1
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Miskel D, Kurzella J, Rings F, Tholen E, Tesfaye D, Schellander K, Salilew-Wondim D, Held-Hoelker E, Große-Brinkhaus C, Hoelker M. Functional COPA is indispensable for early embryo development beyond major genome activation in bovines. Theriogenology 2025; 241:117415. [PMID: 40215828 DOI: 10.1016/j.theriogenology.2025.117415] [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: 01/15/2025] [Revised: 03/28/2025] [Accepted: 03/28/2025] [Indexed: 04/23/2025]
Abstract
Embryonic genome activation is divided into a minor and a major wave of transition to endogenous transcription. In bovines, minor genome activation begins early in the 2-cell stage and is completed by the 8-cell stage when major genome activation becomes dominant. While the activation of genes known to regulate early development have been studied extensively, genes involved in more central cellular functions have not been examined. Taking advantage of the CRISPR Cas9 system, the present study investigated the effect of knocking out the Golgi retrograde protein transporter COPA on early bovine development. After the electroporation of presumptive zygotes with Cas9 ribonucleoproteins targeting COPA exon 6, sequences of 2 (11 %) and 4-cell (16 %) embryos showed knockouts of COPA whereas 8-cell embryos and blastocysts did not, demonstrating that COPA is necessary for development to the 8-cell stage and beyond. Using a repair template containing silent mutations along the target site, COPA loss of wildtype was observed in 5 blastocysts, with successful knock-in of the template on at least one allele. This shows that an edited yet functional copy of COPA can save the developmental capacity of the embryo and demonstrates that Cas9 activity at the target region itself is not responsible for the loss of function. Together, the present study revealed that COPA is necessary for embryonic development, and that the timing of this necessity is before major genome activation onset. More generally, this study further demonstrates the utility of genome editing within reproductive biotechnology for the interrogation of gene function and early embryonic development.
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Affiliation(s)
- Dennis Miskel
- Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany.
| | - Jessica Kurzella
- Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany.
| | - Franca Rings
- Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany.
| | - Ernst Tholen
- Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany.
| | - Dawit Tesfaye
- Department of Biomedical Sciences, Animal Reproduction and Biotechnology Laboratory, Colorado State University, 3105 Rampart Rd, Fort Collins, CO, 80521, United States.
| | - Karl Schellander
- Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany.
| | - Dessie Salilew-Wondim
- Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany; Department of Animal Science, Biotechnology and Reproduction of farm animals, University of Goettingen, Burckhardtweg 2, 37077, Goettingen, Germany.
| | - Eva Held-Hoelker
- Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany; Department of Animal Science, Biotechnology and Reproduction of farm animals, University of Goettingen, Burckhardtweg 2, 37077, Goettingen, Germany.
| | - Christine Große-Brinkhaus
- Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany.
| | - Michael Hoelker
- Department of Animal Science, Biotechnology and Reproduction of farm animals, University of Goettingen, Burckhardtweg 2, 37077, Goettingen, Germany.
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2
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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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3
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Zhang J, Li H, Li L, Wu J, Song L, Liu X, Pan Z, Zhou C, Li W, Liu Z, Jiao M, Hu M, Dong Z, Zhang H, Shi B, Wang Y, Wang D, Carter B, Zhao S, Ren G, Zhao Y, Zhang Y. Super RNA Pol II domains enhance minor ZGA through 3D interaction to ensure the integrity of major transcriptional waves in late-ZGA mammals. CELL GENOMICS 2025:100856. [PMID: 40315839 DOI: 10.1016/j.xgen.2025.100856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Revised: 01/24/2025] [Accepted: 04/02/2025] [Indexed: 05/04/2025]
Abstract
Zygotic genome activation (ZGA) occurs at distinct stages across mammals, with mice initiating ZGA at the 2-cell stage and bovines and humans activating the process in the 4- to 8-cell stages. RNA polymerase II (RNA Pol II) gradually initiates ZGA in mice, but regulation in late-ZGA species remains unclear. Here, RNA Pol II profiling in bovine embryos identified strong intergenic clusters that boost minor ZGA gene expression via chromatin interactions and are named super RNA Pol II domains (SPDs). CRISPRi perturbation of SPDs in bovine embryos decreases the expression of minor ZGA genes, whereas the knockdown of these genes disrupts major ZGA and embryogenesis. Rapid enhancement of minor ZGA genes also occurs in human embryos. Alternatively, mouse and porcine oocytes precociously express these minor ZGA genes without SPDs. Thus, SPDs appear to be an adaptation in bovine embryos, promoting minor ZGA gene expression to comparable levels as early-ZGA species, illuminating species-specific regulation of ZGA timing.
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Affiliation(s)
- Jingcheng Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling 712100, China
| | - Hengkuan Li
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling 712100, China
| | - Linmi Li
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling 712100, China; Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jie Wu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling 712100, China
| | - Linjie Song
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling 712100, China; College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xin Liu
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhangyuan Pan
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Chuan Zhou
- College of Veterinary Medicine, Hunan Agricultural University, Changsha 410000, China
| | - Wenying Li
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling 712100, China; Yazhouwan National Laboratory, 8 Huanjin Road, Yazhou District, Sanya City, Hainan Province 572024, China
| | - Zixiao Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling 712100, China; Yazhouwan National Laboratory, 8 Huanjin Road, Yazhou District, Sanya City, Hainan Province 572024, China
| | - Mei Jiao
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling 712100, China
| | - Mingyang Hu
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Yazhouwan National Laboratory, 8 Huanjin Road, Yazhou District, Sanya City, Hainan Province 572024, China
| | - Zhenyu Dong
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling 712100, China
| | - Hexu Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling 712100, China
| | - Binqiang Shi
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling 712100, China
| | - Yong Wang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling 712100, China
| | - Debao Wang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling 712100, China
| | - Benjamin Carter
- Department of Biochemistry, Purdue University, 175 S University Street, West Lafayette, IN 47907, USA
| | - Shuhong Zhao
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Yazhouwan National Laboratory, 8 Huanjin Road, Yazhou District, Sanya City, Hainan Province 572024, China.
| | - Gang Ren
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling 712100, China; College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
| | - Yunxia Zhao
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Yazhouwan National Laboratory, 8 Huanjin Road, Yazhou District, Sanya City, Hainan Province 572024, China.
| | - Yong Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling 712100, China.
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4
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Davenport KM, Lockhart K, Stoecklein K, Schnabel RD, Spencer TE, Ortega MS. Genome-wide association analyses identify single-nucleotide polymorphisms associated with in vitro embryo cleavage and blastocyst rates in Holstein bulls. J Dairy Sci 2025:S0022-0302(25)00287-5. [PMID: 40306429 DOI: 10.3168/jds.2025-26496] [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: 02/19/2025] [Accepted: 03/31/2025] [Indexed: 05/02/2025]
Abstract
Reproductive success is an essential component of profitable and sustainable dairy operations. Although selection for production traits such as milk yield has led to a decline in fertility in dairy cattle, strategies including assisted reproductive technologies such as in vitro fertilization and embryo transfer, as well as genomic selection for fertility traits, are being implemented to help mitigate this loss. Previous studies have identified genetic markers associated with fertility traits such as daughter pregnancy rate, conception rate, and interval to first conception. However, genetic markers associated with in vitro embryo development have yet to be explored. Therefore, this study aimed to identify genetic markers associated with in vitro embryo cleavage and blastocyst rates with the future goal of creating an index to select bulls with superior abilities to produce embryos in vitro. Rigorous in vitro fertilization trials identified Holstein bulls with divergent abilities to produce embryos that successfully cleave and develop into blastocysts in vitro. A total of 40 bulls with embryo cleavage and blastocyst rate phenotypes were whole genome sequenced. Sequencing was performed on an Illumina platform with PE150 reads followed by cleaning, mapping to ARS-UCD1.2, variant calling with GATK HaplotypeCaller, and quality control following the 1000 Bulls Genomes Project best practices. Genome-wide association analyses identified 819 and 442 SNPs associated with embryo cleavage and blastocyst rates, respectively. Significant regions on chromosomes 15, 18, 21, 22, and 23 were in linkage disequilibrium with QTL previously associated with reproductive traits in cattle. Further, a region on chromosome 28 with the most significant variant associated with cleavage rate contained several synonymous variants in EGLN1, which is a critical component of the hypoxia inducible pathway. An additional region on chromosome 18 associated with cleavage rate contained a missense variant in SMG9, a gene involved in the nonsense-mediated mRNA decay pathway. A region on chromosome 21 associated with blastocyst rate also contained variants in regulatory regions downstream from AEN, a gene required for efficient DNA fragmentation during the p53-dependent apoptosis pathway. In summary, this study identified a preliminary collection of genomic regions associated with embryo cleavage and blastocyst rates in vitro that contain relevant genes and other QTL associated with reproductive traits in cattle. These regions, after validation, could contribute to a selection index for identification of bulls with genetic predispositions to produce a greater number of embryos in vitro for use in assisted reproduction techniques.
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Affiliation(s)
- Kimberly M Davenport
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211; Department of Animal Sciences, Washington State University, Pullman, WA 99164
| | - Kelsey Lockhart
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211
| | - Katy Stoecklein
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211
| | - Thomas E Spencer
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211; Division of Obstetrics, Gynecology, and Women's Health, University of Missouri, Columbia, MO 65211
| | - M Sofia Ortega
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53715.
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5
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Burton A, Torres-Padilla ME. Epigenome dynamics in early mammalian embryogenesis. Nat Rev Genet 2025:10.1038/s41576-025-00831-4. [PMID: 40181107 DOI: 10.1038/s41576-025-00831-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/04/2025] [Indexed: 04/05/2025]
Abstract
During early embryonic development in mammals, the totipotency of the zygote - which is reprogrammed from the differentiated gametes - transitions to pluripotency by the blastocyst stage, coincident with the first cell fate decision. These changes in cellular potency are accompanied by large-scale alterations in the nucleus, including major transcriptional, epigenetic and architectural remodelling, and the establishment of the DNA replication programme. Advances in low-input genomics and loss-of-function methodologies tailored to the pre-implantation embryo now enable these processes to be studied at an unprecedented level of molecular detail in vivo. Such studies have provided new insights into the genome-wide landscape of epigenetic reprogramming and chromatin dynamics during this fundamental period of pre-implantation development.
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Affiliation(s)
- Adam Burton
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, München, Germany
| | - Maria-Elena Torres-Padilla
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, München, Germany.
- Faculty of Biology, Ludwig-Maximilians Universität, München, Germany.
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6
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Pankammoon P, Salinas MBS, Thitaram C, Sathanawongs A. The Complexities of Interspecies Somatic Cell Nuclear Transfer: From Biological and Molecular Insights to Future Perspectives. Int J Mol Sci 2025; 26:3310. [PMID: 40244161 PMCID: PMC11989385 DOI: 10.3390/ijms26073310] [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: 03/11/2025] [Revised: 03/29/2025] [Accepted: 03/31/2025] [Indexed: 04/18/2025] Open
Abstract
For nearly three decades, interspecies somatic cell nuclear transfer (iSCNT) has been explored as a potential tool for cloning, regenerative medicine, and wildlife conservation. However, developmental inefficiencies remain a major challenge, largely due to persistent barriers in nucleocytoplasmic transport, mitonuclear communication, and epigenome crosstalk. This review synthesized peer-reviewed English articles from PubMed, Web of Science, and Scopus, spanning nearly three decades, using relevant keywords to explore the molecular mechanisms underlying iSCNT inefficiencies and potential improvement strategies. We highlight recent findings deepening the understanding of interspecies barriers in iSCNT, emphasizing their interconnected complexities, including the following: (1) nucleocytoplasmic incompatibility may disrupt nuclear pore complex (NPC) assembly and maturation, impairing the nuclear transport of essential transcription factors (TFs), embryonic genome activation (EGA), and nuclear reprogramming; (2) mitonuclear incompatibility could lead to nuclear and mitochondrial DNA (nDNA-mtDNA) mismatches, affecting electron transport chain (ETC) assembly, oxidative phosphorylation, and energy metabolism; (3) these interrelated incompatibilities can further influence epigenetic regulation, potentially leading to incomplete epigenetic reprogramming in iSCNT embryos. Addressing these challenges requires a multifaceted, species-specific approach that balances multiple incompatibilities rather than isolating a single factor. Gaining insight into the molecular interactions between the donor nucleus and recipient cytoplast, coupled with optimizing strategies tailored to specific pairings, could significantly enhance iSCNT efficiency, ultimately transforming experimental breakthroughs into real-world applications in reproductive biotechnology, regenerative medicine, and species conservation.
