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Blanton LV, San Roman AK, Wood G, Buscetta A, Banks N, Skaletsky H, Godfrey AK, Pham TT, Hughes JF, Brown LG, Kruszka P, Lin AE, Kastner DL, Muenke M, Page DC. Stable and robust Xi and Y transcriptomes drive cell-type-specific autosomal and Xa responses in vivo and in vitro in four human cell types. bioRxiv 2024:2024.03.18.585578. [PMID: 38562807 PMCID: PMC10983990 DOI: 10.1101/2024.03.18.585578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Recent in vitro studies of human sex chromosome aneuploidy showed that the Xi ("inactive" X) and Y chromosomes broadly modulate autosomal and Xa ("active" X) gene expression in two cell types. We tested these findings in vivo in two additional cell types. Using linear modeling in CD4+ T cells and monocytes from individuals with one to three X chromosomes and zero to two Y chromosomes, we identified 82 sex-chromosomal and 344 autosomal genes whose expression changed significantly with Xi and/or Y dosage in vivo . Changes in sex-chromosomal expression were remarkably constant in vivo and in vitro across all four cell types examined. In contrast, autosomal responses to Xi and/or Y dosage were largely cell-type-specific, with up to 2.6-fold more variation than sex-chromosomal responses. Targets of the X- and Y-encoded transcription factors ZFX and ZFY accounted for a significant fraction of these autosomal responses both in vivo and in vitro . We conclude that the human Xi and Y transcriptomes are surprisingly robust and stable across the four cell types examined, yet they modulate autosomal and Xa genes - and cell function - in a cell-type-specific fashion. These emerging principles offer a foundation for exploring the wide-ranging regulatory roles of the sex chromosomes across the human body.
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Page DC. David C. Page. Cell Genom 2024; 4:100486. [PMID: 38325340 DOI: 10.1016/j.xgen.2023.100486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 02/09/2024]
Abstract
We talk to David C. Page, corresponding author of "The human Y and inactive X chromosomes similarly modulate autosomal gene expression" in this issue of Cell Genomics, about his paper, the most exciting findings in the paper, and his advice for other scientists.
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San Roman AK, Skaletsky H, Godfrey AK, Bokil NV, Teitz L, Singh I, Blanton LV, Bellott DW, Pyntikova T, Lange J, Koutseva N, Hughes JF, Brown L, Phou S, Buscetta A, Kruszka P, Banks N, Dutra A, Pak E, Lasutschinkow PC, Keen C, Davis SM, Lin AE, Tartaglia NR, Samango-Sprouse C, Muenke M, Page DC. The human Y and inactive X chromosomes similarly modulate autosomal gene expression. Cell Genom 2024; 4:100462. [PMID: 38190107 PMCID: PMC10794785 DOI: 10.1016/j.xgen.2023.100462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/15/2023] [Accepted: 11/14/2023] [Indexed: 01/09/2024]
Abstract
Somatic cells of human males and females have 45 chromosomes in common, including the "active" X chromosome. In males the 46th chromosome is a Y; in females it is an "inactive" X (Xi). Through linear modeling of autosomal gene expression in cells from individuals with zero to three Xi and zero to four Y chromosomes, we found that Xi and Y impact autosomal expression broadly and with remarkably similar effects. Studying sex chromosome structural anomalies, promoters of Xi- and Y-responsive genes, and CRISPR inhibition, we traced part of this shared effect to homologous transcription factors-ZFX and ZFY-encoded by Chr X and Y. This demonstrates sex-shared mechanisms by which Xi and Y modulate autosomal expression. Combined with earlier analyses of sex-linked gene expression, our studies show that 21% of all genes expressed in lymphoblastoid cells or fibroblasts change expression significantly in response to Xi or Y chromosomes.
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Affiliation(s)
| | - Helen Skaletsky
- Whitehead Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
| | - Alexander K Godfrey
- Whitehead Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Neha V Bokil
- Whitehead Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Levi Teitz
- Whitehead Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Isani Singh
- Whitehead Institute, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | - Julian Lange
- Whitehead Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | | | - Laura Brown
- Whitehead Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
| | - Sidaly Phou
- Whitehead Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
| | - Ashley Buscetta
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul Kruszka
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicole Banks
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amalia Dutra
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Evgenia Pak
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | | | - Shanlee M Davis
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Angela E Lin
- Medical Genetics, Massachusetts General for Children, Boston, MA 02114, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Nicole R Tartaglia
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA; Developmental Pediatrics, eXtraOrdinarY Kids Program, Children's Hospital Colorado, Aurora, CO 80011, USA
| | - Carole Samango-Sprouse
- Focus Foundation, Davidsonville, MD 21035, USA; Department of Pediatrics, George Washington University, Washington, DC 20052, USA; Department of Human and Molecular Genetics, Florida International University, Miami, FL 33199, USA
| | - Maximilian Muenke
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David C Page
- Whitehead Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA.
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Mikedis MM, Liu B, de Rooij DG, Page DC. Post-transcriptional repression of mRNA enhances competence to transit from mitosis to meiosis in mouse spermatogenic cells. bioRxiv 2023:2023.09.20.557439. [PMID: 37781613 PMCID: PMC10541148 DOI: 10.1101/2023.09.20.557439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
The special cell cycle known as meiosis transforms diploid germ cells into haploid gametes. In mammalian testes, diploid spermatogenic cells become competent to transition from mitosis to meiosis in response to retinoic acid. In mice, previous studies revealed that MEIOC, alongside binding partners YTHDC2 and RBM46, represses mitotic genes and promotes robust meiotic gene expression in spermatogenic cells that have already initiated meiosis. Here, we molecularly dissect MEIOC-dependent regulation in mouse spermatogenic cells and find that MEIOC actually shapes the transcriptome much earlier, even before meiotic initiation. MEIOC, acting with YTHDC2 and RBM46, destabilizes mRNA targets, including transcriptional repressors E2f6 and Mga, in mitotic spermatogonia. MEIOC thereby derepresses E2F6- and MGA-repressed genes, including Meiosin and other meiosis-associated genes. This confers on spermatogenic cells the molecular competence to, in response to retinoic acid, fully activate the STRA8-MEIOSIN transcriptional regulator, which is required for the meiotic G1/S cell cycle transition and meiotic gene expression. We conclude that in mice, mRNA decay mediated by MEIOC-YTHDC2-RBM46 enhances the competence of mitotic spermatogonia to transit from mitosis to meiosis.
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Affiliation(s)
- Maria M. Mikedis
- Reproductive Sciences Center, Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH United States
- Whitehead Institute, Cambridge, MA, United States
| | - Bingrun Liu
- Whitehead Institute, Cambridge, MA, United States
| | | | - David C. Page
- Whitehead Institute, Cambridge, MA, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA, United States
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5
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Han CZ, Li RZ, Hansen E, Trescott S, Fixsen BR, Nguyen CT, Mora CM, Spann NJ, Bennett HR, Poirion O, Buchanan J, Warden AS, Xia B, Schlachetzki JCM, Pasillas MP, Preissl S, Wang A, O'Connor C, Shriram S, Kim R, Schafer D, Ramirez G, Challacombe J, Anavim SA, Johnson A, Gupta M, Glass IA, Levy ML, Haim SB, Gonda DD, Laurent L, Hughes JF, Page DC, Blurton-Jones M, Glass CK, Coufal NG. Human microglia maturation is underpinned by specific gene regulatory networks. Immunity 2023; 56:2152-2171.e13. [PMID: 37582369 PMCID: PMC10529991 DOI: 10.1016/j.immuni.2023.07.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 04/11/2023] [Accepted: 07/21/2023] [Indexed: 08/17/2023]
Abstract
Microglia phenotypes are highly regulated by the brain environment, but the transcriptional networks that specify the maturation of human microglia are poorly understood. Here, we characterized stage-specific transcriptomes and epigenetic landscapes of fetal and postnatal human microglia and acquired corresponding data in induced pluripotent stem cell (iPSC)-derived microglia, in cerebral organoids, and following engraftment into humanized mice. Parallel development of computational approaches that considered transcription factor (TF) co-occurrence and enhancer activity allowed prediction of shared and state-specific gene regulatory networks associated with fetal and postnatal microglia. Additionally, many features of the human fetal-to-postnatal transition were recapitulated in a time-dependent manner following the engraftment of iPSC cells into humanized mice. These data and accompanying computational approaches will facilitate further efforts to elucidate mechanisms by which human microglia acquire stage- and disease-specific phenotypes.
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Affiliation(s)
- Claudia Z Han
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Rick Z Li
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Emily Hansen
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Samantha Trescott
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Bethany R Fixsen
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Celina T Nguyen
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Cristina M Mora
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Nathanael J Spann
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hunter R Bennett
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Olivier Poirion
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Center for Epigenomics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Justin Buchanan
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Center for Epigenomics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Anna S Warden
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Bing Xia
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Johannes C M Schlachetzki
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Martina P Pasillas
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sebastian Preissl
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Center for Epigenomics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Allen Wang
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Center for Epigenomics, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - Shreya Shriram
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Roy Kim
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Danielle Schafer
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Gabriela Ramirez
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Jean Challacombe
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Samuel A Anavim
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Avalon Johnson
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Mihir Gupta
- Department of Neurosurgery, University of California, San Diego, La Jolla, CA 92037, USA
| | - Ian A Glass
- Department of Pediatrics, University of Washington and Seattle Children's Research Institute, Seattle, WA, USA
| | - Michael L Levy
- Department of Neurosurgery, University of California, San Diego-Rady Children's Hospital, San Diego, CA 92123, USA
| | - Sharona Ben Haim
- Department of Neurosurgery, University of California, San Diego, La Jolla, CA 92037, USA
| | - David D Gonda
- Department of Neurosurgery, University of California, San Diego-Rady Children's Hospital, San Diego, CA 92123, USA
| | - Louise Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - David C Page
- Whitehead Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
| | - Mathew Blurton-Jones
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92696, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Nicole G Coufal
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA; Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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Loehr AR, Timmerman DM, Liu M, Gillis AJ, Matthews M, Bloom JC, Nicholls PK, Page DC, Miller AD, Looijenga LH, Weiss RS. Analysis of a mouse germ cell tumor model establishes pluripotency-associated miRNAs as conserved serum biomarkers for germ cell cancer detection. bioRxiv 2023:2023.09.09.556995. [PMID: 37745561 PMCID: PMC10515752 DOI: 10.1101/2023.09.09.556995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Malignant testicular germ cells tumors (TGCTs) are the most common solid cancers in young men. Current TGCT diagnostics include conventional serum protein markers, but these lack the sensitivity and specificity to serve as accurate markers across all TGCT subtypes. MicroRNAs (miRNAs) are small non-coding regulatory RNAs and informative biomarkers for several diseases. In humans, miRNAs of the miR-371-373 cluster are detectable in the serum of patients with malignant TGCTs and outperform existing serum protein markers for both initial diagnosis and subsequent disease monitoring. We previously developed a genetically engineered mouse model featuring malignant mixed TGCTs consisting of pluripotent embryonal carcinoma (EC) and differentiated teratoma that, like the corresponding human malignancies, originate in utero and are highly chemosensitive. Here, we report that miRNAs in the mouse miR-290-295 cluster, homologs of the human miR-371-373 cluster, were detectable in serum from mice with malignant TGCTs but not from tumor-free control mice or mice with benign teratomas. miR-291-293 were expressed and secreted specifically by pluripotent EC cells, and expression was lost following differentiation induced by the drug thioridazine. Notably, miR-291-293 levels were significantly higher in the serum of pregnant dams carrying tumor-bearing fetuses compared to that of control dams. These findings reveal that expression of the miR-290-295 and miR-371-373 clusters in mice and humans, respectively, is a conserved feature of malignant TGCTs, further validating the mouse model as representative of the human disease. These data also highlight the potential of serum miR-371-373 assays to improve patient outcomes through early TGCT detection, possibly even prenatally.
