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Zheng D, van den Heuvel A, Balog J, Willemsen IM, Kloet S, Tapscott SJ, Mahfouz A, van der Maarel SM. DUX4 activates common and context-specific intergenic transcripts and isoforms. SCIENCE ADVANCES 2025; 11:eadt5356. [PMID: 40333962 PMCID: PMC12057663 DOI: 10.1126/sciadv.adt5356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2024] [Accepted: 04/02/2025] [Indexed: 05/09/2025]
Abstract
DUX4 regulates the expression of genic and nongenic elements and modulates chromatin accessibility during zygotic genome activation in cleavage stage embryos. Its misexpression in skeletal muscle causes facioscapulohumeral dystrophy (FSHD). By leveraging full-length RNA isoform sequencing with short-read RNA sequencing of DUX4-inducible myoblasts, we elucidate an isoform-resolved transcriptome featuring numerous unannotated isoforms from known loci and novel intergenic loci. While DUX4 activates similar programs in early embryos and FSHD muscle, the isoform usage of known DUX4 targets is notably distinct between the two contexts. DUX4 also activates hundreds of previously unannotated intergenic loci dominated by repetitive elements. The transcriptional and epigenetic profiles of these loci in myogenic and embryonic contexts indicate that the usage of DUX4-binding sites at these intergenic loci is influenced by the cellular environment. These findings demonstrate that DUX4 induces context-specific transcriptomic programs, enriching our understanding of DUX4-induced muscle pathology.
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Affiliation(s)
- Dongxu Zheng
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Anita van den Heuvel
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Judit Balog
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Iris M. Willemsen
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Susan Kloet
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Stephen J. Tapscott
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Neurology, University of Washington, Seattle, WA 98195, USA
| | - Ahmed Mahfouz
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, Netherlands
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2
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Zimmerlin L, Angarita A, Park TS, Evans-Moses R, Thomas J, Yan S, Uribe I, Vegas I, Kochendoerfer C, Buys W, Leung AKL, Zambidis ET. Proteogenomic reprogramming to a functional human blastomere-like stem cell state via a PARP-DUX4 regulatory axis. Cell Rep 2025; 44:115671. [PMID: 40338744 DOI: 10.1016/j.celrep.2025.115671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 02/17/2025] [Accepted: 04/16/2025] [Indexed: 05/10/2025] Open
Abstract
Here, we show that conventional human pluripotent stem cells cultured with non-specific tankyrase-PARP1-inhibited conditions underwent proteogenomic reprogramming to functional blastomere-like tankyrase/PARP inhibitor-regulated naive stem cells (TIRN-SC). TIRN-SCs concurrently expressed hundreds of pioneer factors in hybrid 2C-8C-morula-ICM programs that were augmented by induced expression of DUX4. Injection of TIRN-SCs into 8C-staged murine embryos equipotently differentiated human cells to the extra-embryonic and embryonic compartments of chimeric blastocysts and fetuses. Ectopic expression of murine-E-Cadherin in TIRN-SCs further enhanced interspecific chimeric tissue targeting. TIRN-SC-derived trophoblast stem cells efficiently generated placental chimeras. Proteome-ubiquitinome analyses revealed increased TNKS and reduced PARP1 levels and an ADP-ribosylation-deficient, hyper-ubiquitinated proteome that impacted expression of both tankyrase and PARP1 substrates. ChIP-seq of NANOG-SOX2-OCT4 and PARP1 (NSOP) revealed genome-wide NSOP co-binding at DUX4-accessible enhancers of embryonic lineage factors; suggesting a DUX4-NSOP axis regulated TIRN-SC lineage plasticity. TIRN-SCs may serve as valuable models for studying the proteogenomic regulation of pre-lineage human embryogenesis. VIDEO ABSTRACT.
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Affiliation(s)
- Ludovic Zimmerlin
- Institute for Cell Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Ariana Angarita
- Institute for Cell Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Tea Soon Park
- Institute for Cell Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Rebecca Evans-Moses
- Institute for Cell Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Justin Thomas
- Institute for Cell Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Sirui Yan
- Institute for Cell Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Isabel Uribe
- Departments of Biochemistry and Molecular Biology, The Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - Isabella Vegas
- Institute for Cell Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Clara Kochendoerfer
- Institute for Cell Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Willem Buys
- Institute for Cell Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Anthony K L Leung
- Departments of Biochemistry and Molecular Biology, The Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - Elias T Zambidis
- Institute for Cell Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA.
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Xiao Y, Jin W, Ju L, Fu J, Wang G, Yu M, Chen F, Qian K, Wang X, Zhang Y. Tracking single-cell evolution using clock-like chromatin accessibility loci. Nat Biotechnol 2025; 43:784-798. [PMID: 38724668 DOI: 10.1038/s41587-024-02241-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 04/10/2024] [Indexed: 05/18/2025]
Abstract
Single-cell chromatin accessibility sequencing (scATAC-seq) reconstructs developmental trajectory by phenotypic similarity. However, inferring the exact developmental trajectory is challenging. Previous studies showed age-associated DNA methylation (DNAm) changes in specific genomic regions, termed clock-like differential methylation loci (ClockDML). Age-associated DNAm could either result from or result in chromatin accessibility changes at ClockDML. As cells undergo mitosis, the heterogeneity of chromatin accessibility on clock-like loci is reduced, providing a measure of mitotic age. In this study, we developed a method, called EpiTrace, that counts the fraction of opened clock-like loci from scATAC-seq data to determine cell age and perform lineage tracing in various cell lineages and animal species. It shows concordance with known developmental hierarchies, correlates well with DNAm-based clocks and is complementary with mutation-based lineage tracing, RNA velocity and stemness predictions. Applying EpiTrace to scATAC-seq data reveals biological insights with clinically relevant implications, ranging from hematopoiesis, organ development, tumor biology and immunity to cortical gyrification.
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Affiliation(s)
- Yu Xiao
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Wan Jin
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
- Euler Technology, ZGC Life Sciences Park, Beijing, China
| | - Lingao Ju
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jie Fu
- Hong Kong University of Science and Technology, Hong Kong, China
| | - Gang Wang
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Mengxue Yu
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Fangjin Chen
- High Performance Computing Center, Peking-Tsinghua College of Life Sciences, Peking University, Beijing, China
| | - Kaiyu Qian
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
- Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Xinghuan Wang
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China.
- Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China.
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China.
| | - Yi Zhang
- Euler Technology, ZGC Life Sciences Park, Beijing, China.
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Gallo A, Bernardini A, Polettini S, Dolfini D, Gnesutta N, Mantovani R. Multiple Retrotransposon-mediated NF-YA Gene Duplication Events Recurred in Diverse Groups of Mammals at Different Ancestry Levels. Genome Biol Evol 2025; 17:evaf071. [PMID: 40408078 PMCID: PMC12101057 DOI: 10.1093/gbe/evaf071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/10/2025] [Indexed: 05/26/2025] Open
Abstract
NF-Y is a transcription factor trimer formed by Histone Fold subunits NF-YB/NF-YC and NF-YA, which confers sequence-specificity for the CCAAT box, an important cis regulatory element. The subunits are extremely conserved in all eukaryotes and in mammals they are typically encoded by single copy genes. We describe here the presence of a second NF-YA termed NF-YAr for retrogene in diverse groups of mammals (Cetacea, Ruminantia, Ursidae, Sciuridae, hippopotamus, and greater horseshoe bat). NF-YAr retrogenes are located on different chromosomes with respect to the parental gene; they are compact and intronless, or with few annotated introns. Phylogenetic and synteny analyses indicate multiple independent retrotransposition events in the different orders. Analysis of RNA-seq data of Bos taurus suggests expression confined to spermatozoa. Conservation of translation initiation signals around predicted start codons, and of 5'UTR sequences, are consistent with protein expression, suggesting that NF-YAr is a translated, retroposed NF-YA. 3D-informed structural considerations of the predicted protein sequences point at deleterious changes for CCAAT-binding and, potentially, for trimer formation. These findings indicate that multiple independent NF-YA retrotransposition events were fixed in selected orders of mammals, generating a second NF-YA with a strict tissue distribution.
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Affiliation(s)
- Alberto Gallo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Andrea Bernardini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Sofia Polettini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Diletta Dolfini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Nerina Gnesutta
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Roberto Mantovani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
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Hua L, Peng Y, Yan L, Yuan P, Qiao J. Moving toward totipotency: the molecular and cellular features of totipotent and naive pluripotent stem cells. Hum Reprod Update 2025:dmaf006. [PMID: 40299455 DOI: 10.1093/humupd/dmaf006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 01/06/2025] [Indexed: 04/30/2025] Open
Abstract
BACKGROUND Dissecting the key molecular mechanism of embryonic development provides novel insights into embryogenesis and potential intervention strategies for clinical practices. However, the ability to study the molecular mechanisms of early embryo development in humans, such as zygotic genome activation and lineage segregation, is meaningfully constrained by methodological limitations and ethical concerns. Totipotent stem cells have an extended developmental potential to differentiate into embryonic and extraembryonic tissues, providing a suitable model for studying early embryo development. Recently, a series of ground-breaking results on stem cells have identified totipotent-like cells or induced pluripotent stem cells into totipotent-like cells. OBJECTIVE AND RATIONALE This review followed the PRISMA guidelines, surveys the current works of literature on totipotent, naive, and formative pluripotent stem cells, introduces the molecular and biological characteristics of those stem cells, and gives advice for future research. SEARCH METHODS The search method employed the terms 'totipotent' OR 'naive pluripotent stem cell' OR 'formative pluripotent stem cell' for unfiltered search on PubMed, Web of Science, and Cochrane Library. Papers included were those with information on totipotent stem cells, naive pluripotent stem cells, or formative pluripotent stem cells until June 2024 and were published in the English language. Articles that have no relevance to stem cells, or totipotent, naive pluripotent, or formative pluripotent cells were excluded. OUTCOMES There were 152 records included in this review. These publications were divided into four groups according to the species of the cells included in the studies: 67 human stem cell studies, 70 mouse stem cell studies, 9 porcine stem cell studies, and 6 cynomolgus stem cell studies. Naive pluripotent stem cell models have been established in other species such as porcine and cynomolgus. Human and mouse totipotent stem cells, e.g. human 8-cell-like cells, human totipotent blastomere-like cells, and mouse 2-cell-like cells, have been successfully established and exhibit high developmental potency for both embryonic and extraembryonic contributions. However, the observed discrepancies between these cells and real embryos in terms of epigenetics and transcription suggest that further research is warranted. Our results systematically reviewed the established methods, molecular characteristics, and developmental potency of different naive, formative pluripotent, and totipotent stem cells. Furthermore, we provide a parallel comparison between animal and human models, and offer recommendations for future applications to advance early embryo research and assisted reproduction technologies. WIDER IMPLICATIONS Totipotent cell models provide a valuable resource to understand the underlying mechanisms of embryo development and forge new paths toward future treatment of infertility and regenerative medicine. However, current in vitro cell models exhibit epigenetic and transcriptional differences from in vivo embryos, and many cell models are unstable across passages, thus imperfectly recapitulating embryonic development. In this regard, standardizing and expanding current research on totipotent stem cell models are essential to enhance our capability to resemble and decipher embryogenesis.
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Affiliation(s)
- Lingyue Hua
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Yuyang Peng
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Liying Yan
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Peng Yuan
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Jie Qiao
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics, Beijing, China
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Zhang T, Peng Z, Meng F, Li Z, Chen J, Zhou Q, Leng L, Bo H, Lu G, Deng Y, Gu F, Lin G. Maternal transcription factor OTX2 directly induces SETD1A and promotes embryonic genome activation in human pre-implantation embryos. SCIENCE CHINA. LIFE SCIENCES 2025:10.1007/s11427-024-2875-3. [PMID: 40285911 DOI: 10.1007/s11427-024-2875-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2024] [Accepted: 02/18/2025] [Indexed: 04/29/2025]
Abstract
Early embryonic development is controlled by maternal factors originating from mature oocytes. The zygotic genome is activated from a transcriptionally quiescent state through a process called embryonic genome activation (EGA), which involves the depletion and clearance of maternal factors. However, the mechanism by which maternal factors regulate EGA and embryonic development, particularly in humans, remains elusive. In this study, using tri-pronuclear (3PN) embryos and human embryonic stem cells (hESCs), we demonstrated that the maternal transcription factor Orthodenticle Homeobox 2 (OTX2), a paired-like homeobox gene, promotes EGA in human pre-implantation embryos. Knockdown of OTX2 through Trim-Away technology blocked embryonic development and minor EGA gene expression. Overexpression of OTX2 (OTX2OE) in hESCs increased transcript products, primarily at the 2-cell embryo stage genes, including genes encoding methyltransferase of histone H3K4. OTX2OE increased the level of H3K4me3 and increased the open chromatin region that co-occurs with the H3K4me3 region at the 4-cell stage in hESCs. Based on these findings in hESCs, we further verified that OTX2 directly induced the expression of SETD1A by binding to its promoter, leading to increased H3K4me3 levels in both hESCs and 3PN embryos. These findings suggest that the maternal transcription factor OTX2 regulates EGA and early embryogenesis via epigenetic mechanisms.
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Affiliation(s)
- Tianlei Zhang
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410205, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Ziyan Peng
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Fei Meng
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410205, China
| | - Zhuo Li
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410205, China
| | - Junru Chen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, 999078, China
| | - Qinwei Zhou
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410205, China
| | - Lizhi Leng
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410205, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Sciences, Central South University, Changsha, 410008, China
| | - Hao Bo
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410205, China
| | - Guangxiu Lu
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410205, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Sciences, Central South University, Changsha, 410008, China
| | - Yun Deng
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China.
- Laboratory of Zebrafish Genetics, College of Life Sciences, Hunan Normal University, Changsha, 410081, China.
| | - Feng Gu
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, School of Medicine, Hunan Normal University, Engineering Research Center of Reproduction and Translational Medicine of Hunan Province, Changsha, 410013, China.
- Guangxiu Hospital Affiliated with Hunan Normal University (Hunan Guangxiu Hospital), Changsha, 410017, China.
| | - Ge Lin
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410205, China.
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Sciences, Central South University, Changsha, 410008, China.
- Guangxiu Hospital Affiliated with Hunan Normal University (Hunan Guangxiu Hospital), Changsha, 410017, China.
