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Zhang H, Pan Y, Wang M, Wang J, Huang J, Ma R, Yang S, Ma W, Yu S, Cui Y. SETD2 regulates oocytes in vitro maturation through histone methylation and maternal mRNA degradation in yak. Theriogenology 2025; 240:117387. [PMID: 40120144 DOI: 10.1016/j.theriogenology.2025.117387] [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: 12/09/2024] [Revised: 02/26/2025] [Accepted: 03/10/2025] [Indexed: 03/25/2025]
Abstract
In vitro maturation (IVM) of oocytes is a vital aspect of assisted reproductive technology (ART), and its proper application can enhance reproductive efficiency. However, owing to the scarcity of research on the IVM of yak oocytes, its application in yak breeding remains underexplored. Therefore, in this study, we conducted high-throughput mRNA sequencing of immature and mature yak oocytes, which revealed transcriptomic changes during the IVM process in this unique high-altitude domesticated animal. Transcriptomic analysis also identified the histone methyltransferase SET domain-containing 2 (SETD2) as a key factor associated with post-translational modifications during oocyte maturation. To determine the role of SETD2 in oocytes, we employed the SETD2 inhibitor EZM0414 during oocyte maturation. Inhibition of SETD2 resulted in a significant reduction in histone methylation levels, lower oocyte maturation rate in vitro, and suppression of maternal mRNAs degradation suppression (P < 0.05). These findings indicated that SETD2 modulates oocyte maturation by regulating histone methylation and maternal mRNAs degradation. Furthermore, suppression of SETD2 markedly reduced the expression of oocyte secretion-related proteins (TSG6 and GDF9) and cumulus expansion-related protein (PTGS2), demonstrating that oocyte secretion and cumulus expansion were positively correlated with SETD2. Overall, our findings establish SETD2 as an essential regulator of yak oocyte maturation via histone methylation and maternal mRNAs degradation.
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Affiliation(s)
- Hui Zhang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, China; Gansu Provincial Livestock Embryo Engineering Technology Innovation Center, Lanzhou, 730070, China
| | - Yangyang Pan
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, China; Gansu Provincial Livestock Embryo Engineering Technology Innovation Center, Lanzhou, 730070, China
| | - Meng Wang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, China; Gansu Provincial Livestock Embryo Engineering Technology Innovation Center, Lanzhou, 730070, China
| | - Jinglei Wang
- Gansu Provincial Livestock Embryo Engineering Technology Innovation Center, Lanzhou, 730070, China
| | - Jiaxin Huang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, China
| | - Rui Ma
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, China; Gansu Provincial Livestock Embryo Engineering Technology Innovation Center, Lanzhou, 730070, China
| | - Shanshan Yang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, China; Gansu Provincial Livestock Embryo Engineering Technology Innovation Center, Lanzhou, 730070, China
| | - Wenbin Ma
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, China; Gansu Provincial Livestock Embryo Engineering Technology Innovation Center, Lanzhou, 730070, China
| | - Sijiu Yu
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, China; Gansu Provincial Livestock Embryo Engineering Technology Innovation Center, Lanzhou, 730070, China.
| | - Yan Cui
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, China; Gansu Provincial Livestock Embryo Engineering Technology Innovation Center, Lanzhou, 730070, China.