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Affiliation(s)
- Amanda R. Loehr
- Department of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY
| | | | - Michelle Liu
- Department of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY
| | - Ad J.M. Gillis
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Melia Matthews
- Department of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY
| | | | | | - David C. Page
- Whitehead Institute, Cambridge, MA
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA
| | - Andrew D. Miller
- Department of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY
| | | | - Robert S. Weiss
- Department of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY
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Kim JJ, Steinson ER, Lau MS, de Rooij DG, Page DC, Kingston RE. Cell type-specific role of CBX2 and its disordered region in spermatogenesis. Genes Dev 2023; 37:640-660. [PMID: 37553262 PMCID: PMC10499018 DOI: 10.1101/gad.350393.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 07/28/2023] [Indexed: 08/10/2023]
Abstract
Polycomb group (PcG) proteins maintain the repressed state of lineage-inappropriate genes and are therefore essential for embryonic development and adult tissue homeostasis. One critical function of PcG complexes is modulating chromatin structure. Canonical Polycomb repressive complex 1 (cPRC1), particularly its component CBX2, can compact chromatin and phase-separate in vitro. These activities are hypothesized to be critical for forming a repressed physical environment in cells. While much has been learned by studying these PcG activities in cell culture models, it is largely unexplored how cPRC1 regulates adult stem cells and their subsequent differentiation in living animals. Here, we show in vivo evidence of a critical nonenzymatic repressive function of cPRC1 component CBX2 in the male germline. CBX2 is up-regulated as spermatogonial stem cells differentiate and is required to repress genes that were active in stem cells. CBX2 forms condensates (similar to previously described Polycomb bodies) that colocalize with target genes bound by CBX2 in differentiating spermatogonia. Single-cell analyses of mosaic Cbx2 mutant testes show that CBX2 is specifically required to produce differentiating A1 spermatogonia. Furthermore, the region of CBX2 responsible for compaction and phase separation is needed for the long-term maintenance of male germ cells in the animal. These results emphasize that the regulation of chromatin structure by CBX2 at a specific stage of spermatogenesis is critical, which distinguishes this from a mechanism that is reliant on histone modification.
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Affiliation(s)
- Jongmin J Kim
- Department of Molecular Biology, MGH Research Institute, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Emma R Steinson
- Department of Molecular Biology, MGH Research Institute, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Mei Sheng Lau
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology, and Research (A*STAR), Proteos, Singapore 138673, Republic of Singapore
| | - Dirk G de Rooij
- Reproductive Biology Group, Division of Developmental Biology, Department of Biology, Faculty of Science, Utrecht University, Utrecht 3584 CH, the Netherlands
| | - David C Page
- Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Robert E Kingston
- Department of Molecular Biology, MGH Research Institute, Massachusetts General Hospital, Boston, Massachusetts 02114, USA;
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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8
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San Roman AK, Skaletsky H, Godfrey AK, Bokil NV, Teitz L, Singh I, Blanton LV, Bellott DW, Pyntikova T, Lange J, Koutseva N, Hughes JF, Brown L, Phou S, Buscetta A, Kruszka P, Banks N, Dutra A, Pak E, Lasutschinkow PC, Keen C, Davis SM, Lin AE, Tartaglia NR, Samango-Sprouse C, Muenke M, Page DC. The human Y and inactive X chromosomes similarly modulate autosomal gene expression. bioRxiv 2023:2023.06.05.543763. [PMID: 37333288 PMCID: PMC10274745 DOI: 10.1101/2023.06.05.543763] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Somatic cells of human males and females have 45 chromosomes in common, including the "active" X chromosome. In males the 46th chromosome is a Y; in females it is an "inactive" X (Xi). Through linear modeling of autosomal gene expression in cells from individuals with zero to three Xi and zero to four Y chromosomes, we found that Xi and Y impact autosomal expression broadly and with remarkably similar effects. Studying sex-chromosome structural anomalies, promoters of Xi- and Y-responsive genes, and CRISPR inhibition, we traced part of this shared effect to homologous transcription factors - ZFX and ZFY - encoded by Chr X and Y. This demonstrates sex-shared mechanisms by which Xi and Y modulate autosomal expression. Combined with earlier analyses of sex-linked gene expression, our studies show that 21% of all genes expressed in lymphoblastoid cells or fibroblasts change expression significantly in response to Xi or Y chromosomes.
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Affiliation(s)
| | - Helen Skaletsky
- Whitehead Institute; Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute; Cambridge, MA 02142, USA
| | - Alexander K. Godfrey
- Whitehead Institute; Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Neha V. Bokil
- Whitehead Institute; Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Levi Teitz
- Whitehead Institute; Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Isani Singh
- Whitehead Institute; Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | - Julian Lange
- Whitehead Institute; Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | | | | | - Laura Brown
- Whitehead Institute; Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute; Cambridge, MA 02142, USA
| | - Sidaly Phou
- Whitehead Institute; Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute; Cambridge, MA 02142, USA
| | - Ashley Buscetta
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda; MD 20892, USA
| | - Paul Kruszka
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda; MD 20892, USA
| | - Nicole Banks
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda; MD 20892, USA
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health; Bethesda, MD 20892 USA
| | - Amalia Dutra
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD 20892 USA
| | - Evgenia Pak
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD 20892 USA
| | | | | | - Shanlee M. Davis
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Angela E. Lin
- Medical Genetics, Massachusetts General for Children, Boston, MA 02114, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Nicole R. Tartaglia
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Developmental Pediatrics, eXtraOrdinarY Kids Program, Children’s Hospital Colorado, Aurora, CO 80011, USA
| | - Carole Samango-Sprouse
- Focus Foundation, Davidsonville, MD 21035, USA
- Department of Pediatrics, George Washington University, Washington, DC 20052, USA; Department of Human and Molecular Genetics, Florida International University, Miami, FL 33199, USA
| | - Maximilian Muenke
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda; MD 20892, USA
| | - David C. Page
- Whitehead Institute; Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Whitehead Institute; Cambridge, MA 02142, USA
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9
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Arnold AP, Chen X, Grzybowski MN, Ryan JM, Sengelaub DR, Mohanroy T, Furlan VA, Grisham W, Malloy L, Takizawa A, Wiese CB, Vergnes L, Skaletsky H, Page DC, Reue K, Harley VR, Dwinell MR, Geurts AM. A "Four Core Genotypes" rat model to distinguish mechanisms underlying sex-biased phenotypes and diseases. bioRxiv 2023:2023.02.09.527738. [PMID: 36798326 PMCID: PMC9934672 DOI: 10.1101/2023.02.09.527738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Background We have generated a rat model similar to the Four Core Genotypes mouse model, allowing comparison of XX and XY rats with the same type of gonad. The model detects novel sex chromosome effects (XX vs. XY) that contribute to sex differences in any rat phenotype. Methods XY rats were produced with an autosomal transgene of Sry , the testis-determining factor gene, which were fathers of XX and XY progeny with testes. In other rats, CRISPR-Cas9 technology was used to remove Y chromosome factors that initiate testis differentiation, producing fertile XY gonadal females that have XX and XY progeny with ovaries. These groups can be compared to detect sex differences caused by sex chromosome complement (XX vs. XY) and/or by gonadal hormones (rats with testes vs. ovaries). Results We have measured numerous phenotypes to characterize this model, including gonadal histology, breeding performance, anogenital distance, levels of reproductive hormones, body and organ weights, and central nervous system sexual dimorphisms. Serum testosterone levels were comparable in adult XX and XY gonadal males. Numerous phenotypes previously found to be sexually differentiated by the action of gonadal hormones were found to be similar in XX and XY rats with the same type of gonad, suggesting that XX and XY rats with the same type of gonad have comparable levels of gonadal hormones at various stages of development. Conclusion The results establish a powerful new model to discriminate sex chromosome and gonadal hormone effects that cause sexual differences in rat physiology and disease.
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10
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Reichart D, Newby GA, Wakimoto H, Lun M, Gorham JM, Curran JJ, Raguram A, DeLaughter DM, Conner DA, Marsiglia JDC, Kohli S, Chmatal L, Page DC, Zabaleta N, Vandenberghe L, Liu DR, Seidman JG, Seidman C. Efficient in vivo genome editing prevents hypertrophic cardiomyopathy in mice. Nat Med 2023; 29:412-421. [PMID: 36797483 PMCID: PMC9941048 DOI: 10.1038/s41591-022-02190-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 12/16/2022] [Indexed: 02/18/2023]
Abstract
Dominant missense pathogenic variants in cardiac myosin heavy chain cause hypertrophic cardiomyopathy (HCM), a currently incurable disorder that increases risk for stroke, heart failure and sudden cardiac death. In this study, we assessed two different genetic therapies-an adenine base editor (ABE8e) and a potent Cas9 nuclease delivered by AAV9-to prevent disease in mice carrying the heterozygous HCM pathogenic variant myosin R403Q. One dose of dual-AAV9 vectors, each carrying one half of RNA-guided ABE8e, corrected the pathogenic variant in ≥70% of ventricular cardiomyocytes and maintained durable, normal cardiac structure and function. An additional dose provided more editing in the atria but also increased bystander editing. AAV9 delivery of RNA-guided Cas9 nuclease effectively inactivated the pathogenic allele, albeit with dose-dependent toxicities, necessitating a narrow therapeutic window to maintain health. These preclinical studies demonstrate considerable potential for single-dose genetic therapies to correct or silence pathogenic variants and prevent the development of HCM.
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Affiliation(s)
- Daniel Reichart
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Medicine I, University Hospital, LMU Munich, Munich, Germany
| | - Gregory A Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Hiroko Wakimoto
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Mingyue Lun
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Joshua M Gorham
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Justin J Curran
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Aditya Raguram
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Daniel M DeLaughter
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - David A Conner
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | - Sajeev Kohli
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - David C Page
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Whitehead Institute, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nerea Zabaleta
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA
- Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Luk Vandenberghe
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA
- Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - Christine Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Cardiovascular Division, Brigham and Women's Hospital, Boston, MA, USA.
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11
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Korkidakis A, Groff A, Penzias AS, Page DC, Sakkas D. REFINING CELLULAR IDENTITY IN THE HUMAN BLASTOCYST THROUGH SELECTIVE INNER CELL MASS AND TROPHECTODERM BIOPSY. Fertil Steril 2022. [DOI: 10.1016/j.fertnstert.2022.08.224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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12
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Bellott DW, Cho TJ, Jackson EK, Skaletsky H, Hughes JF, Page DC. SHIMS 3.0: Highly efficient single-haplotype iterative mapping and sequencing using ultra-long nanopore reads. PLoS One 2022; 17:e0269692. [PMID: 35700171 PMCID: PMC9197060 DOI: 10.1371/journal.pone.0269692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 05/25/2022] [Indexed: 11/18/2022] Open
Abstract
The reference sequence of structurally complex regions can only be obtained through a highly accurate clone-based approach that we call Single-Haplotype Iterative Mapping and Sequencing (SHIMS). In recent years, improvements to SHIMS have reduced the cost and time required by two orders of magnitude, but internally repetitive clones still require extensive manual effort to transform draft assemblies into reference-quality finished sequences. Here we describe SHIMS 3.0, using ultra-long nanopore reads to augment the Illumina data from SHIMS 2.0 assemblies and resolve internally repetitive structures. This greatly minimizes the need for manual finishing of Illumina-based draft assemblies, allowing a small team with no prior finishing experience to sequence challenging targets with high accuracy. This protocol proceeds from clone-picking to finished assemblies in 2 weeks for about $80 (USD) per clone. We recently used this protocol to produce reference sequence of structurally complex palindromes on chimpanzee and rhesus macaque X chromosomes. Our protocol provides access to structurally complex regions that would otherwise be inaccessible from whole-genome shotgun data or require an impractical amount of manual effort to generate an accurate assembly.