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7
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Cheng Y, Li J, Shang J, Jia X, Bi Y, Gu J, Jiang N, Huan Y, Li Y, Sun M. Comparative analysis of chromatin accessibility in porcine oocytes from follicles of different sizes. Res Vet Sci 2025; 185:105565. [PMID: 39908890 DOI: 10.1016/j.rvsc.2025.105565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2024] [Revised: 01/26/2025] [Accepted: 01/31/2025] [Indexed: 02/07/2025]
Abstract
Chromatin accessibility and transcription levels during oocyte growth are important for oocyte maturation and subsequent development. However, chromatin accessibility changes in porcine oocytes during growth are unclear. The present study demonstrated that porcine oocytes derived from large follicles (LFO) exhibited higher developmental capacity than those derived from small follicles (SFO). Assay for transposase-accessible chromatin using sequencing (ATAC-seq) analysis identified 1117 and 1694 uniquely accessible chromatin peaks in LFO and SFO, respectively. Motif analysis of differential peaks revealed the top 10 significantly enriched transcription factor (TF)-binding motifs in LFO versus SFO, with only one increased peak (Spi1 binding site) and nine decreased peaks (NFYA, ATOH1, ZNF549, Foxn1, HAND2, THRB, NHLH2, FoxP1, and FoxP2 binding sites). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified key processes in the regulation of oocyte growth and maturation. Integration of ATAC-seq and RNA sequencing data revealed the top 10 hub genes involved in chromatin remodeling (MYSM1 and EZH2), histone modification (MYSM1, RNF2, USP1, EZH2, and MIER1), and transcription regulation (MYSM1, ASXL3, and MIER1), as well as those involved in metabolic processes and signal transduction (DOCK7, FGGY, DTL, and DNAJC6). All these genes exhibited increased expression levels in LFO versus SFO. In conclusion, the study demonstrated the dynamic nature of chromatin accessibility during porcine oocyte growth and revealed the TFs and genes closely associated with oocyte growth and maturation. These findings provide new insight into porcine oocyte growth and offer a potential strategy to enhance the in vitro developmental ability of SFO.
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Affiliation(s)
- Yazhuo Cheng
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province 266109, China
| | - Jingyu Li
- Chongqing Key Laboratory of Human Embryo Engineering, Chongqing Health Center for Women and Children, Chongqing 400013, China
| | - Jiyong Shang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province 266109, China
| | - Xilong Jia
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province 266109, China
| | - Yeling Bi
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province 266109, China
| | - Jiaxu Gu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province 266109, China
| | - Nan Jiang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province 266109, China
| | - Yanjun Huan
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province 266109, China
| | - Youwei Li
- College of Haidu, Qingdao Agricultural University, Laiyang, Shandong Province 265200, China.
| | - Mingju Sun
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province 266109, China.
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8
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Dolfini D, Imbriano C, Mantovani R. The role(s) of NF-Y in development and differentiation. Cell Death Differ 2025; 32:195-206. [PMID: 39327506 PMCID: PMC11802806 DOI: 10.1038/s41418-024-01388-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 09/18/2024] [Accepted: 09/19/2024] [Indexed: 09/28/2024] Open
Abstract
NF-Y is a conserved sequence-specific trimeric Transcription Factor -TF- binding to the CCAAT element. We review here the role(s) in development, from pre-implantation embryo to terminally differentiated tissues, by rationalizing and commenting on genetic, genomic, epigenetic and biochemical studies. This effort brings to light the impact of NF-YA isoforms on stemness and differentiation, as well as binding to distal vs promoter proximal sites and connections with selected TFs.
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Affiliation(s)
- Diletta Dolfini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Carol Imbriano
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Modena, Italy
| | - Roberto Mantovani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy.
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9
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Ma G, Fu X, Zhou L, Babarinde IA, Shi L, Yang W, Chen J, Xiao Z, Qiao Y, Ma L, Ou Y, Li Y, Chang C, Deng B, Zhang R, Sun L, Tong G, Li D, Li Y, Hutchins AP. The nuclear matrix stabilizes primed-specific genes in human pluripotent stem cells. Nat Cell Biol 2025; 27:232-245. [PMID: 39789220 DOI: 10.1038/s41556-024-01595-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 12/11/2024] [Indexed: 01/12/2025]
Abstract
The nuclear matrix, a proteinaceous gel composed of proteins and RNA, is an important nuclear structure that supports chromatin architecture, but its role in human pluripotent stem cells (hPSCs) has not been described. Here we show that by disrupting heterogeneous nuclear ribonucleoprotein U (HNRNPU) or the nuclear matrix protein, Matrin-3, primed hPSCs adopted features of the naive pluripotent state, including morphology and upregulation of naive-specific marker genes. We demonstrate that HNRNPU depletion leads to increased chromatin accessibility, reduced DNA contacts and increased nuclear size. Mechanistically, HNRNPU acts as a transcriptional co-factor that anchors promoters of primed-specific genes to the nuclear matrix with POLII to promote their expression and their RNA stability. Overall, HNRNPU promotes cell-type stability and when reduced promotes conversion to earlier embryonic states.
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Affiliation(s)
- Gang Ma
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Xiuling Fu
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Lulu Zhou
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Isaac A Babarinde
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Liyang Shi
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Wenting Yang
- Department of Reproductive Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jiao Chen
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Zhen Xiao
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yu Qiao
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Lisha Ma
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yuhao Ou
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yuhao Li
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Chen Chang
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Boping Deng
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Ran Zhang
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Li Sun
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Guoqing Tong
- Department of Reproductive Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Dongwei Li
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Yiming Li
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China.
| | - Andrew P Hutchins
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
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10
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Chen H. Quantifying Nascent Transcription in Early Embryogenesis. Methods Mol Biol 2025; 2923:143-162. [PMID: 40418448 DOI: 10.1007/978-1-0716-4522-2_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2025]
Abstract
The early embryonic genome exists in a dormant state following fertilization, and it then subsequently undergoes broad activation of zygotic transcription at the early stages of development. A major challenge is the detection of newly made zygotic transcripts and the determination of their activation onset time due to the presence of large and predominantly maternal pool of RNAs. Here we describe a detailed method to measure the zygotic transcription during zygotic genome activation (ZGA) of Xenopus early embryos using metabolic labeling of nascent transcripts with 5-ethynyl uridine (5-EU) followed by purifying and sequencing the nascent EU-RNAs (EU-RNA-seq). This method is highly sensitive in detecting early zygotic transcripts that are not detected by total RNA-seq and determines the actual onset time of transcriptional activation for zygotic genes. The method is applicable to a wide variety of embryonic model systems and has already afforded novel insights into gene regulation in early embryogenesis.
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Affiliation(s)
- Hui Chen
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA.
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11
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Levin-Ferreyra F, Kodali S, Cui Y, Pashos ARS, Pessina P, Brumbaugh J, Di Stefano B. Transposable element activity captures human pluripotent cell states. EMBO Rep 2025; 26:329-352. [PMID: 39668246 PMCID: PMC11772670 DOI: 10.1038/s44319-024-00343-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2024] [Revised: 11/21/2024] [Accepted: 11/25/2024] [Indexed: 12/14/2024] Open
Abstract
Human pluripotent stem cells (hPSCs) exist in multiple, transcriptionally distinct states and serve as powerful models for studying human development. Despite their significance, the molecular determinants and pathways governing these pluripotent states remain incompletely understood. Here, we demonstrate that transposable elements act as sensitive indicators of distinct pluripotent cell states. We engineered hPSCs with fluorescent reporters to capture the temporal expression dynamics of two state-specific transposable elements, LTR5_Hs, and MER51B. This dual reporter system enables real-time monitoring and isolation of stem cells transitioning from naïve to primed pluripotency and further towards differentiation, serving as a more accurate readout of pluripotency states compared to conventional systems. Unexpectedly, we identified a rare, metastable cell population within primed hPSCs, marked by transcripts related to preimplantation embryo development and which is associated with a DNA damage response. Moreover, our system establishes the chromatin factor NSD1 and the RNA-binding protein FUS as potent molecular safeguards of primed pluripotency. Our study introduces a novel system for investigating cellular potency and provides key insights into the regulation of embryonic development.
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Affiliation(s)
- Florencia Levin-Ferreyra
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Srikanth Kodali
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Yingzhi Cui
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Alison R S Pashos
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
- University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO, USA
- Charles C. Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Patrizia Pessina
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Justin Brumbaugh
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
- University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO, USA
- Charles C. Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Bruno Di Stefano
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA.
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
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12
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Liang H, Deng J, Luo T, Luo H, Li F, Wu K, Lin C. Chromatin accessibility reveals potential prognostic value of the peak set associated with smoking history in patients with lung adenocarcinoma. Heliyon 2024; 10:e41006. [PMID: 39720074 PMCID: PMC11665461 DOI: 10.1016/j.heliyon.2024.e41006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 12/03/2024] [Accepted: 12/04/2024] [Indexed: 12/26/2024] Open
Abstract
Considerable differences in molecular characteristics have been defined between non-smoker and smokers in patients with lung adenocarcinoma (LUAD), yet studies on open chromatin patterns associated with LUAD progression caused by smoking are still lacking. Here, we constructed a novel network based on correlations between each ATAC-seq peak from TCGA data using our previously developed algorithm. Subsequently, principal component analysis was performed on LUAD samples with retained peaks filtered by the correlation network, and pathway analysis was conducted to identify potential pathways involved. We identified a set of peaks that discriminated smokers in LUAD patients according to levels of exposure to tobacco quantified in pack-years. These peaks were also significantly associated with progression-free survival and overall survival of these patients. Further examination of the gene set related to those peaks revealed that the comprising genes, such as KRT19, B3GNT3, CLDN7 and CLDN3 are strongly associated with LUAD development. They are consistent with the important roles of the associated pathways in LUAD oncogenesis induced by smoking, including estrogen response, apical junction and glycolysis pathways. In summary, our study may provide valuable insights into exploring ATAC-seq peaks and understanding smoking-related LUAD carcinogenesis from a perspective of open chromatin changes.
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Affiliation(s)
- Han Liang
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), BGI Research, Hangzhou 310000, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, BGI Research, Shenzhen 518083, China
- BGI Genomics, Shenzhen 518083, China
| | - Jianlian Deng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tian Luo
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), BGI Research, Hangzhou 310000, China
- BGI Genomics, Shenzhen 518083, China
| | - Huijuan Luo
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), BGI Research, Hangzhou 310000, China
- BGI Genomics, Shenzhen 518083, China
| | - Fuqiang Li
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), BGI Research, Hangzhou 310000, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, BGI Research, Shenzhen 518083, China
- BGI Genomics, Shenzhen 518083, China
| | - Kui Wu
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), BGI Research, Hangzhou 310000, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, BGI Research, Shenzhen 518083, China
- BGI Genomics, Shenzhen 518083, China
| | - Cong Lin
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), BGI Research, Hangzhou 310000, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, BGI Research, Shenzhen 518083, China
- BGI Genomics, Shenzhen 518083, China
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13
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Jarosz AS, Halo JV. Transcription of Endogenous Retroviruses: Broad and Precise Mechanisms of Control. Viruses 2024; 16:1312. [PMID: 39205286 PMCID: PMC11359688 DOI: 10.3390/v16081312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 08/07/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024] Open
Abstract
Endogenous retroviruses (ERVs) are the remnants of retroviral germline infections and are highly abundant in the genomes of vertebrates. At one time considered to be nothing more than inert 'junk' within genomes, ERVs have been tolerated within host genomes over vast timescales, and their study continues to reveal complex co-evolutionary histories within their respective host species. For example, multiple instances have been characterized of ERVs having been 'borrowed' for normal physiology, from single copies to ones involved in various regulatory networks such as innate immunity and during early development. Within the cell, the accessibility of ERVs is normally tightly controlled by epigenetic mechanisms such as DNA methylation or histone modifications. However, these silencing mechanisms of ERVs are reversible, and epigenetic alterations to the chromatin landscape can thus lead to their aberrant expression, as is observed in abnormal cellular environments such as in tumors. In this review, we focus on ERV transcriptional control and draw parallels and distinctions concerning the loss of regulation in disease, as well as their precise regulation in early development.
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Affiliation(s)
- Abigail S. Jarosz
- Science and Mathematics Division, Lorrain County Community College, Lorrain, OH 44035, USA;
| | - Julia V. Halo
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
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14
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Hu Y, He Z, Li Z, Wang Y, Wu N, Sun H, Zhou Z, Hu Q, Cong X. Lactylation: the novel histone modification influence on gene expression, protein function, and disease. Clin Epigenetics 2024; 16:72. [PMID: 38812044 PMCID: PMC11138093 DOI: 10.1186/s13148-024-01682-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 05/20/2024] [Indexed: 05/31/2024] Open
Abstract
Lactic acid, traditionally considered as a metabolic waste product arising from glycolysis, has undergone a resurgence in scientific interest since the discovery of the Warburg effect in tumor cells. Numerous studies have proved that lactic acid could promote angiogenesis and impair the function of immune cells within tumor microenvironments. Nevertheless, the precise molecular mechanisms governing these biological functions remain inadequately understood. Recently, lactic acid has been found to induce a posttranslational modification, lactylation, that may offer insight into lactic acid's non-metabolic functions. Notably, the posttranslational modification of proteins by lactylation has emerged as a crucial mechanism by which lactate regulates cellular processes. This article provides an overview of the discovery of lactate acidification, outlines the potential "writers" and "erasers" responsible for protein lactylation, presents an overview of protein lactylation patterns across different organisms, and discusses the diverse physiological roles of lactylation. Besides, the article highlights the latest research progress concerning the regulatory functions of protein lactylation in pathological processes and underscores its scientific significance for future investigations.
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Affiliation(s)
- Yue Hu
- Department of Tissues Bank, China-Japan Union Hospital of Jilin University, Changchun, 130033, China
| | - Zhenglin He
- China-Japan Union Hospital of Jilin University, Jilin University, Changchun, 130033, China
| | - Zongjun Li
- China-Japan Union Hospital of Jilin University, Jilin University, Changchun, 130033, China
| | - Yihan Wang
- China-Japan Union Hospital of Jilin University, Jilin University, Changchun, 130033, China
| | - Nan Wu
- Department of Tissues Bank, China-Japan Union Hospital of Jilin University, Changchun, 130033, China
- Department of Dermatology, China-Japan Union Hospital of Jilin University, Changchun, 130033, China
| | - Hongyan Sun
- Department of Tissues Bank, China-Japan Union Hospital of Jilin University, Changchun, 130033, China
| | - Zilong Zhou
- Department of Tissues Bank, China-Japan Union Hospital of Jilin University, Changchun, 130033, China
| | - Qianying Hu
- Department of Tissues Bank, China-Japan Union Hospital of Jilin University, Changchun, 130033, China
| | - Xianling Cong
- Department of Tissues Bank, China-Japan Union Hospital of Jilin University, Changchun, 130033, China.
- Department of Dermatology, China-Japan Union Hospital of Jilin University, Changchun, 130033, China.
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15
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Gong X, He W, Jin W, Ma H, Wang G, Li J, Xiao Y, Zhao Y, Chen Q, Guo H, Yang J, Qi Y, Dong W, Fu M, Li X, Liu J, Liu X, Yin A, Zhang Y, Wei Y. Disruption of maternal vascular remodeling by a fetal endoretrovirus-derived gene in preeclampsia. Genome Biol 2024; 25:117. [PMID: 38715110 PMCID: PMC11075363 DOI: 10.1186/s13059-024-03265-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 04/30/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Preeclampsia, one of the most lethal pregnancy-related diseases, is associated with the disruption of uterine spiral artery remodeling during placentation. However, the early molecular events leading to preeclampsia remain unknown. RESULTS By analyzing placentas from preeclampsia, non-preeclampsia, and twin pregnancies with selective intrauterine growth restriction, we show that the pathogenesis of preeclampsia is attributed to immature trophoblast and maldeveloped endothelial cells. Delayed epigenetic reprogramming during early extraembryonic tissue development leads to generation of excessive immature trophoblast cells. We find reduction of de novo DNA methylation in these trophoblast cells results in selective overexpression of maternally imprinted genes, including the endoretrovirus-derived gene PEG10 (paternally expressed gene 10). PEG10 forms virus-like particles, which are transferred from the trophoblast to the closely proximate endothelial cells. In normal pregnancy, only a low amount of PEG10 is transferred to maternal cells; however, in preeclampsia, excessive PEG10 disrupts maternal vascular development by inhibiting TGF-beta signaling. CONCLUSIONS Our study reveals the intricate epigenetic mechanisms that regulate trans-generational genetic conflict and ultimately ensure proper maternal-fetal interface formation.