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Reimão-Pinto MM, Castillo-Hair SM, Seelig G, Schier AF. The regulatory landscape of 5' UTRs in translational control during zebrafish embryogenesis. Dev Cell 2025; 60:1498-1515.e8. [PMID: 39818206 DOI: 10.1016/j.devcel.2024.12.038] [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: 12/14/2023] [Revised: 07/22/2024] [Accepted: 12/19/2024] [Indexed: 01/18/2025]
Abstract
The 5' UTRs of mRNAs are critical for translation regulation during development, but their in vivo regulatory features are poorly characterized. Here, we report the regulatory landscape of 5' UTRs during early zebrafish embryogenesis using a massively parallel reporter assay of 18,154 sequences coupled to polysome profiling. We found that the 5' UTR suffices to confer temporal dynamics to translation initiation and identified 86 motifs enriched in 5' UTRs with distinct ribosome recruitment capabilities. A quantitative deep learning model, Danio Optimus 5-Prime (DaniO5P), identified a combined role for 5' UTR length, translation initiation site context, upstream AUGs, and sequence motifs on ribosome recruitment. DaniO5P predicts the activities of maternal and zygotic 5' UTR isoforms and indicates that modulating 5' UTR length and motif grammar contributes to translation initiation dynamics. This study provides a first quantitative model of 5' UTR-based translation regulation in development and lays the foundation for identifying the underlying molecular effectors.
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Affiliation(s)
| | - Sebastian M Castillo-Hair
- Department of Electrical & Computer Engineering, University of Washington, Seattle, WA 98195, USA; eScience Institute, University of Washington, Seattle, WA 98195, USA
| | - Georg Seelig
- Department of Electrical & Computer Engineering, University of Washington, Seattle, WA 98195, USA; Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA
| | - Alexander F Schier
- Biozentrum, University of Basel, 4056 Basel, Switzerland; Allen Discovery Center for Cell Lineage Tracing, Seattle, WA 98195, USA.
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3
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Tomuro K, Iwasaki S. Advances in ribosome profiling technologies. Biochem Soc Trans 2025:BST20253061. [PMID: 40380882 DOI: 10.1042/bst20253061] [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: 03/09/2025] [Accepted: 04/30/2025] [Indexed: 05/19/2025]
Abstract
Ribosome profiling (or Ribo-seq) has emerged as a powerful approach for revealing the regulatory mechanisms of protein synthesis, on the basis of deep sequencing of ribosome footprints. Recent innovations in Ribo-seq technologies have significantly enhanced their sensitivity, specificity, and resolution. In this review, we outline emerging Ribo-seq derivatives that overcome barriers in low inputs, rRNA contamination, data calibration, and single-cell applications. These advances enable detailed insights into translational control across diverse biological contexts.
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Affiliation(s)
- Kotaro Tomuro
- RNA Systems Biochemistry Laboratory, Pioneering Research Institute, RIKEN, Wako, Saitama 351-0198, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, Pioneering Research Institute, RIKEN, Wako, Saitama 351-0198, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan
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Qi X, Ji H, Bianchi E, Hall SJ, Avellino G, Berg W, Bearelly P, Sigman M, Wu Z, Spade DJ. Downregulation of spermatogenesis-associated transcripts in the spermatozoa of idiopathic infertile men. Andrology 2025. [PMID: 40346865 DOI: 10.1111/andr.70060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2025] [Revised: 04/11/2025] [Accepted: 04/28/2025] [Indexed: 05/12/2025]
Abstract
BACKGROUND Approximately half of male factor infertility cases are idiopathic, indicating a need for new methods to supplement male fertility assessment. OBJECTIVES The objective of this study was to identify differences in the sperm transcriptomes of men with different clinical fertility status. We hypothesized that sperm mRNA profiling could distinguish men presenting for fertility assessment from proven fertile men. MATERIALS AND METHODS We compared two groups of study participants: men who presented for infertility assessment (n = 53, "infertility"), and men without a history of infertility who had fathered a child and were presenting for vasectomy (n = 14, "proven fertile" control). Study participants provided a semen sample for semen analysis and sperm mRNA sequencing. Differentially abundant genes were identified, and a gene expression summary score was constructed to test the ability of RNA-seq data to differentiate between study populations. RESULTS The semen parameter that best differentiated between study populations was motility (area under the ROC curve = 0.746). In RNA-seq analysis, 1885 total differentially abundant transcripts were identified (q < 0.05, fold difference ≥ 2), 1004 (53.3%) of which were downregulated in infertility study participants. The Gene Ontology term, spermatogenesis, was enriched, with 40 out of 44 differentially abundant genes downregulated in infertility study participants. A gene expression summary score consisting of 100 upregulated and 100 downregulated genes was able to differentiate between the two groups of study participants. DISCUSSION Sperm mRNAs differed between proven fertile and infertility study men. Known fertility-associated genes, including PRM1 and PRM2, and potentially novel fertility markers, including HOOK1 and SPATA6, were downregulated in infertility study samples. Future studies should test these results for reproducibility and test whether novel biomarker candidates can provide mechanistic information about etiologies of idiopathic male infertility. CONCLUSION Our results support the hypothesis that sperm mRNA abundance differs by clinical fertility status.