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Affiliation(s)
- Daniel W. Bellott
- Whitehead Institute, Cambridge, Massachusetts, United States of America
- * E-mail:
| | - Ting-Jan Cho
- Whitehead Institute, Cambridge, Massachusetts, United States of America
| | - Emily K. Jackson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Helen Skaletsky
- Whitehead Institute, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts, United States of America
| | | | - David C. Page
- Whitehead Institute, Cambridge, Massachusetts, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts, United States of America
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13
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Hughes JF, Skaletsky H, Nicholls PK, Drake A, Pyntikova T, Cho TJ, Bellott DW, Page DC. A gene deriving from the ancestral sex chromosomes was lost from the X and retained on the Y chromosome in eutherian mammals. BMC Biol 2022; 20:133. [PMID: 35676717 PMCID: PMC9178871 DOI: 10.1186/s12915-022-01338-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 05/25/2022] [Indexed: 11/14/2022] Open
Abstract
Background The mammalian X and Y chromosomes originated from a pair of ordinary autosomes. Over the past ~180 million years, the X and Y have become highly differentiated and now only recombine with each other within a short pseudoautosomal region. While the X chromosome broadly preserved its gene content, the Y chromosome lost ~92% of the genes it once shared with the X chromosome. PRSSLY is a Y-linked gene identified in only a few mammalian species that was thought to be acquired, not ancestral. However, PRSSLY’s presence in widely divergent species—bull and mouse—led us to further investigate its evolutionary history. Results We discovered that PRSSLY is broadly conserved across eutherians and has ancient origins. PRSSLY homologs are found in syntenic regions on the X chromosome in marsupials and on autosomes in more distant animals, including lizards, indicating that PRSSLY was present on the ancestral autosomes but was lost from the X and retained on the Y in eutherian mammals. We found that across eutheria, PRSSLY’s expression is testis-specific, and, in mouse, it is most robustly expressed in post-meiotic germ cells. The closest paralog to PRSSLY is the autosomal gene PRSS55, which is expressed exclusively in testes, involved in sperm differentiation and migration, and essential for male fertility in mice. Outside of eutheria, in species where PRSSLY orthologs are not Y-linked, we find expression in a broader range of somatic tissues, suggesting that PRSSLY has adopted a germ-cell-specific function in eutherians. Finally, we generated Prssly mutant mice and found that they are fully fertile but produce offspring with a modest female-biased sex ratio compared to controls. Conclusions PRSSLY appears to be the first example of a gene that derives from the mammalian ancestral sex chromosomes that was lost from the X and retained on the Y. Although the function of PRSSLY remains to be determined, it may influence the sex ratio by promoting the survival or propagation of Y-bearing sperm. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01338-8.
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Affiliation(s)
| | - Helen Skaletsky
- Whitehead Institute, Cambridge, MA, 02142, USA.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA, 02142, USA
| | - Peter K Nicholls
- Whitehead Institute, Cambridge, MA, 02142, USA.,Present Address: Faculty of Life Sciences, University of Bradford, BD71DP, Bradford, UK
| | | | | | | | | | - David C Page
- Whitehead Institute, Cambridge, MA, 02142, USA.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA, 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
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14
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Ling L, Li F, Yang P, Oates RD, Silber S, Kurischko C, Luca FC, Leu NA, Zhang J, Yue Q, Skaletsky H, Brown LG, Rozen S, Page DC, Wang PJ, Zheng K. Genetic characterization of a missense mutation in the X-linked TAF7L gene identified in an oligozoospermic man. Biol Reprod 2022; 107:157-167. [PMID: 35554494 PMCID: PMC9310510 DOI: 10.1093/biolre/ioac093] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 04/18/2022] [Accepted: 05/02/2022] [Indexed: 11/14/2022] Open
Abstract
While hundreds of knockout mice show infertility as a major phenotype, causative genic mutations of male infertility in humans remain rather limited. Here we report the identification of a missense mutation (D136G) in the X-linked TAF7L gene as a potential cause of oligozoospermia in men. The human aspartate (D136) is evolutionally conserved across species, and its change to glycine (G) is predicted to be detrimental. Genetic complementation experiments in budding yeast demonstrate that the conserved aspartate or its analogous asparagine (N) residue in yeast TAF7 is essential for cell viability and thus its mutation to glycine is lethal. Although the corresponding D144G substitution in the mouse Taf7l gene does not affect male fertility, RNA-seq analyses reveal alterations in transcriptome profiles in the Taf7l (D144G) mutant testes. These results support this TAF7L mutation as a risk factor for oligozoospermia in humans.
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Affiliation(s)
- Li Ling
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Fangfang Li
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Pinglan Yang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Robert D Oates
- Department of Urology, Boston University Medical Center, Boston, MA 02118, USA
| | - Sherman Silber
- Infertility Center of St. Louis, St. Luke's Hospital, St. Louis, MO 63017, USA
| | - Cornelia Kurischko
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - Francis C Luca
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - N Adrian Leu
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - Jinwen Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Qiuling Yue
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Helen Skaletsky
- Howard Hughes Medical Institute, Whitehead Institute, and Department of Biology, Massachusetts Institute of Technology, 455 Main Street, Cambridge, MA 02142, USA
| | - Laura G Brown
- Howard Hughes Medical Institute, Whitehead Institute, and Department of Biology, Massachusetts Institute of Technology, 455 Main Street, Cambridge, MA 02142, USA
| | - Steve Rozen
- Duke-NUS Graduate Medical School Singapore, 8 College Road, 169857, Singapore
| | - David C Page
- Howard Hughes Medical Institute, Whitehead Institute, and Department of Biology, Massachusetts Institute of Technology, 455 Main Street, Cambridge, MA 02142, USA
| | - P Jeremy Wang
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - Ke Zheng
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
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15
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Jackson EK, Bellott DW, Skaletsky H, Page DC. GC-biased gene conversion in X-chromosome palindromes conserved in human, chimpanzee, and rhesus macaque. G3 Genes|Genomes|Genetics 2021; 11:6317831. [PMID: 34849781 PMCID: PMC8981503 DOI: 10.1093/g3journal/jkab224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/28/2021] [Indexed: 12/03/2022]
Abstract
Gene conversion is GC-biased across a wide range of taxa. Large palindromes on mammalian
sex chromosomes undergo frequent gene conversion that maintains arm-to-arm sequence
identity greater than 99%, which may increase their susceptibility to the effects of
GC-biased gene conversion. Here, we demonstrate a striking history of GC-biased gene
conversion in 12 palindromes conserved on the X chromosomes of human, chimpanzee, and
rhesus macaque. Primate X-chromosome palindrome arms have significantly higher GC content
than flanking single-copy sequences. Nucleotide replacements that occurred in human and
chimpanzee palindrome arms over the past 7 million years are one-and-a-half times as
GC-rich as the ancestral bases they replaced. Using simulations, we show that our observed
pattern of nucleotide replacements is consistent with GC-biased gene conversion with a
magnitude of 70%, similar to previously reported values based on analyses of human
meioses. However, GC-biased gene conversion since the divergence of human and rhesus
macaque explains only a fraction of the observed difference in GC content between
palindrome arms and flanking sequence, suggesting that palindromes are older than 29
million years and/or had elevated GC content at the time of their formation. This work
supports a greater than 2:1 preference for GC bases over AT bases during gene conversion
and demonstrates that the evolution and composition of mammalian sex chromosome
palindromes is strongly influenced by GC-biased gene conversion.
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Affiliation(s)
- Emily K Jackson
- Whitehead Institute, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Helen Skaletsky
- Whitehead Institute, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
| | - David C Page
- Whitehead Institute, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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16
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Jackson EK, Bellott DW, Cho TJ, Skaletsky H, Hughes JF, Pyntikova T, Page DC. Large palindromes on the primate X Chromosome are preserved by natural selection. Genome Res 2021; 31:1337-1352. [PMID: 34290043 PMCID: PMC8327919 DOI: 10.1101/gr.275188.120] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 05/17/2021] [Indexed: 12/27/2022]
Abstract
Mammalian sex chromosomes carry large palindromes that harbor protein-coding gene families with testis-biased expression. However, there are few known examples of sex-chromosome palindromes conserved between species. We identified 26 palindromes on the human X Chromosome, constituting more than 2% of its sequence, and characterized orthologous palindromes in the chimpanzee and the rhesus macaque using a clone-based sequencing approach that incorporates full-length nanopore reads. Many of these palindromes are missing or misassembled in the current reference assemblies of these species' genomes. We find that 12 human X palindromes have been conserved for at least 25 million years, with orthologs in both chimpanzee and rhesus macaque. Insertions and deletions between species are significantly depleted within the X palindromes' protein-coding genes compared to their noncoding sequence, demonstrating that natural selection has preserved these gene families. The spacers that separate the left and right arms of palindromes are a site of localized structural instability, with seven of 12 conserved palindromes showing no spacer orthology between human and rhesus macaque. Analysis of the 1000 Genomes Project data set revealed that human X-palindrome spacers are enriched for deletions relative to arms and flanking sequence, including a common spacer deletion that affects 13% of human X Chromosomes. This work reveals an abundance of conserved palindromes on primate X Chromosomes and suggests that protein-coding gene families in palindromes (most of which remain poorly characterized) promote X-palindrome survival in the face of ongoing structural instability.
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Affiliation(s)
- Emily K Jackson
- Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | - Ting-Jan Cho
- Whitehead Institute, Cambridge, Massachusetts 02142, USA
| | - Helen Skaletsky
- Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
| | | | | | - David C Page
- Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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17
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Abstract
In each generation, the germline is tasked with producing somatic lineages that form the body, and segregating a population of cells for gametogenesis. During animal development, when do cells of the germline irreversibly commit to producing gametes? Integrating findings from diverse species, we conclude that the final commitment of the germline to gametogenesis - the process of germ cell determination - occurs after primordial germ cells (PGCs) colonize the gonads. Combining this understanding with medical findings, we present a model whereby germ cell tumors arise from cells that failed to undertake germ cell determination, regardless of their having colonized the gonads. We propose that the diversity of cell types present in these tumors reflects the broad developmental potential of migratory PGCs.
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Affiliation(s)
- Peter K Nicholls
- Whitehead Institute, 455 Main Street, Cambridge, MA 02142, USA.,Faculty of Life Sciences, University of Bradford, Bradford BD7 1DP, UK
| | - David C Page
- Whitehead Institute, 455 Main Street, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
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18
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Bellott DW, Page DC. Dosage-sensitive functions in embryonic development drove the survival of genes on sex-specific chromosomes in snakes, birds, and mammals. Genome Res 2021; 31:198-210. [PMID: 33479023 PMCID: PMC7849413 DOI: 10.1101/gr.268516.120] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 12/04/2020] [Indexed: 12/18/2022]
Abstract
Different ancestral autosomes independently evolved into sex chromosomes in snakes, birds, and mammals. In snakes and birds, females are ZW and males are ZZ; in mammals, females are XX and males are XY. Although X and Z Chromosomes retain nearly all ancestral genes, sex-specific W and Y Chromosomes suffered extensive genetic decay. In both birds and mammals, the genes that survived on sex-specific chromosomes are enriched for broadly expressed, dosage-sensitive regulators of gene expression, subject to strong purifying selection. To gain deeper insight into the processes that govern survival on sex-specific chromosomes, we carried out a meta-analysis of survival across 41 species-three snakes, 24 birds, and 14 mammals-doubling the number of ancestral genes under investigation and increasing our power to detect enrichments among survivors relative to nonsurvivors. Of 2564 ancestral genes, representing an eighth of the ancestral amniote genome, only 324 survive on present-day sex-specific chromosomes. Survivors are enriched for dosage-sensitive developmental processes, particularly development of neural crest-derived structures, such as the face. However, there was no enrichment for expression in sex-specific tissues, involvement in sex determination or gonadogenesis pathways, or conserved sex-biased expression. Broad expression and dosage sensitivity contributed independently to gene survival, suggesting that pleiotropy imposes additional constraints on the evolution of dosage compensation. We propose that maintaining the viability of the heterogametic sex drove gene survival on amniote sex-specific chromosomes, and that subtle modulation of the expression of survivor genes and their autosomal orthologs has disproportionately large effects on development and disease.