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Affiliation(s)
- Peachanika Pankammoon
- Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand; (P.P.); (C.T.)
| | - Marvin Bryan Segundo Salinas
- Department of Basic Veterinary Sciences, College of Veterinary Science and Medicine, Central Luzon State University, Science City of Muñoz 3120, Nueva Ecija, Philippines;
| | - Chatchote Thitaram
- Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand; (P.P.); (C.T.)
- Elephant, Wildlife and Companion Animals Research Group, Chiang Mai University, Chiang Mai 50100, Thailand
| | - Anucha Sathanawongs
- Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand; (P.P.); (C.T.)
- Elephant, Wildlife and Companion Animals Research Group, Chiang Mai University, Chiang Mai 50100, Thailand
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7
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Kojima ML, Hoppe C, Giraldez AJ. The maternal-to-zygotic transition: reprogramming of the cytoplasm and nucleus. Nat Rev Genet 2025; 26:245-267. [PMID: 39587307 PMCID: PMC11928286 DOI: 10.1038/s41576-024-00792-0] [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] [Accepted: 10/08/2024] [Indexed: 11/27/2024]
Abstract
A fertilized egg is initially transcriptionally silent and relies on maternally provided factors to initiate development. For embryonic development to proceed, the oocyte-inherited cytoplasm and the nuclear chromatin need to be reprogrammed to create a permissive environment for zygotic genome activation (ZGA). During this maternal-to-zygotic transition (MZT), which is conserved in metazoans, transient totipotency is induced and zygotic transcription is initiated to form the blueprint for future development. Recent technological advances have enhanced our understanding of MZT regulation, revealing common themes across species and leading to new fundamental insights about transcription, mRNA decay and translation.
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Affiliation(s)
- Mina L Kojima
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Caroline Hoppe
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA.
- Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA.
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8
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Oomen ME, Rodriguez-Terrones D, Kurome M, Zakhartchenko V, Mottes L, Simmet K, Noll C, Nakatani T, Mourra-Diaz CM, Aksoy I, Savatier P, Göke J, Wolf E, Kaessmann H, Torres-Padilla ME. An atlas of transcription initiation reveals regulatory principles of gene and transposable element expression in early mammalian development. Cell 2025; 188:1156-1174.e20. [PMID: 39837330 DOI: 10.1016/j.cell.2024.12.013] [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: 04/11/2023] [Revised: 10/26/2024] [Accepted: 12/10/2024] [Indexed: 01/23/2025]
Abstract
Transcriptional activation of the embryonic genome (EGA) is a major developmental landmark enabling the embryo to become independent from maternal control. The magnitude and control of transcriptional reprogramming during this event across mammals remains poorly understood. Here, we developed Smart-seq+5' for high sensitivity, full-length transcript coverage and simultaneous capture of 5' transcript information from single cells and single embryos. Using Smart-seq+5', we profiled 34 developmental stages in 5 mammalian species and provide an extensive characterization of the transcriptional repertoire of early development before, during, and after EGA. We demonstrate widespread transposable element (TE)-driven transcription across species, including, remarkably, of DNA transposons. We identify 19,657 TE-driven genic transcripts, suggesting extensive TE co-option in early development over evolutionary timescales. TEs display similar expression dynamics across species and species-specific patterns, suggesting shared and divergent regulation. Our work provides a powerful resource for understanding transcriptional regulation of mammalian development.
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Affiliation(s)
- Marlies E Oomen
- Institute of Epigenetics and Stem Cells, Helmholtz Munich, Munich, Germany
| | | | - Mayuko Kurome
- Genzentrum, Ludwig-Maximilians-Universität, Munich, Germany
| | | | - Lorenza Mottes
- Institute of Epigenetics and Stem Cells, Helmholtz Munich, Munich, Germany
| | - Kilian Simmet
- Genzentrum, Ludwig-Maximilians-Universität, Munich, Germany
| | - Camille Noll
- Institute of Epigenetics and Stem Cells, Helmholtz Munich, Munich, Germany
| | | | | | - Irene Aksoy
- Université Lyon 1, INSERM U1208, INRAE USC 1361, 69500 Bron, France
| | - Pierre Savatier
- Université Lyon 1, INSERM U1208, INRAE USC 1361, 69500 Bron, France; Platform PrimaStem, INSERM U1208, INRAE USC 1361, 69500 Bron, France
| | - Jonathan Göke
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore; Department of Statistics and Data Science, National University of Singapore, Singapore, Singapore
| | - Eckhard Wolf
- Genzentrum, Ludwig-Maximilians-Universität, Munich, Germany
| | - Henrik Kaessmann
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Maria-Elena Torres-Padilla
- Institute of Epigenetics and Stem Cells, Helmholtz Munich, Munich, Germany; Faculty of Biology, Ludwig-Maximilians Universität, Munich, Germany.
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Pankammoon P, Qing Y, Zhao H, Jiao D, Li H, Wang F, Wiriyahdamrong T, Guo J, Li W, Chuammitri P, Thitaram C, Wei H, Sathanowongs A. Transcriptomic insights into developmental arrest in fluorescent labeling transgenic Asian elephant ( Elephas maximus) embryos via inter-order cloning. Front Cell Dev Biol 2025; 13:1532962. [PMID: 40092629 PMCID: PMC11907086 DOI: 10.3389/fcell.2025.1532962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2024] [Accepted: 01/27/2025] [Indexed: 03/19/2025] Open
Abstract
Introduction Asian elephants (Elephas maximus) provide a unique model for studying cloning in large mammals. As an endangered species with declining populations and limited oocyte availability, interspecies somatic cell nuclear transfer (iSCNT) combined with transcriptomic analysis holds promise for advancing iSCNT embryonic arrest development and further facilitating applications in conservation efforts, therapeutic cloning, and regenerative medicine. Methods This study conducted low-input RNA sequencing analyses on transgenic Asian elephant-pig (AE-P) inter-order cloned embryos expressing enhanced green fluorescent protein (EGFP) at the 2- and 4-cell stages. Differential gene expressions, pathway enrichment, and hub gene analyses were performed to identify the molecular mechanisms and core genes influencing normal and arrest development. Results and Discussion Approximately 25% of clean reads successfully aligned with the Asian elephant genome. The transcriptomic analysis revealed that inter-order cloned embryos with earlier cleavage at the 2- and 4-cell stages exhibited signs of residual transcriptomic memory and incomplete epigenetic reprogramming, while arrested embryos showed indications of nucleocytoplasmic incompatibility and nDNA-mtDNA mismatch. Hub gene analyses indicated core genes such as NDUFC2, NDUFS3, NDUFAB1, SDHC, SDHB, NUP54, NUP43, NUP37, NDC1, CDK1, and CCNB1 linked to energy production, nucleocytoplasmic transport, and cell cycle regulation highlighting the overall challenges in cloning Asian elephant inter-order embryos. Altogether, the analysis of high-throughput sequencing enhances the reliability of iSCNT production in this study, advancing our understanding of cellular reprogramming and molecular roadblocks in AE-P inter-order cloned embryos. Transcriptomic analyses have identified key factors contributing to developmental barriers in iSCNT, offering valuable insights into the complexities of these challenges.
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Affiliation(s)
| | - Yubo Qing
- Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
- Science and Technology Department of Yunnan Province, Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Heng Zhao
- Science and Technology Department of Yunnan Province, Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Deling Jiao
- Science and Technology Department of Yunnan Province, Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Honghui Li
- Science and Technology Department of Yunnan Province, Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Fengchong Wang
- Science and Technology Department of Yunnan Province, Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- College of Animal Science, Yunnan Agricultural University, Kunming, China
| | - Thanapa Wiriyahdamrong
- Science and Technology Department of Yunnan Province, Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- College of Animal Science, Yunnan Agricultural University, Kunming, China
| | - Jianxiong Guo
- Science and Technology Department of Yunnan Province, Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
| | - Wengui Li
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | | | - Chatchote Thitaram
- Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Hongjiang Wei
- Science and Technology Department of Yunnan Province, Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
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10
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Sangalli JR, Nociti RP, Chiaratti MR, Bridi A, Botigelli RC, Ambrizi DR, de Almeida Saraiva HFR, Perecin F, da Silveira JC, Ross PJ, Meirelles FV. Beta-hydroxybutyrate alters bovine preimplantation embryo development through transcriptional and epigenetic mechanisms†. Biol Reprod 2025; 112:253-272. [PMID: 39668404 DOI: 10.1093/biolre/ioae175] [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: 10/11/2023] [Revised: 07/10/2024] [Accepted: 11/25/2024] [Indexed: 12/14/2024] Open
Abstract
Developing embryos are susceptible to fluctuations in the nutrients and metabolites concentrations within the reproductive tract, which can lead to alterations in their developmental trajectory. Ketotic dairy cows have diminished fertility, and elevated levels of the ketone body beta-hydroxybutyrate (BHB) have been associated with poor embryonic development. We used an in vitro model based on either in vitro fertilization (IVF) or parthenogenesis to investigate the effects of BHB on the preimplantation bovine embryo development, epigenome, and transcriptome. Embryo culture medium was supplemented with BHB at a similar concentration to that present in the blood of cows suffering with severe ketosis, followed by analysis of blastocysts formation rate, diameter, total number of cells, levels of H3K9 beta-hydroxybutyrylation (H3K9bhb), apoptosis, and transcriptional alterations. As a result, we observed that BHB reduced the blastocysts rates, the diameter and the total number of cells in both parthenotes and IVF embryos. Exposure to BHB for either 3 or 7 days greatly increased the H3K9bhb levels in parthenotes at the 8-cells and blastocyst stages, and affected the expression of HDAC1, TET1, DNMT1, KDM6B, NANOG, and MTHFD2 genes. Additionally, culture of IVF embryos with BHB for 7 days dramatically increased H3K9bhb and reduced NANOG in blastocysts. RNA-seq analysis of IVF blastocysts revealed that BHB modulated the expression of 118 genes, which were involved with biological processes such as embryonic development, implantation, reproduction, proliferation, and metabolism. These findings provided valuable insights into the mechanisms through which BHB disrupts preimplantation embryonic development and affects the fertility in dairy cows.
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Affiliation(s)
- Juliano Rodrigues Sangalli
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of Sao Paulo Pirassununga, São Paulo, Brazil
| | - Ricardo Perecin Nociti
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of Sao Paulo Pirassununga, São Paulo, Brazil
- Centre de Recherche en Reproduction Animale (CRRA), Faculty of Veterinary Medicine, University of Montreal Saint-Hyacinthe, Quebec, Canada
| | - Marcos Roberto Chiaratti
- Department of Genetics and Evolution, Center of Biological and Health Sciences, Federal University of São Carlos, São Paulo, Brazil
| | - Alessandra Bridi
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of Sao Paulo Pirassununga, São Paulo, Brazil
| | | | - Dewison Ricardo Ambrizi
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of Sao Paulo Pirassununga, São Paulo, Brazil
| | | | - Felipe Perecin
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of Sao Paulo Pirassununga, São Paulo, Brazil
| | - Juliano Coelho da Silveira
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of Sao Paulo Pirassununga, São Paulo, Brazil
| | - Pablo Juan Ross
- Department of Animal Science, University of California, Davis, California, USA
| | - Flávio Vieira Meirelles
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of Sao Paulo Pirassununga, São Paulo, Brazil
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11
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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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12
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Liu Z, Li D, Deng M, Zhou L, Wang J, Liu L, Mao W, Lu H, Xu X, Wang F, Wan Y. METTL3 improves the development of somatic cell nuclear transfer embryos through AURKB and H3S10ph in goats. Int J Biol Macromol 2025; 286:138546. [PMID: 39653227 DOI: 10.1016/j.ijbiomac.2024.138546] [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: 07/02/2024] [Revised: 12/06/2024] [Accepted: 12/06/2024] [Indexed: 12/12/2024]
Abstract
Developmental abnormalities are more common in somatic cell nuclear transfer (SCNT) embryos due to epigenetic barriers that occur during the maternal-to-zygotic transition (MZT). N6-methyladenosine (m6A) is an RNA epigenetic modification that plays a significant role in numerous biological processes. However, the relationship between m6A and SCNT embryonic development is largely unexplored. In the present study, we found that the low expression of m6A methyltransferase-like 3 (METTL3) was associated with developmental arrest before zygotic genome activation (ZGA) in goat SCNT embryos and that karyokinesis defects were evident during their development. Notably, we demonstrated that METTL3 overexpression rescued the karyokinesis abnormalities, enhanced embryonic development and elevated the blastocyst formation rate. Further experiments revealed that METTL3 could mitigate the defects of maternal mRNA degradation, enhance the translation of Aurora kinase B (AURKB) and increase the phosphorylation of serine 10 on histone H3 (H3S10ph) to ensure the normal karyokinesis in SCNT embryos before ZGA in goats. Overall, our study highlights the essential role of METTL3 in enhancing the development of goat SCNT embryos. These findings indicate that METTL3 is critical for optimal SCNT efficiency and advance our understanding of m6A's role in embryonic development.
