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Estill MS, Hauser R, Krawetz SA. RNA element discovery from germ cell to blastocyst. Nucleic Acids Res 2019; 47:2263-2275. [PMID: 30576549 PMCID: PMC6411832 DOI: 10.1093/nar/gky1223] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 10/31/2018] [Accepted: 11/24/2018] [Indexed: 12/19/2022] Open
Abstract
Recent studies have shown that tissue-specific transcriptomes contain multiple types of RNAs that are transcribed from intronic and intergenic sequences. The current study presents a tool for the discovery of transcribed, unannotated sequence elements from RNA-seq libraries. This RNA Element (RE) discovery algorithm (REDa) was applied to a spectrum of tissues and cells representing germline, embryonic, and somatic tissues and examined as a function of differentiation through the first set of cell divisions of human development. This highlighted extensive transcription throughout the genome, yielding previously unidentified human spermatogenic RNAs. Both exonic and novel X-chromosome REs were subject to robust meiotic sex chromosome inactivation, although an extensive de-repression occurred in the post-meiotic stages of spermatogenesis. Surprisingly, 2.4% of the 10,395 X chromosome exonic REs were present in mature sperm. Transcribed genomic repetitive sequences, including simple centromeric repeats, HERVE and HSAT1, were also shown to be associated with RE expression during spermatogenesis. These results suggest that pervasive intergenic repetitive sequence expression during human spermatogenesis may play a role in regulating chromatin dynamics. Repetitive REs switching repeat classes during differentiation upon fertilization and embryonic genome activation was evident.
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MESH Headings
- Algorithms
- Blastocyst/cytology
- Blastocyst/metabolism
- Cell Differentiation
- Cell Line
- Chromatin/genetics
- Chromatin/metabolism
- Chromosomes, Human, X/genetics
- Embryonic Development/genetics
- Exons/genetics
- Female
- Fertilization
- Gene Expression Regulation, Developmental
- Genomics
- Humans
- Liver/cytology
- Liver/metabolism
- Male
- Meiosis/genetics
- Oocytes/cytology
- Oocytes/metabolism
- Poly A/analysis
- Poly A/genetics
- Poly A/isolation & purification
- RNA, Messenger/analysis
- RNA, Messenger/genetics
- RNA, Messenger/isolation & purification
- Regulatory Sequences, Ribonucleic Acid/genetics
- Repetitive Sequences, Nucleic Acid
- Sequence Analysis, RNA
- Spermatogenesis/genetics
- Spermatozoa/cytology
- Spermatozoa/metabolism
- Transcription, Genetic
- X Chromosome Inactivation
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Affiliation(s)
- Molly S Estill
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
| | - Russ Hauser
- Vincent Memorial Obstetrics and Gynecology Service, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Departments of Environmental Health and Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Stephen A Krawetz
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48201, USA
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Mulugeta E, Wassenaar E, Sleddens-Linkels E, van IJcken WFJ, Heard E, Grootegoed JA, Just W, Gribnau J, Baarends WM. Genomes of Ellobius species provide insight into the evolutionary dynamics of mammalian sex chromosomes. Genome Res 2016; 26:1202-10. [PMID: 27510564 PMCID: PMC5052041 DOI: 10.1101/gr.201665.115] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 07/11/2016] [Indexed: 11/24/2022]
Abstract
The X and Y sex chromosomes of placental mammals show hallmarks of a tumultuous evolutionary past. The X Chromosome has a rich and conserved gene content, while the Y Chromosome has lost most of its genes. In the Transcaucasian mole vole Ellobius lutescens, the Y Chromosome including Sry has been lost, and both females and males have a 17,X diploid karyotype. Similarly, the closely related Ellobius talpinus, has a 54,XX karyotype in both females and males. Here, we report the sequencing and assembly of the E. lutescens and E. talpinus genomes. The results indicate that the loss of the Y Chromosome in E. lutescens and E. talpinus occurred in two independent events. Four functional homologs of mouse Y-Chromosomal genes were detected in both female and male E. lutescens, of which three were also detected in the E. talpinus genome. One of these is Eif2s3y, known as the only Y-derived gene that is crucial for successful male meiosis. Female and male E. lutescens can carry one and the same X Chromosome with a largely conserved gene content, including all genes known to function in X Chromosome inactivation. The availability of the genomes of these mole vole species provides unique models to study the dynamics of sex chromosome evolution.