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Affiliation(s)
- Xiaoli Gong
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Wei He
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Wan Jin
- Euler Technology, Beijing, China
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hongwei Ma
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, China
- Department Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Gang Wang
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
- Human Genetic Resources Preservation Center of Hubei Province, Wuhan, China
- Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jiaxin Li
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Yu Xiao
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
- Human Genetic Resources Preservation Center of Hubei Province, Wuhan, China
- Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yangyu Zhao
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | | | | | - Jiexia Yang
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Yiming Qi
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Wei Dong
- Maternity Ward, Haidian Maternal and Child Health Hospital, Beijing, China
| | - Meng Fu
- Department of Obstetrics and Gynecology, Haidian Maternal and Child Health Hospital, Beijing, China
| | - Xiaojuan Li
- Euler Technology, Beijing, China
- Present Address: International Max Planck Research School for Genome Science, and University of Göttingen, Göttingen Center for Molecular Biosciences, Göttingen, Germany
| | | | - Xinghui Liu
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, China.
- Department Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China.
| | - Aihua Yin
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China.
| | - Yi Zhang
- Euler Technology, Beijing, China.
| | - Yuan Wei
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.
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16
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Saha D, Animireddy S, Bartholomew B. The SWI/SNF ATP-dependent chromatin remodeling complex in cell lineage priming and early development. Biochem Soc Trans 2024; 52:603-616. [PMID: 38572912 PMCID: PMC11088921 DOI: 10.1042/bst20230416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/05/2024]
Abstract
ATP dependent chromatin remodelers have pivotal roles in transcription, DNA replication and repair, and maintaining genome integrity. SWI/SNF remodelers were first discovered in yeast genetic screens for factors involved in mating type switching or for using alternative energy sources therefore termed SWI/SNF complex (short for SWItch/Sucrose NonFermentable). The SWI/SNF complexes utilize energy from ATP hydrolysis to disrupt histone-DNA interactions and shift, eject, or reposition nucleosomes making the underlying DNA more accessible to specific transcription factors and other regulatory proteins. In development, SWI/SNF orchestrates the precise activation and repression of genes at different stages, safe guards the formation of specific cell lineages and tissues. Dysregulation of SWI/SNF have been implicated in diseases such as cancer, where they can drive uncontrolled cell proliferation and tumor metastasis. Additionally, SWI/SNF defects are associated with neurodevelopmental disorders, leading to disruption of neural development and function. This review offers insights into recent developments regarding the roles of the SWI/SNF complex in pluripotency and cell lineage primining and the approaches that have helped delineate its importance. Understanding these molecular mechanisms is crucial for unraveling the intricate processes governing embryonic stem cell biology and developmental transitions and may potentially apply to human diseases linked to mutations in the SWI/SNF complex.
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Affiliation(s)
- Dhurjhoti Saha
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77054, U.S.A
| | - Srinivas Animireddy
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77054, U.S.A
| | - Blaine Bartholomew
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77054, U.S.A
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17
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Schultheis H, Bentsen M, Heger V, Looso M. Uncovering uncharacterized binding of transcription factors from ATAC-seq footprinting data. Sci Rep 2024; 14:9275. [PMID: 38654130 DOI: 10.1038/s41598-024-59989-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 04/17/2024] [Indexed: 04/25/2024] Open
Abstract
Transcription factors (TFs) are crucial epigenetic regulators, which enable cells to dynamically adjust gene expression in response to environmental signals. Computational procedures like digital genomic footprinting on chromatin accessibility assays such as ATACseq can be used to identify bound TFs in a genome-wide scale. This method utilizes short regions of low accessibility signals due to steric hindrance of DNA bound proteins, called footprints (FPs), which are combined with motif databases for TF identification. However, while over 1600 TFs have been described in the human genome, only ~ 700 of these have a known binding motif. Thus, a substantial number of FPs without overlap to a known DNA motif are normally discarded from FP analysis. In addition, the FP method is restricted to organisms with a substantial number of known TF motifs. Here we present DENIS (DE Novo motIf diScovery), a framework to generate and systematically investigate the potential of de novo TF motif discovery from FPs. DENIS includes functionality (1) to isolate FPs without binding motifs, (2) to perform de novo motif generation and (3) to characterize novel motifs. Here, we show that the framework rediscovers artificially removed TF motifs, quantifies de novo motif usage during an early embryonic development example dataset, and is able to analyze and uncover TF activity in organisms lacking canonical motifs. The latter task is exemplified by an investigation of a scATAC-seq dataset in zebrafish which covers different cell types during hematopoiesis.
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Affiliation(s)
- Hendrik Schultheis
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Mette Bentsen
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Vanessa Heger
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Mario Looso
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany.
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18
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Kong X, Li R, Chen M, Zheng R, Wang J, Sun C, Qu Y. Endogenous retrovirus HERVH-derived lncRNA UCA1 controls human trophoblast development. Proc Natl Acad Sci U S A 2024; 121:e2318176121. [PMID: 38483994 PMCID: PMC10962953 DOI: 10.1073/pnas.2318176121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 02/12/2024] [Indexed: 03/19/2024] Open
Abstract
Endogenous retroviruses (ERVs) are frequently reactivated in mammalian placenta. It has been proposed that ERVs contribute to shaping the gene regulatory network of mammalian trophoblasts, dominantly acting as species- and placental-specific enhancers. However, whether and how ERVs control human trophoblast development through alternative pathways remains poorly understood. Besides the well-recognized function of human endogenous retrovirus-H (HERVH) in maintaining pluripotency of early human epiblast, here we present a unique role of HERVH on trophoblast lineage development. We found that the LTR7C/HERVH subfamily exhibits an accessible chromatin state in the human trophoblast lineage. Particularly, the LTR7C/HERVH-derived Urothelial Cancer Associated 1 (UCA1), a primate-specific long non-coding RNA (lncRNA), is transcribed in human trophoblasts and promotes the proliferation of human trophoblast stem cells (hTSCs), whereas its ectopic expression compromises human trophoblast syncytialization coinciding with increased interferon signaling pathway. Importantly, UCA1 upregulation is detectable in placental samples from early-onset preeclampsia (EO-PE) patients and the transcriptome of EO-PE placenta exhibits considerable similarities to that of the syncytiotrophoblasts differentiated from UCA1-overexpressing hTSCs, supporting up-regulated UCA1 as a potential biomarker of this disease. Altogether, our data shed light on the versatile regulatory role of HERVH in early human development and provide a unique mechanism whereby ERVs exert a function in human placentation and placental syndromes.
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Affiliation(s)
- Xuhui Kong
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou510080, China
- Key Laboratory for Stem Cells and Tissue Engineering, Sun Yat-sen University, Ministry of Education, Guangzhou510080, China
| | - Ruiqi Li
- Reproductive and Genetic Hospital of Kapok, Hainan571400, China
- Department of Obstetrics and Gynecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou510120, China
- The First People’s Hospital of Kashgar, Kashgar844000, China
| | - Manqi Chen
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou510080, China
- Key Laboratory for Stem Cells and Tissue Engineering, Sun Yat-sen University, Ministry of Education, Guangzhou510080, China
| | - Rongyan Zheng
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou510080, China
- Key Laboratory for Stem Cells and Tissue Engineering, Sun Yat-sen University, Ministry of Education, Guangzhou510080, China
| | - Jichang Wang
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou510080, China
- Key Laboratory for Stem Cells and Tissue Engineering, Sun Yat-sen University, Ministry of Education, Guangzhou510080, China
| | - Chuanbo Sun
- Laboratory of Medical Systems Biology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou510623, China
| | - Yuliang Qu
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou510080, China
- Key Laboratory for Stem Cells and Tissue Engineering, Sun Yat-sen University, Ministry of Education, Guangzhou510080, China
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19
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Gawriyski L, Tan Z, Liu X, Chowdhury I, Malaymar Pinar D, Zhang Q, Weltner J, Jouhilahti EM, Wei GH, Kere J, Varjosalo M. Interaction network of human early embryonic transcription factors. EMBO Rep 2024; 25:1589-1622. [PMID: 38297188 PMCID: PMC10933267 DOI: 10.1038/s44319-024-00074-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 02/02/2024] Open
Abstract
Embryonic genome activation (EGA) occurs during preimplantation development and is characterized by the initiation of de novo transcription from the embryonic genome. Despite its importance, the regulation of EGA and the transcription factors involved in this process are poorly understood. Paired-like homeobox (PRDL) family proteins are implicated as potential transcriptional regulators of EGA, yet the PRDL-mediated gene regulatory networks remain uncharacterized. To investigate the function of PRDL proteins, we are identifying the molecular interactions and the functions of a subset family of the Eutherian Totipotent Cell Homeobox (ETCHbox) proteins, seven PRDL family proteins and six other transcription factors (TFs), all suggested to participate in transcriptional regulation during preimplantation. Using mass spectrometry-based interactomics methods, AP-MS and proximity-dependent biotin labeling, and chromatin immunoprecipitation sequencing we derive the comprehensive regulatory networks of these preimplantation TFs. By these interactomics tools we identify more than a thousand high-confidence interactions for the 21 studied bait proteins with more than 300 interacting proteins. We also establish that TPRX2, currently assigned as pseudogene, is a transcriptional activator.
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Affiliation(s)
- Lisa Gawriyski
- University of Helsinki, Institute of Biotechnology, Helsinki, Finland
- Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Zenglai Tan
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Xiaonan Liu
- University of Helsinki, Institute of Biotechnology, Helsinki, Finland
| | | | - Dicle Malaymar Pinar
- University of Helsinki, Institute of Biotechnology, Helsinki, Finland
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey
| | - Qin Zhang
- Ministry of Education Key Laboratory of Metabolism and Molecular Medicine & Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cancer Institute, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Jere Weltner
- Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Eeva-Mari Jouhilahti
- Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Gong-Hong Wei
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
- Ministry of Education Key Laboratory of Metabolism and Molecular Medicine & Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cancer Institute, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Juha Kere
- Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
- Karolinska Institutet, Department of Biosciences and Nutrition, Huddinge, Sweden
| | - Markku Varjosalo
- University of Helsinki, Institute of Biotechnology, Helsinki, Finland.
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland.
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20
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Ishii S, Kakizuka T, Park SJ, Tagawa A, Sanbo C, Tanabe H, Ohkawa Y, Nakanishi M, Nakai K, Miyanari Y. Genome-wide ATAC-see screening identifies TFDP1 as a modulator of global chromatin accessibility. Nat Genet 2024; 56:473-482. [PMID: 38361031 DOI: 10.1038/s41588-024-01658-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 01/08/2024] [Indexed: 02/17/2024]
Abstract
Chromatin accessibility is a hallmark of active regulatory regions and is functionally linked to transcriptional networks and cell identity. However, the molecular mechanisms and networks that govern chromatin accessibility have not been thoroughly studied. Here we conducted a genome-wide CRISPR screening combined with an optimized ATAC-see protocol to identify genes that modulate global chromatin accessibility. In addition to known chromatin regulators like CREBBP and EP400, we discovered a number of previously unrecognized proteins that modulate chromatin accessibility, including TFDP1, HNRNPU, EIF3D and THAP11 belonging to diverse biological pathways. ATAC-seq analysis upon their knockouts revealed their distinct and specific effects on chromatin accessibility. Remarkably, we found that TFDP1, a transcription factor, modulates global chromatin accessibility through transcriptional regulation of canonical histones. In addition, our findings highlight the manipulation of chromatin accessibility as an approach to enhance various cell engineering applications, including genome editing and induced pluripotent stem cell reprogramming.
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Affiliation(s)
- Satoko Ishii
- The Graduate University for Advanced Studies, SOKENDAI, Okazaki, Japan
- National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan
| | - Taishi Kakizuka
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Sung-Joon Park
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Ayako Tagawa
- WPI Nano Life Science Institute, Kanazawa University, Kanazawa, Japan
| | - Chiaki Sanbo
- National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan
| | - Hideyuki Tanabe
- Research Center for Integrative Evolutionary Science, SOKENDAI, Hayama, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | | | - Kenta Nakai
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yusuke Miyanari
- WPI Nano Life Science Institute, Kanazawa University, Kanazawa, Japan.
- Cancer Research Institute, Kanazawa University, Kanazawa, Japan.
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21
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Dolfini D, Gnesutta N, Mantovani R. Expression and function of NF-Y subunits in cancer. Biochim Biophys Acta Rev Cancer 2024; 1879:189082. [PMID: 38309445 DOI: 10.1016/j.bbcan.2024.189082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/05/2024]
Abstract
NF-Y is a Transcription Factor (TF) targeting the CCAAT box regulatory element. It consists of the NF-YB/NF-YC heterodimer, each containing an Histone Fold Domain (HFD), and the sequence-specific subunit NF-YA. NF-YA expression is associated with cell proliferation and absent in some post-mitotic cells. The review summarizes recent findings impacting on cancer development. The logic of the NF-Y regulome points to pro-growth, oncogenic genes in the cell-cycle, metabolism and transcriptional regulation routes. NF-YA is involved in growth/differentiation decisions upon cell-cycle re-entry after mitosis and it is widely overexpressed in tumors, the HFD subunits in some tumor types or subtypes. Overexpression of NF-Y -mostly NF-YA- is oncogenic and decreases sensitivity to anti-neoplastic drugs. The specific roles of NF-YA and NF-YC isoforms generated by alternative splicing -AS- are discussed, including the prognostic value of their levels, although the specific molecular mechanisms of activity are still to be deciphered.
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Affiliation(s)
- Diletta Dolfini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, Milano 20133, Italy
| | - Nerina Gnesutta
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, Milano 20133, Italy
| | - Roberto Mantovani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, Milano 20133, Italy.