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Affiliation(s)
- Xinran Qi
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, USA
| | - Han Ji
- Department of Biostatistics, Brown University, Providence, Rhode Island, USA
| | - Enrica Bianchi
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, USA
| | - Susan J Hall
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, USA
| | - Gabriella Avellino
- Department of Surgery, Division of Urology, Brown University, Providence, Rhode Island, USA
| | - William Berg
- Department of Surgery, Division of Urology, Brown University, Providence, Rhode Island, USA
| | - Priyanka Bearelly
- Department of Surgery, Division of Urology, Brown University, Providence, Rhode Island, USA
| | - Mark Sigman
- Department of Surgery, Division of Urology, Brown University, Providence, Rhode Island, USA
| | - Zhijin Wu
- Department of Biostatistics, Brown University, Providence, Rhode Island, USA
| | - Daniel J Spade
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, USA
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Camlin NJ. Protein-targeting reverse genetic approaches: the future of oocyte and preimplantation embryo research. Mol Hum Reprod 2025; 31:gaaf008. [PMID: 40100642 PMCID: PMC12000532 DOI: 10.1093/molehr/gaaf008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2024] [Revised: 02/10/2025] [Indexed: 03/20/2025] Open
Abstract
Reverse genetic approaches are the standard in molecular biology to determine a protein's function. Traditionally, nucleic acid targeting via gene knockout (DNA) and knockdown (RNA) has been the method of choice to remove proteins-of-interest. However, the nature of mammalian oocyte maturation and preimplantation embryo development can make nucleic acid-targeting approaches difficult. Gene knockout allows time for compensatory mechanisms and secondary phenotypes to develop which can make interpretation of a protein's function difficult. Furthermore, genes can be essential for animal and/or oocyte survival, and therefore, gene knockout is not always a viable approach to investigate oocyte maturation and preimplantation embryo development. Conversely, RNA-targeting approaches, i.e. RNA interference (RNAi) and morpholinos, rely on protein half-life and therefore are unable to knockdown every protein-of-interest. An increasing number of reverse genetic approaches that directly target proteins have been developed to overcome the limitations of nucleic acid-based approaches, including Trim-Away and auxin-inducible degradation. These protein-targeting approaches give researchers exquisite and fast control of protein loss. This review will discuss how Trim-Away and auxin-inducible degradation can overcome many of the challenges of nucleic acid-based reverse genetic approaches. Furthermore, it highlights the unique research opportunities these approaches afford, such as targeting post-translationally modified proteins.
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Affiliation(s)
- Nicole J Camlin
- Cell and Molecular Biology, School of Biological, Environmental and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, USA
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Yang G, Xin Q, Dean J. ZNHIT3 Regulates Translation to Ensure Cell Lineage Differentiation in Mouse Preimplantation Development. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025:e2413599. [PMID: 40178020 DOI: 10.1002/advs.202413599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2024] [Revised: 03/13/2025] [Indexed: 04/05/2025]
Abstract
Upon fertilization, the mouse zygotic genome is activated and maternal RNAs as well as proteins are degraded. Early developmental programs are built on proteins encoded by zygotic mouse genes that are needed to guide early cell fate commitment. The box C/D snoRNA ribonucleoprotein (snoRNP) complex is required for rRNA biogenesis, ribosome assembly and pre-mRNA splicing essential for protein translation. Zinc finger, HIT type 3 (encoded by Znhit3) is previously identified as a component in the assembly of the box C/D snoRNP complex. Using gene-edited mice, it identifies Znhit3 as an early embryonic gene whose ablation reduces protein translation and prevents mouse embryos development beyond the morula stage. The absence of ZNHIT3 leads to decreased snoRNA and rRNA abundance which causes defects of ribosomes and mRNA splicing. Microinjection of Znhit3 cRNA partially rescues the phenotype and confirms that ZNHIT3 is required for mRNA translation during preimplantation development.