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Affiliation(s)
- Zifei Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; Changzhou Maternal and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University; Changzhou Key Laboratory of Maternal and Child Health Medicine, Changzhou 213003, Jiangsu, China
| | - Dongxu Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Mingtian Deng
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Lei Zhou
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jingang Wang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Liang Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Weijia Mao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Honghui Lu
- Department of Animal Husbandry & Veterinary, Haimen distinct, Nantong 226000, China
| | - Xinsong Xu
- Department of Animal Husbandry & Veterinary, Haimen distinct, Nantong 226000, China
| | - Feng Wang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yongjie Wan
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
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13
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Yaşar B, Boskovic N, Ivask M, Weltner J, Jouhilahti EM, Vill P, Skoog T, Jaakma Ü, Kere J, Bürglin TR, Katayama S, Org T, Kurg A. Molecular cloning of PRD-like homeobox genes expressed in bovine oocytes and early IVF embryos. BMC Genomics 2024; 25:1048. [PMID: 39506635 PMCID: PMC11542365 DOI: 10.1186/s12864-024-10969-w] [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: 05/03/2024] [Accepted: 10/28/2024] [Indexed: 11/08/2024] Open
Abstract
BACKGROUND Embryonic genome activation (EGA) is a critical step in early embryonic development, as it marks the transition from relying on maternal factors to the initiation of transcription from embryo's own genome. The factors associated with EGA are not well understood and need further investigation. PRD-like (PRDL) homeodomain transcription factors (TFs) are considered to play crucial roles in this early event during development but these TFs have evolved differently, even within mammalian lineages. Different numbers of PRDL TFs have been predicted in bovine (Bos taurus); however, their divergent evolution requires species-specific confirmation and functional investigations. RESULTS In this study, we conducted molecular cloning of mRNAs for the PRDL TFs ARGFX, DUXA, LEUTX, NOBOX, TPRX1, TPRX2, and TPRX3 in bovine oocytes or in vitro fertilized (IVF) preimplantation embryos. Our results confirmed the expression of PRDL TF genes in early bovine development at the cDNA level and uncovered their structures. For each investigated PRDL TF gene, we isolated at least one homeodomain-encoding cDNA fragment, indicative of DNA binding and thus potential role in transcriptional regulation in developing bovine embryos. Additionally, our cDNA cloning approach allowed us to reveal breed-related differences in bovine, as evidenced by the identification of a high number of single nucleotide variants (SNVs) across the PRDL class homeobox genes. Subsequently, we observed the prediction of the 9aa transactivation domain (9aaTAD) motif in the putative protein sequence of TPRX3 leading us to conduct functional analysis of this gene. We demonstrated that the TPRX3 overexpression in bovine fibroblast induces not only protein-coding genes but also short noncoding RNAs involved in splicing and RNA editing. We supported this finding by identifying a shared set of genes between our and published bovine early embryo development datasets. CONCLUSIONS Providing full-length cDNA evidence for previously predicted homeobox genes that belong to PRDL class improves the annotation of the bovine genome. Updating the annotation with seven developmentally-important genes will enhance the accuracy of RNAseq analysis with datasets derived from bovine preimplantation embryos. In addition, the absence of TPRX3 in humans highlights the species-specific and TF-specific regulation of biological processes during early embryo development.
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Affiliation(s)
- Barış Yaşar
- Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.
- Department of Medicine Huddinge, Karolinska Institutet, Huddinge, Sweden.
| | - Nina Boskovic
- Department of Medicine Huddinge, Karolinska Institutet, Huddinge, Sweden
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Marilin Ivask
- Chair of Animal Breeding and Biotechnology, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia
- Department of Pathophysiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Jere Weltner
- Folkhälsan Research Centre, Helsinki, Finland
- Stem Cells and Metabolism and Research Program, University of Helsinki, Helsinki, Finland
| | - Eeva-Mari Jouhilahti
- Folkhälsan Research Centre, Helsinki, Finland
- Stem Cells and Metabolism and Research Program, University of Helsinki, Helsinki, Finland
| | - Piibe Vill
- Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Tiina Skoog
- Department of Medicine Huddinge, Karolinska Institutet, Huddinge, Sweden
| | - Ülle Jaakma
- Chair of Animal Breeding and Biotechnology, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Juha Kere
- Department of Medicine Huddinge, Karolinska Institutet, Huddinge, Sweden
- Folkhälsan Research Centre, Helsinki, Finland
- Stem Cells and Metabolism and Research Program, University of Helsinki, Helsinki, Finland
| | - Thomas R Bürglin
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Shintaro Katayama
- Department of Medicine Huddinge, Karolinska Institutet, Huddinge, Sweden
- Folkhälsan Research Centre, Helsinki, Finland
- Stem Cells and Metabolism and Research Program, University of Helsinki, Helsinki, Finland
| | - Tõnis Org
- Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Centre for Genomics, Evolution and Medicine, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Ants Kurg
- Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
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14
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Current JZ, Chaney HL, Zhang M, Dugan EM, Chimino GL, Yao J. Characterization of bovine long non-coding RNAs, OOSNCR1, OOSNCR2 and OOSNCR3, and their roles in oocyte maturation and early embryonic development. Reprod Biol 2024; 24:100915. [PMID: 38936296 DOI: 10.1016/j.repbio.2024.100915] [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: 10/31/2023] [Revised: 06/11/2024] [Accepted: 06/16/2024] [Indexed: 06/29/2024]
Abstract
In mammals, early embryogenesis relies heavily on the regulation of maternal transcripts including protein-coding and non-coding RNAs stored in oocytes. In this study, the expression of three bovine oocyte expressed long non-coding RNAs (lncRNAs), OOSNCR1, OOSNCR2, and OOSNCR3, was characterized in somatic tissues, the ovarian follicle, and throughout early embryonic development. Moreover, the functional requirement of each transcript during oocyte maturation and early embryonic development was investigated using a siRNA-mediated knockdown approach. Tissue distribution analysis revealed that OOSNCR1, OOSNCR2 and OOSNCR3 are predominantly expressed in fetal ovaries. Follicular cell expression analysis revealed that these lncRNAs are highly expressed in the oocytes, with minor expression detected in the cumulus cells (CCs) and mural granulosa cells (mGCs). The expression for all three genes was highest during oocyte maturation, decreased at fertilization, and ceased altogether by the 16-cell stage. Knockdown of OOSNCR1, OOSNCR2 and OOSNCR3 in immature oocytes was achieved by microinjection of the cumulus-enclosed germinal vesicle (GV) oocytes with siRNAs targeting these lncRNAs. Knockdown of OOSNCR1, OOSNCR2 and OOSNCR3 did not affect cumulus expansion, but oocyte survival at 12 h post-insemination was significantly reduced. In addition, knockdown of OOSNCR1, OOSNCR2 and OOSNCR3 in immature oocytes resulted in a decreased rate of blastocyst development, and reduced expression of genes associated with oocyte competency such as nucleoplasmin 2 (NPM2), growth differentiation factor 9 (GDF9), bone morphogenetic protein 15 (BMP15), and JY-1 in MII oocytes. The data herein suggest a functional requirement of OOSNCR1, OOSNCR2, and OOSNCR3 during bovine oocyte maturation and early embryogenesis.
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Affiliation(s)
- Jaelyn Z Current
- Laboratory of Animal Biotechnology and Genomics, Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, United States
| | - Heather L Chaney
- Laboratory of Animal Biotechnology and Genomics, Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, United States
| | - Mingxiang Zhang
- Laboratory of Animal Biotechnology and Genomics, Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, United States
| | - Emily M Dugan
- Laboratory of Animal Biotechnology and Genomics, Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, United States
| | - Gianna L Chimino
- Laboratory of Animal Biotechnology and Genomics, Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, United States
| | - Jianbo Yao
- Laboratory of Animal Biotechnology and Genomics, Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, United States.
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15
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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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16
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Schettini GP, Morozyuk M, Biase FH. Identification of novel cattle (Bos taurus) genes and biological insights of their function in pre-implantation embryo development. BMC Genomics 2024; 25:775. [PMID: 39118001 PMCID: PMC11313146 DOI: 10.1186/s12864-024-10685-5] [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: 05/29/2024] [Accepted: 08/02/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND Appropriate regulation of genes expressed in oocytes and embryos is essential for acquisition of developmental competence in mammals. Here, we hypothesized that several genes expressed in oocytes and pre-implantation embryos remain unknown. Our goal was to reconstruct the transcriptome of oocytes (germinal vesicle and metaphase II) and pre-implantation cattle embryos (blastocysts) using short-read and long-read sequences to identify putative new genes. RESULTS We identified 274,342 transcript sequences and 3,033 of those loci do not match a gene present in official annotations and thus are potential new genes. Notably, 63.67% (1,931/3,033) of potential novel genes exhibited coding potential. Also noteworthy, 97.92% of the putative novel genes overlapped annotation with transposable elements. Comparative analysis of transcript abundance identified that 1,840 novel genes (recently added to the annotation) or potential new genes were differentially expressed between developmental stages (FDR < 0.01). We also determined that 522 novel or potential new genes (448 and 34, respectively) were upregulated at eight-cell embryos compared to oocytes (FDR < 0.01). In eight-cell embryos, 102 novel or putative new genes were co-expressed (|r|> 0.85, P < 1 × 10-8) with several genes annotated with gene ontology biological processes related to pluripotency maintenance and embryo development. CRISPR-Cas9 genome editing confirmed that the disruption of one of the novel genes highly expressed in eight-cell embryos reduced blastocyst development (ENSBTAG00000068261, P = 1.55 × 10-7). CONCLUSIONS Our results revealed several putative new genes that need careful annotation. Many of the putative new genes have dynamic regulation during pre-implantation development and are important components of gene regulatory networks involved in pluripotency and blastocyst formation.
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Affiliation(s)
- Gustavo P Schettini
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Michael Morozyuk
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Fernando H Biase
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
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17
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Ouyang Z, Liu F, Li W, Wang J, Chen B, Zheng Y, Li Y, Tao H, Xu X, Li C, Cong Y, Li H, Bo X, Chen H. The developmental and evolutionary characteristics of transcription factor binding site clustered regions based on an explainable machine learning model. Nucleic Acids Res 2024; 52:7610-7626. [PMID: 38813828 PMCID: PMC11260490 DOI: 10.1093/nar/gkae441] [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: 01/22/2024] [Revised: 04/26/2024] [Accepted: 05/10/2024] [Indexed: 05/31/2024] Open
Abstract
Gene expression is temporally and spatially regulated by the interaction of transcription factors (TFs) and cis-regulatory elements (CREs). The uneven distribution of TF binding sites across the genome poses challenges in understanding how this distribution evolves to regulate spatio-temporal gene expression and consequent heritable phenotypic variation. In this study, chromatin accessibility profiles and gene expression profiles were collected from several species including mammals (human, mouse, bovine), fish (zebrafish and medaka), and chicken. Transcription factor binding sites clustered regions (TFCRs) at different embryonic stages were characterized to investigate regulatory evolution. The study revealed dynamic changes in TFCR distribution during embryonic development and species evolution. The synchronization between TFCR complexity and gene expression was assessed across species using RegulatoryScore. Additionally, an explainable machine learning model highlighted the importance of the distance between TFCR and promoter in the coordinated regulation of TFCRs on gene expression. Our results revealed the developmental and evolutionary dynamics of TFCRs during embryonic development from fish, chicken to mammals. These data provide valuable resources for exploring the relationship between transcriptional regulation and phenotypic differences during embryonic development.