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22
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Hossain MJ, Nyame P, Monde K. Species-Specific Transcription Factors Associated with Long Terminal Repeat Promoters of Endogenous Retroviruses: A Comprehensive Review. Biomolecules 2024; 14:280. [PMID: 38540701 PMCID: PMC10968565 DOI: 10.3390/biom14030280] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/19/2024] [Accepted: 02/24/2024] [Indexed: 11/11/2024] Open
Abstract
Endogenous retroviruses (ERVs) became a part of the eukaryotic genome through endogenization millions of years ago. Moreover, they have lost their innate capability of virulence or replication. Nevertheless, in eukaryotic cells, they actively engage in various activities that may be advantageous or disadvantageous to the cells. The mechanisms by which transcription is triggered and implicated in cellular processes are complex. Owing to the diversity in the expression of transcription factors (TFs) in cells and the TF-binding motifs of viruses, the comprehensibility of ERV initiation and its impact on cellular functions are unclear. Currently, several factors are known to be related to their initiation. TFs that bind to the viral long-terminal repeat (LTR) are critical initiators. This review discusses the TFs shown to actively associate with ERV stimulation across species such as humans, mice, pigs, monkeys, zebrafish, Drosophila, and yeast. A comprehensive summary of the expression of previously reported TFs may aid in identifying similarities between animal species and endogenous viruses. Moreover, an in-depth understanding of ERV expression will assist in elucidating their physiological roles in eukaryotic cell development and in clarifying their relationship with endogenous retrovirus-associated diseases.
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Affiliation(s)
| | | | - Kazuaki Monde
- Department of Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan; (M.J.H.); (P.N.)
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23
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Wang T, Peng J, Fan J, Tang N, Hua R, Zhou X, Wang Z, Wang L, Bai Y, Quan X, Wang Z, Zhang L, Luo C, Zhang W, Kang X, Liu J, Li L, Li L. Single-cell multi-omics profiling of human preimplantation embryos identifies cytoskeletal defects during embryonic arrest. Nat Cell Biol 2024; 26:263-277. [PMID: 38238450 DOI: 10.1038/s41556-023-01328-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 12/01/2023] [Indexed: 02/16/2024]
Abstract
Human in vitro fertilized embryos exhibit low developmental capabilities, and the mechanisms that underlie embryonic arrest remain unclear. Here using a single-cell multi-omics sequencing approach, we simultaneously analysed alterations in the transcriptome, chromatin accessibility and the DNA methylome in human embryonic arrest due to unexplained reasons. Arrested embryos displayed transcriptome disorders, including a distorted microtubule cytoskeleton, increased genomic instability and impaired glycolysis, which were coordinated with multiple epigenetic reprogramming defects. We identified Aurora A kinase (AURKA) repression as a cause of embryonic arrest. Mechanistically, arrested embryos induced through AURKA inhibition resembled the reprogramming abnormalities of natural embryonic arrest in terms of the transcriptome, the DNA methylome, chromatin accessibility and H3K4me3 modifications. Mitosis-independent sequential activation of the zygotic genome in arrested embryos showed that YY1 contributed to human major zygotic genome activation. Collectively, our study decodes the reprogramming abnormalities and mechanisms of human embryonic arrest and the key regulators of zygotic genome activation.
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Affiliation(s)
- Teng Wang
- Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Junhua Peng
- Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Jiaqi Fan
- Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Ni Tang
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
- Key Laboratory for Reproductive Medicine of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
- Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
| | - Rui Hua
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, P. R. China
| | - Xueliang Zhou
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
- Key Laboratory for Reproductive Medicine of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
- Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
| | - Zhihao Wang
- Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Longfei Wang
- Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Yanling Bai
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
- Key Laboratory for Reproductive Medicine of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
- Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
| | - Xiaowan Quan
- Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Zimeng Wang
- Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Li Zhang
- Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Chen Luo
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, P. R. China
| | - Weiqing Zhang
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, P. R. China
| | - Xiangjin Kang
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
- Key Laboratory for Reproductive Medicine of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
- Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
| | - Jianqiao Liu
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
- Key Laboratory for Reproductive Medicine of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
- Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
| | - Lei Li
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China.
- Key Laboratory for Reproductive Medicine of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China.
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China.
- Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China.
| | - Lin Li
- Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China.
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24
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Dou C, Wu L, Zhang J, He H, Xu T, Yu Z, Su P, Zhang X, Wang J, Miao YL, Zhou J. The transcriptional activator Klf5 recruits p300-mediated H3K27ac for maintaining trophoblast stem cell pluripotency. J Mol Cell Biol 2024; 15:mjad045. [PMID: 37533201 PMCID: PMC10768793 DOI: 10.1093/jmcb/mjad045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 04/14/2023] [Accepted: 05/11/2023] [Indexed: 08/04/2023] Open
Abstract
The effective proliferation and differentiation of trophoblast stem cells (TSCs) is indispensable for the development of the placenta, which is the key to maintaining normal fetal growth during pregnancy. Kruppel-like factor 5 (Klf5) is implicated in the activation of pluripotency gene expression in embryonic stem cells (ESCs), yet its function in TSCs is poorly understood. Here, we showed that Klf5 knockdown resulted in the downregulation of core TSC-specific genes, consequently causing rapid differentiation of TSCs. Consistently, Klf5-depleted embryos lost the ability to establish TSCs in vitro. At the molecular level, Klf5 preferentially occupied the proximal promoter regions and maintained an open chromatin architecture of key TSC-specific genes. Deprivation of Klf5 impaired the enrichment of p300, a major histone acetyl transferase of H3 lysine 27 acetylation (H3K27ac), and further reduced the occupancy of H3K27ac at promoter regions, leading to decreased transcriptional activity of TSC pluripotency genes. Thus, our findings highlight a novel mechanism of Klf5 in regulating the self-renewal and differentiation of TSCs and provide a reference for understanding placental development and improving pregnancy rates.
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Affiliation(s)
- Chengli Dou
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Linhui Wu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Jingjing Zhang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Hainan He
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Tian Xu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Zhisheng Yu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Peng Su
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Xia Zhang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Junling Wang
- Department of Reproductive Medicine, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic, Edong Healthcare Group, Huangshi 435000, China
| | - Yi-Liang Miao
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jilong Zhou
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
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25
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Alanis-Lobato G, Bartlett TE, Huang Q, Simon CS, McCarthy A, Elder K, Snell P, Christie L, Niakan KK. MICA: a multi-omics method to predict gene regulatory networks in early human embryos. Life Sci Alliance 2024; 7:e202302415. [PMID: 37879938 PMCID: PMC10599980 DOI: 10.26508/lsa.202302415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 10/27/2023] Open
Abstract
Recent advances in single-cell omics have transformed characterisation of cell types in challenging-to-study biological contexts. In contexts with limited single-cell samples, such as the early human embryo inference of transcription factor-gene regulatory network (GRN) interactions is especially difficult. Here, we assessed application of different linear or non-linear GRN predictions to single-cell simulated and human embryo transcriptome datasets. We also compared how expression normalisation impacts on GRN predictions, finding that transcripts per million reads outperformed alternative methods. GRN inferences were more reproducible using a non-linear method based on mutual information (MI) applied to single-cell transcriptome datasets refined with chromatin accessibility (CA) (called MICA), compared with alternative network prediction methods tested. MICA captures complex non-monotonic dependencies and feedback loops. Using MICA, we generated the first GRN inferences in early human development. MICA predicted co-localisation of the AP-1 transcription factor subunit proto-oncogene JUND and the TFAP2C transcription factor AP-2γ in early human embryos. Overall, our comparative analysis of GRN prediction methods defines a pipeline that can be applied to single-cell multi-omics datasets in especially challenging contexts to infer interactions between transcription factor expression and target gene regulation.
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Affiliation(s)
| | | | - Qiulin Huang
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, London, UK
- Department of Physiology, Development and Neuroscience, The Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Claire S Simon
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, London, UK
| | - Afshan McCarthy
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, London, UK
| | | | | | | | - Kathy K Niakan
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, London, UK
- Department of Physiology, Development and Neuroscience, The Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
- Wellcome - Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Epigenetics Programme, Babraham Institute, Cambridge, UK
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26
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Wilkinson AL, Zorzan I, Rugg-Gunn PJ. Epigenetic regulation of early human embryo development. Cell Stem Cell 2023; 30:1569-1584. [PMID: 37858333 DOI: 10.1016/j.stem.2023.09.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/18/2023] [Accepted: 09/25/2023] [Indexed: 10/21/2023]
Abstract
Studies of mammalian development have advanced our understanding of the genetic, epigenetic, and cellular processes that orchestrate embryogenesis and have uncovered new insights into the unique aspects of human embryogenesis. Recent studies have now produced the first epigenetic maps of early human embryogenesis, stimulating new ideas about epigenetic reprogramming, cell fate control, and the potential mechanisms underpinning developmental plasticity in human embryos. In this review, we discuss these new insights into the epigenetic regulation of early human development and the importance of these processes for safeguarding development. We also highlight unanswered questions and key challenges that remain to be addressed.
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Affiliation(s)
| | - Irene Zorzan
- Epigenetics Programme, Babraham Institute, Cambridge, UK
| | - Peter J Rugg-Gunn
- Epigenetics Programme, Babraham Institute, Cambridge, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge, UK; Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK.
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27
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Torre D, Francoeur NJ, Kalma Y, Gross Carmel I, Melo BS, Deikus G, Allette K, Flohr R, Fridrikh M, Vlachos K, Madrid K, Shah H, Wang YC, Sridhar SH, Smith ML, Eliyahu E, Azem F, Amir H, Mayshar Y, Marazzi I, Guccione E, Schadt E, Ben-Yosef D, Sebra R. Isoform-resolved transcriptome of the human preimplantation embryo. Nat Commun 2023; 14:6902. [PMID: 37903791 PMCID: PMC10616205 DOI: 10.1038/s41467-023-42558-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 10/15/2023] [Indexed: 11/01/2023] Open
Abstract
Human preimplantation development involves extensive remodeling of RNA expression and splicing. However, its transcriptome has been compiled using short-read sequencing data, which fails to capture most full-length mRNAs. Here, we generate an isoform-resolved transcriptome of early human development by performing long- and short-read RNA sequencing on 73 embryos spanning the zygote to blastocyst stages. We identify 110,212 unannotated isoforms transcribed from known genes, including highly conserved protein-coding loci and key developmental regulators. We further identify 17,964 isoforms from 5,239 unannotated genes, which are largely non-coding, primate-specific, and highly associated with transposable elements. These isoforms are widely supported by the integration of published multi-omics datasets, including single-cell 8CLC and blastoid studies. Alternative splicing and gene co-expression network analyses further reveal that embryonic genome activation is associated with splicing disruption and transient upregulation of gene modules. Together, these findings show that the human embryo transcriptome is far more complex than currently known, and will act as a valuable resource to empower future studies exploring development.
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Affiliation(s)
- Denis Torre
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Yael Kalma
- Fertility and IVF Institute, Tel-Aviv Sourasky Medical Center, Affiliated to Tel Aviv University, Tel Aviv, 64239, Israel
| | - Ilana Gross Carmel
- Fertility and IVF Institute, Tel-Aviv Sourasky Medical Center, Affiliated to Tel Aviv University, Tel Aviv, 64239, Israel
| | - Betsaida S Melo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Gintaras Deikus
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kimaada Allette
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ron Flohr
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, 69978, Israel
- CORAL - Center Of Regeneration and Longevity, Tel-Aviv Sourasky Medical Center, Tel Aviv, 64239, Israel
| | - Maya Fridrikh
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Kent Madrid
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Hardik Shah
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ying-Chih Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Shwetha H Sridhar
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Melissa L Smith
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, 40202, USA
| | - Efrat Eliyahu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Foad Azem
- Fertility and IVF Institute, Tel-Aviv Sourasky Medical Center, Affiliated to Tel Aviv University, Tel Aviv, 64239, Israel
| | - Hadar Amir
- Fertility and IVF Institute, Tel-Aviv Sourasky Medical Center, Affiliated to Tel Aviv University, Tel Aviv, 64239, Israel
| | - Yoav Mayshar
- Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Ivan Marazzi
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, University of California, Irvine, CA, 92697, USA
| | - Ernesto Guccione
- Center for OncoGenomics and Innovative Therapeutics (COGIT); Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eric Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Dalit Ben-Yosef
- Fertility and IVF Institute, Tel-Aviv Sourasky Medical Center, Affiliated to Tel Aviv University, Tel Aviv, 64239, Israel.
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, 69978, Israel.
- CORAL - Center Of Regeneration and Longevity, Tel-Aviv Sourasky Medical Center, Tel Aviv, 64239, Israel.
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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28
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Li J, Yuan P, Ma G, Liu Y, Zhang Q, Wang W, Guo Y. The composition dynamics of transposable elements in human blastocysts. J Hum Genet 2023; 68:681-688. [PMID: 37308564 DOI: 10.1038/s10038-023-01169-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/11/2023] [Accepted: 06/03/2023] [Indexed: 06/14/2023]
Abstract
Transposable elements (TEs) are mobile DNA sequences that can replicate themselves and play significant roles in embryo development and chromosomal structure remodeling. In this study, we investigated the variation of TEs in blastocysts with different parental genetic backgrounds. We analyzed the proportions of 1137 TEs subfamilies from six classes at the DNA level using Bowtie2 and PopoolationTE2 in 196 blastocysts with abnormal parental chromosomal diseases. Our findings revealed that the parental karyotype was the dominant factor influencing TEs frequencies. Out of the 1116 subfamilies, different frequencies were observed in blastocysts with varying parental karyotypes. The development stage of blastocysts was the second most crucial factor influencing TEs proportions. A total of 614 subfamilies exhibited different proportions at distinct blastocyst stages. Notably, subfamily members belonging to the Alu family showed a high proportion at stage 6, while those from the LINE class exhibited a high proportion at stage 3 and a low proportion at stage 6. Moreover, the proportions of some TEs subfamilies also varied depending on blastocyst karyotype, inner cell mass status, and outer trophectoderm status. We found that 48 subfamilies displayed different proportions between balanced and unbalanced blastocysts. Additionally, 19 subfamilies demonstrated varying proportions among different inner cell mass scores, and 43 subfamilies exhibited different proportions among outer trophectoderm scores. This study suggests that the composition of TEs subfamilies may be influenced by various factors and undergoes dynamic modulation during embryo development.
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Affiliation(s)
- Jian Li
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ping Yuan
- IVF Center, Department of Obstetrics and Gynecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- IVF Center, The First People's Hospital of Kashi Prefecture, Kashi, China
| | - Guangwei Ma
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Ying Liu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Reproductive Medical Center, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Qingxue Zhang
- IVF Center, Department of Obstetrics and Gynecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wenjun Wang
- IVF Center, Department of Obstetrics and Gynecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.
| | - Yabin Guo
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.
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29
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Chen Y, Xie D, Ma X, Xue X, Liu M, Xiao X, Lai C, Xu X, Chen X, Chen Y, Zhang Z, XuHan X, Lai Z, Lin Y. Genome-wide high-throughput chromosome conformation capture analysis reveals hierarchical chromatin interactions during early somatic embryogenesis. PLANT PHYSIOLOGY 2023; 193:555-577. [PMID: 37313777 DOI: 10.1093/plphys/kiad348] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 05/04/2023] [Accepted: 05/23/2023] [Indexed: 06/15/2023]
Abstract
Somatic embryogenesis (SE), like zygotic embryo development, is a progressive process. Early SE is the beginning of a switch from a somatic to an embryogenic state and is an important stage for initiating chromatin reprogramming of SE. Previous studies suggest that changes in chromatin accessibility occur during early SE, although information on the 3D structure of chromatin is not yet available. Here, we present a chromosome-level genome assembly of longan (Dimocarpus longan) using PacBio combined with high-through chromosome conformation capture scaffolding, which resulted in a 446 Mb genome assembly anchored onto 15 scaffolds. During early SE, chromatin was concentrated and then decondensed, and a large number of long terminal repeat retrotransposons (LTR-RTs) were enriched in the local chromatin interaction region, suggesting LTR-RTs were involved in chromatin reorganization. Early SE was accompanied by the transformation from A to B compartments, and the interactions between B compartments were enhanced. Results from chromatin accessibility, monomethylation of histone H3 at lysine 4 (H3K4me1) modification, and transcription analyses further revealed a gene regulatory network for cell wall thickening during SE. Particularly, we found that the H3K4me1 differential peak binding motif showed abnormal activation of ethylene response factor transcription factors and participation in SE. The chromosome-level genomic and multiomics analyses revealed the 3D conformation of chromatin during early SE, providing insight into the molecular mechanisms underlying cell wall thickening and the potential regulatory networks of TFs during early SE in D. longan. These results provide additional clues for revealing the molecular mechanisms of plant SE.