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Affiliation(s)
- Guanghui Yang
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Qiliang Xin
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jurrien Dean
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD, 20892, USA
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Dowdle ME, Lykke-Andersen J. Cytoplasmic mRNA decay and quality control machineries in eukaryotes. Nat Rev Genet 2025:10.1038/s41576-024-00810-1. [PMID: 39870755 DOI: 10.1038/s41576-024-00810-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2024] [Indexed: 01/29/2025]
Abstract
mRNA degradation pathways have key regulatory roles in gene expression. The intrinsic stability of mRNAs in the cytoplasm of eukaryotic cells varies widely in a gene- and isoform-dependent manner and can be regulated by cellular cues, such as kinase signalling, to control mRNA levels and spatiotemporal dynamics of gene expression. Moreover, specialized quality control pathways exist to rid cells of non-functional mRNAs produced by errors in mRNA processing or mRNA damage that negatively impact translation. Recent advances in structural, single-molecule and genome-wide methods have provided new insights into the central machineries that carry out mRNA turnover, the mechanisms by which mRNAs are targeted for degradation and the general principles that govern mRNA stability at a global level. This improved understanding of mRNA degradation in the cytoplasm of eukaryotic cells is finding practical applications in the design of therapeutic mRNAs.
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Affiliation(s)
- Megan E Dowdle
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Jens Lykke-Andersen
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA.
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Demond H, Khan S, Castillo-Fernandez J, Hanna CW, Kelsey G. Transcriptome and DNA methylation profiling during the NSN to SN transition in mouse oocytes. BMC Mol Cell Biol 2025; 26:2. [PMID: 39754059 PMCID: PMC11697814 DOI: 10.1186/s12860-024-00527-3] [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: 08/12/2024] [Accepted: 12/27/2024] [Indexed: 01/06/2025] Open
Abstract
BACKGROUND During the latter stages of their development, mammalian oocytes under dramatic chromatin reconfiguration, transitioning from a non-surrounded nucleolus (NSN) to a surrounded nucleolus (SN) stage, and concomitant transcriptional silencing. Although the NSN-SN transition is known to be essential for developmental competence of the oocyte, less is known about the accompanying molecular changes. Here we examine the changes in the transcriptome and DNA methylation during the NSN to SN transition in mouse oocytes. RESULTS To study the transcriptome and DNA methylation dynamics during the NSN to SN transition, we used single-cell (sc)M&T-seq to generate scRNA-seq and sc-bisulphite-seq (scBS-seq) data from GV oocytes classified as NSN or SN by Hoechst staining of their nuclei. Transcriptome analysis showed a lower number of detected transcripts in SN compared with NSN oocytes as well as downregulation of 576 genes, which were enriched for processes related to mRNA processing. We used the transcriptome data to generate a classifier that can infer chromatin stage in scRNA-seq datasets. The classifier was successfully tested in multiple published datasets of mouse models with a known skew in NSN: SN ratios. Analysis of the scBS-seq data showed increased DNA methylation in SN compared to NSN oocytes, which was most pronounced in regions with intermediate levels of methylation. Overlap with chromatin immunoprecipitation and sequencing (ChIP-seq) data for the histone modifications H3K36me3, H3K4me3 and H3K27me3 showed that regions gaining methylation in SN oocytes are enriched for overlapping H3K36me3 and H3K27me3, which is an unusual combination, as these marks do not typically coincide. CONCLUSIONS We characterise the transcriptome and DNA methylation changes accompanying the NSN-SN transition in mouse oocytes. We develop a classifier that can be used to infer chromatin status in single-cell or bulk RNA-seq data, enabling identification of altered chromatin transition in genetic knock-outs, and a quality control to identify skewed NSN-SN proportions that could otherwise confound differential gene expression analysis. We identify late-methylating regions in SN oocytes that are associated with an unusual combination of chromatin modifications, which may be regions with high chromatin plasticity and transitioning between H3K27me3 and H3K36me3, or reflect heterogeneity on a single-cell level.