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Affiliation(s)
| | - David C Page
- Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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19
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Hughes JF, Skaletsky H, Pyntikova T, Koutseva N, Raudsepp T, Brown LG, Bellott DW, Cho TJ, Dugan-Rocha S, Khan Z, Kremitzki C, Fronick C, Graves-Lindsay TA, Fulton L, Warren WC, Wilson RK, Owens E, Womack JE, Murphy WJ, Muzny DM, Worley KC, Chowdhary BP, Gibbs RA, Page DC. Sequence analysis in Bos taurus reveals pervasiveness of X-Y arms races in mammalian lineages. Genome Res 2020; 30:1716-1726. [PMID: 33208454 PMCID: PMC7706723 DOI: 10.1101/gr.269902.120] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 10/28/2020] [Indexed: 12/28/2022]
Abstract
Studies of Y Chromosome evolution have focused primarily on gene decay, a consequence of suppression of crossing-over with the X Chromosome. Here, we provide evidence that suppression of X-Y crossing-over unleashed a second dynamic: selfish X-Y arms races that reshaped the sex chromosomes in mammals as different as cattle, mice, and men. Using super-resolution sequencing, we explore the Y Chromosome of Bos taurus (bull) and find it to be dominated by massive, lineage-specific amplification of testis-expressed gene families, making it the most gene-dense Y Chromosome sequenced to date. As in mice, an X-linked homolog of a bull Y-amplified gene has become testis-specific and amplified. This evolutionary convergence implies that lineage-specific X-Y coevolution through gene amplification, and the selfish forces underlying this phenomenon, were dominatingly powerful among diverse mammalian lineages. Together with Y gene decay, X-Y arms races molded mammalian sex chromosomes and influenced the course of mammalian evolution.
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Affiliation(s)
| | - Helen Skaletsky
- Whitehead Institute, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
| | | | | | - Terje Raudsepp
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843, USA
| | - Laura G Brown
- Whitehead Institute, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
| | | | - Ting-Jan Cho
- Whitehead Institute, Cambridge, Massachusetts 02142, USA
| | - Shannon Dugan-Rocha
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Ziad Khan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Colin Kremitzki
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Catrina Fronick
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Tina A Graves-Lindsay
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Lucinda Fulton
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Wesley C Warren
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Richard K Wilson
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Elaine Owens
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843, USA
| | - James E Womack
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843, USA
| | - William J Murphy
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Kim C Worley
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Bhanu P Chowdhary
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - David C Page
- Whitehead Institute, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
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20
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Mikedis MM, Fan Y, Nicholls PK, Endo T, Jackson EK, Cobb SA, de Rooij DG, Page DC. DAZL mediates a broad translational program regulating expansion and differentiation of spermatogonial progenitors. eLife 2020; 9:56523. [PMID: 32686646 PMCID: PMC7445011 DOI: 10.7554/elife.56523] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 07/20/2020] [Indexed: 01/28/2023] Open
Abstract
Fertility across metazoa requires the germline-specific DAZ family of RNA-binding proteins. Here we examine whether DAZL directly regulates progenitor spermatogonia using a conditional genetic mouse model and in vivo biochemical approaches combined with chemical synchronization of spermatogenesis. We find that the absence of Dazl impairs both expansion and differentiation of the spermatogonial progenitor population. In undifferentiated spermatogonia, DAZL binds the 3' UTRs of ~2,500 protein-coding genes. Some targets are known regulators of spermatogonial proliferation and differentiation while others are broadly expressed, dosage-sensitive factors that control transcription and RNA metabolism. DAZL binds 3' UTR sites conserved across vertebrates at a UGUU(U/A) motif. By assessing ribosome occupancy in undifferentiated spermatogonia, we find that DAZL increases translation of its targets. In total, DAZL orchestrates a broad translational program that amplifies protein levels of key spermatogonial and gene regulatory factors to promote the expansion and differentiation of progenitor spermatogonia.
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Affiliation(s)
| | - Yuting Fan
- Whitehead Institute, Cambridge, United States.,Reproductive Medicine Center, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | | | | | - Emily K Jackson
- Whitehead Institute, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | | | | | - David C Page
- Whitehead Institute, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, United States
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21
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Godfrey AK, Naqvi S, Chmátal L, Chick JM, Mitchell RN, Gygi SP, Skaletsky H, Page DC. Quantitative analysis of Y-Chromosome gene expression across 36 human tissues. Genome Res 2020; 30:860-873. [PMID: 32461223 PMCID: PMC7370882 DOI: 10.1101/gr.261248.120] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 05/18/2020] [Indexed: 02/07/2023]
Abstract
Little is known about how human Y-Chromosome gene expression directly contributes to differences between XX (female) and XY (male) individuals in nonreproductive tissues. Here, we analyzed quantitative profiles of Y-Chromosome gene expression across 36 human tissues from hundreds of individuals. Although it is often said that Y-Chromosome genes are lowly expressed outside the testis, we report many instances of elevated Y-Chromosome gene expression in a nonreproductive tissue. A notable example is EIF1AY, which encodes eukaryotic translation initiation factor 1A Y-linked, together with its X-linked homolog EIF1AX. Evolutionary loss of a Y-linked microRNA target site enabled up-regulation of EIF1AY, but not of EIF1AX, in the heart. Consequently, this essential translation initiation factor is nearly twice as abundant in male as in female heart tissue at the protein level. Divergence between the X and Y Chromosomes in regulatory sequence can therefore lead to tissue-specific Y-Chromosome-driven sex biases in expression of critical, dosage-sensitive regulatory genes.
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Affiliation(s)
- Alexander K Godfrey
- Whitehead Institute, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Sahin Naqvi
- Whitehead Institute, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Lukáš Chmátal
- Whitehead Institute, Cambridge, Massachusetts 02142, USA
| | - Joel M Chick
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Richard N Mitchell
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Helen Skaletsky
- Whitehead Institute, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
| | - David C Page
- Whitehead Institute, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
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22
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Naqvi S, Godfrey AK, Hughes JF, Goodheart ML, Mitchell RN, Page DC. Conservation, acquisition, and functional impact of sex-biased gene expression in mammals. Science 2020; 365:365/6450/eaaw7317. [PMID: 31320509 DOI: 10.1126/science.aaw7317] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 06/12/2019] [Indexed: 12/15/2022]
Abstract
Sex differences abound in human health and disease, as they do in other mammals used as models. The extent to which sex differences are conserved at the molecular level across species and tissues is unknown. We surveyed sex differences in gene expression in human, macaque, mouse, rat, and dog, across 12 tissues. In each tissue, we identified hundreds of genes with conserved sex-biased expression-findings that, combined with genomic analyses of human height, explain ~12% of the difference in height between females and males. We surmise that conserved sex biases in expression of genes otherwise operating equivalently in females and males contribute to sex differences in traits. However, most sex-biased expression arose during the mammalian radiation, which suggests that careful attention to interspecies divergence is needed when modeling human sex differences.
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Affiliation(s)
- Sahin Naqvi
- Whitehead Institute, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alexander K Godfrey
- Whitehead Institute, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Mary L Goodheart
- Whitehead Institute, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
| | - Richard N Mitchell
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - David C Page
- Whitehead Institute, Cambridge, MA 02142, USA. .,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
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23
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Gura MA, Mikedis MM, Seymour KA, de Rooij DG, Page DC, Freiman RN. Dynamic and regulated TAF gene expression during mouse embryonic germ cell development. PLoS Genet 2020; 16:e1008515. [PMID: 31914128 PMCID: PMC7010400 DOI: 10.1371/journal.pgen.1008515] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 02/10/2020] [Accepted: 11/11/2019] [Indexed: 12/02/2022] Open
Abstract
Germ cells undergo many developmental transitions before ultimately becoming either eggs or sperm, and during embryonic development these transitions include epigenetic reprogramming, quiescence, and meiosis. To begin understanding the transcriptional regulation underlying these complex processes, we examined the spatial and temporal expression of TAF4b, a variant TFIID subunit required for fertility, during embryonic germ cell development. By analyzing published datasets and using our own experimental system to validate these expression studies, we determined that both Taf4b mRNA and protein are highly germ cell-enriched and that Taf4b mRNA levels dramatically increase from embryonic day 12.5–18.5. Surprisingly, additional mRNAs encoding other TFIID subunits are coordinately upregulated through this time course, including Taf7l and Taf9b. The expression of several of these germ cell-enriched TFIID genes is dependent upon Dazl and/or Stra8, known regulators of germ cell development and meiosis. Together, these data suggest that germ cells employ a highly specialized and dynamic form of TFIID to drive the transcriptional programs that underlie mammalian germ cell development. Assisted reproductive therapy and fertility preservation are increasingly used to improve human reproduction across the world, yet there are still many unanswered questions regarding what factors govern the development of eggs and sperm and how these factors work together. We previously identified a subunit of the general transcription factor TFIID, TAF4b, that is essential for fertility. However, many basic characteristics of how Taf4b and its associated TFIID family members contribute to the formation of healthy sperm and eggs in mice and humans remain unknown. In this study, we find that mouse Taf4b and several closely related TFIID subunits become highly abundant during mouse embryonic gonad development, specifically in the cells that ultimately become eggs and sperm. Here, we analyzed data from public repositories and isolated these developing cells to examine their gene expression patterns throughout embryonic development. Together these data suggest that the dynamic expression of Taf4b and other TFIID family members are dependent on the well-established reproductive cell regulators Dazl and Stra8. This understanding of Taf4b gene expression and regulation in mouse reproductive cell development is likely conserved during development of human cells and offers novel insights into the interconnectedness of the factors that govern the formation of healthy eggs and sperm.
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Affiliation(s)
- Megan A. Gura
- Brown University, MCB Graduate Program and Department of Molecular Biology, Cell Biology and Biochemistry, Providence, RI, United States of America
| | | | - Kimberly A. Seymour
- Brown University, MCB Graduate Program and Department of Molecular Biology, Cell Biology and Biochemistry, Providence, RI, United States of America
| | | | - David C. Page
- Whitehead Institute, Cambridge, MA, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States of America
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA, United States of America
| | - Richard N. Freiman
- Brown University, MCB Graduate Program and Department of Molecular Biology, Cell Biology and Biochemistry, Providence, RI, United States of America
- * E-mail:
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24
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Dokshin GA, Davis GM, Sawle AD, Eldridge MD, Nicholls PK, Gourley TE, Romer KA, Molesworth LW, Tatnell HR, Ozturk AR, de Rooij DG, Hannon GJ, Page DC, Mello CC, Carmell MA. GCNA Interacts with Spartan and Topoisomerase II to Regulate Genome Stability. Dev Cell 2020; 52:53-68.e6. [PMID: 31839538 PMCID: PMC7227305 DOI: 10.1016/j.devcel.2019.11.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 08/14/2019] [Accepted: 11/13/2019] [Indexed: 12/22/2022]
Abstract
GCNA proteins are expressed across eukarya in pluripotent cells and have conserved functions in fertility. GCNA homologs Spartan (DVC-1) and Wss1 resolve DNA-protein crosslinks (DPCs), including Topoisomerase-DNA adducts, during DNA replication. Here, we show that GCNA mutants in mouse and C. elegans display defects in genome maintenance including DNA damage, aberrant chromosome condensation, and crossover defects in mouse spermatocytes and spontaneous genomic rearrangements in C. elegans. We show that GCNA and topoisomerase II (TOP2) physically interact in both mice and worms and colocalize on condensed chromosomes during mitosis in C. elegans embryos. Moreover, C. elegans gcna-1 mutants are hypersensitive to TOP2 poison. Together, our findings support a model in which GCNA provides genome maintenance functions in the germline and may do so, in part, by promoting the resolution of TOP2 DPCs.