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Affiliation(s)
- Zhangyi Ouyang
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Feng Liu
- College of Medical Informatics, Chongqing Medical University, Chongqing 400016, China
| | - Wanying Li
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Junting Wang
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Bijia Chen
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Yang Zheng
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Yaru Li
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Huan Tao
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Xiang Xu
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Cheng Li
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking University, Beijing 100871, China
| | - Yuwen Cong
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Hao Li
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Xiaochen Bo
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Hebing Chen
- Academy of Military Medical Sciences, Beijing 100850, China
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18
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Ghasemi Z, Alizadeh Mogadam Masouleh A, Rashki Ghaleno L, Akbarinejad V, Rezazadeh Valojerdi M, Shahverdi A. Maternal nutrition and fetal imprinting of the male progeny. Anim Reprod Sci 2024; 265:107470. [PMID: 38657462 DOI: 10.1016/j.anireprosci.2024.107470] [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: 12/28/2023] [Revised: 03/28/2024] [Accepted: 03/30/2024] [Indexed: 04/26/2024]
Abstract
The global population as well as the demand for human food is rapidly growing worldwide, which necessitates improvement of efficiency in livestock operations. In this context, environmental factors during fetal and/or neonatal life have been observed to influence normal physical and physiological function of an individual during adulthood, and this phenomenon is called fetal or developmental programming. While numerous studies have reported the impact of maternal factors on development of the female progeny, limited information is available on the potential effects of fetal programming on reproductive function of the male offspring. Therefore, the objective for this review article was to focus on available literature regarding the impact of maternal factors, particularly maternal nutrition, on reproductive system of the male offspring. To this end, we highlighted developmental programming of the male offspring in domestic species (i.e., pig, cow and sheep) as well as laboratory species (i.e., mice and rat) during pregnancy and lactation. In this sense, we pointed out the effects of maternal nutrition on various functions of the male offspring including hypothalamic-pituitary axis, hormonal levels, testicular tissue and semen parameters.
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Affiliation(s)
- Zahrasadat Ghasemi
- Department of Embryology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran; Animal Core Facility, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - AliReza Alizadeh Mogadam Masouleh
- Department of Embryology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran; Gyn-medicum, Center for Reproductive Medicine, Göttingen, Germany; Institute of Pharmacology and Toxicology, University Medical Center Göttingen, Göttingen, Germany.
| | - Leila Rashki Ghaleno
- Department of Embryology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Vahid Akbarinejad
- Department of Theriogenology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Mojtaba Rezazadeh Valojerdi
- Department of Embryology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran; Department of Anatomy, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Abdolhossein Shahverdi
- Department of Embryology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
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19
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McGraw MS, Bishman JA, Daigneault BW. Efficiency of embryo complementation and pluripotency maintenance following multiple passaging of in vitro-derived bovine embryos. Reprod Fertil Dev 2024; 36:RD24018. [PMID: 38902907 DOI: 10.1071/rd24018] [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: 02/02/2024] [Accepted: 05/28/2024] [Indexed: 06/22/2024] Open
Abstract
Context Current methods to obtain bovine embryos of high genetic merit include approaches that require skilled techniques for low-efficiency cloning strategies. Aims The overall goal herein was to identify the efficacy of alternative methods for producing multiple embryos through blastomere complementation while determining maintenance of cell pluripotency. Methods Bovine oocytes were fertilised in vitro to produce 4-cell embryos from which blastomeres were isolated and cultured as 2-cell aggregates using a well-of-the-well system. Aggregates were returned to incubation up to 7days (Passage 1). A second passage of complement embryos was achieved by splitting 4-cell Passage 1 embryos. Passaged embryos reaching the blastocyst stage were characterised for cell number and cell lineage specification in replicate with non-reconstructed zona-intact embryos. Key results Passage 1 and 2 embryo complements yielded 29% and 25% blastocyst development, respectively. Passage 1 embryos formed blastocysts, but with a reduction in expression of SOX2 and decreased size compared to non-reconstructed zona-intact embryos. Passage 2 embryos had a complete lack of SOX2 expression and a reduction in transcript abundance of SOX2 and SOX17, suggesting loss of pluripotency markers that primarily affected inner cell mass (ICM) and hypoblast formation. Conclusions In vitro fertilised bovine embryos can be reconstructed with multiple passaging to generate genetically identical embryos. Increased passaging drives trophectoderm cell lineage specification while compromising ICM formation. Implications These results may provide an alternative strategy for producing genetically identical bovine embryos through blastomere complementation with applications towards the development of trophoblast and placental models of early development.
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Affiliation(s)
- Maura S McGraw
- Department of Animal Sciences, University of Florida, 2250 Shealy Drive, Gainesville, FL 32611, USA
| | - Jordan A Bishman
- Department of Animal Sciences, University of Florida, 2250 Shealy Drive, Gainesville, FL 32611, USA
| | - Bradford W Daigneault
- Department of Animal Sciences, University of Florida, 2250 Shealy Drive, Gainesville, FL 32611, USA
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Scatolin GN, Ming H, Wang Y, Iyyappan R, Gutierrez-Castillo E, Zhu L, Sagheer M, Song C, Bondioli K, Jiang Z. Single-cell transcriptional landscapes of bovine peri-implantation development. iScience 2024; 27:109605. [PMID: 38633001 PMCID: PMC11022056 DOI: 10.1016/j.isci.2024.109605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 03/14/2024] [Accepted: 03/25/2024] [Indexed: 04/19/2024] Open
Abstract
Supporting healthy pregnancy outcomes requires a comprehensive understanding of the molecular and cellular programs of peri-implantation development, when most pregnancy failure occurs. Here, we present single-cell transcriptomes of bovine peri-implantation embryo development at day 12, 14, 16, and 18 post-fertilization. We defined the cellular composition and gene expression of embryonic disc, hypoblast, and trophoblast lineages in bovine peri-implantation embryos, and identified markers and pathway signaling that represent distinct stages of bovine peri-implantation lineages; the expression of selected markers was validated in peri-implantation embryos. Using detailed time-course transcriptomic analyses, we revealed a previously unrecognized primitive trophoblast cell lineage. We also characterized conserved and divergence peri-implantation lineage programs between bovine and other mammalian species. Finally, we established cell-cell communication signaling underlies embryonic and extraembryonic cell interaction to ensure proper early development. These data provide foundational information to discover essential biological signaling underpinning bovine peri-implantation development.
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Affiliation(s)
| | - Hao Ming
- Department of Animal Sciences, Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Yinjuan Wang
- School of Animal Sciences, AgCenter, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Rajan Iyyappan
- Department of Animal Sciences, Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | | | - Linkai Zhu
- Department of Animal Sciences, Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Masroor Sagheer
- Department of Animal Sciences, Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Chao Song
- Department of Animal Sciences, Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Kenneth Bondioli
- School of Animal Sciences, AgCenter, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Zongliang Jiang
- Department of Animal Sciences, Genetics Institute, University of Florida, Gainesville, FL 32610, USA
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21
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Oomen ME, Torres-Padilla ME. Jump-starting life: balancing transposable element co-option and genome integrity in the developing mammalian embryo. EMBO Rep 2024; 25:1721-1733. [PMID: 38528171 PMCID: PMC11015026 DOI: 10.1038/s44319-024-00118-5] [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: 12/07/2023] [Revised: 02/23/2024] [Accepted: 03/05/2024] [Indexed: 03/27/2024] Open
Abstract
Remnants of transposable elements (TEs) are widely expressed throughout mammalian embryo development. Originally infesting our genomes as selfish elements and acting as a source of genome instability, several of these elements have been co-opted as part of a complex system of genome regulation. Many TEs have lost transposition ability and their transcriptional potential has been tampered as a result of interactions with the host throughout evolutionary time. It has been proposed that TEs have been ultimately repurposed to function as gene regulatory hubs scattered throughout our genomes. In the early embryo in particular, TEs find a perfect environment of naïve chromatin to escape transcriptional repression by the host. As a consequence, it is thought that hosts found ways to co-opt TE sequences to regulate large-scale changes in chromatin and transcription state of their genomes. In this review, we discuss several examples of TEs expressed during embryo development, their potential for co-option in genome regulation and the evolutionary pressures on TEs and on our genomes.
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Affiliation(s)
- Marlies E Oomen
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, München, Germany
| | - Maria-Elena Torres-Padilla
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, München, Germany.
- Faculty of Biology, Ludwig-Maximilians Universität, München, Germany.
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22
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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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23
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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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24
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Zeng Y, Hoshino Y, Susami K, Honda S, Minami N, Ikeda S. Evaluating histone modification analysis of individual preimplantation embryos. BMC Genomics 2024; 25:75. [PMID: 38238676 PMCID: PMC10795292 DOI: 10.1186/s12864-024-09984-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 01/06/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND We previously reported a modification of the CUT&Tag method (NTU-CAT) that allows genome-wide histone modification analysis in individual preimplantation embryos. In the present study, NTU-CAT was further simplified by taking advantage of the Well-of-the-Well (WOW) system, which enables the processing of multiple embryos in a shorter time with less reagent and cell loss during the procedure (WOW-CUT&Tag, WOW-CAT). RESULTS WOW-CAT allowed histone modification profiling from not only a single blastocyst but also from a portion of it. WOW-CAT generated similar H3K4me3 profiles as NTU-CAT, but they were closer to the profiles produced by chromatin immunoprecipitation-sequencing, such as a valley-like trend and relatively lower false positive rates, indicating that WOW-CAT may attenuate the bias of Tn5 transposase to cut open chromatin regions. Simultaneous WOW-CAT of two halves of single blastocysts was conducted to analyze two different histone modifications (H3K4me3 and H3K27ac) within the same embryo. Furthermore, trophectoderm cells were biopsied and subjected to WOW-CAT in anticipation of preimplantation diagnosis of histone modifications. WOW-CAT allowed the monitoring of epigenetic modifications in the main body of the embryo. For example, analysis of H3K4me3 modifications of XIST and DDX3Y in trophectoderm biopsies could be used to sex embryos in combination with quantitative PCR, but without the need for deep sequencing. CONCLUSIONS These results suggest the applicability of WOW-CAT for flexible epigenetic analysis of individual embryos in preimplantation epigenetic diagnosis.
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Affiliation(s)
- Yiren Zeng
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Yoichiro Hoshino
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Kazuki Susami
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Shinnosuke Honda
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Naojiro Minami
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Shuntaro Ikeda
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan.
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25
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Luo ZB, Yang LH, Han SZ, Chang SY, Liu H, An ZY, Zhang XL, Quan BH, Yin XJ, Kang JD. Cyclophosphamide reduces gene transcriptional activity and embryo in vitro development by inhibiting NF-κB expression through decreasing AcH4K12. Chem Biol Interact 2024; 387:110806. [PMID: 37980972 DOI: 10.1016/j.cbi.2023.110806] [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: 09/27/2023] [Revised: 11/07/2023] [Accepted: 11/10/2023] [Indexed: 11/21/2023]
Abstract
Cyclophosphamide (CTX), a widely used chemotherapeutic agent for cancer treatment, has been associated with long-term toxicity and detrimental effects on oocytes and ovaries, resulting in female reproductive dysfunction. This study aimed to investigate the potential impact of CTX on in vitro maturation (IVM) injury of porcine oocytes and subsequent embryonic development, as well as its effects on epigenetic modification and gene activation during early embryonic development. The results demonstrated that CTX treatment caused aberrant spindle structure and mitochondrial dysfunction during oocyte maturation, inducing DNA damage and early apoptosis, which consequently disrupted meiotic maturation. Indeed, CTX significantly reduced the in vitro developmental capacity of porcine embryos, and induced DNA damage and apoptosis in in vitro fertilization (IVF) blastocysts. Importantly, CTX induced abnormal histone modification of AcH4K12 in early porcine embryos. Moreover, addition of LBH589 before zygotic genome activation (ZGA) effectively increased AcH4K12 levels and restored the protein expression of NF-κB, which can effectively enhance the in vitro developmental potential of IVF embryos. The DNA damage and apoptosis induced by CTX compromised the quality of the blastocysts, which were recovered by supplementation with LBH589. This restoration was accompanied by down-regulation of BAX mRNA expression and up-regulation of BCL2, POU5F1, SOX2 and SOD1 mRNA expression. These findings indicated that CTX caused abnormal histone modification of AcH4K12 in early porcine embryos and reduced the protein expression of NF-κB, a key regulator of early embryo development, which may block subsequent ZGA processes.
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Affiliation(s)
- Zhao-Bo Luo
- Department of Animal Science, College of Agriculture, Yanbian University, Yanji, Jilin, 133002, China
| | - Liu-Hui Yang
- Department of Animal Science, College of Agriculture, Yanbian University, Yanji, Jilin, 133002, China
| | - Sheng-Zhong Han
- Department of Animal Science, College of Agriculture, Yanbian University, Yanji, Jilin, 133002, China
| | - Shuang-Yan Chang
- Department of Animal Science, College of Agriculture, Yanbian University, Yanji, Jilin, 133002, China
| | - Hongye Liu
- Department of Animal Science, College of Agriculture, Yanbian University, Yanji, Jilin, 133002, China
| | - Zhi-Yong An
- Department of Animal Science, College of Agriculture, Yanbian University, Yanji, Jilin, 133002, China
| | - Xiu-Li Zhang
- Department of Animal Science, College of Agriculture, Yanbian University, Yanji, Jilin, 133002, China
| | - Biao-Hu Quan
- Department of Animal Science, College of Agriculture, Yanbian University, Yanji, Jilin, 133002, China; Jilin Provincial Key Laboratory of Transgenic Animal and Embryo Engineering, Yanbian University, Yanji, Jilin, 133002, China
| | - Xi-Jun Yin
- Department of Animal Science, College of Agriculture, Yanbian University, Yanji, Jilin, 133002, China; Jilin Provincial Key Laboratory of Transgenic Animal and Embryo Engineering, Yanbian University, Yanji, Jilin, 133002, China.
| | - Jin-Dan Kang
- Department of Animal Science, College of Agriculture, Yanbian University, Yanji, Jilin, 133002, China; Jilin Provincial Key Laboratory of Transgenic Animal and Embryo Engineering, Yanbian University, Yanji, Jilin, 133002, China.