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Affiliation(s)
- Hannah Demond
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK
- Laboratory of Integrative Biology (LIBi), Centro de Excelencia en Medicina Traslacional (CEMT), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
- BMRC, Biomedical Research Consortium Chile, Santiago, Chile
- Institute of Pathology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Soumen Khan
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK
| | | | - Courtney W Hanna
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK
- Loke Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3EG, UK
| | - Gavin Kelsey
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK.
- Loke Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK.
- Wellcome-MRC Institute of Metabolic Science-Metabolic Research Laboratories, Cambridge, CB2 0QQ, UK.
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Yang J, Bu J, Liu B, Liu Y, Zhang Z, Li Z, Lu F, Zhu B, Li Y. MARTRE family proteins negatively regulate CCR4-NOT activity to protect poly(A) tail length and promote translation of maternal mRNA. Nat Commun 2025; 16:248. [PMID: 39747175 PMCID: PMC11696134 DOI: 10.1038/s41467-024-55610-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 12/17/2024] [Indexed: 01/04/2025] Open
Abstract
The mammalian early embryo development requires translation of maternal mRNA inherited from the oocyte. While poly(A) tail length influences mRNA translation efficiency during the oocyte-to-embryo transition (OET), molecular mechanisms regulating maternal RNA poly(A) tail length are not fully understood. In this study, we identified MARTRE, a previously uncharacterized protein family (MARTRE1-MARTRE6), as regulators expressed during mouse OET that modulate poly(A) tail length. MARTRE inhibits deadenylation through the direct interaction with the deadenylase CCR4-NOT, and ectopic expression of Martre stabilized mRNA by attenuating poly(A) tail shortening. Deletion of the Martre gene locus results in shortened poly(A) tails and decreased translation efficiency of actively translated mRNAs in mouse zygotes, but does not affect maternal mRNA decay. MARTRE proteins thus fine-tune maternal mRNA translation by negatively regulating the deadenylating activity of CCR4-NOT. Moreover, Martre knockout embryos show delayed 2-cell stage progression and compromised preimplantation development. Together, our findings highlight protection of long poly(A) tails from active deadenylation as an important mechanism to coordinate translation of maternal mRNA.
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Affiliation(s)
- Jing Yang
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jiachen Bu
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Bowen Liu
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yusheng Liu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Zhuqiang Zhang
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ziyi Li
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Falong Lu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
| | - Bing Zhu
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
- New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Yingfeng Li
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
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Lv X, Zhang H, Wu L. Advances in PIWI-piRNA function in female reproduction in mammals. Acta Biochim Biophys Sin (Shanghai) 2024; 57:148-156. [PMID: 39544003 PMCID: PMC11802344 DOI: 10.3724/abbs.2024195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Accepted: 10/18/2024] [Indexed: 11/17/2024] Open
Abstract
PIWI-interacting RNAs (piRNAs), which associate with PIWI clade Argonaute proteins to form piRNA-induced silencing complexes (piRISCs) in germline cells, are responsible for maintaining genomic integrity and reproductive function through transcriptional or post-transcriptional suppression of transposable elements and regulation of protein-coding genes. Recent discoveries of crucial PIWI-piRNA functions in oogenesis and embryogenesis in golden hamsters suggest an indispensable role in female fertility that has been obscured in the predominant mouse model of PIWI-piRNA pathway regulation. In particular, studies of piRNA expression dynamics, functional redundancies, and compositional variations across mammal species have advanced our understanding of piRNA functions in male and, especially, female reproduction. These findings further support the use of hamsters as a more representative model of piRNA biology in mammals. In addition to discussing these new perspectives, the current review also covers emerging directions for piRNA research, its implications for female fertility, and our fundamental understanding of reproductive mechanisms.