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Affiliation(s)
- Gregoriy A Dokshin
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Gregory M Davis
- School of Health and Life Sciences, Federation University, VIC 3841, Australia
| | - Ashley D Sawle
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Matthew D Eldridge
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | | | - Taylin E Gourley
- School of Health and Life Sciences, Federation University, VIC 3841, Australia
| | - Katherine A Romer
- Whitehead Institute, 455 Main Street, Cambridge, MA 02142, USA; Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Luke W Molesworth
- School of Health and Life Sciences, Federation University, VIC 3841, Australia
| | - Hannah R Tatnell
- School of Health and Life Sciences, Federation University, VIC 3841, Australia
| | - Ahmet R Ozturk
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Dirk G de Rooij
- Whitehead Institute, 455 Main Street, Cambridge, MA 02142, USA; Reproductive Biology Group, Division of Developmental Biology, Department of Biology, Faculty of Science, Utrecht University, Utrecht 3584, the Netherlands; Center for Reproductive Medicine, Academic Medical Center, University of Amsterdam 1105, the Netherlands
| | - Gregory J Hannon
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - David C Page
- Whitehead Institute, 455 Main Street, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
| | - Craig C Mello
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| | - Michelle A Carmell
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Whitehead Institute, 455 Main Street, Cambridge, MA 02142, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
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25
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Kruszka P, Buscetta A, Acosta MT, Banks N, Addissie YA, Toro C, Luby M, Latour L, Vezina G, Page DC, Muenke M. Circle of Willis anomalies in Turner syndrome: Absent A1 segment of the anterior cerebral artery. Birth Defects Res 2019; 111:1584-1588. [PMID: 31626395 DOI: 10.1002/bdr2.1609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 09/24/2019] [Accepted: 10/09/2019] [Indexed: 11/09/2022]
Abstract
PURPOSE Turner syndrome (TS) is the most common sex chromosome disorder in women and is associated with a higher than expected death rate secondary to cerebrovascular disease, including stroke. This study evaluates the cerebral vascular anatomy of individuals with TS. METHODS Twenty-one women with TS had brain magnetic resonance angiography (MRA). These MRAs were evaluated in a blinded manner with a control group of 25 men and 25 women who had MRA imaging for multiple indications including migraine headaches, psychiatric disorders, and seizures. RESULTS Twenty-nine percent of women with TS were missing an A1 segment of the anterior cerebral artery (ACA) compared to 0% in the control group (p < .001). There were no other significant differences in the circle of Willis (COW) in women with TS compared with the control group. A complete COW was found in 3 of 21 (14%) of women with TS and 12 of 47 (26%) controls (p = .36). CONCLUSION Women with TS have a significantly different intracranial vascular anatomy, specifically the absence of the A1 segment of the ACA when compared to male and female controls. More research in brain imaging in women with TS and stroke and other cerebrovascular diseases is needed to determine the clinical significance of this anomaly.
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Affiliation(s)
- Paul Kruszka
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Ashley Buscetta
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Maria T Acosta
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland.,Undiagnosed Disease Network, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Nicole Banks
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Yonit A Addissie
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Camilo Toro
- Undiagnosed Disease Network, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Marie Luby
- Stroke Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | - Lawrence Latour
- Stroke Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | - Gilbert Vezina
- The Children's Research Institute, Children's National Health System, Washington, DC
| | - David C Page
- Whitehead Institute, Cambridge, Massachusetts.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts
| | - Maximilian Muenke
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
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26
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Lesch BJ, Tothova Z, Morgan EA, Liao Z, Bronson RT, Ebert BL, Page DC. Intergenerational epigenetic inheritance of cancer susceptibility in mammals. eLife 2019; 8:e39380. [PMID: 30963999 PMCID: PMC6456297 DOI: 10.7554/elife.39380] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 03/03/2019] [Indexed: 12/11/2022] Open
Abstract
Susceptibility to cancer is heritable, but much of this heritability remains unexplained. Some 'missing' heritability may be mediated by epigenetic changes in the parental germ line that do not involve transmission of genetic variants from parent to offspring. We report that deletion of the chromatin regulator Kdm6a (Utx) in the paternal germ line results in elevated tumor incidence in genetically wild type mice. This effect increases following passage through two successive generations of Kdm6a male germline deletion, but is lost following passage through a wild type germ line. The H3K27me3 mark is redistributed in sperm of Kdm6a mutants, and we define approximately 200 H3K27me3-marked regions that exhibit increased DNA methylation, both in sperm of Kdm6a mutants and in somatic tissue of progeny. Hypermethylated regions in enhancers may alter regulation of genes involved in cancer initiation or progression. Epigenetic changes in male gametes may therefore impact cancer susceptibility in adult offspring.
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Affiliation(s)
| | - Zuzana Tothova
- Department of Medicine, Division of HematologyBrigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
- Broad Institute of MIT and HarvardCambridgeUnited States
| | - Elizabeth A Morgan
- Department of PathologyBrigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Zhicong Liao
- Department of GeneticsYale School of MedicineNew HavenUnited States
- Yale Cancer CenterYale School of MedicineNew HavenUnited States
| | - Roderick T Bronson
- Department of PathologyTufts University School of Medicine and Veterinary MedicineNorth GraftonUnited States
| | - Benjamin L Ebert
- Department of Medicine, Division of HematologyBrigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
- Broad Institute of MIT and HarvardCambridgeUnited States
| | - David C Page
- Whitehead InstituteCambridgeUnited States
- Department of BiologyMassachusetts Institute of TechnologyCambridgeUnited States
- Howard Hughes Medical Institute, Whitehead InstituteCambridgeUnited States
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27
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Ly P, Brunner SF, Shoshani O, Kim DH, Lan W, Pyntikova T, Flanagan AM, Behjati S, Page DC, Campbell PJ, Cleveland DW. Chromosome segregation errors generate a diverse spectrum of simple and complex genomic rearrangements. Nat Genet 2019; 51:705-715. [PMID: 30833795 PMCID: PMC6441390 DOI: 10.1038/s41588-019-0360-8] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 01/23/2019] [Indexed: 01/05/2023]
Abstract
Cancer genomes are frequently characterized by numerical and structural chromosomal abnormalities. Here we integrated a centromere-specific inactivation approach with selection for a conditionally essential gene, a strategy termed CEN-SELECT, to systematically interrogate the structural landscape of mis-segregated chromosomes. We show that single-chromosome mis-segregation into a micronucleus can directly trigger a broad spectrum of genomic rearrangement types. Cytogenetic profiling revealed that mis-segregated chromosomes exhibit 120-fold-higher susceptibility to developing seven major categories of structural aberrations, including translocations, insertions, deletions, and complex reassembly through chromothripsis coupled to classical non-homologous end joining. Whole-genome sequencing of clonally propagated rearrangements identified random patterns of clustered breakpoints with copy-number alterations resulting in interspersed gene deletions and extrachromosomal DNA amplification events. We conclude that individual chromosome segregation errors during mitotic cell division are sufficient to drive extensive structural variations that recapitulate genomic features commonly associated with human disease.
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Affiliation(s)
- Peter Ly
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA.
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | | | - Ofer Shoshani
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Dong Hyun Kim
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Weijie Lan
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA
| | | | - Adrienne M Flanagan
- University College London Cancer Institute, London, UK
- Department of Histopathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, UK
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - David C Page
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Don W Cleveland
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA.
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28
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Kojima ML, de Rooij DG, Page DC. Amplification of a broad transcriptional program by a common factor triggers the meiotic cell cycle in mice. eLife 2019; 8:43738. [PMID: 30810530 PMCID: PMC6392498 DOI: 10.7554/elife.43738] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 02/10/2019] [Indexed: 12/22/2022] Open
Abstract
The germ line provides the cellular link between generations of multicellular organisms, its cells entering the meiotic cell cycle only once each generation. However, the mechanisms governing this initiation of meiosis remain poorly understood. Here, we examined cells undergoing meiotic initiation in mice, and we found that initiation involves the dramatic upregulation of a transcriptional network of thousands of genes whose expression is not limited to meiosis. This broad gene expression program is directly upregulated by STRA8, encoded by a germ cell-specific gene required for meiotic initiation. STRA8 binds its own promoter and those of thousands of other genes, including meiotic prophase genes, factors mediating DNA replication and the G1-S cell-cycle transition, and genes that promote the lengthy prophase unique to meiosis I. We conclude that, in mice, the robust amplification of this extraordinarily broad transcription program by a common factor triggers initiation of meiosis.
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Affiliation(s)
- Mina L Kojima
- Whitehead Institute, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | | | - David C Page
- Whitehead Institute, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, United States
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29
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San Roman AK, Page DC. A strategic research alliance: Turner syndrome and sex differences. Am J Med Genet C Semin Med Genet 2019; 181:59-67. [PMID: 30790449 DOI: 10.1002/ajmg.c.31677] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 01/06/2019] [Indexed: 12/11/2022]
Abstract
Sex chromosome constitution varies in the human population, both between the sexes (46,XX females and 46,XY males), and within the sexes (e.g., 45,X and 46,XX females, and 47,XXY and 46,XY males). Coincident with this genetic variation are numerous phenotypic differences between males and females, and individuals with sex chromosome aneuploidy. However, the molecular mechanisms by which sex chromosome constitution impacts phenotypes at the cellular, tissue, and organismal levels remain largely unexplored. Thus, emerges a fundamental question connecting the study of sex differences and sex chromosome aneuploidy syndromes: How does sex chromosome constitution influence phenotype? Here, we focus on Turner syndrome (TS), associated with the 45,X karyotype, and its synergies with the study of sex differences. We review findings from evolutionary studies of the sex chromosomes, which identified genes that are most likely to contribute to phenotypes as a result of variation in sex chromosome constitution. We then explore strategies for investigating the direct effects of the sex chromosomes, and the evidence for specific sex chromosome genes impacting phenotypes. In sum, we argue that integrating the study of TS with sex differences offers a mutually beneficial alliance to identify contributions of the sex chromosomes to human development, health, and disease.
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Affiliation(s)
| | - David C Page
- Whitehead Institute, Cambridge, Massachusetts.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
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30
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Romer KA, de Rooij DG, Kojima ML, Page DC. Corrigendum to "Isolating mitotic and meiotic germ cells from male mice by developmental synchronization, staging, and sorting" [Dev. Biol. 443 (2018) 19-34]. Dev Biol 2019; 445:113. [PMID: 30416000 DOI: 10.1016/j.ydbio.2018.10.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Katherine A Romer
- Whitehead Institute, 455 Main Street, Cambridge, MA 02142, USA; Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Dirk G de Rooij
- Whitehead Institute, 455 Main Street, Cambridge, MA 02142, USA
| | - Mina L Kojima
- Whitehead Institute, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David C Page
- Whitehead Institute, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Whitehead Institute, 455 Main Street, Cambridge, MA 02142, USA.
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31
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Romer KA, de Rooij DG, Kojima ML, Page DC. Isolating mitotic and meiotic germ cells from male mice by developmental synchronization, staging, and sorting. Dev Biol 2018; 443:19-34. [PMID: 30149006 DOI: 10.1016/j.ydbio.2018.08.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 08/23/2018] [Accepted: 08/23/2018] [Indexed: 01/06/2023]
Abstract
Isolating discrete populations of germ cells from the mouse testis is challenging, because the adult testis contains germ cells at every step of spermatogenesis, in addition to somatic cells. We present a novel method for isolating precise, high-purity populations of male germ cells. We first synchronize germ cell development in vivo by manipulating retinoic acid metabolism, and perform histological staging to verify synchronization. We use fluorescence-activated cell sorting to separate the synchronized differentiating germ cells from contaminating somatic cells and undifferentiated spermatogonia. We achieve ~90% purity at each step of development from undifferentiated spermatogonia through late meiotic prophase. Utilizing this "3 S" method (synchronize, stage, and sort), we can separate germ cell types that were previously challenging or impossible to distinguish, with sufficient yield for epigenetic and biochemical studies. 3 S expands the toolkit of germ cell sorting methods, and should facilitate detailed characterization of molecular and biochemical changes that occur during the mitotic and meiotic phases of spermatogenesis.
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Affiliation(s)
- Katherine A Romer
- Whitehead Institute, 455 Main Street, Cambridge, MA 02142, USA; Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Dirk G de Rooij
- Whitehead Institute, 455 Main Street, Cambridge, MA 02142, USA
| | - Mina L Kojima
- Whitehead Institute, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David C Page
- Whitehead Institute, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Whitehead Institute, 455 Main Street, Cambridge, MA 02142, USA.
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Teitz LS, Pyntikova T, Skaletsky H, Page DC. Selection Has Countered High Mutability to Preserve the Ancestral Copy Number of Y Chromosome Amplicons in Diverse Human Lineages. Am J Hum Genet 2018; 103:261-275. [PMID: 30075113 DOI: 10.1016/j.ajhg.2018.07.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/10/2018] [Indexed: 02/07/2023] Open
Abstract
Amplicons-large, highly identical segmental duplications-are a prominent feature of mammalian Y chromosomes. Although they encode genes essential for fertility, these amplicons differ vastly between species, and little is known about the selective constraints acting on them. Here, we develop computational tools to detect amplicon copy number with unprecedented accuracy from high-throughput sequencing data. We find that one-sixth (16.9%) of 1,216 males from the 1000 Genomes Project have at least one deleted or duplicated amplicon. However, each amplicon's reference copy number is scrupulously maintained among divergent branches of the Y chromosome phylogeny, including the ancient branch A00, indicating that the reference copy number is ancestral to all modern human Y chromosomes. Using phylogenetic analyses and simulations, we demonstrate that this pattern of variation is incompatible with neutral evolution and instead displays hallmarks of mutation-selection balance. We also observe cases of amplicon rescue, in which deleted amplicons are restored through subsequent duplications. These results indicate that, contrary to the lack of constraint suggested by the differences between species, natural selection has suppressed amplicon copy number variation in diverse human lineages.