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26
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D’Occhio MJ, Campanile G, Baruselli PS, Porto Neto LR, Hayes BJ, Snr AC, Fortes MRS. Pleomorphic adenoma gene1 in reproduction and implication for embryonic survival in cattle: a review. J Anim Sci 2024; 102:skae103. [PMID: 38586898 PMCID: PMC11056886 DOI: 10.1093/jas/skae103] [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: 12/07/2023] [Accepted: 04/05/2024] [Indexed: 04/09/2024] Open
Abstract
The pleomorphic adenoma gene1 (PLAG1) encodes a DNA-binding, C2H2 zinc-finger protein which acts as a transcription factor that regulates the expression of diverse genes across different organs and tissues; hence, the name pleomorphic. Rearrangements of the PLAG1 gene, and/or overexpression, are associated with benign tumors and cancers in a variety of tissues. This is best described for pleomorphic adenoma of the salivary glands in humans. The most notable expression of PLAG1 occurs during embryonic and fetal development, with lesser expression after birth. Evidence has accumulated of a role for PLAG1 protein in normal early embryonic development and placentation in mammals. PLAG1 protein influences the expression of the ike growth factor 2 (IGF2) gene and production of IGF2 protein. IGF2 is an important mitogen in ovarian follicles/oocytes, embryos, and fetuses. The PLAG1-IGF2 axis, therefore, provides one pathway whereby PLAG1 protein can influence embryonic survival and pregnancy. PLAG1 also influences over 1,000 other genes in embryos including those associated with ribosomal assembly and proteins. Brahman (Bos indicus) heifers homozygous for the PLAG1 variant, rs109815800 (G > T), show greater fertility than contemporary heifers with either one, or no copy, of the variant. Greater fertility in heifers homozygous for rs109815800 could be the result of early puberty and/or greater embryonic survival. The present review first looks at the broader roles of the PLAG1 gene and PLAG1 protein and then focuses on the emerging role of PLAG1/PLAG1 in embryonic development and pregnancy. A deeper understanding of factors which influence embryonic development is required for the next transformational increase in embryonic survival and successful pregnancy for both in vivo and in vitro derived embryos in cattle.
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Affiliation(s)
- Michael J D’Occhio
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - Giuseppe Campanile
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples, Italy
| | - Pietro S Baruselli
- Faculty of Veterinary Medicine and Animal Science, Department of Animal Reproduction, University of Sao Paulo, Sao Paulo, Brazil
| | | | - Ben J Hayes
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Alf Collins Snr
- CBV Brahman, Marlborough, Central Queensland, QLD, Australia
| | - Marina R S Fortes
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
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27
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Yu T, Zhang C, Song W, Zhao X, Cheng Y, Liu J, Su J. Single-cell RNA-seq and single-cell bisulfite-sequencing reveal insights into yak preimplantation embryogenesis. J Biol Chem 2024; 300:105562. [PMID: 38097189 PMCID: PMC10821408 DOI: 10.1016/j.jbc.2023.105562] [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: 03/24/2023] [Revised: 11/17/2023] [Accepted: 12/03/2023] [Indexed: 01/13/2024] Open
Abstract
Extensive epigenetic reprogramming occurs during preimplantation embryonic development. However, the impact of DNA methylation in plateau yak preimplantation embryos and how epigenetic reprogramming contributes to transcriptional regulatory networks are unclear. In this study, we quantified gene expression and DNA methylation in oocytes and a series of yak embryos at different developmental stages and at single-cell resolution using single-cell bisulfite-sequencing and RNA-seq. We characterized embryonic genome activation and maternal transcript degradation and mapped epigenetic reprogramming events critical for embryonic development. Through cross-species transcriptome analysis, we identified 31 conserved maternal hub genes and 39 conserved zygotic hub genes, including SIN3A, PRC1, HDAC1/2, and HSPD1. Notably, by combining single-cell DNA methylation and transcriptome analysis, we identified 43 candidate methylation driver genes, such as AURKA, NUSAP1, CENPF, and PLK1, that may be associated with embryonic development. Finally, using functional approaches, we further determined that the epigenetic modifications associated with the histone deacetylases HDAC1/2 are essential for embryonic development and that the deubiquitinating enzyme USP7 may affect embryonic development by regulating DNA methylation. Our data represent an extensive resource on the transcriptional dynamics of yak embryonic development and DNA methylation remodeling, and provide new insights into strategies for the conservation of germplasm resources, as well as a better understanding of mammalian early embryonic development that can be applied to investigate the causes of early developmental disorders.
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Affiliation(s)
- Tong Yu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Chengtu Zhang
- Academician Zhang Yong Innovation Center, Xining Animal Disease Control Center, Xining, Qinghai, China
| | - Weijia Song
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Xinyi Zhao
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuyao Cheng
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Jun Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.
| | - Jianmin Su
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.
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28
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Perera CD, Idrees M, Khan AM, Haider Z, Ullah S, Kang JS, Lee SH, Kang SM, Kong IK. PDGFRβ Activation Induced the Bovine Embryonic Genome Activation via Enhanced NFYA Nuclear Localization. Int J Mol Sci 2023; 24:17047. [PMID: 38069370 PMCID: PMC10707662 DOI: 10.3390/ijms242317047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Embryonic genome activation (EGA) is a critical step during embryonic development. Several transcription factors have been identified that play major roles in initiating EGA; however, this gradual and complex mechanism still needs to be explored. In this study, we investigated the role of nuclear transcription factor Y subunit A (NFYA) in bovine EGA and bovine embryonic development and its relationship with the platelet-derived growth factor receptor-β (PDGFRβ) by using a potent selective activator (PDGF-BB) and inhibitor (CP-673451) of PDGF receptors. Activation and inhibition of PDGFRβ using PDGF-BB and CP-673451 revealed that NFYA expression is significantly (p < 0.05) affected by the PDGFRβ. In addition, PDGFRβ mRNA expression was significantly increased (p < 0.05) in the activator group and significantly decreased (p < 0.05) in the inhibitor group when compared with PDGFRα. Downregulation of NFYA following PDGFRβ inhibition was associated with the expression of critical EGA-related genes, bovine embryo development rate, and implantation potential. Moreover, ROS and mitochondrial apoptosis levels and expression of pluripotency-related markers necessary for inner cell mass development were also significantly (p < 0.05) affected by the downregulation of NFYA while interrupting trophoblast cell (CDX2) differentiation. In conclusion, the PDGFRβ-NFYA axis is critical for bovine embryonic genome activation and embryonic development.
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Affiliation(s)
- Chalani Dilshani Perera
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea; (C.D.P.); (M.I.); (A.M.K.); (Z.H.); (S.U.); (J.-S.K.); (S.-H.L.); (S.-M.K.)
| | - Muhammad Idrees
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea; (C.D.P.); (M.I.); (A.M.K.); (Z.H.); (S.U.); (J.-S.K.); (S.-H.L.); (S.-M.K.)
- Institute of Agriculture and Life Science (IALS), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Abdul Majid Khan
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea; (C.D.P.); (M.I.); (A.M.K.); (Z.H.); (S.U.); (J.-S.K.); (S.-H.L.); (S.-M.K.)
| | - Zaheer Haider
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea; (C.D.P.); (M.I.); (A.M.K.); (Z.H.); (S.U.); (J.-S.K.); (S.-H.L.); (S.-M.K.)
| | - Safeer Ullah
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea; (C.D.P.); (M.I.); (A.M.K.); (Z.H.); (S.U.); (J.-S.K.); (S.-H.L.); (S.-M.K.)
| | - Ji-Su Kang
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea; (C.D.P.); (M.I.); (A.M.K.); (Z.H.); (S.U.); (J.-S.K.); (S.-H.L.); (S.-M.K.)
| | - Seo-Hyun Lee
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea; (C.D.P.); (M.I.); (A.M.K.); (Z.H.); (S.U.); (J.-S.K.); (S.-H.L.); (S.-M.K.)
| | - Seon-Min Kang
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea; (C.D.P.); (M.I.); (A.M.K.); (Z.H.); (S.U.); (J.-S.K.); (S.-H.L.); (S.-M.K.)
| | - Il-Keun Kong
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea; (C.D.P.); (M.I.); (A.M.K.); (Z.H.); (S.U.); (J.-S.K.); (S.-H.L.); (S.-M.K.)
- Institute of Agriculture and Life Science (IALS), Gyeongsang National University, Jinju 52828, Republic of Korea
- The King Kong Corp. Ltd., Gyeongsang National University, Jinju 52828, Republic of Korea
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29
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Jiang Z. Molecular and cellular programs underlying the development of bovine pre-implantation embryos. Reprod Fertil Dev 2023; 36:34-42. [PMID: 38064195 PMCID: PMC10962643 DOI: 10.1071/rd23146] [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] [Indexed: 12/18/2023] Open
Abstract
Early embryonic mortality is a major cause of infertility in cattle, yet the underlying molecular causes remain a mystery. Over the past half century, assisted reproductive technologies such as in vitro fertilisation and somatic cell nuclear transfer have been used to improve cattle reproductive efficiency; however, reduced embryo developmental potential is seen compared to their in vivo counterparts. Recent years have seen exciting progress across bovine embryo research, including genomic profiling of embryogenesis, new methods for improving embryo competence, and experimenting on building bovine embryos from stem cell cultures. These advances are beginning to define bovine embryo molecular and cellular programs and could potentially lead to improved embryo health. Here, I highlight the current status of molecular determinants and cellular programs of bovine embryo development and new opportunities to improve the bovine embryo health.
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Affiliation(s)
- Zongliang Jiang
- Department of Animal Sciences, Genetics Institute, University of Florida, Gainesville, FL 32610, USA
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30
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Yuan C, Tang L, Lopdell T, Petrov VA, Oget-Ebrad C, Moreira GCM, Gualdrón Duarte JL, Sartelet A, Cheng Z, Salavati M, Wathes DC, Crowe MA, Coppieters W, Littlejohn M, Charlier C, Druet T, Georges M, Takeda H. An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants. Genome Res 2023; 33:1848-1864. [PMID: 37751945 PMCID: PMC10691486 DOI: 10.1101/gr.277947.123] [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: 04/01/2023] [Accepted: 09/19/2023] [Indexed: 09/28/2023]
Abstract
We report the generation of an organism-wide catalog of 976,813 cis-acting regulatory elements for the bovine detected by the assay for transposase accessible chromatin using sequencing (ATAC-seq). We regroup these regulatory elements in 16 components by nonnegative matrix factorization. Correlation between the genome-wide density of peaks and transcription start sites, correlation between peak accessibility and expression of neighboring genes, and enrichment in transcription factor binding motifs support their regulatory potential. Using a previously established catalog of 12,736,643 variants, we show that the proportion of single-nucleotide polymorphisms mapping to ATAC-seq peaks is higher than expected and that this is owing to an approximately 1.3-fold higher mutation rate within peaks. Their site frequency spectrum indicates that variants in ATAC-seq peaks are subject to purifying selection. We generate eQTL data sets for liver and blood and show that variants that drive eQTL fall into liver- and blood-specific ATAC-seq peaks more often than expected by chance. We combine ATAC-seq and eQTL data to estimate that the proportion of regulatory variants mapping to ATAC-seq peaks is approximately one in three and that the proportion of variants mapping to ATAC-seq peaks that are regulatory is approximately one in 25. We discuss the implication of these findings on the utility of ATAC-seq information to improve the accuracy of genomic selection.