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Affiliation(s)
- Yan Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Dejian Xie
- Beijing Research Center, Wuhan Frasergen Bioinformatics Co., Ltd, Beijing 100081, China
| | - Xiangwei Ma
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xiaodong Xue
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Mengyu Liu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xuechen Xiao
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Chunwang Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xiaoping Xu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xiaohui Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Zihao Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xu XuHan
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- Institut de la Recherche Interdisciplinaire de Toulouse, IRIT-ARI, Toulouse 31300, France
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
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30
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Luo H, Hu X, Wu H, Zaib G, Chai W, Cui H. Activation of lnc-ALVE1-AS1 inhibited ALV-J replication through triggering the TLR3 pathway in chicken macrophage like cell line. Vet Res Commun 2023; 47:431-443. [PMID: 35715584 DOI: 10.1007/s11259-022-09960-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 06/14/2022] [Indexed: 11/27/2022]
Abstract
Endogenous retroviruses (ERVs) are remnants of the historical retroviral infections, and their derived transcripts with viral signatures are important sources of long noncoding RNAs (lncRNAs). We have previously shown that the chicken ERV-derived lncRNA lnc-ALVE1-AS1 exerts antiviral innate immunity in chicken embryo fibroblasts. However, it is not clear whether this endogenous retroviral RNA has a similar function in immune cells. Here, we found that lnc-ALVE1-AS1 was persistently inhibited in chicken macrophages after avian leukosis virus subgroup J (ALV-J) infection. Furthermore, overexpression of lnc-ALVE1-AS1 significantly inhibited the replication of exogenous ALV-J, whereas knockdown of lnc-ALVE1-AS1 promoted the replication of ALV-J in chicken macrophages. This phenomenon is attributed to the induction of antiviral innate immunity by lnc-ALVE1-AS1 in macrophages, whereas knockdown of lnc-ALVE1-AS1 had the opposite effect. Mechanistically, lnc-ALVE1-AS1 can be sensed by the cytosolic pattern recognition receptor TLR3 and trigger the type I interferons response. The present study provides novel insights into the antiviral defense of ERV-derived lncRNAs in macrophages and offers new strategies for future antiviral solutions.
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Affiliation(s)
- Huan Luo
- Institute of Epigenetics and Epigenomics, College of Animal Science and Technology, Yangzhou University, No. 48 East Wenhui Road, Yangzhou, 225009, Jiangsu, China
| | - Xuming Hu
- Institute of Epigenetics and Epigenomics, College of Animal Science and Technology, Yangzhou University, No. 48 East Wenhui Road, Yangzhou, 225009, Jiangsu, China.
- Joint International Research Laboratory of Agricultural & Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
- Jiangsu Co-Innovation Center for Prevention & Control of Important Animal Infectious Diseases & Zoonoses, Yangzhou, 225009, Jiangsu, China.
| | - Huixian Wu
- Institute of Epigenetics and Epigenomics, College of Animal Science and Technology, Yangzhou University, No. 48 East Wenhui Road, Yangzhou, 225009, Jiangsu, China
| | - Gul Zaib
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Wenxian Chai
- Changzhou Animal Disease Prevention and Control Center, Changzhou, 213002, Jiangsu, China
| | - Hengmi Cui
- Institute of Epigenetics and Epigenomics, College of Animal Science and Technology, Yangzhou University, No. 48 East Wenhui Road, Yangzhou, 225009, Jiangsu, China
- Joint International Research Laboratory of Agricultural & Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou, 225009, Jiangsu, China
- Jiangsu Co-Innovation Center for Prevention & Control of Important Animal Infectious Diseases & Zoonoses, Yangzhou, 225009, Jiangsu, China
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31
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Guo J, Zhao H, Zhang J, Lv X, Zhang S, Su R, Zheng W, Dai J, Meng F, Gong F, Lu G, Xue Y, Lin G. Selective Translation of Maternal mRNA by eIF4E1B Controls Oocyte to Embryo Transition. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2205500. [PMID: 36755190 PMCID: PMC10104655 DOI: 10.1002/advs.202205500] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 01/17/2023] [Indexed: 06/18/2023]
Abstract
Maternal messenger ribonucleic acids (mRNAs) are driven by a highly orchestrated scheme of recruitment to polysomes and translational activation. However, selecting and regulating individual mRNAs for the translation from a competitive pool of mRNAs are little-known processes. This research shows that the maternal eukaryotic translation initiation factor 4e1b (Eif4e1b) expresses during the oocyte-to-embryo transition (OET), and maternal deletion of Eif4e1b leads to multiple defects concerning oogenesis and embryonic developmental competence during OET. The linear amplification of complementary deoxyribonucleic acid (cDNA) ends, and sequencing (LACE-seq) is used to identify the distinct subset of mRNA and its CG-rich binding sites within the 5' untranslated region (UTR) targeted by eIF4E1B. The proteomics analyses indicate that eIF4E1B-specific bound genes show stronger downregulation at the protein level, which further verify a group of proteins that plays a crucial role in oocyte maturation and embryonic developmental competence is insufficiently synthesized in Eif4e1b-cKO oocytes during OET. Moreover, the biochemical results in vitro are combined to further confirm the maternal-specific translation activation model assembled by eIF4E1B and 3'UTR-associated mRNA binding proteins. The findings demonstrate the indispensability of eIF4E1B for selective translation activation in mammalian oocytes and provide a potential network regulated by eIF4E1B in OET.
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Affiliation(s)
- Jing Guo
- Clinical Research Center for Reproduction and Genetics in Hunan ProvinceReproductive and Genetic Hospital of CITIC‐XiangyaChangsha410078P. R. China
| | - Hailian Zhao
- Key Laboratory of RNA BiologyInstitute of BiophysicsChinese Academy of SciencesBeijing100101P. R. China
- University of Chinese Academy of SciencesBeijing100049P. R. China
| | - Jue Zhang
- Clinical Research Center for Reproduction and Genetics in Hunan ProvinceReproductive and Genetic Hospital of CITIC‐XiangyaChangsha410078P. R. China
| | - Xiangjiang Lv
- Laboratory of Reproductive and Stem Cell EngineeringNHC Key Laboratory of Human Stem Cell and Reproductive EngineeringCentral South UniversityChangsha410078P. R. China
| | - Shen Zhang
- Clinical Research Center for Reproduction and Genetics in Hunan ProvinceReproductive and Genetic Hospital of CITIC‐XiangyaChangsha410078P. R. China
| | - Ruibao Su
- Key Laboratory of RNA BiologyInstitute of BiophysicsChinese Academy of SciencesBeijing100101P. R. China
- University of Chinese Academy of SciencesBeijing100049P. R. China
| | - Wei Zheng
- Clinical Research Center for Reproduction and Genetics in Hunan ProvinceReproductive and Genetic Hospital of CITIC‐XiangyaChangsha410078P. R. China
| | - Jing Dai
- Clinical Research Center for Reproduction and Genetics in Hunan ProvinceReproductive and Genetic Hospital of CITIC‐XiangyaChangsha410078P. R. China
- Laboratory of Reproductive and Stem Cell EngineeringNHC Key Laboratory of Human Stem Cell and Reproductive EngineeringCentral South UniversityChangsha410078P. R. China
| | - Fei Meng
- Clinical Research Center for Reproduction and Genetics in Hunan ProvinceReproductive and Genetic Hospital of CITIC‐XiangyaChangsha410078P. R. China
| | - Fei Gong
- Clinical Research Center for Reproduction and Genetics in Hunan ProvinceReproductive and Genetic Hospital of CITIC‐XiangyaChangsha410078P. R. China
- Laboratory of Reproductive and Stem Cell EngineeringNHC Key Laboratory of Human Stem Cell and Reproductive EngineeringCentral South UniversityChangsha410078P. R. China
| | - Guangxiu Lu
- Clinical Research Center for Reproduction and Genetics in Hunan ProvinceReproductive and Genetic Hospital of CITIC‐XiangyaChangsha410078P. R. China
- Laboratory of Reproductive and Stem Cell EngineeringNHC Key Laboratory of Human Stem Cell and Reproductive EngineeringCentral South UniversityChangsha410078P. R. China
| | - Yuanchao Xue
- Key Laboratory of RNA BiologyInstitute of BiophysicsChinese Academy of SciencesBeijing100101P. R. China
- University of Chinese Academy of SciencesBeijing100049P. R. China
| | - Ge Lin
- Clinical Research Center for Reproduction and Genetics in Hunan ProvinceReproductive and Genetic Hospital of CITIC‐XiangyaChangsha410078P. R. China
- Laboratory of Reproductive and Stem Cell EngineeringNHC Key Laboratory of Human Stem Cell and Reproductive EngineeringCentral South UniversityChangsha410078P. R. China
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32
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Gawriyski L, Jouhilahti EM, Yoshihara M, Fei L, Weltner J, Airenne TT, Trokovic R, Bhagat S, Tervaniemi MH, Murakawa Y, Salokas K, Liu X, Miettinen S, Bürglin TR, Sahu B, Otonkoski T, Johnson MS, Katayama S, Varjosalo M, Kere J. Comprehensive characterization of the embryonic factor LEUTX. iScience 2023; 26:106172. [PMID: 36876139 PMCID: PMC9978639 DOI: 10.1016/j.isci.2023.106172] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 12/01/2022] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
The paired-like homeobox transcription factor LEUTX is expressed in human preimplantation embryos between the 4- and 8-cell stages, and then silenced in somatic tissues. To characterize the function of LEUTX, we performed a multiomic characterization of LEUTX using two proteomics methods and three genome-wide sequencing approaches. Our results show that LEUTX stably interacts with the EP300 and CBP histone acetyltransferases through its 9 amino acid transactivation domain (9aaTAD), as mutation of this domain abolishes the interactions. LEUTX targets genomic cis-regulatory sequences that overlap with repetitive elements, and through these elements it is suggested to regulate the expression of its downstream genes. We find LEUTX to be a transcriptional activator, upregulating several genes linked to preimplantation development as well as 8-cell-like markers, such as DPPA3 and ZNF280A. Our results support a role for LEUTX in preimplantation development as an enhancer binding protein and as a potent transcriptional activator.
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Affiliation(s)
- Lisa Gawriyski
- Stem Cells and Metabolism Research Program, University of Helsinki, 00290 Helsinki, Finland
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
- Folkhälsan Research Center, 00290 Helsinki, Finland
| | - Eeva-Mari Jouhilahti
- Stem Cells and Metabolism Research Program, University of Helsinki, 00290 Helsinki, Finland
- Folkhälsan Research Center, 00290 Helsinki, Finland
| | - Masahito Yoshihara
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183 Huddinge, Sweden
| | - Liangru Fei
- Applied Tumor Genomics Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Jere Weltner
- Stem Cells and Metabolism Research Program, University of Helsinki, 00290 Helsinki, Finland
- Folkhälsan Research Center, 00290 Helsinki, Finland
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, 14186 Stockholm, Sweden
- Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, 14186 Stockholm, Sweden
| | - Tomi T. Airenne
- Structural Bioinformatics Laboratory and InFLAMES Research Flagship Center, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Ras Trokovic
- Stem Cells and Metabolism Research Program, University of Helsinki, 00290 Helsinki, Finland
| | - Shruti Bhagat
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183 Huddinge, Sweden
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Mari H. Tervaniemi
- Stem Cells and Metabolism Research Program, University of Helsinki, 00290 Helsinki, Finland
- Folkhälsan Research Center, 00290 Helsinki, Finland
| | - Yasuhiro Murakawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Medical Systems Genomics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- IFOM-ETS, Milan, Italy
| | - Kari Salokas
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Xiaonan Liu
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Sini Miettinen
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | | | - Biswajyoti Sahu
- Applied Tumor Genomics Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
- Centre for Molecular Medicine Norway (NCMM), University of Oslo, 0349 Oslo, Norway
| | - Timo Otonkoski
- Stem Cells and Metabolism Research Program, University of Helsinki, 00290 Helsinki, Finland
- Children’s Hospital, Helsinki University Hospital and University of Helsinki, 00290 Helsinki, Finland
| | - Mark S. Johnson
- Structural Bioinformatics Laboratory and InFLAMES Research Flagship Center, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Shintaro Katayama
- Stem Cells and Metabolism Research Program, University of Helsinki, 00290 Helsinki, Finland
- Folkhälsan Research Center, 00290 Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183 Huddinge, Sweden
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Juha Kere
- Stem Cells and Metabolism Research Program, University of Helsinki, 00290 Helsinki, Finland
- Folkhälsan Research Center, 00290 Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183 Huddinge, Sweden
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33
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Zhou C, Halstead MM, Bonnet‐Garnier A, Schultz RM, Ross PJ. Histone remodeling reflects conserved mechanisms of bovine and human preimplantation development. EMBO Rep 2023; 24:e55726. [PMID: 36779365 PMCID: PMC9986824 DOI: 10.15252/embr.202255726] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 02/14/2023] Open
Abstract
How histone modifications regulate changes in gene expression during preimplantation development in any species remains poorly understood. Using CUT&Tag to overcome limiting amounts of biological material, we profiled two activating (H3K4me3 and H3K27ac) and two repressive (H3K9me3 and H3K27me3) marks in bovine oocytes, 2-, 4-, and 8-cell embryos, morula, blastocysts, inner cell mass, and trophectoderm. In oocytes, broad bivalent domains mark developmental genes, and prior to embryonic genome activation (EGA), H3K9me3 and H3K27me3 co-occupy gene bodies, suggesting a global mechanism for transcription repression. During EGA, chromatin accessibility is established before canonical H3K4me3 and H3K27ac signatures. Embryonic transcription is required for this remodeling, indicating that maternally provided products alone are insufficient for reprogramming. Last, H3K27me3 plays a major role in restriction of cellular potency, as blastocyst lineages are defined by differential polycomb repression and transcription factor activity. Notably, inferred regulators of EGA and blastocyst formation strongly resemble those described in humans, as opposed to mice. These similarities suggest that cattle are a better model than rodents to investigate the molecular basis of human preimplantation development.