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Affiliation(s)
- Xiaolong Lv
- />Key Laboratory of RNA Science and EngineeringShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghai200031China
| | - Hongdao Zhang
- />Key Laboratory of RNA Science and EngineeringShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghai200031China
| | - Ligang Wu
- />Key Laboratory of RNA Science and EngineeringShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghai200031China
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Ming H, Iyyappan R, Kakavand K, Dvoran M, Susor A, Jiang Z. Spatiotemporal dynamics and selectivity of mRNA translation during mouse pre-implantation development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.28.620693. [PMID: 39553972 PMCID: PMC11565823 DOI: 10.1101/2024.10.28.620693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2024]
Abstract
Translational regulation is pivotal during preimplantation development. However, how mRNAs are selected for temporal regulation and their dynamic utilization and fate during this period are still unknown. Using a high-resolution ribosome profiling approach, we analyzed the transcriptome, as well as monosome- and polysome-bound RNAs of mouse oocytes and embryos, defining an unprecedented extent of spatiotemporal translational landscapes during this rapid developmental phase. We observed previously unknown mechanisms of translational selectivity, i.e., stage-wise deferral of loading monosome-bound mRNAs to polysome for active translation, continuous translation of both monosome and polysome-bound mRNAs at the same developmental stage, and priming to monosomes after initial activation. We showed that a eukaryotic initiation factor Eif1ad3, which is exclusively translated in the 2-Cell embryo, is required for ribosome biogenesis post embryonic genome activation. Our study thus provides genome-wide datasets and analyses of spatiotemporal translational dynamics accompanying mammalian germ cell and embryonic development and reveals the contribution of a novel translation initiation factor to mammalian pre-implantation development.
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Affiliation(s)
- Hao Ming
- Department of Animal Sciences, Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Rajan Iyyappan
- Department of Animal Sciences, Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Kianoush Kakavand
- Laboratory of Biochemistry and Molecular Biology of Germ Cells, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Rumburska 89, 277 21 Libechov, Czech Republic
| | - Michal Dvoran
- Laboratory of Biochemistry and Molecular Biology of Germ Cells, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Rumburska 89, 277 21 Libechov, Czech Republic
| | - Andrej Susor
- Laboratory of Biochemistry and Molecular Biology of Germ Cells, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Rumburska 89, 277 21 Libechov, Czech Republic
| | - Zongliang Jiang
- Department of Animal Sciences, Genetics Institute, University of Florida, Gainesville, FL 32610, USA
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Giaccari C, Cecere F, Argenziano L, Pagano A, Riccio A. New insights into oocyte cytoplasmic lattice-associated proteins. Trends Genet 2024; 40:880-890. [PMID: 38955588 DOI: 10.1016/j.tig.2024.06.002] [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: 04/16/2024] [Revised: 06/06/2024] [Accepted: 06/07/2024] [Indexed: 07/04/2024]
Abstract
Oocyte maturation and preimplantation embryo development are critical to successful pregnancy outcomes and the correct establishment and maintenance of genomic imprinting. Thanks to novel technologies and omics studies in human patients and mouse models, the importance of the proteins associated with the cytoplasmic lattices (CPLs), highly abundant structures found in the cytoplasm of mammalian oocytes and preimplantation embryos, in the maternal to zygotic transition is becoming increasingly evident. This review highlights the recent discoveries on the role of these proteins in protein storage and other oocyte cytoplasmic processes, epigenetic reprogramming, and zygotic genome activation (ZGA). A better comprehension of these events may significantly improve clinical diagnosis and pave the way for targeted interventions aiming to correct or mitigate female fertility issues and genomic imprinting disorders.