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Affiliation(s)
- Eskeatnaf Mulugeta
- Department of Developmental Biology, Erasmus MC, 3015CN, Rotterdam, The Netherlands; Institut Curie, Genetics and Developmental Biology Unit, 75248, Paris, France
| | - Evelyne Wassenaar
- Department of Developmental Biology, Erasmus MC, 3015CN, Rotterdam, The Netherlands
| | | | | | - Edith Heard
- Institut Curie, Genetics and Developmental Biology Unit, 75248, Paris, France
| | - J Anton Grootegoed
- Department of Developmental Biology, Erasmus MC, 3015CN, Rotterdam, The Netherlands
| | - Walter Just
- Institute of Human Genetics, University of Ulm, 89081, Ulm, Germany
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus MC, 3015CN, Rotterdam, The Netherlands
| | - Willy M Baarends
- Department of Developmental Biology, Erasmus MC, 3015CN, Rotterdam, The Netherlands
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Federici F, Mulugeta E, Schoenmakers S, Wassenaar E, Hoogerbrugge JW, van der Heijden GW, van Cappellen WA, Slotman JA, van IJcken WFJ, Laven JSE, Grootegoed JA, Baarends WM. Incomplete meiotic sex chromosome inactivation in the domestic dog. BMC Genomics 2015; 16:291. [PMID: 25884295 PMCID: PMC4399420 DOI: 10.1186/s12864-015-1501-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/30/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In mammalian meiotic prophase, homologous chromosome recognition is aided by formation and repair of programmed DNA double-strand breaks (DSBs). Subsequently, stable associations form through homologous chromosome synapsis. In male mouse meiosis, the largely heterologous X and Y chromosomes synapse only in their short pseudoautosomal regions (PARs), and DSBs persist along the unsynapsed non-homologous arms of these sex chromosomes. Asynapsis of these arms and the persistent DSBs then trigger transcriptional silencing through meiotic sex chromosome inactivation (MSCI), resulting in formation of the XY body. This inactive state is partially maintained in post-meiotic haploid spermatids (postmeiotic sex chromatin repression, PSCR). For the human, establishment of MSCI and PSCR have also been reported, but X-linked gene silencing appears to be more variable compared to mouse. To gain more insight into the regulation and significance of MSCI and PSCR among different eutherian species, we have performed a global analysis of XY pairing dynamics, DSB repair, MSCI and PSCR in the domestic dog (Canis lupus familiaris), for which the complete genome sequence has recently become available, allowing a thorough comparative analyses. RESULTS In addition to PAR synapsis between X and Y, we observed extensive self-synapsis of part of the dog X chromosome, and rapid loss of known markers of DSB repair from that part of the X. Sequencing of RNA from purified spermatocytes and spermatids revealed establishment of MSCI. However, the self-synapsing region of the X displayed higher X-linked gene expression compared to the unsynapsed area in spermatocytes, and was post-meiotically reactivated in spermatids. In contrast, genes in the PAR, which are expected to escape MSCI, were expressed at very low levels in both spermatocytes and spermatids. Our comparative analysis was then used to identify two X-linked genes that may escape MSCI in spermatocytes, and 21 that are specifically re-activated in spermatids of human, mouse and dog. CONCLUSIONS Our data indicate that MSCI is incomplete in the dog. This may be partially explained by extensive, but transient, self-synapsis of the X chromosome, in association with rapid completion of meiotic DSB repair. In addition, our comparative analysis identifies novel candidate male fertility genes.
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Affiliation(s)
- Federica Federici
- Department of Developmental Biology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Eskeatnaf Mulugeta
- Department of Developmental Biology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands. .,Present address: Institut Curie, Genetics and Developmental Biology, Unit 11 et 13 rue Pierre et Marie Curie, 75248, Paris, Cedex 05, France.
| | - Sam Schoenmakers
- Department of Developmental Biology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands. .,Department of Obstetrics and Gynaecology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Evelyne Wassenaar
- Department of Developmental Biology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Jos W Hoogerbrugge
- Department of Developmental Biology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Godfried W van der Heijden
- Department of Developmental Biology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands. .,Department of Obstetrics and Gynaecology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Wiggert A van Cappellen
- Department of Pathology, Erasmus Optical Imaging Centre, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Johan A Slotman
- Department of Pathology, Erasmus Optical Imaging Centre, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Wilfred F J van IJcken
- Erasmus Center for Biomics, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.