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Affiliation(s)
- Chuan Zhou
- Department of Animal Science University of CaliforniaDavisCAUSA
| | - Michelle M Halstead
- Université Paris‐Saclay, UVSQ, INRAE, BREEDJouy‐en‐JosasFrance
- Ecole Nationale Vétérinaire d'Alfort, BREEDMaisons‐AlfortFrance
| | - Amélie Bonnet‐Garnier
- Université Paris‐Saclay, UVSQ, INRAE, BREEDJouy‐en‐JosasFrance
- Ecole Nationale Vétérinaire d'Alfort, BREEDMaisons‐AlfortFrance
| | - Richard M Schultz
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary MedicineUniversity of CaliforniaDavisCAUSA
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Pablo J Ross
- Department of Animal Science University of CaliforniaDavisCAUSA
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34
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Hernandez Mora JR, Buhigas C, Clark S, Del Gallego Bonilla R, Daskeviciute D, Monteagudo-Sánchez A, Poo-Llanillo ME, Medrano JV, Simón C, Meseguer M, Kelsey G, Monk D. Single-cell multi-omic analysis profiles defective genome activation and epigenetic reprogramming associated with human pre-implantation embryo arrest. Cell Rep 2023; 42:112100. [PMID: 36763500 DOI: 10.1016/j.celrep.2023.112100] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 10/14/2022] [Accepted: 01/26/2023] [Indexed: 02/11/2023] Open
Abstract
During pre-implantation stages of mammalian development, maternally stored material promotes both the erasure of the sperm and oocyte epigenetic profiles and is responsible for concomitant genome activation. Here, we have utilized single-cell methylome and transcriptome sequencing (scM&T-seq) to quantify both mRNA expression and DNA methylation in oocytes and a developmental series of human embryos at single-cell resolution. We fully characterize embryonic genome activation and maternal transcript degradation and map key epigenetic reprogramming events in developmentally high-quality embryos. By comparing these signatures with early embryos that have undergone spontaneous cleavage-stage arrest, as determined by time-lapse imaging, we identify embryos that fail to appropriately activate their genomes or undergo epigenetic reprogramming. Our results indicate that a failure to successfully accomplish these essential milestones impedes the developmental potential of pre-implantation embryos and is likely to have important implications, similar to aneuploidy, for the success of assisted reproductive cycles.
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Affiliation(s)
| | - Claudia Buhigas
- Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7JT, UK
| | - Stephen Clark
- The Babraham Institute, Babraham, Cambridge CB22 3AT, UK
| | | | - Dagne Daskeviciute
- Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7JT, UK
| | | | | | - Jose Vicente Medrano
- IVI-RMA Global and Health Research Institute la Fe, 46026 Valencia, Spain; Department of Obstetrics and Gynecology, Valencia University and INCLIVA, 46010 Valencia, Spain
| | - Carlos Simón
- Department of Obstetrics and Gynecology, Valencia University and INCLIVA, 46010 Valencia, Spain; Department of Obstetrics and Gynecology, BIDMC, Harvard University, Boston, MA 02215, USA
| | - Marcos Meseguer
- IVI-RMA Global and Health Research Institute la Fe, 46026 Valencia, Spain
| | - Gavin Kelsey
- The Babraham Institute, Babraham, Cambridge CB22 3AT, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EL, UK; Wellcome-MRC Institute of Metabolic Science-Metabolic Research Laboratories, Cambridge CB2 0QQ, UK
| | - David Monk
- Bellvitge Institute for Biomedical Research, 08908 Barcelona, Spain; Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7JT, UK.
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Zhang X, Zhang C, Zhou D, Zhang T, Chen X, Ren J, He C, Meng F, Zhou Q, Yang Q, Dai C, Lin G, Zeng S, Leng L. Telomeres cooperate in zygotic genome activation by affecting DUX4/ Dux transcription. iScience 2023; 26:106158. [PMID: 36843839 PMCID: PMC9950522 DOI: 10.1016/j.isci.2023.106158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/03/2022] [Accepted: 02/03/2023] [Indexed: 02/10/2023] Open
Abstract
Zygotic genome activation (ZGA) is initiated once the genome chromatin state is organized in the newly formed zygote. Telomeres are specialized chromatin structures at the ends of chromosomes and are reset during early embryogenesis, while the details and significance of telomere changes in preimplantation embryos remain unclear. We demonstrated that the telomere length was shortened in the minor ZGA stage and significantly elongated in the major ZGA stage of human and mouse embryos. Expression of the ZGA pioneer factor DUX4/Dux was negatively correlated with the telomere length. ATAC sequencing data revealed that the chromatin accessibility peaks on the DUX4 promoter region (i.e., the subtelomere of chromosome 4q) were transiently augmented in human minor ZGA. Reduction of telomeric heterochromatin H3K9me3 in the telomeric region also synergistically activated DUX4 expression with p53 in human embryonic stem cells. We propose herein that telomeres regulate the expression of DUX4/Dux through chromatin remodeling and are thereby involved in ZGA.
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Affiliation(s)
- Xiaorui Zhang
- Hospital of Hunan Guangxiu, Hunan Normal University, Hunan 410001, China,Reproductive and Genetic Hospital of Citic-Xiangya, Hunan 410008, China,Hunan International Scientific and Technological Cooperation Base of Development and Carcinogenesis, Changsha, China,Department of Reproductive Medicine, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi 710061, China
| | - Changquan Zhang
- NHC Key Laboratory of Human Stem and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, China
| | - Di Zhou
- NHC Key Laboratory of Human Stem and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, China,Hunan International Scientific and Technological Cooperation Base of Development and Carcinogenesis, Changsha, China
| | - Tianlei Zhang
- Reproductive and Genetic Hospital of Citic-Xiangya, Hunan 410008, China
| | - Xueqin Chen
- NHC Key Laboratory of Human Stem and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, China
| | - Jinlin Ren
- Hospital of Hunan Guangxiu, Hunan Normal University, Hunan 410001, China
| | - Caixia He
- NHC Key Laboratory of Human Stem and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, China,Hunan International Scientific and Technological Cooperation Base of Development and Carcinogenesis, Changsha, China
| | - Fei Meng
- Reproductive and Genetic Hospital of Citic-Xiangya, Hunan 410008, China
| | - Qinwei Zhou
- Reproductive and Genetic Hospital of Citic-Xiangya, Hunan 410008, China
| | - Qiaohui Yang
- NHC Key Laboratory of Human Stem and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, China
| | - Congling Dai
- Reproductive and Genetic Hospital of Citic-Xiangya, Hunan 410008, China,NHC Key Laboratory of Human Stem and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, China
| | - Ge Lin
- Reproductive and Genetic Hospital of Citic-Xiangya, Hunan 410008, China,NHC Key Laboratory of Human Stem and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, China,Hunan International Scientific and Technological Cooperation Base of Development and Carcinogenesis, Changsha, China,Corresponding author
| | - Sicong Zeng
- Hospital of Hunan Guangxiu, Hunan Normal University, Hunan 410001, China,Reproductive and Genetic Hospital of Citic-Xiangya, Hunan 410008, China,Hunan International Scientific and Technological Cooperation Base of Development and Carcinogenesis, Changsha, China,Corresponding author
| | - Lizhi Leng
- Reproductive and Genetic Hospital of Citic-Xiangya, Hunan 410008, China,NHC Key Laboratory of Human Stem and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, China,Hunan International Scientific and Technological Cooperation Base of Development and Carcinogenesis, Changsha, China,Corresponding author
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36
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Moya-Jódar M, Ullate-Agote A, Barlabé P, Rodríguez-Madoz JR, Abizanda G, Barreda C, Carvajal-Vergara X, Vilas-Zornoza A, Romero JP, Garate L, Agirre X, Coppiello G, Prósper F, Aranguren XL. Revealing cell populations catching the early stages of human embryo development in naive pluripotent stem cell cultures. Stem Cell Reports 2022; 18:64-80. [PMID: 36563688 PMCID: PMC9860119 DOI: 10.1016/j.stemcr.2022.11.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 11/15/2022] [Accepted: 11/18/2022] [Indexed: 12/24/2022] Open
Abstract
Naive human pluripotent stem cells (hPSCs) are defined as the in vitro counterpart of the human preimplantation embryo's epiblast and are used as a model system to study developmental processes. In this study, we report the discovery and characterization of distinct cell populations coexisting with epiblast-like cells in 5iLAF naive human induced PSC (hiPSC) cultures. It is noteworthy that these populations closely resemble different cell types of the human embryo at early developmental stages. While epiblast-like cells represent the main cell population, interestingly we detect a cell population with gene and transposable element expression profile closely resembling the totipotent eight-cell (8C)-stage human embryo, and three cell populations analogous to trophectoderm cells at different stages of their maturation process: transition, early, and mature stages. Moreover, we reveal the presence of cells resembling primitive endoderm. Thus, 5iLAF naive hiPSC cultures provide an excellent opportunity to model the earliest events of human embryogenesis, from the 8C stage to the peri-implantation period.
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Affiliation(s)
- Marta Moya-Jódar
- Program of Regenerative Medicine, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona 31008, Spain,Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona 31008, Spain
| | - Asier Ullate-Agote
- Program of Regenerative Medicine, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona 31008, Spain,Advanced Genomics Laboratory, Program of Hemato-Oncology, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Paula Barlabé
- Program of Regenerative Medicine, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona 31008, Spain,Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona 31008, Spain
| | - Juan Roberto Rodríguez-Madoz
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), IDISNA, University of Navarra, Pamplona, Spain,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Pamplona, Spain
| | - Gloria Abizanda
- Program of Regenerative Medicine, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona 31008, Spain,Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona 31008, Spain
| | - Carolina Barreda
- Program of Regenerative Medicine, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona 31008, Spain,Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona 31008, Spain
| | - Xonia Carvajal-Vergara
- Program of Regenerative Medicine, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona 31008, Spain,Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona 31008, Spain
| | - Amaia Vilas-Zornoza
- Advanced Genomics Laboratory, Program of Hemato-Oncology, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Pamplona, Spain
| | - Juan Pablo Romero
- Advanced Genomics Laboratory, Program of Hemato-Oncology, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain,10x Genomics, 6230 Stoneridge Mall Road, Pleasanton, CA 94588, USA
| | - Leire Garate
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), IDISNA, University of Navarra, Pamplona, Spain,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Pamplona, Spain
| | - Xabier Agirre
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), IDISNA, University of Navarra, Pamplona, Spain,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Pamplona, Spain
| | - Giulia Coppiello
- Program of Regenerative Medicine, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona 31008, Spain,Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona 31008, Spain
| | - Felipe Prósper
- Program of Regenerative Medicine, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona 31008, Spain; Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona 31008, Spain; Hemato-Oncology Program, Center for Applied Medical Research (CIMA), IDISNA, University of Navarra, Pamplona, Spain; Hematology Department, Clínica Universidad de Navarra, University of Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Pamplona, Spain.
| | - Xabier L. Aranguren
- Program of Regenerative Medicine, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona 31008, Spain,Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona 31008, Spain,Corresponding author
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Zhai Y, Yu H, An X, Zhang Z, Zhang M, Zhang S, Li Q, Li Z. Profiling the transcriptomic signatures and identifying the patterns of zygotic genome activation - a comparative analysis between early porcine embryos and their counterparts in other three mammalian species. BMC Genomics 2022; 23:772. [PMID: 36434523 PMCID: PMC9700911 DOI: 10.1186/s12864-022-09015-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 11/15/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND The transcriptional changes around zygotic genome activation (ZGA) in preimplantation embryos are critical for studying mechanisms of embryonic developmental arrest and searching for key transcription factors. However, studies on the transcription profile of porcine ZGA are limited. RESULTS In this study, we performed RNA sequencing in porcine in vivo developed (IVV) and somatic cell nuclear transfer (SCNT) embryo at different stages and compared the transcriptional activity of porcine embryos with mouse, bovine and human embryos. The results showed that the transcriptome map of the early porcine embryos was significantly changed at the 4-cell stage, and 5821 differentially expressed genes (DEGs) in SCNT embryos failed to be reprogrammed or activated during ZGA, which mainly enrichment to metabolic pathways. c-MYC was identified as the highest expressed transcription factor during ZGA. By treating with 10,058-F4, an inhibitor of c-MYC, the cleavage rate (38.33 ± 3.4%) and blastocyst rate (23.33 ± 4.3%) of porcine embryos were significantly lower than those of the control group (50.82 ± 2.7% and 34.43 ± 1.9%). Cross-species analysis of transcriptome during ZGA showed that pigs and bovines had the highest similarity coefficient in biological processes. KEGG pathway analysis indicated that there were 10 co-shared pathways in the four species. CONCLUSIONS Our results reveal that embryos with impaired developmental competence may be arrested at an early stage of development. c-MYC helps promote ZGA and preimplantation embryonic development in pigs. Pigs and bovines have the highest coefficient of similarity in biological processes during ZGA. This study provides an important reference for further studying the reprogramming regulatory mechanism of porcine embryos during ZGA.
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Affiliation(s)
- Yanhui Zhai
- grid.64924.3d0000 0004 1760 5735Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, 130021 China
| | - Hao Yu
- grid.64924.3d0000 0004 1760 5735College of Animal Science, Jilin University, Changchun, 130062 Jilin China
| | - Xinglan An
- grid.64924.3d0000 0004 1760 5735Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, 130021 China
| | - Zhiren Zhang
- grid.452930.90000 0004 1757 8087Zhuhai People’s Hospital (Zhuhai hospital affiliated with Jinan University), Zhuhai, 519000 Guangdong China
| | - Meng Zhang
- grid.64924.3d0000 0004 1760 5735Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, 130021 China
| | - Sheng Zhang
- grid.64924.3d0000 0004 1760 5735Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, 130021 China
| | - Qi Li
- grid.64924.3d0000 0004 1760 5735Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, 130021 China
| | - Ziyi Li
- grid.64924.3d0000 0004 1760 5735Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, 130021 China
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38
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Pontis J, Pulver C, Playfoot CJ, Planet E, Grun D, Offner S, Duc J, Manfrin A, Lutolf MP, Trono D. Primate-specific transposable elements shape transcriptional networks during human development. Nat Commun 2022; 13:7178. [PMID: 36418324 PMCID: PMC9684439 DOI: 10.1038/s41467-022-34800-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/08/2022] [Indexed: 11/24/2022] Open
Abstract
The human genome contains more than 4.5 million inserts derived from transposable elements (TEs), the result of recurrent waves of invasion and internal propagation throughout evolution. For new TE copies to be inherited, they must become integrated in the genome of the germline or pre-implantation embryo, which requires that their source TE be expressed at these stages. Accordingly, many TEs harbor DNA binding sites for the pluripotency factors OCT4, NANOG, SOX2, and KLFs and are transiently expressed during embryonic genome activation. Here, we describe how many primate-restricted TEs have additional binding sites for lineage-specific transcription factors driving their expression during human gastrulation and later steps of fetal development. These TE integrants serve as lineage-specific enhancers fostering the transcription, amongst other targets, of KRAB-zinc finger proteins (KZFPs) of comparable evolutionary age, which in turn corral the activity of TE-embedded regulatory sequences in a similarly lineage-restricted fashion. Thus, TEs and their KZFP controllers play broad roles in shaping transcriptional networks during early human development.