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Affiliation(s)
- Can Yuan
- Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Lijing Tang
- Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Thomas Lopdell
- Research and Development, Livestock Improvement Corporation, Hamilton 3240, New Zealand
| | - Vyacheslav A Petrov
- Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Claire Oget-Ebrad
- Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | | | - José Luis Gualdrón Duarte
- Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Arnaud Sartelet
- Clinical Department of Ruminant, University of Liège, 4000 Liège, Belgium
| | - Zhangrui Cheng
- Royal Veterinary College, Hatfield, Herts AL9 7TA, United Kingdom
| | - Mazdak Salavati
- Royal Veterinary College, Hatfield, Herts AL9 7TA, United Kingdom
| | - D Claire Wathes
- Royal Veterinary College, Hatfield, Herts AL9 7TA, United Kingdom
| | - Mark A Crowe
- School of Veterinary Medicine, University College Dublin, Dublin 4, Ireland
| | - Wouter Coppieters
- GIGA Genomics platform, GIGA Institute, University of Liège, 4000 Liège, Belgium
| | - Mathew Littlejohn
- Research and Development, Livestock Improvement Corporation, Hamilton 3240, New Zealand
| | - Carole Charlier
- Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Tom Druet
- Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Michel Georges
- Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium;
| | - Haruko Takeda
- Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
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Huang Y, Zhang J, Li X, Wu Z, Xie G, Wang Y, Liu Z, Jiao M, Zhang H, Shi B, Wang Y, Zhang Y. Chromatin accessibility memory of donor cells disrupts bovine somatic cell nuclear transfer blastocysts development. FASEB J 2023; 37:e23111. [PMID: 37531300 DOI: 10.1096/fj.202300131rrr] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 06/30/2023] [Accepted: 07/11/2023] [Indexed: 08/04/2023]
Abstract
The post-transfer developmental capacity of bovine somatic cell nuclear transfer (SCNT) blastocysts is reduced, implying that abnormalities in gene expression regulation are present at blastocyst stage. Chromatin accessibility, as an indicator for transcriptional regulatory elements mediating gene transcription activity, has heretofore been largely unexplored in SCNT embryos, especially at blastocyst stage. In the present study, single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) of in vivo and SCNT blastocysts were conducted to segregate lineages and demonstrate the aberrant chromatin accessibility of transcription factors (TFs) related to inner cell mass (ICM) development in SCNT blastocysts. Pseudotime analysis of lineage segregation further reflected dysregulated chromatin accessibility dynamics of TFs in the ICM of SCNT blastocysts compared to their in vivo counterparts. ATAC- and ChIP-seq results of SCNT donor cells revealed that the aberrant chromatin accessibility in the ICM of SCNT blastocysts was due to the persistence of chromatin accessibility memory at corresponding loci in the donor cells, with strong enrichment of trimethylation of histone H3 at lysine 4 (H3K4me3) at these loci. Correction of the aberrant chromatin accessibility through demethylation of H3K4me3 by KDM5B diminished the expression of related genes (e.g., BCL11B) and significantly improved the ICM proliferation in SCNT blastocysts. This effect was confirmed by knocking down BCL11B in SCNT embryos to down-regulate p21 and alleviate the inhibition of ICM proliferation. These findings expand our understanding of the chromatin accessibility abnormalities in SCNT blastocysts and BCL11B may be a potential target to improve SCNT efficiency.
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Affiliation(s)
- Yuemeng Huang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Jingcheng Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Xinmei Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zhipei Wu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Guoxiang Xie
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yong Wang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Zhengqing Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Mei Jiao
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Hexu Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Binqiang Shi
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Yu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yong Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
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Zhang KY, Guo J, Zhan CL, Yuan CS, Min CG, Li ZQ, Liu HY, Wang J, Zhao J, Lu WF, Ma X. β-hydroxybutyrate impairs bovine oocyte maturation via pyruvate dehydrogenase (PDH) associated energy metabolism abnormality. Front Pharmacol 2023; 14:1243243. [PMID: 37637420 PMCID: PMC10450765 DOI: 10.3389/fphar.2023.1243243] [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: 06/20/2023] [Accepted: 08/03/2023] [Indexed: 08/29/2023] Open
Abstract
Background: Ketosis is one of the most frequent and costly metabolic disorders in high-producing dairy cows, and negatively associated with the health and reproductive performance of bovine. Ketosis is mainly caused by the accumulation of ketone body β-hydroxybutyric acid and its diagnosis is based on β-hydroxybutyrate (βHB) concentration in blood. Methods: In this study, we investigated the effects of βHB on bovine oocyte maturation in the concentration of subclinical (1.2 mM) βHB and clinical (3.6 mM). Results: The results showed βHB disrupted bovine oocyte maturation and development capacity. Further analysis showed that βHB induced oxidative stress and mitochondrial dysfunction, as indicated by the increased level of reactive oxygen species (ROS), disrupted mitochondrial structure and distribution, and depolarized membrane potential. Furthermore, oxidative stress triggered early apoptosis, as shown by the enhanced levels of Caspase-3 and Annexin-V. Moreover, 3.6 mM βHB induced the disruption of the pyruvate dehydrogenase (PDH) activity, showing with the decrease of the global acetylation modification and the increase of the abnormal spindle rate. Conclusion: Our study showed that βHB in subclinical/clinical concentration had toxic effects on mitochondrial function and PDH activity, which might affect energy metabolism and epigenetic modification of bovine oocytes and embryos.
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Affiliation(s)
- Kai-Yan Zhang
- Key Laboratory of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China
- Jilin Provincial International Joint Research Center of Animal Breeding and Reproduction Technology, Jilin Agricultural University, Changchun, Jilin, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Jing Guo
- Key Laboratory of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China
- Jilin Provincial International Joint Research Center of Animal Breeding and Reproduction Technology, Jilin Agricultural University, Changchun, Jilin, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Cheng-Lin Zhan
- Key Laboratory of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China
- Jilin Provincial International Joint Research Center of Animal Breeding and Reproduction Technology, Jilin Agricultural University, Changchun, Jilin, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Chong-Shan Yuan
- Key Laboratory of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China
- Jilin Provincial International Joint Research Center of Animal Breeding and Reproduction Technology, Jilin Agricultural University, Changchun, Jilin, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Chang-Guo Min
- Key Laboratory of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China
- Jilin Provincial International Joint Research Center of Animal Breeding and Reproduction Technology, Jilin Agricultural University, Changchun, Jilin, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Zhi-Qiang Li
- Key Laboratory of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China
- Jilin Provincial International Joint Research Center of Animal Breeding and Reproduction Technology, Jilin Agricultural University, Changchun, Jilin, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Hong-Yu Liu
- Key Laboratory of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China
- Jilin Provincial International Joint Research Center of Animal Breeding and Reproduction Technology, Jilin Agricultural University, Changchun, Jilin, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Jun Wang
- Key Laboratory of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China
- Jilin Provincial International Joint Research Center of Animal Breeding and Reproduction Technology, Jilin Agricultural University, Changchun, Jilin, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Jing Zhao
- Key Laboratory of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China
- Jilin Provincial International Joint Research Center of Animal Breeding and Reproduction Technology, Jilin Agricultural University, Changchun, Jilin, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Wen-Fa Lu
- Key Laboratory of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China
- Jilin Provincial International Joint Research Center of Animal Breeding and Reproduction Technology, Jilin Agricultural University, Changchun, Jilin, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Xin Ma
- Key Laboratory of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China
- Jilin Provincial International Joint Research Center of Animal Breeding and Reproduction Technology, Jilin Agricultural University, Changchun, Jilin, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
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Rabel RAC, Marchioretto PV, Bangert EA, Wilson K, Milner DJ, Wheeler MB. Pre-Implantation Bovine Embryo Evaluation-From Optics to Omics and Beyond. Animals (Basel) 2023; 13:2102. [PMID: 37443900 DOI: 10.3390/ani13132102] [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: 05/22/2023] [Revised: 06/16/2023] [Accepted: 06/17/2023] [Indexed: 07/15/2023] Open
Abstract
Approximately 80% of the ~1.5 million bovine embryos transferred in 2021 were in vitro produced. However, only ~27% of the transferred IVP embryos will result in live births. The ~73% pregnancy failures are partly due to transferring poor-quality embryos, a result of erroneous stereomicroscopy-based morphological evaluation, the current method of choice for pre-transfer embryo evaluation. Numerous microscopic (e.g., differential interference contrast, electron, fluorescent, time-lapse, and artificial-intelligence-based microscopy) and non-microscopic (e.g., genomics, transcriptomics, epigenomics, proteomics, metabolomics, and nuclear magnetic resonance) methodologies have been tested to find an embryo evaluation technique that is superior to morphologic evaluation. Many of these research tools can accurately determine embryo quality/viability; however, most are invasive, expensive, laborious, technically sophisticated, and/or time-consuming, making them futile in the context of in-field embryo evaluation. However accurate they may be, using complex methods, such as RNA sequencing, SNP chips, mass spectrometry, and multiphoton microscopy, at thousands of embryo production/collection facilities is impractical. Therefore, future research is warranted to innovate field-friendly, simple benchtop tests using findings already available, particularly from omics-based research methodologies. Time-lapse monitoring and artificial-intelligence-based automated image analysis also have the potential for accurate embryo evaluation; however, further research is warranted to innovate economically feasible options for in-field applications.
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Affiliation(s)
- R A Chanaka Rabel
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Paula V Marchioretto
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Elizabeth A Bangert
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Kenneth Wilson
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Derek J Milner
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Matthew B Wheeler
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Biomedical and Translational Sciences, Carle-Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Scatolin GN, Ming H, Wang Y, Zhu L, Castillo EG, Bondioli K, Jiang Z. Single-cell transcriptional landscapes of bovine peri-implantation development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.13.544813. [PMID: 37398069 PMCID: PMC10312721 DOI: 10.1101/2023.06.13.544813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
UNLABELLED Supporting healthy pregnancy outcomes requires a comprehensive understanding of the cellular hierarchy and underlying molecular mechanisms during peri-implantation development. Here, we present a single-cell transcriptome-wide view of the bovine peri-implantation embryo development at day 12, 14, 16 and 18, when most of the pregnancy failure occurs in cattle. We defined the development and dynamic progression of cellular composition and gene expression of embryonic disc, hypoblast, and trophoblast lineages during bovine peri-implantation development. Notably, the comprehensive transcriptomic mapping of trophoblast development revealed a previously unrecognized primitive trophoblast cell lineage that is responsible for pregnancy maintenance in bovine prior to the time when binucleate cells emerge. We analyzed novel markers for the cell lineage development during bovine early development. We also identified cell-cell communication signaling underling embryonic and extraembryonic cell interaction to ensure proper early development. Collectively, our work provides foundational information to discover essential biological pathways underpinning bovine peri-implantation development and the molecular causes of the early pregnancy failure during this critical period. SIGNIFICANCE STATEMENT Peri-implantation development is essential for successful reproduction in mammalian species, and cattle have a unique process of elongation that proceeds for two weeks prior to implantation and represents a period when many pregnancies fail. Although the bovine embryo elongation has been studied histologically, the essential cellular and molecular factors governing lineage differentiation remain unexplored. This study profiled the transcriptome of single cells in the bovine peri-implantation development throughout day 12, 14, 16, and 18, and identified peri-implantation stage-related features of cell lineages. The candidate regulatory genes, factors, pathways and embryonic and extraembryonic cell interactions were also prioritized to ensure proper embryo elongation in cattle.
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Grow EJ, Liu Y, Fan Z, Perisse IV, Patrick T, Regouski M, Shadle S, Polejaeva I, White KL, Cairns BR. Chromatin Reprogramming of In Vitro Fertilized and Somatic Cell Nuclear Transfer Bovine Embryos During Embryonic Genome Activation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.10.536281. [PMID: 37090641 PMCID: PMC10120652 DOI: 10.1101/2023.04.10.536281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Reprogramming of the gamete into a developmentally competent embryo identity is a fundamental aspect of preimplantation development. One of the most important processes of this reprogramming is the transcriptional awakening during embryonic genome activation (EGA), which robustly occurs in fertilized embryos but is defective in most somatic cell nuclear transfer (SCNT) embryos. However, little is known about the genome-wide underlying chromatin landscape during EGA in SCNT embryos and how it differs from a fertilized embryo. By profiling open chromatin genome-wide in both types of bovine embryos, we find that SCNT embryos fail to reprogram a subset of the EGA gene targets that are normally activated in fertilized embryos. Importantly, a small number of transcription factor (TF) motifs explain most chromatin regions that fail to open in SCNT embryos suggesting that over-expression of a limited number of TFs may provide more robust reprogramming. One such TF, the zygotically-expressed bovine gene DUXC which is a homologue of EGA factors DUX/DUX4 in mouse/human, is alone capable of activating ∼84% of all EGA transcripts that fail to activate normally in SCNT embryos. Additionally, single-cell chromatin profiling revealed low intra-embryo heterogeneity but high inter-embryo heterogeneity in SCNT embryos and an uncoupling of cell division and open chromatin reprogramming during EGA. Surprisingly, our data also indicate that transcriptional defects may arise downstream of promoter chromatin opening in SCNT embryos, suggesting additional mechanistic insights into how and why transcription at EGA is dysregulated. We anticipate that our work will lead to altered SCNT protocols to increase the developmental competency of bovine SCNT embryos.