| | - Joop S E Laven
- Department of Obstetrics and Gynaecology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
| | - J Anton Grootegoed
- Department of Developmental Biology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Willy M Baarends
- Department of Developmental Biology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
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Sin HS, Ichijima Y, Koh E, Namiki M, Namekawa SH. Human postmeiotic sex chromatin and its impact on sex chromosome evolution. Genome Res 2012; 22:827-36. [PMID: 22375025 PMCID: PMC3337429 DOI: 10.1101/gr.135046.111] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Sex chromosome inactivation is essential epigenetic programming in male germ cells. However, it remains largely unclear how epigenetic silencing of sex chromosomes impacts the evolution of the mammalian genome. Here we demonstrate that male sex chromosome inactivation is highly conserved between humans and mice and has an impact on the genetic evolution of human sex chromosomes. We show that, in humans, sex chromosome inactivation established during meiosis is maintained into spermatids with the silent compartment postmeiotic sex chromatin (PMSC). Human PMSC is illuminated with epigenetic modifications such as trimethylated lysine 9 of histone H3 and heterochromatin proteins CBX1 and CBX3, which implicate a conserved mechanism underlying the maintenance of sex chromosome inactivation in mammals. Furthermore, our analyses suggest that male sex chromosome inactivation has impacted multiple aspects of the evolutionary history of mammalian sex chromosomes: amplification of copy number, retrotranspositions, acquisition of de novo genes, and acquisition of different expression profiles. Most strikingly, profiles of escape genes from postmeiotic silencing diverge significantly between humans and mice. Escape genes exhibit higher rates of amino acid changes compared with non-escape genes, suggesting that they are beneficial for reproductive fitness and may allow mammals to cope with conserved postmeiotic silencing during the evolutionary past. Taken together, we propose that the epigenetic silencing mechanism impacts the genetic evolution of sex chromosomes and contributed to speciation and reproductive diversity in mammals.
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Affiliation(s)
- Ho-Su Sin
- Division of Reproductive Sciences, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
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de Vries M, Vosters S, Merkx G, D'Hauwers K, Wansink DG, Ramos L, de Boer P. Human male meiotic sex chromosome inactivation. PLoS One 2012; 7:e31485. [PMID: 22355370 PMCID: PMC3280304 DOI: 10.1371/journal.pone.0031485] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 01/09/2012] [Indexed: 11/30/2022] Open
Abstract
In mammalian male gametogenesis the sex chromosomes are distinctive in both gene activity and epigenetic strategy. At first meiotic prophase the heteromorphic X and Y chromosomes are placed in a separate chromatin domain called the XY body. In this process, X,Y chromatin becomes highly phosphorylated at S139 of H2AX leading to the repression of gonosomal genes, a process known as meiotic sex chromosome inactivation (MSCI), which has been studied best in mice. Post-meiotically this repression is largely maintained. Disturbance of MSCI in mice leads to harmful X,Y gene expression, eventuating in spermatocyte death and sperm heterogeneity. Sperm heterogeneity is a characteristic of the human male. For this reason we were interested in the efficiency of MSCI in human primary spermatocytes. We investigated MSCI in pachytene spermatocytes of seven probands: four infertile men and three fertile controls, using direct and indirect in situ methods. A considerable degree of variation in the degree of MSCI was detected, both between and within probands. Moreover, in post-meiotic stages this variation was observed as well, indicating survival of spermatocytes with incompletely inactivated sex chromosomes. Furthermore, we investigated the presence of H3K9me3 posttranslational modifications on the X and Y chromatin. Contrary to constitutive centromeric heterochromatin, this heterochromatin marker did not specifically accumulate on the XY body, with the exception of the heterochromatic part of the Y chromosome. This may reflect the lower degree of MSCI in man compared to mouse. These results point at relaxation of MSCI, which can be explained by genetic changes in sex chromosome composition during evolution and candidates as a mechanism behind human sperm heterogeneity.
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Affiliation(s)
- Marieke de Vries
- Department of Obstetrics and Gynaecology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Sanne Vosters
- Department of Obstetrics and Gynaecology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Gerard Merkx
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Kathleen D'Hauwers
- Department of Urology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Derick G. Wansink
- Department of Cell Biology, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Liliana Ramos
- Department of Obstetrics and Gynaecology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Peter de Boer
- Department of Obstetrics and Gynaecology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
- * E-mail:
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