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Affiliation(s)
- Julien Pontis
- Laboratory of Virology and Genetics, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.
| | - Cyril Pulver
- Laboratory of Virology and Genetics, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Christopher J Playfoot
- Laboratory of Virology and Genetics, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Evarist Planet
- Laboratory of Virology and Genetics, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Delphine Grun
- Laboratory of Virology and Genetics, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Sandra Offner
- Laboratory of Virology and Genetics, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Julien Duc
- Laboratory of Virology and Genetics, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Andrea Manfrin
- Laboratory for Stem Cell Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Matthias P Lutolf
- Laboratory for Stem Cell Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Didier Trono
- Laboratory of Virology and Genetics, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.
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39
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Li C, Zhang Y, Leng L, Pan X, Zhao D, Li X, Huang J, Bolund L, Lin G, Luo Y, Xu F. The single-cell expression profile of transposable elements and transcription factors in human early biparental and uniparental embryonic development. Front Cell Dev Biol 2022; 10:1020490. [PMID: 36438554 PMCID: PMC9691860 DOI: 10.3389/fcell.2022.1020490] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/17/2022] [Indexed: 10/24/2023] Open
Abstract
Transposable elements (TEs) and transcription factors (TFs) are involved in the precise regulation of gene expression during the preimplantation stage. Activation of TEs is a key event for mammalian embryonic genome activation and preimplantation early embryonic development. TFs are involved in the regulation of drastic changes in gene expression patterns, but an inventory of the interplay between TEs and TFs during normal/abnormal human embryonic development is still lacking. Here we used single-cell RNA sequencing data generated from biparental and uniparental embryos to perform an integrative analysis of TE and TF expression. Our results showed that endogenous retroviruses (ERVs) are mainly expressed during the minor embryonic genome activation (EGA) process of early embryos, while Alu is gradually expressed in the middle and later stages. Some important ERVs (e.g., LTR5_Hs, MLT2A1) and Alu TEs are expressed at significantly lower levels in androgenic embryos. Integrative analysis revealed that the expression of the transcription factors CTCF and POU5F1 is correlated with the differential expression of ERV TEs. Comparative coexpression network analysis further showed distinct expression levels of important TFs (e.g., LEUTX and ZSCAN5A) in dizygotic embryos vs. parthenogenetic and androgenic embryos. This systematic investigation of TE and TF expression in human early embryonic development by single-cell RNA sequencing provides valuable insights into mammalian embryonic development.
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Affiliation(s)
- Conghui Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Yue Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong, China
| | - Lizhi Leng
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Key Laboratory of Reproductive and Stem Cells Engineering, Ministry of Health, Changsha, China
- Reproductive & Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Xiaoguang Pan
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Depeng Zhao
- Department of Reproductive Medicine, Affiliated Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, China
| | - Xuemei Li
- Department of Reproductive Medicine, Affiliated Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, China
| | - Jinrong Huang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lars Bolund
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Ge Lin
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Key Laboratory of Reproductive and Stem Cells Engineering, Ministry of Health, Changsha, China
- Reproductive & Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Yonglun Luo
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Fengping Xu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- BGI Cell, BGI-Shenzhen, Shenzhen, China
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40
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Paloviita P, Vuoristo S. The non-coding genome in early human development - Recent advancements. Semin Cell Dev Biol 2022; 131:4-13. [PMID: 35177347 DOI: 10.1016/j.semcdb.2022.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/08/2022] [Accepted: 02/08/2022] [Indexed: 12/14/2022]
Abstract
Not that long ago, the human genome was discovered to be mainly non-coding, that is comprised of DNA sequences that do not code for proteins. The initial paradigm that non-coding is also non-functional was soon overturned and today the work to uncover the functions of non-coding DNA and RNA in human early embryogenesis has commenced. Early human development is characterized by large-scale changes in genomic activity and the transcriptome that are partly driven by the coordinated activation and repression of repetitive DNA elements scattered across the genome. Here we provide examples of recent novel discoveries of non-coding DNA and RNA interactions and mechanisms that ensure accurate non-coding activity during human maternal-to-zygotic transition and lineage segregation. These include studies on small and long non-coding RNAs, transposable element regulation, and RNA tailing in human oocytes and early embryos. High-throughput approaches to dissect the non-coding regulatory networks governing early human development are a foundation for functional studies of specific genomic elements and molecules that has only begun and will provide a wider understanding of early human embryogenesis and causes of infertility.
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Affiliation(s)
- Pauliina Paloviita
- Department of Obstetrics and Gynaecology, University of Helsinki, 00014 Helsinki, Finland
| | - Sanna Vuoristo
- Department of Obstetrics and Gynaecology, University of Helsinki, 00014 Helsinki, Finland.
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41
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Yu H, Chen M, Hu Y, Ou S, Yu X, Liang S, Li N, Yang M, Kong X, Sun C, Jia S, Zhang Q, Liu L, Hurst LD, Li R, Wang W, Wang J. Dynamic reprogramming of H3K9me3 at hominoid-specific retrotransposons during human preimplantation development. Cell Stem Cell 2022; 29:1031-1050.e12. [PMID: 35803225 DOI: 10.1016/j.stem.2022.06.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 04/06/2022] [Accepted: 06/08/2022] [Indexed: 12/13/2022]
Abstract
Reprogramming of H3K9me3-dependent heterochromatin is required for early development. How H3K9me3 is involved in early human development remains, however, largely unclear. Here, we resolve the temporal landscape of H3K9me3 during human preimplantation development and its regulation for diverse hominoid-specific retrotransposons. At the 8-cell stage, H3K9me3 reprogramming at hominoid-specific retrotransposons termed SINE-VNTR-Alu (SVA) facilitates interaction between certain promoters and SVA-derived enhancers, promoting the zygotic genome activation. In trophectoderm, de novo H3K9me3 domains prevent pluripotent transcription factors from binding to hominoid-specific retrotransposons-derived regulatory elements for inner cell mass (ICM)-specific genes. H3K9me3 re-establishment at SVA elements in the ICM is associated with higher transcription of DNA repair genes, when compared with naive human pluripotent stem cells. Our data demonstrate that species-specific reorganization of H3K9me3-dependent heterochromatin at hominoid-specific retrotransposons plays important roles during early human development, shedding light on how the epigenetic regulation for early development has evolved in mammals.
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Affiliation(s)
- Hanwen Yu
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Manqi Chen
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Yuanlang Hu
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China; The First Affiliated Hospital, Jinan University, Guangzhou 510630, China
| | - Songbang Ou
- Department of Obstetrics and Gynaecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Xiu Yu
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Shiqi Liang
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Niannian Li
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China; Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Mingzhu Yang
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Xuhui Kong
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Chuanbo Sun
- Laboratory of Medical Systems Biology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Shiqi Jia
- The First Affiliated Hospital, Jinan University, Guangzhou 510630, China
| | - Qingxue Zhang
- Department of Obstetrics and Gynaecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China; Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Laurence D Hurst
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Ruiqi Li
- Department of Obstetrics and Gynaecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.
| | - Wenjun Wang
- Department of Obstetrics and Gynaecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.
| | - Jichang Wang
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China.
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42
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Liu Q, Chen X, Qiao J. Advances in studying human gametogenesis and embryonic development in China. Biol Reprod 2022; 107:12-26. [PMID: 35788258 DOI: 10.1093/biolre/ioac134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 05/21/2022] [Accepted: 06/20/2022] [Indexed: 11/12/2022] Open
Abstract
Reproductive medicine in China has developed rapidly since 1988 due to the support from the government and scientific exploration. However, the success rate of assisted reproduction technology (ART) is around 30-40% and many unknown "black boxes" in gametogenesis and embryo development are still present. With the development of single-cell and low-input sequencing technologies, the network of transcriptome and epigenetic regulation (DNA methylation, chromatin accessibility, and histone modifications) during the development of human primordial germ cells (PGCs), gametes and embryos has been investigated in depth. Furthermore, pre-implantation genetic testing (PGT) has also rapidly developed. In this review, we summarize and analyze China's outstanding progress in these fields.
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Affiliation(s)
- Qiang Liu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Xi Chen
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Jie Qiao
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Research Units of Comprehensive Diagnosis and Treatment of Oocyte Maturation Arrest, Chinese Academy of Medical Sciences, Beijing, China
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43
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Zhang T, Zheng R, Li M, Yan C, Lan X, Tong B, Lu P, Jiang W. Active endogenous retroviral elements in human pluripotent stem cells play a role in regulating host gene expression. Nucleic Acids Res 2022; 50:4959-4973. [PMID: 35451484 PMCID: PMC9122532 DOI: 10.1093/nar/gkac265] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 03/22/2022] [Accepted: 04/01/2022] [Indexed: 12/20/2022] Open
Abstract
Human endogenous retroviruses, also called LTR elements, can be bound by transcription factors and marked by different histone modifications in different biological contexts. Recently, individual LTR or certain subclasses of LTRs such as LTR7/HERVH and LTR5_Hs/HERVK families have been identified as cis-regulatory elements. However, there are still many LTR elements with unknown functions. Here, we dissected the landscape of histone modifications and regulatory map of LTRs by integrating 98 ChIP-seq data in human embryonic stem cells (ESCs), and annotated the active LTRs enriching enhancer/promoter-related histone marks. Notably, we found that MER57E3 functionally acted as proximal regulatory element to activate respective ZNF gene. Additionally, HERVK transcript could mainly function in nucleus to activate the adjacent genes. Since LTR5_Hs/LTR5 was bound by many early embryo-specific transcription factors, we further investigated the expression dynamics in different pluripotent states. LTR5_Hs/LTR5/HERVK exhibited higher expression level in naïve ESCs and extended pluripotent stem cells (EPSCs). Functionally, the LTR5_Hs/LTR5 with high activity could serve as a distal enhancer to regulate the host genes. Ultimately, our study not only provides a comprehensive regulatory map of LTRs in human ESCs, but also explores the regulatory models of MER57E3 and LTR5_Hs/LTR5 in host genome.
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Affiliation(s)
- Tianzhe Zhang
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Ran Zheng
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Mao Li
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Chenchao Yan
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Xianchun Lan
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Bei Tong
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Pei Lu
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Wei Jiang
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Human Genetics Resource Preservation Center of Wuhan University, Wuhan 430071, China
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan 430071, China
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Pepin AS, Lafleur C, Lambrot R, Dumeaux V, Kimmins S. Sperm histone H3 lysine 4 tri-methylation serves as a metabolic sensor of paternal obesity and is associated with the inheritance of metabolic dysfunction. Mol Metab 2022; 59:101463. [PMID: 35183795 PMCID: PMC8931445 DOI: 10.1016/j.molmet.2022.101463] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/12/2022] [Accepted: 02/14/2022] [Indexed: 11/28/2022] Open
Abstract
OBJECTIVE Parental environmental exposures can strongly influence descendant risks for adult disease. How paternal obesity changes the sperm chromatin leading to the acquisition of metabolic disease in offspring remains controversial and ill-defined. The objective of this study was to assess (1) whether obesity induced by a high-fat diet alters sperm histone methylation; (2) whether paternal obesity can induce metabolic disturbances across generations; (3) whether there could be cumulative damage to the sperm epigenome leading to enhanced metabolic dysfunction in descendants; and (4) whether obesity-sensitive regions associate with embryonic epigenetic and transcriptomic profiles. Using a genetic mouse model of epigenetic inheritance, we investigated the role of histone H3 lysine 4 methylation (H3K4me3) in the paternal transmission of metabolic dysfunction. This transgenic mouse overexpresses the histone demethylase enzyme KDM1A in the developing germline and has an altered sperm epigenome at the level of histone H3K4 methylation. We hypothesized that challenging transgenic sires with a high-fat diet would further erode the sperm epigenome and lead to enhanced metabolic disturbances in the next generations. METHODS To assess whether paternal obesity can have inter- or transgenerational impacts, and if so to identify potential mechanisms of this non-genetic inheritance, we used wild-type C57BL/6NCrl and transgenic males with a pre-existing altered sperm epigenome. To induce obesity, sires were fed either a control or high-fat diet (10% or 60% kcal fat, respectively) for 10-12 weeks, then bred to wild-type C57BL/6NCrl females fed a regular diet. F1 and F2 descendants were characterized for metabolic phenotypes by examining the effects of paternal obesity by sex, on body weight, fat mass distribution, the liver transcriptome, intraperitoneal glucose, and insulin tolerance tests. To determine whether obesity altered the F0 sperm chromatin, native chromatin immunoprecipitation-sequencing targeting H3K4me3 was performed. To gain insight into mechanisms of paternal transmission, we compared our sperm H3K4me3 profiles with embryonic and placental chromatin states, histone modification, and gene expression profiles. RESULTS Obesity-induced alterations in H3K4me3 occurred in genes implicated in metabolic, inflammatory, and developmental processes. These processes were associated with offspring metabolic dysfunction and corresponded to genes enriched for H3K4me3 in embryos and overlapped embryonic and placenta gene expression profiles. Transgenerational susceptibility to metabolic disease was only observed when obese F0 had a pre-existing modified sperm epigenome. This coincided with increased H3K4me3 alterations in sperm and more severe phenotypes affecting their offspring. CONCLUSIONS Our data suggest sperm H3K4me3 might serve as a metabolic sensor that connects paternal diet with offspring phenotypes via the placenta. This non-DNA-based knowledge of inheritance has the potential to improve our understanding of how environment shapes heritability and may lead to novel routes for the prevention of disease. This study highlights the need to further study the connection between the sperm epigenome, placental development, and children's health. SUMMARY SENTENCE Paternal obesity impacts sperm H3K4me3 and is associated with placenta, embryonic and metabolic outcomes in descendants.
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Affiliation(s)
- Anne-Sophie Pepin
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Christine Lafleur
- Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC H9X 3V9, Canada
| | - Romain Lambrot
- Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC H9X 3V9, Canada
| | - Vanessa Dumeaux
- Department of Biology, PERFORM Center, Concordia University, Montreal, QC H4B 1R6, Canada
| | - Sarah Kimmins
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, QC H3G 1Y6, Canada; Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC H9X 3V9, Canada.
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45
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Mazid MA, Ward C, Luo Z, Liu C, Li Y, Lai Y, Wu L, Li J, Jia W, Jiang Y, Liu H, Fu L, Yang Y, Ibañez DP, Lai J, Wei X, An J, Guo P, Yuan Y, Deng Q, Wang Y, Liu Y, Gao F, Wang J, Zaman S, Qin B, Wu G, Maxwell PH, Xu X, Liu L, Li W, Esteban MA. Rolling back human pluripotent stem cells to an eight-cell embryo-like stage. Nature 2022; 605:315-324. [PMID: 35314832 DOI: 10.1038/s41586-022-04625-0] [Citation(s) in RCA: 129] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 03/10/2022] [Indexed: 11/08/2022]
Abstract
After fertilization, the quiescent zygote experiences a burst of genome activation that initiates a short-lived totipotent state. Understanding the process of totipotency in human cells would have broad applications. However, in contrast to in mice1,2, demonstration of the time of zygotic genome activation or the eight-cell (8C) stage in in vitro cultured human cells has not yet been reported, and the study of embryos is limited by ethical and practical considerations. Here we describe a transgene-free, rapid and controllable method for producing 8C-like cells (8CLCs) from human pluripotent stem cells. Single-cell analysis identified key molecular events and gene networks associated with this conversion. Loss-of-function experiments identified fundamental roles for DPPA3, a master regulator of DNA methylation in oocytes3, and TPRX1, a eutherian totipotent cell homeobox (ETCHbox) family transcription factor that is absent in mice4. DPPA3 induces DNA demethylation throughout the 8CLC conversion process, whereas TPRX1 is a key executor of 8CLC gene networks. We further demonstrate that 8CLCs can produce embryonic and extraembryonic lineages in vitro or in vivo in the form of blastoids5 and complex teratomas. Our approach provides a resource to uncover the molecular process of early human embryogenesis.