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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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Macrae TA, Fothergill-Robinson J, Ramalho-Santos M. Regulation, functions and transmission of bivalent chromatin during mammalian development. Nat Rev Mol Cell Biol 2023; 24:6-26. [PMID: 36028557 DOI: 10.1038/s41580-022-00518-2] [Citation(s) in RCA: 85] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2022] [Indexed: 12/25/2022]
Abstract
Cells differentiate and progress through development guided by a dynamic chromatin landscape that mediates gene expression programmes. During development, mammalian cells display a paradoxical chromatin state: histone modifications associated with gene activation (trimethylated histone H3 Lys4 (H3K4me3)) and with gene repression (trimethylated H3 Lys27 (H3K27me3)) co-occur at promoters of developmental genes. This bivalent chromatin modification state is thought to poise important regulatory genes for expression or repression during cell-lineage specification. In this Review, we discuss recent work that has expanded our understanding of the molecular basis of bivalent chromatin and its contributions to mammalian development. We describe the factors that establish bivalency, especially histone-lysine N-methyltransferase 2B (KMT2B) and Polycomb repressive complex 2 (PRC2), and consider evidence indicating that PRC1 shapes bivalency and may contribute to its transmission between generations. We posit that bivalency is a key feature of germline and embryonic stem cells, as well as other types of stem and progenitor cells. Finally, we discuss the relevance of bivalent chromtin to human development and cancer, and outline avenues of future research.
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Affiliation(s)
- Trisha A Macrae
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA.
| | - Julie Fothergill-Robinson
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Miguel Ramalho-Santos
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada.
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Gene Expression of Aquaporins (AQPs) in Cumulus Oocytes Complex and Embryo of Cattle. Animals (Basel) 2022; 13:ani13010098. [PMID: 36611707 PMCID: PMC9817902 DOI: 10.3390/ani13010098] [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: 10/18/2022] [Revised: 11/20/2022] [Accepted: 12/07/2022] [Indexed: 12/28/2022] Open
Abstract
Aquaporins (AQPs) are proteins with various functions related to proper cell function and early development in mammals. The aim of this study was to evaluate the presence of AQPs and determine their mRNA levels in the cumulus oocyte complex (COC) of four bovine breeds and in blastocysts of five bovine crosses. Grade I, II and III COCs were collected by ovum pick up from non-lactating heifers of the Brahaman, Holstein, Gir and Romosinuano breeds. Embryos were produced in vitro up to the blastocyst stage of the bovine ♀Gir × ♂Holstein, ♀Holstein × ♂Gir, ♀Brahman × ♂Holstein, ♀Holstein × ♂Brahman, and ♀Romosinuano × ♂Holstein crosses. mRNA expression of AQP1-AQP12b was estimated in COC and embryos by real-time-PCR. The presence of the twelve AQPs in the COCs and bovine embryos was established. Additionally, significant differences were determined in the expression of AQP6 and AQP12b in COCs, as well as in transcripts levels of AQP4, AQP8 and AQP9 from bovine embryos. Gene expression of AQPs in COCs and bovine embryos is consistent with the previously described biological functions. This is the first report of AQPs in COC of Gir, Brahman, Holstein and Romosinuano and embryos of five crossbreeds between Bos indicus and B. taurus.
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Lee H, You SY, Han DW, La H, Park C, Yoo S, Kang K, Kang MH, Choi Y, Hong K. Dynamic Change of R-Loop Implicates in the Regulation of Zygotic Genome Activation in Mouse. Int J Mol Sci 2022; 23:ijms232214345. [PMID: 36430821 PMCID: PMC9699122 DOI: 10.3390/ijms232214345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022] Open
Abstract
In mice, zygotic genome activation (ZGA) occurs in two steps: minor ZGA at the one-cell stage and major ZGA at the two-cell stage. Regarding the regulation of gene transcription, minor ZGA is known to have unique features, including a transcriptionally permissive state of chromatin and insufficient splicing processes. The molecular characteristics may originate from extremely open chromatin states in the one-cell stage zygotes, yet the precise underlying mechanism has not been well studied. Recently, the R-loop, a triple-stranded nucleic acid structure of the DNA/RNA hybrid, has been implicated in gene transcription and DNA replication. Therefore, in the present study, we examined the changes in R-loop dynamics during mouse zygotic development, and its roles in zygotic transcription or DNA replication. Our analysis revealed that R-loops persist in the genome of metaphase II oocytes and preimplantation embryos from the zygote to the blastocyst stage. In particular, zygotic R-loop levels dynamically change as development proceeds, showing that R-loop levels decrease as pronucleus maturation occurs. Mechanistically, R-loop dynamics are likely linked to ZGA, as inhibition of either DNA replication or transcription at the time of minor ZGA decreases R-loop levels in the pronuclei of zygotes. However, the induction of DNA damage by treatment with anticancer agents, including cisplatin or doxorubicin, does not elicit genome-wide changes in zygotic R-loop levels. Therefore, our study suggests that R-loop formation is mechanistically associated with the regulation of mouse ZGA, especially minor ZGA, by modulating gene transcription and DNA replication.
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Affiliation(s)
- Hyeonji Lee
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029, Republic of Korea
| | - Seong-Yeob You
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029, Republic of Korea
| | - Dong Wook Han
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, Wuyi University, Jiangmen 529020, China
| | - Hyeonwoo La
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029, Republic of Korea
| | - Chanhyeok Park
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029, Republic of Korea
| | - Seonho Yoo
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029, Republic of Korea
| | - Kiye Kang
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029, Republic of Korea
| | - Min-Hee Kang
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029, Republic of Korea
| | - Youngsok Choi
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029, Republic of Korea
| | - Kwonho Hong
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029, Republic of Korea
- Correspondence:
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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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41
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Genome-wide chromatin accessibility analysis unveils open chromatin convergent evolution during polyploidization in cotton. Proc Natl Acad Sci U S A 2022; 119:e2209743119. [PMID: 36279429 PMCID: PMC9636936 DOI: 10.1073/pnas.2209743119] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Allopolyploidization, resulting in divergent genomes in the same cell, is believed to trigger a “genome shock”, leading to broad genetic and epigenetic changes. However, little is understood about chromatin and gene-expression dynamics as underlying driving forces during allopolyploidization. Here, we examined the genome-wide DNase I-hypersensitive site (DHS) and its variations in domesticated allotetraploid cotton (
Gossypium hirsutum
and
Gossypium barbadense
, AADD) and its extant AA (
Gossypium arboreum
) and DD (
Gossypium raimondii
) progenitors. We observed distinct DHS distributions between
G. arboreum
and
G. raimondii
. In contrast, the DHSs of the two subgenomes of
G. hirsutum
and
G. barbadense
showed a convergent distribution. This convergent distribution of DHS was also present in the wild allotetraploids
Gossypium darwinii
and
G. hirsutum
var.
yucatanense
, but absent from a resynthesized hybrid of
G. arboreum
and
G. raimondii
, suggesting that it may be a common feature in polyploids, and not a consequence of domestication after polyploidization. We revealed that putative
cis
-regulatory elements (CREs) derived from polyploidization-related DHSs were dominated by several families, including Dof, ERF48, and BPC1. Strikingly, 56.6% of polyploidization-related DHSs were derived from transposable elements (TEs). Moreover, we observed positive correlations between DHS accessibility and the histone marks H3K4me3, H3K27me3, H3K36me3, H3K27ac, and H3K9ac, indicating that coordinated interplay among histone modifications, TEs, and CREs drives the DHS landscape dynamics under polyploidization. Collectively, these findings advance our understanding of the regulatory architecture in plants and underscore the complexity of regulome evolution during polyploidization.
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42
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Zhu L, Zhou T, Iyyappan R, Ming H, Dvoran M, Wang Y, Chen Q, Roberts RM, Susor A, Jiang Z. High-resolution ribosome profiling reveals translational selectivity for transcripts in bovine preimplantation embryo development. Development 2022; 149:dev200819. [PMID: 36227586 PMCID: PMC9687001 DOI: 10.1242/dev.200819] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 09/26/2022] [Indexed: 11/06/2022]
Abstract
High-resolution ribosome fractionation and low-input ribosome profiling of bovine oocytes and preimplantation embryos has enabled us to define the translational landscapes of early embryo development at an unprecedented level. We analyzed the transcriptome and the polysome- and non-polysome-bound RNA profiles of bovine oocytes (germinal vesicle and metaphase II stages) and early embryos at the two-cell, eight-cell, morula and blastocyst stages, and revealed four modes of translational selectivity: (1) selective translation of non-abundant mRNAs; (2) active, but modest translation of a selection of highly expressed mRNAs; (3) translationally suppressed abundant to moderately abundant mRNAs; and (4) mRNAs associated specifically with monosomes. A strong translational selection of low-abundance transcripts involved in metabolic pathways and lysosomes was found throughout bovine embryonic development. Notably, genes involved in mitochondrial function were prioritized for translation. We found that translation largely reflected transcription in oocytes and two-cell embryos, but observed a marked shift in the translational control in eight-cell embryos that was associated with the main phase of embryonic genome activation. Subsequently, transcription and translation become more synchronized in morulae and blastocysts. Taken together, these data reveal a unique spatiotemporal translational regulation that accompanies bovine preimplantation development.
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Affiliation(s)
- Linkai Zhu
- School of Animal Sciences, AgCenter, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557-0352, USA
| | - Rajan Iyyappan
- Laboratory of Biochemistry and Molecular Biology of Germ Cells, Institute of Animal Physiology and Genetics, CAS, 277 21 Liběchov, Czech Republic
| | - Hao Ming
- School of Animal Sciences, AgCenter, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Michal Dvoran
- Laboratory of Biochemistry and Molecular Biology of Germ Cells, Institute of Animal Physiology and Genetics, CAS, 277 21 Liběchov, Czech Republic
| | - Yinjuan Wang
- School of Animal Sciences, AgCenter, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Qi Chen
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 92521, USA
| | - R. Michael Roberts
- Department of Animal Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211-7310, USA
| | - Andrej Susor
- Laboratory of Biochemistry and Molecular Biology of Germ Cells, Institute of Animal Physiology and Genetics, CAS, 277 21 Liběchov, Czech Republic
| | - Zongliang Jiang
- School of Animal Sciences, AgCenter, Louisiana State University, Baton Rouge, LA 70803, USA
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43
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Bekaert B, Boel A, Cosemans G, De Witte L, Menten B, Heindryckx B. CRISPR/Cas gene editing in the human germline. Semin Cell Dev Biol 2022; 131:93-107. [PMID: 35305903 DOI: 10.1016/j.semcdb.2022.03.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 12/14/2022]
Abstract
The ease and efficacy of CRISPR/Cas9 germline gene editing in animal models paved the way to human germline gene editing (HGGE), by which permanent changes can be introduced into the embryo. Distinct genes can be knocked out to examine their function during embryonic development. Alternatively, specific sequences can be introduced which can be applied to correct disease-causing mutations. To date, it has been shown that the success of HGGE is dependent on various experimental parameters and that various hurdles (i.e. loss-of-heterozygosity and mosaicism) need to be overcome before clinical applications should be considered. Due to the shortage of human germline material and the ethical constraints concerning HGGE, alternative models such as stem cells have been evaluated as well, in terms of their predictive value on the genetic outcome for HGGE approaches. This review will give an overview of the state of the art of HGGE in oocytes and embryos, and its accompanying challenges.
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Affiliation(s)
- B Bekaert
- Ghent-Fertility And Stem cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - A Boel
- Ghent-Fertility And Stem cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - G Cosemans
- Ghent-Fertility And Stem cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - L De Witte
- Center for Medical Genetics Ghent, Ghent University, Department of Biomolecular Medicine, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - B Menten
- Center for Medical Genetics Ghent, Ghent University, Department of Biomolecular Medicine, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - B Heindryckx
- Ghent-Fertility And Stem cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium.