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Naqvi S, Bellott DW, Lin KS, Page DC. Conserved microRNA targeting reveals preexisting gene dosage sensitivities that shaped amniote sex chromosome evolution. Genome Res 2018; 28:474-483. [PMID: 29449410 PMCID: PMC5880238 DOI: 10.1101/gr.230433.117] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 02/06/2018] [Indexed: 02/02/2023]
Abstract
Mammalian X and Y Chromosomes evolved from an ordinary autosomal pair. Genetic decay of the Y led to X Chromosome inactivation (XCI) in females, but some Y-linked genes were retained during the course of sex chromosome evolution, and many X-linked genes did not become subject to XCI. We reconstructed gene-by-gene dosage sensitivities on the ancestral autosomes through phylogenetic analysis of microRNA (miRNA) target sites and compared these preexisting characteristics to the current status of Y-linked and X-linked genes in mammals. Preexisting heterogeneities in dosage sensitivity, manifesting as differences in the extent of miRNA-mediated repression, predicted either the retention of a Y homolog or the acquisition of XCI following Y gene decay. Analogous heterogeneities among avian Z-linked genes predicted either the retention of a W homolog or gene-specific dosage compensation following W gene decay. Genome-wide analyses of human copy number variation indicate that these heterogeneities consisted of sensitivity to both increases and decreases in dosage. We propose a model of XY/ZW evolution incorporating such preexisting dosage sensitivities in determining the evolutionary fates of individual genes. Our findings thus provide a more complete view of the role of dosage sensitivity in shaping the mammalian and avian sex chromosomes and reveal an important role for post-transcriptional regulatory sequences (miRNA target sites) in sex chromosome evolution.
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Affiliation(s)
- Sahin Naqvi
- Whitehead Institute, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | - Kathy S Lin
- Whitehead Institute, Cambridge, Massachusetts 02142, USA.,Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - David C Page
- Whitehead Institute, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
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Soh YQS, Mikedis MM, Kojima M, Godfrey AK, de Rooij DG, Page DC. Meioc maintains an extended meiotic prophase I in mice. PLoS Genet 2017; 13:e1006704. [PMID: 28380054 PMCID: PMC5397071 DOI: 10.1371/journal.pgen.1006704] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 04/19/2017] [Accepted: 03/20/2017] [Indexed: 01/13/2023] Open
Abstract
The meiosis-specific chromosomal events of homolog pairing, synapsis, and recombination occur over an extended meiotic prophase I that is many times longer than prophase of mitosis. Here we show that, in mice, maintenance of an extended meiotic prophase I requires the gene Meioc, a germ-cell specific factor conserved in most metazoans. In mice, Meioc is expressed in male and female germ cells upon initiation of and throughout meiotic prophase I. Mouse germ cells lacking Meioc initiate meiosis: they undergo pre-meiotic DNA replication, they express proteins involved in synapsis and recombination, and a subset of cells progress as far as the zygotene stage of prophase I. However, cells in early meiotic prophase—as early as the preleptotene stage—proceed to condense their chromosomes and assemble a spindle, as if having progressed to metaphase. Meioc-deficient spermatocytes that have initiated synapsis mis-express CYCLIN A2, which is normally expressed in mitotic spermatogonia, suggesting a failure to properly transition to a meiotic cell cycle program. MEIOC interacts with YTHDC2, and the two proteins pull-down an overlapping set of mitosis-associated transcripts. We conclude that when the meiotic chromosomal program is initiated, Meioc is simultaneously induced so as to extend meiotic prophase. Specifically, MEIOC, together with YTHDC2, promotes a meiotic (as opposed to mitotic) cell cycle program via post-transcriptional control of their target transcripts. Meiosis is the specialized cell division that halves the genetic content of germ cells to produce haploid gametes. This reductive division is preceded by a preparative phase of the cell cycle, meiotic prophase I, during which several meiosis-specific chromosomal events occur. Across sexually reproducing organisms, prophase of meiosis I is dramatically longer than mitotic prophase. However, it was not known in mammals how and why meiotic prophase I is extended. We have identified a mouse mutant in which this extended prophase I is disrupted: germ cells lacking Meioc initiate meiosis, but prematurely proceed to metaphase. Mutant male meiotic germ cells mis-express a cell cycle regulator that is normally expressed in mitotic male germ cells, suggesting that Meioc is required for germ cells to properly transition to a meiotic cell cycle program. Biochemical analyses of proteins and transcripts that associate with MEIOC protein suggest that MEIOC may promote the transition from a mitotic to meiotic cell cycle program by post-transcriptionally regulating target transcripts. Our studies indicate that in mammals, as in other sexually reproducing organisms, meiotic prophase I must be extended to allow time for meiotic chromosomal events to reach completion.
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Affiliation(s)
- Y. Q. Shirleen Soh
- Whitehead Institute, Cambridge, MA, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | | | - Mina Kojima
- Whitehead Institute, Cambridge, MA, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Alexander K. Godfrey
- Whitehead Institute, Cambridge, MA, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | | | - David C. Page
- Whitehead Institute, Cambridge, MA, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States of America
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA, United States of America
- * E-mail:
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35
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Ly P, Teitz LS, Kim DH, Shoshani O, Skaletsky H, Fachinetti D, Page DC, Cleveland DW. Selective Y centromere inactivation triggers chromosome shattering in micronuclei and repair by non-homologous end joining. Nat Cell Biol 2016; 19:68-75. [PMID: 27918550 DOI: 10.1038/ncb3450] [Citation(s) in RCA: 174] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 11/02/2016] [Indexed: 12/14/2022]
Abstract
Chromosome missegregation into a micronucleus can cause complex and localized genomic rearrangements known as chromothripsis, but the underlying mechanisms remain unresolved. Here we developed an inducible Y centromere-selective inactivation strategy by exploiting a CENP-A/histone H3 chimaera to directly examine the fate of missegregated chromosomes in otherwise diploid human cells. Using this approach, we identified a temporal cascade of events that are initiated following centromere inactivation involving chromosome missegregation, fragmentation, and re-ligation that span three consecutive cell cycles. Following centromere inactivation, a micronucleus harbouring the Y chromosome is formed in the first cell cycle. Chromosome shattering, producing up to 53 dispersed fragments from a single chromosome, is triggered by premature micronuclear condensation prior to or during mitotic entry of the second cycle. Lastly, canonical non-homologous end joining (NHEJ), but not homology-dependent repair, is shown to facilitate re-ligation of chromosomal fragments in the third cycle. Thus, initial errors in cell division can provoke further genomic instability through fragmentation of micronuclear DNAs coupled to NHEJ-mediated reassembly in the subsequent interphase.
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Affiliation(s)
- Peter Ly
- Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Levi S Teitz
- Department of Biology, Massachusetts Institute of Technology and Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
| | - Dong H Kim
- Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Ofer Shoshani
- Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Helen Skaletsky
- Howard Hughes Medical Institute and Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
| | - Daniele Fachinetti
- Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - David C Page
- Department of Biology, Massachusetts Institute of Technology and Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute and Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
| | - Don W Cleveland
- Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093, USA
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36
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Carmell MA, Dokshin GA, Skaletsky H, Hu YC, van Wolfswinkel JC, Igarashi KJ, Bellott DW, Nefedov M, Reddien PW, Enders GC, Uversky VN, Mello CC, Page DC. A widely employed germ cell marker is an ancient disordered protein with reproductive functions in diverse eukaryotes. eLife 2016; 5. [PMID: 27718356 PMCID: PMC5098910 DOI: 10.7554/elife.19993] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/05/2016] [Indexed: 12/17/2022] Open
Abstract
The advent of sexual reproduction and the evolution of a dedicated germline in multicellular organisms are critical landmarks in eukaryotic evolution. We report an ancient family of GCNA (germ cell nuclear antigen) proteins that arose in the earliest eukaryotes, and feature a rapidly evolving intrinsically disordered region (IDR). Phylogenetic analysis reveals that GCNA proteins emerged before the major eukaryotic lineages diverged; GCNA predates the origin of a dedicated germline by a billion years. Gcna gene expression is enriched in reproductive cells across eukarya - either just prior to or during meiosis in single-celled eukaryotes, and in stem cells and germ cells of diverse multicellular animals. Studies of Gcna-mutant C. elegans and mice indicate that GCNA has functioned in reproduction for at least 600 million years. Homology to IDR-containing proteins implicated in DNA damage repair suggests that GCNA proteins may protect the genomic integrity of cells carrying a heritable genome.
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Affiliation(s)
| | - Gregoriy A Dokshin
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States
| | - Helen Skaletsky
- Whitehead Institute, Cambridge, United States.,Howard Hughes Medical Institute, Chevy Chase, United States
| | | | | | | | | | - Michael Nefedov
- BACPAC Resources, Children's Hospital Oakland, Oakland, United States
| | - Peter W Reddien
- Whitehead Institute, Cambridge, United States.,Howard Hughes Medical Institute, Chevy Chase, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - George C Enders
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, United States
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, United States
| | - Craig C Mello
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States.,Howard Hughes Medical Institute, Chevy Chase, United States
| | - David C Page
- Whitehead Institute, Cambridge, United States.,Howard Hughes Medical Institute, Chevy Chase, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
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37
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Lesch BJ, Silber SJ, McCarrey JR, Page DC. Corrigendum: Parallel evolution of male germline epigenetic poising and somatic development in animals. Nat Genet 2016; 48:1296. [PMID: 27681290 DOI: 10.1038/ng1016-1296b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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38
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Lesch BJ, Silber SJ, McCarrey JR, Page DC. Parallel evolution of male germline epigenetic poising and somatic development in animals. Nat Genet 2016; 48:888-94. [PMID: 27294618 DOI: 10.1038/ng.3591] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 05/17/2016] [Indexed: 12/20/2022]
Abstract
Changes in gene regulation frequently underlie changes in morphology during evolution, and differences in chromatin state have been linked with changes in anatomical structure and gene expression across evolutionary time. Here we assess the relationship between evolution of chromatin state in germ cells and evolution of gene regulatory programs governing somatic development. We examined the poised (H3K4me3/H3K27me3 bivalent) epigenetic state in male germ cells from five mammalian and one avian species. We find that core genes poised in germ cells from multiple amniote species are ancient regulators of morphogenesis that sit at the top of transcriptional hierarchies controlling somatic tissue development, whereas genes that gain poising in germ cells from individual species act downstream of core poised genes during development in a species-specific fashion. We propose that critical regulators of animal development gained an epigenetically privileged state in germ cells, manifested in amniotes by H3K4me3/H3K27me3 poising, early in metazoan evolution.
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Affiliation(s)
| | - Sherman J Silber
- Infertility Center of St. Louis, St. Luke's Hospital, St. Louis, Missouri, USA
| | - John R McCarrey
- Department of Biology, University of Texas at San Antonio, San Antonio, Texas, USA
| | - David C Page
- Whitehead Institute, Cambridge, Massachusetts, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts, USA
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39
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Yang F, Silber S, Leu NA, Oates RD, Marszalek JD, Skaletsky H, Brown LG, Rozen S, Page DC, Wang PJ. TEX11 is mutated in infertile men with azoospermia and regulates genome-wide recombination rates in mouse. EMBO Mol Med 2016; 7:1198-210. [PMID: 26136358 PMCID: PMC4568952 DOI: 10.15252/emmm.201404967] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Genome-wide recombination is essential for genome stability, evolution, and speciation. Mouse Tex11, an X-linked meiosis-specific gene, promotes meiotic recombination and chromosomal synapsis. Here, we report that TEX11 is mutated in infertile men with non-obstructive azoospermia and that an analogous mutation in the mouse impairs meiosis. Genetic screening of a large cohort of idiopathic infertile men reveals that TEX11 mutations, including frameshift and splicing acceptor site mutations, cause infertility in 1% of azoospermic men. Functional evaluation of three analogous human TEX11 missense mutations in transgenic mouse models identified one mutation (V748A) as a potential infertility allele and found two mutations non-causative. In the mouse model, an intronless autosomal Tex11 transgene functionally substitutes for the X-linked Tex11 gene, providing genetic evidence for the X-to-autosomal retrotransposition evolution phenomenon. Furthermore, we find that TEX11 protein levels modulate genome-wide recombination rates in both sexes. These studies indicate that TEX11 alleles affecting expression level or substituting single amino acids may contribute to variations in recombination rates between sexes and among individuals in humans.