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Affiliation(s)
- Md Abdul Mazid
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Carl Ward
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Zhiwei Luo
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | | | - Yunpan Li
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yiwei Lai
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- BGI-Shenzhen, Shenzhen, China
| | - Liang Wu
- University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Jinxiu Li
- University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Wenqi Jia
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yu Jiang
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Key Laboratory of Zoonoses Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Hao Liu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Lixin Fu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yueli Yang
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Key Laboratory of Zoonoses Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - David P Ibañez
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Junjian Lai
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xiaoyu Wei
- University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Juan An
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Pengcheng Guo
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Key Laboratory of Zoonoses Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yue Yuan
- University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Qiuting Deng
- University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | | | | | - Fei Gao
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | | | - Shahriar Zaman
- Department of Genetic Engineering and Biotechnology, Faculty of Life and Earth Sciences, University of Rajshahi, Rajshahi, Bangladesh
| | - Baoming Qin
- Laboratory of Metabolism and Cell Fate, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | | | - Patrick H Maxwell
- Cambridge Institute for Medical Research, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China
| | | | - Wenjuan Li
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
| | - Miguel A Esteban
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
- BGI-Shenzhen, Shenzhen, China.
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Key Laboratory of Zoonoses Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China.
- Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing, China.
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Vuoristo S, Bhagat S, Hydén-Granskog C, Yoshihara M, Gawriyski L, Jouhilahti EM, Ranga V, Tamirat M, Huhtala M, Kirjanov I, Nykänen S, Krjutškov K, Damdimopoulos A, Weltner J, Hashimoto K, Recher G, Ezer S, Paluoja P, Paloviita P, Takegami Y, Kanemaru A, Lundin K, Airenne TT, Otonkoski T, Tapanainen JS, Kawaji H, Murakawa Y, Bürglin TR, Varjosalo M, Johnson MS, Tuuri T, Katayama S, Kere J. DUX4 is a multifunctional factor priming human embryonic genome activation. iScience 2022; 25:104137. [PMID: 35402882 PMCID: PMC8990217 DOI: 10.1016/j.isci.2022.104137] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 02/04/2022] [Accepted: 03/18/2022] [Indexed: 12/13/2022] Open
Abstract
Double homeobox 4 (DUX4) is expressed at the early pre-implantation stage in human embryos. Here we show that induced human DUX4 expression substantially alters the chromatin accessibility of non-coding DNA and activates thousands of newly identified transcribed enhancer-like regions, preferentially located within ERVL-MaLR repeat elements. CRISPR activation of transcribed enhancers by C-terminal DUX4 motifs results in the increased expression of target embryonic genome activation (EGA) genes ZSCAN4 and KHDC1P1. We show that DUX4 is markedly enriched in human zygotes, followed by intense nuclear DUX4 localization preceding and coinciding with minor EGA. DUX4 knockdown in human zygotes led to changes in the EGA transcriptome but did not terminate the embryos. We also show that the DUX4 protein interacts with the Mediator complex via the C-terminal KIX binding motif. Our findings contribute to the understanding of DUX4 as a regulator of the non-coding genome.
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Affiliation(s)
- Sanna Vuoristo
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177 Huddinge, Sweden.,Department of Obstetrics and Gynecology, 00014, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | - Shruti Bhagat
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177 Huddinge, Sweden.,RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Instutute for the Advanced Study of Human Biology, Kyoto University, Kyoto 606-8501, Japan
| | | | - Masahito Yoshihara
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177 Huddinge, Sweden
| | - Lisa Gawriyski
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Eeva-Mari Jouhilahti
- Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland
| | - Vipin Ranga
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
| | - Mahlet Tamirat
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
| | - Mikko Huhtala
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
| | - Ida Kirjanov
- Department of Obstetrics and Gynecology, 00014, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | - Sonja Nykänen
- Department of Obstetrics and Gynecology, 00014, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | - Kaarel Krjutškov
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177 Huddinge, Sweden.,Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland.,Competence Centre for Health Technologies, 51010 Tartu, Estonia.,University of Tartu, Department of Obstetrics and Gynecology, Institute of Clinical Medicine, 50406 Tartu, Estonia
| | | | - Jere Weltner
- Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland
| | - Kosuke Hashimoto
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Gaëlle Recher
- Laboratoire Photonique Numérique et Nanosciences, CNRS, Institut d'Optique Graduate School, University of Bordeaux, UMR 5298, 33400 Bordeaux, France
| | - Sini Ezer
- Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland.,Folkhälsan Research Center, 00290 Helsinki, Finland
| | - Priit Paluoja
- Competence Centre for Health Technologies, 51010 Tartu, Estonia.,Institute of Clinical Medicine, University of Tartu, 50090 Tartu, Estonia.,University of Helsinki, Doctoral Program in Population Health, 00014 Helsinki, Finland
| | - Pauliina Paloviita
- Department of Obstetrics and Gynecology, 00014, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | | | | | - Karolina Lundin
- Department of Obstetrics and Gynecology, 00014, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | - Tomi T Airenne
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
| | - Timo Otonkoski
- Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland.,Children's Hospital, Helsinki University Central Hospital, 00290
| | - Juha S Tapanainen
- Department of Obstetrics and Gynecology, 00014, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland.,Reproductive Medicine Unit, Helsinki University Hospital, 00290 Helsinki, Finland.,Oulu University Hospital, 90220 Oulu, Finland
| | - Hideya Kawaji
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako 351-0198, Japan.,Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Yasuhiro Murakawa
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Instutute for the Advanced Study of Human Biology, Kyoto University, Kyoto 606-8501, Japan.,IFOM, The FIRC Institute of Molecular Oncology, 20139 Milan, Italy.,Department of Medical Systems Genomics, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Thomas R Bürglin
- Department of Biomedicine, University of Basel, 4031 Basel, Switzerland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Mark S Johnson
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
| | - Timo Tuuri
- Department of Obstetrics and Gynecology, 00014, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland.,Reproductive Medicine Unit, Helsinki University Hospital, 00290 Helsinki, Finland
| | - Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177 Huddinge, Sweden.,Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland.,Folkhälsan Research Center, 00290 Helsinki, Finland
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177 Huddinge, Sweden.,Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland.,Folkhälsan Research Center, 00290 Helsinki, Finland
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Taubenschmid-Stowers J, Rostovskaya M, Santos F, Ljung S, Argelaguet R, Krueger F, Nichols J, Reik W. 8C-like cells capture the human zygotic genome activation program in vitro. Cell Stem Cell 2022; 29:449-459.e6. [PMID: 35216671 PMCID: PMC8901440 DOI: 10.1016/j.stem.2022.01.014] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/26/2021] [Accepted: 01/28/2022] [Indexed: 01/12/2023]
Abstract
The activation of the embryonic genome marks the first major wave of transcription in the developing organism. Zygotic genome activation (ZGA) in mouse 2-cell embryos and 8-cell embryos in humans is crucial for development. Here, we report the discovery of human 8-cell-like cells (8CLCs) among naive embryonic stem cells, which transcriptionally resemble the 8-cell human embryo. They express ZGA markers, including ZSCAN4 and LEUTX, and transposable elements, such as HERVL and MLT2A1. 8CLCs show reduced SOX2 levels and can be identified using TPRX1 and H3.Y marker proteins in vitro. Overexpression of the transcription factor DUX4 and spliceosome inhibition increase human ZGA-like transcription. Excitingly, the 8CLC markers TPRX1 and H3.Y are also expressed in ZGA-stage 8-cell human embryos and may thus be relevant in vivo. 8CLCs provide a unique opportunity to characterize human ZGA-like transcription and might provide critical insights into early events in embryogenesis in humans.
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Affiliation(s)
| | | | - Fátima Santos
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
| | - Sebastian Ljung
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | | | - Felix Krueger
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Jennifer Nichols
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EL, UK
| | - Wolf Reik
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK; Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
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48
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Sahinyan K, Blackburn DM, Simon MM, Lazure F, Kwan T, Bourque G, Soleimani VD. Application of ATAC-Seq for genome-wide analysis of the chromatin state at single myofiber resolution. eLife 2022; 11:72792. [PMID: 35188098 PMCID: PMC8901173 DOI: 10.7554/elife.72792] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 02/09/2022] [Indexed: 12/11/2022] Open
Abstract
Myofibers are the main components of skeletal muscle, which is the largest tissue in the body. Myofibers are highly adaptive and can be altered under different biological and disease conditions. Therefore, transcriptional and epigenetic studies on myofibers are crucial to discover how chromatin alterations occur in the skeletal muscle under different conditions. However, due to the heterogenous nature of skeletal muscle, studying myofibers in isolation proves to be a challenging task. Single-cell sequencing has permitted the study of the epigenome of isolated myonuclei. While this provides sequencing with high dimensionality, the sequencing depth is lacking, which makes comparisons between different biological conditions difficult. Here, we report the first implementation of single myofiber ATAC-Seq, which allows for the sequencing of an individual myofiber at a depth sufficient for peak calling and for comparative analysis of chromatin accessibility under various physiological and disease conditions. Application of this technique revealed significant differences in chromatin accessibility between resting and regenerating myofibers, as well as between myofibers from a mouse model of Duchenne Muscular Dystrophy (mdx) and wild-type (WT) counterparts. This technique can lead to a wide application in the identification of chromatin regulatory elements and epigenetic mechanisms in muscle fibers during development and in muscle-wasting diseases.
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Affiliation(s)
- Korin Sahinyan
- Department of Human Genetics, McGill University, Montreal, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Canada
| | - Darren M Blackburn
- Department of Human Genetics, McGill University, Montreal, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Canada
| | - Marie-Michelle Simon
- Department of Human Genetics, McGill University, Montreal, Canada.,McGill Genome Centre, Montreal, Canada
| | - Felicia Lazure
- Department of Human Genetics, McGill University, Montreal, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Canada
| | - Tony Kwan
- Department of Human Genetics, McGill University, Montreal, Canada.,McGill Genome Centre, Montreal, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, Canada.,McGill Genome Centre, Montreal, Canada.,Canadian Centre for Computational Genomics, Montreal, Canada
| | - Vahab D Soleimani
- Department of Human Genetics, McGill University, Montreal, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Canada
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49
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Masteika IF, Sathya A, Homma S, Miller BM, Boyce FM, Miller JB. Downstream events initiated by expression of FSHD-associated DUX4: Studies of nucleocytoplasmic transport, γH2AX accumulation, and Bax/Bak-dependence. Biol Open 2022; 11:274475. [PMID: 35191484 PMCID: PMC8890089 DOI: 10.1242/bio.059145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/12/2022] [Indexed: 12/15/2022] Open
Abstract
Abnormal expression in skeletal muscle of the double homeobox transcription factor DUX4 underlies pathogenesis in facioscapulohumeral muscular dystrophy (FSHD). Though multiple changes are known to be initiated by aberrant DUX4 expression, the downstream events initiated by DUX4 remain incompletely understood. In this study, we examined plausible downstream events initiated by DUX4. First, we found that nucleocytoplasmic protein export appeared to be decreased upon DUX4 expression as indicated by nuclear accumulation of a shuttle-GFP reporter. Second, building on studies from other labs, we showed that phospho(Ser139)-H2AX (γH2AX), an indicator of double-strand DNA breaks, accumulated both in human FSHD1 myotube nuclei upon endogenous DUX4 expression and in Bax-/-;Bak-/- (double knockout), SV40-immortalized mouse embryonic fibroblasts upon exogenous DUX4 expression. In contrast, DUX4-induced caspase 3/7 activation was prevented in Bax-/-;Bak-/- double knockout SV40-MEFs, but not by single knockouts of Bax, Bak, or Bid. Thus, aberrant DUX4 expression appeared to alter nucleocytoplasmic protein transport and generate double-strand DNA breaks in FSHD1 myotube nuclei, and the Bax/Bak pathway is required for DUX4-induced caspase activation but not γH2AX accumulation. These results add to our knowledge of downstream events induced by aberrant DUX4 expression and suggest possibilities for further mechanistic investigation.
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Affiliation(s)
- Isabel F Masteika
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Anvitha Sathya
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Sachiko Homma
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Bess M Miller
- Biological & Biomedical Sciences Program, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Frederick M Boyce
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Jeffrey Boone Miller
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts 02118, USA
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50
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Salavati M, Woolley SA, Cortés Araya Y, Halstead MM, Stenhouse C, Johnsson M, Ashworth CJ, Archibald AL, Donadeu FX, Hassan MA, Clark EL. Profiling of open chromatin in developing pig (Sus scrofa) muscle to identify regulatory regions. G3 (BETHESDA, MD.) 2022; 12:6460335. [PMID: 34897420 PMCID: PMC9210303 DOI: 10.1093/g3journal/jkab424] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
There is very little information about how the genome is regulated in domestic pigs (Sus scrofa). This lack of knowledge hinders efforts to define and predict the effects of genetic variants in pig breeding programs. To address this knowledge gap, we need to identify regulatory sequences in the pig genome starting with regions of open chromatin. We used the "Improved Protocol for the Assay for Transposase-Accessible Chromatin (Omni-ATAC-Seq)" to identify putative regulatory regions in flash-frozen semitendinosus muscle from 24 male piglets. We collected samples from the smallest-, average-, and largest-sized male piglets from each litter through five developmental time points. Of the 4661 ATAC-Seq peaks identified that represent regions of open chromatin, >50% were within 1 kb of known transcription start sites. Differential read count analysis revealed 377 ATAC-Seq defined genomic regions where chromatin accessibility differed significantly across developmental time points. We found regions of open chromatin associated with downregulation of genes involved in muscle development that were present in small-sized fetal piglets but absent in large-sized fetal piglets at day 90 of gestation. The dataset that we have generated provides a resource for studies of genome regulation in pigs and contributes valuable functional annotation information to filter genetic variants for use in genomic selection in pig breeding programs.
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Affiliation(s)
- Mazdak Salavati
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Shernae A Woolley
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Yennifer Cortés Araya
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Michelle M Halstead
- Department of Animal Science, University of California Davis, Davis, CA 95616, USA
| | - Claire Stenhouse
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
- Department of Animal Science, Texas A&M University, College Station, TX 77843, USA
| | - Martin Johnsson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala 750 07, Sweden
| | - Cheryl J Ashworth
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Alan L Archibald
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Francesc X Donadeu
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Musa A Hassan
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Emily L Clark
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
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