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44
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Jiang T, Ling Z, Zhou Z, Chen X, Chen L, Liu S, Sun Y, Yang J, Yang B, Huang J, Huang L. Construction of a transposase accessible chromatin landscape reveals chromatin state of repeat elements and potential causal variant for complex traits in pigs. J Anim Sci Biotechnol 2022; 13:112. [PMID: 36217153 PMCID: PMC9552403 DOI: 10.1186/s40104-022-00767-3] [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: 04/18/2022] [Accepted: 08/10/2022] [Indexed: 11/13/2022] Open
Abstract
Background A comprehensive landscape of chromatin states for multiple mammalian tissues is essential for elucidating the molecular mechanism underlying regulatory variants on complex traits. However, the genome-wide chromatin accessibility has been only reported in limited tissue types in pigs. Results Here we report a genome-wide landscape of chromatin accessibility of 20 tissues in two female pigs at ages of 6 months using ATAC-seq, and identified 557,273 merged peaks, which greatly expanded the pig regulatory element repository. We revealed tissue-specific regulatory elements which were associated with tissue-relevant biological functions. We identified both positive and negative significant correlations between the regulatory elements and gene transcripts, which showed distinct distributions in terms of their strength and distances from corresponding genes. We investigated the presence of transposable elements (TEs) in open chromatin regions across all tissues, these included identifications of porcine endogenous retroviruses (PERVs) exhibiting high accessibility in liver and homology of porcine specific virus sequences to universally accessible transposable elements. Furthermore, we prioritized a potential causal variant for polyunsaturated fatty acid in the muscle. Conclusions Our data provides a novel multi-tissues accessible chromatin landscape that serve as an important resource for interpreting regulatory sequences in tissue-specific and conserved biological functions, as well as regulatory variants of loci associated with complex traits in pigs. Supplementary Information The online version contains supplementary material available at 10.1186/s40104-022-00767-3.
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Affiliation(s)
- Tao Jiang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Ziqi Ling
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Zhimin Zhou
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xiaoyun Chen
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Liqing Chen
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Sha Liu
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Yingchun Sun
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jiawen Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Bin Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Jianzhen Huang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Lusheng Huang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
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45
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Low Expression of Mitofusin 1 Gene Leads to Mitochondrial Dysfunction and Embryonic Genome Activation Failure in Ovine-Bovine Inter-Species Cloned Embryos. Int J Mol Sci 2022; 23:ijms231710145. [PMID: 36077543 PMCID: PMC9456037 DOI: 10.3390/ijms231710145] [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: 06/29/2022] [Revised: 08/27/2022] [Accepted: 08/30/2022] [Indexed: 11/17/2022] Open
Abstract
Inter-species somatic cell nuclear transfer (iSCNT) is significant in the study of biological problems such as embryonic genome activation and the mitochondrial function of embryos. Here, we used iSCNT as a model to determine whether abnormal embryo genome activation was caused by mitochondrial dysfunction. First, we found the ovine-bovine iSCNT embryos were developmentally blocked at the 8-cell stage. The reactive oxygen species level, mitochondrial membrane potential, and ATP level in ovine-bovine cloned embryos were significantly different from both bovine-bovine and IVF 8-cell stage embryos. RNA sequencing and q-PCR analysis revealed that mitochondrial transport, mitochondrial translational initiation, mitochondrial large ribosomal subunit, and mitochondrial outer membrane genes were abnormally expressed in the ovine-bovine embryos, and the mitochondrial outer membrane and mitochondrial ribosome large subunit genes, mitochondrial fusion gene 1, and ATPase Na+/K+ transporting subunit beta 3 gene were expressed at lower levels in the ovine-bovine cloned embryos. Furthermore, we found that overexpression and knockdown of Mfn1 significantly affected mitochondrial fusion and subsequent biological functions such as production of ATP, mitochondrial membrane potential, reactive oxygen species and gene expressions in cloned embryos. These findings enhance our understanding of the mechanism by which the Mfn1 gene regulates embryonic development and embryonic genome activation events.
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46
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Idrees M, Kumar V, Khan AM, Joo MD, Uddin Z, Lee KW, Kong IK. Hesperetin activated SIRT1 neutralizes cadmium effects on the early bovine embryo development. Theriogenology 2022; 189:209-221. [DOI: 10.1016/j.theriogenology.2022.06.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 12/12/2022]
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47
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Kelly CJ, Chitko-McKown CG, Chuong EB. Ruminant-specific retrotransposons shape regulatory evolution of bovine immunity. Genome Res 2022; 32:1474-1486. [PMID: 35948370 PMCID: PMC9435751 DOI: 10.1101/gr.276241.121] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 05/05/2022] [Indexed: 02/03/2023]
Abstract
Cattle are an important livestock species, and mapping the genomic architecture of agriculturally relevant traits such as disease susceptibility is a major challenge in the bovine research community. Lineage-specific transposable elements (TEs) are increasingly recognized to contribute to gene regulatory evolution and variation, but this possibility has been largely unexplored in ruminant genomes. We conducted epigenomic profiling of the type II interferon (IFN) response in bovine cells and found thousands of ruminant-specific TEs including MER41_BT and Bov-A2 elements predicted to act as IFN-inducible enhancer elements. CRISPR knockout experiments in bovine cells established that critical immune factors including IFNAR2 and IL2RB are transcriptionally regulated by TE-derived enhancers. Finally, population genomic analysis of 38 individuals revealed that a subset of polymorphic TE insertions may function as enhancers in modern cattle. Our study reveals that lineage-specific TEs have shaped the evolution of ruminant IFN responses and potentially continue to contribute to immune gene regulatory differences across modern breeds and individuals. Together with previous work in human cells, our findings demonstrate that lineage-specific TEs have been independently co-opted to regulate IFN-inducible gene expression in multiple species, supporting TE co-option as a recurrent mechanism driving the evolution of IFN-inducible transcriptional networks.
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Affiliation(s)
- Conor J Kelly
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80309, USA
| | - Carol G Chitko-McKown
- USDA, ARS, Roman L. Hruska US Meat Animal Research Center (MARC), Clay Center, Nebraska 68933, USA
| | - Edward B Chuong
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80309, USA
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48
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Hu R, Xu Y, Han B, Chen Y, Li W, Guan G, Hu P, Zhou Y, Xu Q, Chen L. MiR-202-3p determines embryo viability during mid-blastula transition. Front Cell Dev Biol 2022; 10:897826. [PMID: 36003151 PMCID: PMC9393261 DOI: 10.3389/fcell.2022.897826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 07/13/2022] [Indexed: 11/13/2022] Open
Abstract
Developmental growth is an intricate process involving the coordinated regulation of the expression of various genes, and microRNAs (miRNAs) play crucial roles in diverse processes throughout animal development. The mid-blastula transition (MBT) is a developmental milestone when maternal RNAs are cleared and the zygotic genome programmed asynchronous cell division begins to drive embryogenesis. While mechanisms underlying MBT have been intensively revealed, factors regulating cell proliferation at the transition remain largely unknown. We report here a microRNA, miR-202-3p to be a key factor that determines embryonic fate during MBT in zebrafish. A miR-202-3p antagomir specifically terminated embryo development at the mid-blastula stage. In vivo deletion of the miR-202 locus recapitulated the fatal phenotypes, which were rescued only by miR-202-3p or its precursor. Transcriptome comparison revealed >250 RNAs including both maternal and zygotic origins were dysregulated at MBT in the miR-202−/− embryos, corresponding with arrays of homeostatic disorders leading to massive apoptosis. A trio of genes: nfkbiaa, perp and mgll, known to be intimately involved with cell proliferation and survival, were identified as direct targets of miR-202-3p. Importantly, over- or under-expression of any of the trio led to developmental delay or termination at the blastula or gastrula stages. Furthermore, nfkbiaa and perp were shown to inter-regulate each other. Thus, miR-202-3p mediates a regulatory network whose components interact closely during MBT to determine embryonic viability and development.
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Affiliation(s)
- Ruiqin Hu
- International Joint Research Centre for Marine Biosciences (Ministry of Science and Technology), College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education) and International Research Centre for Marine Biosciences, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Yanna Xu
- International Joint Research Centre for Marine Biosciences (Ministry of Science and Technology), College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education) and International Research Centre for Marine Biosciences, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Bingshe Han
- International Joint Research Centre for Marine Biosciences (Ministry of Science and Technology), College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education) and International Research Centre for Marine Biosciences, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Yi Chen
- International Joint Research Centre for Marine Biosciences (Ministry of Science and Technology), College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education) and International Research Centre for Marine Biosciences, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Wenhao Li
- International Joint Research Centre for Marine Biosciences (Ministry of Science and Technology), College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education) and International Research Centre for Marine Biosciences, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Guijun Guan
- International Joint Research Centre for Marine Biosciences (Ministry of Science and Technology), College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education) and International Research Centre for Marine Biosciences, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Peng Hu
- International Joint Research Centre for Marine Biosciences (Ministry of Science and Technology), College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education) and International Research Centre for Marine Biosciences, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Yan Zhou
- International Joint Research Centre for Marine Biosciences (Ministry of Science and Technology), College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education) and International Research Centre for Marine Biosciences, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Qianghua Xu
- International Joint Research Centre for Marine Biosciences (Ministry of Science and Technology), College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education) and International Research Centre for Marine Biosciences, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, College of Marine Science, Shanghai Ocean University, Shanghai, China
| | - Liangbiao Chen
- International Joint Research Centre for Marine Biosciences (Ministry of Science and Technology), College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education) and International Research Centre for Marine Biosciences, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- *Correspondence: Liangbiao Chen,
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49
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Zhang M, Current JZ, Chaney HL, Yao J. Identification of the DNA binding element of ZNFO, an oocyte-specific zinc finger transcription factor in cattle. Gene 2022; 834:146655. [PMID: 35680024 DOI: 10.1016/j.gene.2022.146655] [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: 03/18/2022] [Revised: 05/14/2022] [Accepted: 06/02/2022] [Indexed: 11/04/2022]
Abstract
The maternal effect genes are essential components of oocyte competence, which orchestrate the early developmental events before zygotic genome activation (ZGA). The Krüppel-associated box (KRAB) domain-containing zinc finger proteins (KRAB-ZFPs) constitute the largest transcription factor family in mammals. As a novel maternal effect gene, ZNFO was identified previously in our laboratory. The gene codes for a KRAB-ZFP specifically expressed in bovine oocytes and early embryos and gene silencing experiments have demonstrated that ZNFO is required for early embryonic development in cattle. In the present study, we identified a consensus sequence, ATATCCTGTTTAAACCCC, as the DNA binding element of ZNFO (ZNFOBE) using a library of random oligonucleotides by cyclic amplification of sequence target (CAST) analysis. Sequence-specific binding of ZNFO to the DNA binding element was confirmed by an electrophoretic mobility shift assay (EMSA), and the key nucleotides in the ZNFOBE that are required for specific binding by ZNFO were further determined by a competitive EMSA using mutant competitors. Through a luciferase-based reporter assay, it was confirmed that the interaction between ZNFO and ZNFOBE is required for the repressive function of ZNFO. These results provide an essential step towards the identification of ZNFO regulated genes that play important roles during early embryonic development.
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Affiliation(s)
- Mingxiang Zhang
- Laboratory of Animal Biotechnology and Genomics, Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA
| | - Jaelyn Z Current
- Laboratory of Animal Biotechnology and Genomics, Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA
| | - Heather L Chaney
- Laboratory of Animal Biotechnology and Genomics, Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA
| | - Jianbo Yao
- Laboratory of Animal Biotechnology and Genomics, Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA.
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Genome-wide profiling of histone H3K4me3 and H3K27me3 modifications in individual blastocysts by CUT&Tag without a solid support (NON-TiE-UP CUT&Tag). Sci Rep 2022; 12:11727. [PMID: 35821505 PMCID: PMC9276795 DOI: 10.1038/s41598-022-15417-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 06/23/2022] [Indexed: 11/09/2022] Open
Abstract
Individual analysis of the epigenome of preimplantation embryos is useful for characterizing each embryo and for investigating the effects of environmental factors on their epigenome. However, it is difficult to analyze genome-wide epigenetic modifications, especially histone modifications, in a large number of single embryos due to the small number of cells and the complexity of the analysis methods. To solve this problem, we further modified the CUT&Tag method, which can analyze histone modifications in a small number of cells, such that the embryo is handled as a cell mass in the reaction solutions in the absence of the solid-phase magnetic beads that are used for antibody and enzyme reactions in the conventional method (NON-TiE-UP CUT&Tag; NTU-CAT). By using bovine blastocysts as a model, we showed that genome-wide profiles of representative histone modifications, H3K4me3 and H3K27me3, could be obtained by NTU-CAT that are in overall agreement with the conventional chromatin immunoprecipitation-sequencing (ChIP-seq) method, even from single embryos. However, this new approach has limitations that require attention, including false positive and negative peaks and lower resolution for broad modifications. Despite these limitations, we consider NTU-CAT a promising replacement for ChIP-seq with the great advantage of being able to analyze individual embryos.
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