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Affiliation(s)
- Carlo Giaccari
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania 'Luigi Vanvitelli,' Caserta, Italy
| | - Francesco Cecere
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania 'Luigi Vanvitelli,' Caserta, Italy
| | - Lucia Argenziano
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania 'Luigi Vanvitelli,' Caserta, Italy
| | - Angela Pagano
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania 'Luigi Vanvitelli,' Caserta, Italy
| | - Andrea Riccio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania 'Luigi Vanvitelli,' Caserta, Italy; Institute of Genetics and Biophysics (IGB) 'Adriano Buzzati-Traverso,' Consiglio Nazionale delle Ricerche (CNR), Naples, Italy.
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Pérez-Gómez A, Hamze JG, Flores-Borobia I, Galiano-Cogolludo B, Lamas-Toranzo I, González-Brusi L, Ramos-Ibeas P, Bermejo-Álvarez P. HH5 double-carrier embryos fail to progress through early conceptus elongation. J Dairy Sci 2024; 107:6371-6382. [PMID: 38642647 DOI: 10.3168/jds.2023-24482] [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: 11/28/2023] [Accepted: 03/14/2024] [Indexed: 04/22/2024]
Abstract
Massive genotyping in cattle has uncovered several deleterious haplotypes that cause preterm mortality. Holstein haplotype 5 (HH5) is a deleterious haplotype present in the Holstein Friesian population that involves the ablation of the transcription factor B1 mitochondrial (TFB1M) gene. The developmental stage at which HH5 double-carrier (DC, homozygous) embryos or fetuses die remains unknown and this is a relevant information to estimate the economic losses associated with the inadvertent cross between carriers. To determine whether HH5 DC survive to maternal recognition of pregnancy, embryonic day (E) 14 embryos were flushed from superovulated carrier cows inseminated with a carrier bull. Double-carrier E14 conceptuses were recovered at Mendelian rates but they failed to achieve early elongation, as evidenced by a drastic reduction of their extra-embryonic membranes, which were >26-fold shorter than those of carrier or noncarrier embryos. To assess development at earlier stages, TFB1M knockout (KO) embryos-functionally equivalent to DC embryos-were generated by clustered regularly interspaced short palindromic repeats (CRISPR) technology and cultured to the blastocyst stage, in vitro culture day (D) 8, and to the early embryonic disc stage, D12. No significant effect of TFB1M ablation was observed on the differentiation and proliferation of embryonic lineages and relative mitochondrial DNA (mtDNA) content up to D12. In conclusion, HH5 DC embryos are able to develop to early embryonic disc stage but fail to undergo early conceptus elongation, which is required for pregnancy recognition.
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Affiliation(s)
- A Pérez-Gómez
- Animal Reproduction Department, INIA, CSIC, 28040 Madrid, Spain
| | - J G Hamze
- Animal Reproduction Department, INIA, CSIC, 28040 Madrid, Spain; Department of Cell Biology and Histology, Universidad de Murcia, International Excellence Campus for Higher Education and Research (Campus Mare Nostrum), 30100 Murcia, Spain
| | | | | | - I Lamas-Toranzo
- Animal Reproduction Department, INIA, CSIC, 28040 Madrid, Spain; Department of Cell Biology and Histology, Universidad de Murcia, International Excellence Campus for Higher Education and Research (Campus Mare Nostrum), 30100 Murcia, Spain
| | - L González-Brusi
- Animal Reproduction Department, INIA, CSIC, 28040 Madrid, Spain; Department of Cell Biology and Histology, Universidad de Murcia, International Excellence Campus for Higher Education and Research (Campus Mare Nostrum), 30100 Murcia, Spain
| | - P Ramos-Ibeas
- Animal Reproduction Department, INIA, CSIC, 28040 Madrid, Spain
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