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Affiliation(s)
- Fang Yang
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sherman Silber
- Infertility Center of St. Louis, St. Luke's Hospital, St. Louis, MO, USA
| | - N Adrian Leu
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Robert D Oates
- Department of Urology, Boston University Medical Center, Boston, MA, USA
| | - Janet D Marszalek
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA, USA
| | - Helen Skaletsky
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA, USA
| | - Laura G Brown
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA, USA
| | - Steve Rozen
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA, USA Duke-Nus Graduate Medical School Singapore, Singapore City, Singapore
| | - David C Page
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA, USA Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - P Jeremy Wang
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
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Kern DM, Nicholls PK, Page DC, Cheeseman IM. A mitotic SKAP isoform regulates spindle positioning at astral microtubule plus ends. J Cell Biol 2016; 213:315-28. [PMID: 27138257 PMCID: PMC4862331 DOI: 10.1083/jcb.201510117] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 03/30/2016] [Indexed: 12/14/2022] Open
Abstract
The Astrin/SKAP complex regulates mitotic chromosome alignment and centrosome integrity, but previous work found conflicting results for SKAP function. Here, Kern et al. demonstrate that a previously unappreciated short SKAP isoform mediates mitotic spindle positioning at astral microtubule plus ends. The Astrin/SKAP complex plays important roles in mitotic chromosome alignment and centrosome integrity, but previous work found conflicting results for SKAP function. Here, we demonstrate that SKAP is expressed as two distinct isoforms in mammals: a longer, testis-specific isoform that was used for the previous studies in mitotic cells and a novel, shorter mitotic isoform. Unlike the long isoform, short SKAP rescues SKAP depletion in mitosis and displays robust microtubule plus-end tracking, including localization to astral microtubules. Eliminating SKAP microtubule binding results in severe chromosome segregation defects. In contrast, SKAP mutants specifically defective for plus-end tracking facilitate proper chromosome segregation but display spindle positioning defects. Cells lacking SKAP plus-end tracking have reduced Clasp1 localization at microtubule plus ends and display increased lateral microtubule contacts with the cell cortex, which we propose results in unbalanced dynein-dependent cortical pulling forces. Our work reveals an unappreciated role for the Astrin/SKAP complex as an astral microtubule mediator of mitotic spindle positioning.
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Affiliation(s)
- David M Kern
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142 Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Peter K Nicholls
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
| | - David C Page
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142 Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139 Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - Iain M Cheeseman
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142 Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
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Abstract
Mammals have the oldest sex chromosome system known: the mammalian X and Y chromosomes evolved from ordinary autosomes beginning at least 180 million years ago. Despite their shared ancestry, mammalian Y chromosomes display enormous variation among species in size, gene content, and structural complexity. Several unique features of the Y chromosome--its lack of a homologous partner for crossing over, its functional specialization for spermatogenesis, and its high degree of sequence amplification--contribute to this extreme variation. However, amid this evolutionary turmoil many commonalities have been revealed that have contributed to our understanding of the selective pressures driving the evolution and biology of the Y chromosome. Two biological themes have defined Y-chromosome research over the past six decades: testis determination and spermatogenesis. A third biological theme begins to emerge from recent insights into the Y chromosome's roles beyond the reproductive tract--a theme that promises to broaden the reach of Y-chromosome research by shedding light on fundamental sex differences in human health and disease.
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Affiliation(s)
- Jennifer F Hughes
- Whitehead Institute, Howard Hughes Medical Institute, and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142;
| | - David C Page
- Whitehead Institute, Howard Hughes Medical Institute, and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142;
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Wu Y, Abbey CK, Chen X, Liu J, Page DC, Alagoz O, Peissig P, Onitilo AA, Burnside ES. Developing a utility decision framework to evaluate predictive models in breast cancer risk estimation. J Med Imaging (Bellingham) 2015; 2:041005. [PMID: 26835489 DOI: 10.1117/1.jmi.2.4.041005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 07/20/2015] [Indexed: 12/14/2022] Open
Abstract
Combining imaging and genetic information to predict disease presence and progression is being codified into an emerging discipline called "radiogenomics." Optimal evaluation methodologies for radiogenomics have not been well established. We aim to develop a decision framework based on utility analysis to assess predictive models for breast cancer diagnosis. We garnered Gail risk factors, single nucleotide polymorphisms (SNPs), and mammographic features from a retrospective case-control study. We constructed three logistic regression models built on different sets of predictive features: (1) Gail, (2) Gail + Mammo, and (3) Gail + Mammo + SNP. Then we generated receiver operating characteristic (ROC) curves for three models. After we assigned utility values for each category of outcomes (true negatives, false positives, false negatives, and true positives), we pursued optimal operating points on ROC curves to achieve maximum expected utility of breast cancer diagnosis. We performed McNemar's test based on threshold levels at optimal operating points, and found that SNPs and mammographic features played a significant role in breast cancer risk estimation. Our study comprising utility analysis and McNemar's test provides a decision framework to evaluate predictive models in breast cancer risk estimation.
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Affiliation(s)
- Yirong Wu
- University of Wisconsin-Madison , Department of Radiology, 600 Highland Avenue, Madison, Wisconsin 53792, United States
| | - Craig K Abbey
- University of California-Santa Barbara , Department of Psychological and Brain Sciences, 251 UCEN Road, Santa Barbara, California 93106, United States
| | - Xianqiao Chen
- Wuhan University of Technology , School of Computer Science and Technology, 1178 Heping Avenue, Wuhan, Hubei 430070, China
| | - Jie Liu
- University of Washington-Seattle , Department of Genome Sciences, 3720 15th Avenue, Seattle, Washington 98105, United States
| | - David C Page
- University of Wisconsin-Madison , Department of Biostatistics and Medical Informatics, 600 Highland Avenue, Madison, Wisconsin 53706, United States
| | - Oguzhan Alagoz
- University of Wisconsin-Madison , Department of Industrial and Systems Engineering, 1513 University Avenue, Madison, Wisconsin 53706, United States
| | - Peggy Peissig
- Marshfield Clinic Research Foundation , 1000 North Oak Avenue, Marshfield, Wisconsin 54449, United States
| | - Adedayo A Onitilo
- Marshfield Clinic Research Foundation, 1000 North Oak Avenue, Marshfield, Wisconsin 54449, United States; Marshfield Clinic Weston Center, Department of Hematology/Oncology, 3501 Cranberry Boulevard, Weston, Wisconsin 54476, United States
| | - Elizabeth S Burnside
- University of Wisconsin-Madison , Department of Radiology, 600 Highland Avenue, Madison, Wisconsin 53792, United States
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Hughes JF, Skaletsky H, Koutseva N, Pyntikova T, Page DC. Sex chromosome-to-autosome transposition events counter Y-chromosome gene loss in mammals. Genome Biol 2015; 16:104. [PMID: 26017895 PMCID: PMC4446799 DOI: 10.1186/s13059-015-0667-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 05/06/2015] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Although the mammalian X and Y chromosomes evolved from a single pair of autosomes, they are highly differentiated: the Y chromosome is dramatically smaller than the X and has lost most of its genes. The surviving genes are a specialized set with extraordinary evolutionary longevity. Most mammalian lineages have experienced delayed, or relatively recent, loss of at least one conserved Y-linked gene. An extreme example of this phenomenon is in the Japanese spiny rat, where the Y chromosome has disappeared altogether. In this species, many Y-linked genes were rescued by transposition to new genomic locations, but until our work presented here, this has been considered an isolated case. RESULTS We describe eight cases of genes that have relocated to autosomes in mammalian lineages where the corresponding Y-linked gene has been lost. These gene transpositions originated from either the X or Y chromosomes, and are observed in diverse mammalian lineages: occurring at least once in marsupials, apes, and cattle, and at least twice in rodents and marmoset. For two genes--EIF1AX/Y and RPS4X/Y--transposition to autosomes occurred independently in three distinct lineages. CONCLUSIONS Rescue of Y-linked gene loss through transposition to autosomes has previously been reported for a single isolated rodent species. However, our findings indicate that this compensatory mechanism is widespread among mammalian species. Thus, Y-linked gene loss emerges as an additional driver of gene transposition from the sex chromosomes, a phenomenon thought to be driven primarily by meiotic sex chromosome inactivation.
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Affiliation(s)
| | - Helen Skaletsky
- Whitehead Institute, Cambridge, MA, 02142, USA. .,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA, 02142, USA.
| | | | | | - David C Page
- Whitehead Institute, Cambridge, MA, 02142, USA. .,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA, 02142, USA. .,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.
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44
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Backeljauw PF, Bondy C, Chernausek SD, Cernich JT, Cole DA, Fasciano LP, Foodim J, Hawley S, Hong DS, Knickmeyer RC, Kruszka P, Lin AE, Lippe BM, Lorigan GA, Maslen CL, Mauras N, Page DC, Pemberton VL, Prakash SK, Quigley CA, Ranallo KC, Reiss AL, Sandberg DE, Scurlock C, Silberbach M. Proceedings from the Turner Resource Network symposium: the crossroads of health care research and health care delivery. Am J Med Genet A 2015; 167A:1962-71. [PMID: 25920614 DOI: 10.1002/ajmg.a.37121] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 03/06/2015] [Indexed: 01/15/2023]
Abstract
Turner syndrome, a congenital condition that affects ∼1/2,500 births, results from absence or structural alteration of the second sex chromosome. There has been substantial effort by numerous clinical and genetic research groups to delineate the clinical, pathophysiological, cytogenetic, and molecular features of this multisystem condition. Questions about the molecular-genetic and biological basis of many of the clinical features remain unanswered, and health care providers and families seek improved care for affected individuals. The inaugural "Turner Resource Network (TRN) Symposium" brought together individuals with Turner syndrome and their families, advocacy group leaders, clinicians, basic scientists, physician-scientists, trainees and other stakeholders with interest in the well-being of individuals and families living with the condition. The goal of this symposium was to establish a structure for a TRN that will be a patient-powered organization involving those living with Turner syndrome, their families, clinicians, and scientists. The TRN will identify basic and clinical questions that might be answered with registries, clinical trials, or through bench research to promote and advocate for best practices and improved care for individuals with Turner syndrome. The symposium concluded with the consensus that two rationales justify the creation of a TRN: inadequate attention has been paid to the health and psychosocial issues facing girls and women who live with Turner syndrome; investigations into the susceptibility to common disorders such as cardiovascular or autoimmune diseases caused by sex chromosome deficiencies will increase understanding of disease susceptibilities in the general population.
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Affiliation(s)
- Philippe F Backeljauw
- Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Carolyn Bondy
- Endocrine Branch NICHD, National Institutes of Health, Bethesda, Maryland
| | | | | | - David A Cole
- Hagley Museum and Library in Wilmington, Wilmington, Delaware
| | | | | | - Scott Hawley
- Stowers Institute for Medical Research, Kansas City, Missouri
| | | | - Rebecca C Knickmeyer
- Department of Psychiatry, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Paul Kruszka
- National Human Genome Research Institute NIH, Bethesda, Maryland
| | - Angela E Lin
- Genetics Unit, MassGeneral Hospital for Children, Boston, Massachusetts
| | - Barbara M Lippe
- David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio
| | - Cheryl L Maslen
- Oregon Health and Sciences University School of Medicine, Portland, Oregon
| | - Nelly Mauras
- Nemours Children's Clinic, Jacksonville, Florida
| | - David C Page
- Whitehead Institute, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | | | | | - Charmian A Quigley
- Pediatric Endocrinology, Indiana University School of Medicine, Indianapolis, Indiana
| | | | - Allan L Reiss
- Center for Interdisciplinary Brain Sciences Research, Stanford University, Palo Alto, California
| | - David E Sandberg
- Department of Pediatrics, Child Health Evaluation and Research (CHEAR) Unit, University of Michigan, Ann Arbor, Michigan
| | - Cindy Scurlock
- Turner Syndrome Society of the United States, Houston, Texas
| | - Michael Silberbach
- Oregon Health and Sciences University School of Medicine, Portland, Oregon
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45
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Hu YC, Nicholls PK, Soh YQS, Daniele JR, Junker JP, van Oudenaarden A, Page DC. Licensing of primordial germ cells for gametogenesis depends on genital ridge signaling. PLoS Genet 2015; 11:e1005019. [PMID: 25739037 PMCID: PMC4349450 DOI: 10.1371/journal.pgen.1005019] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 01/22/2015] [Indexed: 01/07/2023] Open
Abstract
In mouse embryos at mid-gestation, primordial germ cells (PGCs) undergo licensing to become gametogenesis-competent cells (GCCs), gaining the capacity for meiotic initiation and sexual differentiation. GCCs then initiate either oogenesis or spermatogenesis in response to gonadal cues. Germ cell licensing has been considered to be a cell-autonomous and gonad-independent event, based on observations that some PGCs, having migrated not to the gonad but to the adrenal gland, nonetheless enter meiosis in a time frame parallel to ovarian germ cells -- and do so regardless of the sex of the embryo. Here we test the hypothesis that germ cell licensing is cell-autonomous by examining the fate of PGCs in Gata4 conditional mutant (Gata4 cKO) mouse embryos. Gata4, which is expressed only in somatic cells, is known to be required for genital ridge initiation. PGCs in Gata4 cKO mutants migrated to the area where the genital ridge, the precursor of the gonad, would ordinarily be formed. However, these germ cells did not undergo licensing and instead retained characteristics of PGCs. Our results indicate that licensing is not purely cell-autonomous but is induced by the somatic genital ridge. During embryonic development, stem cell-like primordial germ cells travel across the developing embryo to the genital ridge, which gives rise to the gonad. Around the time of their arrival, the primordial germ cells gain the capacity to undertake sexual specialization and meiosis—a process called germ cell licensing. Based on the observation that meiosis and sexual differentiation can occur when primordial germ cells stray into the area of the adrenal gland, the primordial germ cell has been thought to be responsible for its own licensing. We tested this notion by examining the licensing process in mutant mouse embryos that did not form a genital ridge. We discovered that in the absence of the genital ridge, primordial germ cells migrate across the developing embryo properly, but instead of undergoing licensing, these cells retain their primordial germ cell characteristics. We conclude that licensing of embryonic primordial germ cells for gametogenesis is dependent on signaling from the genital ridge.
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Affiliation(s)
- Yueh-Chiang Hu
- Whitehead Institute, Cambridge, Massachusetts, United States of America
| | - Peter K. Nicholls
- Whitehead Institute, Cambridge, Massachusetts, United States of America
| | - Y. Q. Shirleen Soh
- Whitehead Institute, Cambridge, Massachusetts, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Joseph R. Daniele
- Whitehead Institute, Cambridge, Massachusetts, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Jan Philipp Junker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Hubrecht Institute—KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, Utrecht, Netherlands
| | - Alexander van Oudenaarden
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Hubrecht Institute—KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, Utrecht, Netherlands
| | - David C. Page
- Whitehead Institute, Cambridge, Massachusetts, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts, United States of America
- * E-mail:
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Wu Y, Liu J, Del Rio AM, Page DC, Alagoz O, Peissig P, Onitilo AA, Burnside ES. Developing a clinical utility framework to evaluate prediction models in radiogenomics. Proc SPIE Int Soc Opt Eng 2015; 9416. [PMID: 27095854 DOI: 10.1117/12.2081954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Combining imaging and genetic information to predict disease presence and behavior is being codified into an emerging discipline called "radiogenomics." Optimal evaluation methodologies for radiogenomics techniques have not been established. We aim to develop a clinical decision framework based on utility analysis to assess prediction models for breast cancer. Our data comes from a retrospective case-control study, collecting Gail model risk factors, genetic variants (single nucleotide polymorphisms-SNPs), and mammographic features in Breast Imaging Reporting and Data System (BI-RADS) lexicon. We first constructed three logistic regression models built on different sets of predictive features: (1) Gail, (2) Gail+SNP, and (3) Gail+SNP+BI-RADS. Then, we generated ROC curves for three models. After we assigned utility values for each category of findings (true negative, false positive, false negative and true positive), we pursued optimal operating points on ROC curves to achieve maximum expected utility (MEU) of breast cancer diagnosis. We used McNemar's test to compare the predictive performance of the three models. We found that SNPs and BI-RADS features augmented the baseline Gail model in terms of the area under ROC curve (AUC) and MEU. SNPs improved sensitivity of the Gail model (0.276 vs. 0.147) and reduced specificity (0.855 vs. 0.912). When additional mammographic features were added, sensitivity increased to 0.457 and specificity to 0.872. SNPs and mammographic features played a significant role in breast cancer risk estimation (p-value < 0.001). Our decision framework comprising utility analysis and McNemar's test provides a novel framework to evaluate prediction models in the realm of radiogenomics.
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Affiliation(s)
- Yirong Wu
- Dept. of Radiology, UW Madison, WI, USA
| | - Jie Liu
- Dept. of Computer Science, UW Madison, WI, USA
| | | | | | - Oguzhan Alagoz
- Dept. of Industrial and Systems Engineering, UW Madison, WI, USA
| | - Peggy Peissig
- Marshfield Clinic Research Foundation, Marshfield, WI, USA
| | - Adedayo A Onitilo
- Marshfield Clinic Research Foundation, Marshfield, WI, USA; Dept. of Hematology/Oncology, Marshfield Clinic Weston Center, Weston, WI, USA
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47
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Abstract
Poised (bivalent) chromatin is defined by the simultaneous presence of histone modifications associated with both gene activation and repression. This epigenetic feature was first observed at promoters of lineage-specific regulatory genes in embryonic stem cells in culture. More recent work has shown that, in vivo, mammalian germ cells maintain poised chromatin at promoters of many genes that regulate somatic development, and that they retain this state from fetal stages through meiosis and gametogenesis. We hypothesize that the poised chromatin state is essential for germ cell identity and function. We propose three roles for poised chromatin in the mammalian germ line: prevention of DNA methylation, maintenance of germ cell identity and preparation for totipotency. We discuss these roles in the context of recently proposed models for germline potency and epigenetic inheritance.
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Affiliation(s)
- Bluma J Lesch
- Whitehead Institute, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - David C Page
- Whitehead Institute, 9 Cambridge Center, Cambridge, MA 02142, USA Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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48
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Soh YQS, Alföldi J, Pyntikova T, Brown LG, Graves T, Minx PJ, Fulton RS, Kremitzki C, Koutseva N, Mueller JL, Rozen S, Hughes JF, Owens E, Womack JE, Murphy WJ, Cao Q, de Jong P, Warren WC, Wilson RK, Skaletsky H, Page DC. Sequencing the mouse Y chromosome reveals convergent gene acquisition and amplification on both sex chromosomes. Cell 2014; 159:800-13. [PMID: 25417157 DOI: 10.1016/j.cell.2014.09.052] [Citation(s) in RCA: 213] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 09/04/2014] [Accepted: 09/22/2014] [Indexed: 01/27/2023]
Abstract
We sequenced the MSY (male-specific region of the Y chromosome) of the C57BL/6J strain of the laboratory mouse Mus musculus. In contrast to theories that Y chromosomes are heterochromatic and gene poor, the mouse MSY is 99.9% euchromatic and contains about 700 protein-coding genes. Only 2% of the MSY derives from the ancestral autosomes that gave rise to the mammalian sex chromosomes. Instead, all but 45 of the MSY's genes belong to three acquired, massively amplified gene families that have no homologs on primate MSYs but do have acquired, amplified homologs on the mouse X chromosome. The complete mouse MSY sequence brings to light dramatic forces in sex chromosome evolution: lineage-specific convergent acquisition and amplification of X-Y gene families, possibly fueled by antagonism between acquired X-Y homologs. The mouse MSY sequence presents opportunities for experimental studies of a sex-specific chromosome in its entirety, in a genetically tractable model organism.
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Affiliation(s)
- Y Q Shirleen Soh
- Whitehead Institute, 9 Cambridge Center, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Jessica Alföldi
- Whitehead Institute, 9 Cambridge Center, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | | | - Laura G Brown
- Whitehead Institute, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
| | - Tina Graves
- The Genome Institute, Washington University School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108, USA
| | - Patrick J Minx
- The Genome Institute, Washington University School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108, USA
| | - Robert S Fulton
- The Genome Institute, Washington University School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108, USA
| | - Colin Kremitzki
- The Genome Institute, Washington University School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108, USA
| | - Natalia Koutseva
- Whitehead Institute, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Jacob L Mueller
- Whitehead Institute, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Steve Rozen
- Whitehead Institute, 9 Cambridge Center, Cambridge, MA 02142, USA
| | | | - Elaine Owens
- College of Veterinary Medicine and Biomedical Sciences, 4458 Texas A&M University, College Station, TX 77843, USA
| | - James E Womack
- College of Veterinary Medicine and Biomedical Sciences, 4458 Texas A&M University, College Station, TX 77843, USA
| | - William J Murphy
- College of Veterinary Medicine and Biomedical Sciences, 4458 Texas A&M University, College Station, TX 77843, USA
| | - Qing Cao
- BACPAC Resources, Children's Hospital Oakland, 747 52nd Street, Oakland, CA 94609, USA
| | - Pieter de Jong
- BACPAC Resources, Children's Hospital Oakland, 747 52nd Street, Oakland, CA 94609, USA
| | - Wesley C Warren
- The Genome Institute, Washington University School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108, USA
| | - Richard K Wilson
- The Genome Institute, Washington University School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108, USA
| | - Helen Skaletsky
- Whitehead Institute, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
| | - David C Page
- Whitehead Institute, 9 Cambridge Center, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA.
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49
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Koenig PA, Nicholls PK, Schmidt FI, Hagiwara M, Maruyama T, Frydman GH, Watson N, Page DC, Ploegh HL. The E2 ubiquitin-conjugating enzyme UBE2J1 is required for spermiogenesis in mice. J Biol Chem 2014; 289:34490-502. [PMID: 25320092 DOI: 10.1074/jbc.m114.604132] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
ER-resident proteins destined for degradation are dislocated into the cytosol by components of the ER quality control machinery for proteasomal degradation. Dislocation substrates are ubiquitylated in the cytosol by E2 ubiquitin-conjugating/E3 ligase complexes. UBE2J1 is one of the well-characterized E2 enzymes that participate in this process. However, the physiological function of Ube2j1 is poorly defined. We find that Ube2j1(-/-) mice have reduced viability and fail to thrive early after birth. Male Ube2j1(-/-) mice are sterile due to a defect in late spermatogenesis. Ultrastructural analysis shows that removal of the cytoplasm is incomplete in Ube2j1(-/-) elongating spermatids, compromising the release of mature elongate spermatids into the lumen of the seminiferous tubule. Our findings identify an essential function for the ubiquitin-proteasome-system in spermiogenesis and define a novel, non-redundant physiological function for the dislocation step of ER quality control.
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Affiliation(s)
- Paul-Albert Koenig
- From the Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
| | - Peter K Nicholls
- From the Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
| | - Florian I Schmidt
- From the Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
| | - Masatoshi Hagiwara
- From the Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
| | - Takeshi Maruyama
- From the Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
| | - Galit H Frydman
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Nicki Watson
- From the Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
| | - David C Page
- From the Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, and Howard Hughes Medical Institute, Cambridge, Massachusetts 02142
| | - Hidde L Ploegh
- From the Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, and
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50
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Bellott DW, Hughes JF, Skaletsky H, Brown LG, Pyntikova T, Cho TJ, Koutseva N, Zaghlul S, Graves T, Rock S, Kremitzki C, Fulton RS, Dugan S, Ding Y, Morton D, Khan Z, Lewis L, Buhay C, Wang Q, Watt J, Holder M, Lee S, Nazareth L, Alföldi J, Rozen S, Muzny DM, Warren WC, Gibbs RA, Wilson RK, Page DC. Erratum: Corrigendum: Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators. Nature 2014. [DOI: 10.1038/nature13719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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