“Digital chromosome banding”: A scRNA-seq-based chromosome banding method distinguishes real and pseudo sex body
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE233871 | GEO | 2026/08/12
REPOSITORIES: GEO
Similar Datasets
Project description:During spermatogenesis, the unsynapsed XY chromosomes undergo meiotic sex chromosome inactivation (MSCI) and form a heterochromatic XY body. Defects in MSCI lead to meiotic arrest and male infertility. Although DNA damage response (DDR) factors are established as key initiators of MSCI, how transcriptional silencing is subsequently achieved remains elusive. Here, we identify the nucleolar components NPM1, SENP3, and rRNA as essential downstream effectors of DDR signaling in MSCI. During pachytene, these components migrate to and transiently cover the XY body during MSCI establishment, before becoming restricted to a corner of the XY body. Genetic deletion of Npm1 or Senp3, or inhibition of rRNA transcription severely impairs MSCI. Mechanistically, SENP3-mediated deSUMOylation of NPM1 promotes its interaction with rRNA, enabling liquid-liquid phase separation, via which they exclude Pol II from the XY body. Together, these data reveal a previously unrecognized role of nucleolar components in the transcriptional regulation of MSCI in mammalian spermatogenesis.
2026-02-11 | GSE196779 | GEO
Project description:Meiotic progression in mammals is governed by tightly coordinated transcriptional programs and surveillance mechanisms that ensure the successful pairing, synapsis, and segregation of homologous chromosomes. In spermatocytes, homolog pairing is safeguarded by the pachytene checkpoint, whose mechanism is critically involves meiotic sex chromosome inactivation (MSCI), a silencing mechanism that targets the largely unsynapsed X and Y chromosomes during pachytene. HORMAD2, a HORMA domain-containing protein, plays a key role in MSCI. Although in vitro studies have implicated SYCP2 in recruiting HORMAD proteins to chromosome axes, the mechanism and physiological relevance of this interaction during meiosis has remained unclear. To gain transcriptome-level insights into how loss of HORMAD2 axial recruitment affects meiotic progression and sex chromosome regulation, we performed single-cell RNA sequencing (scRNA-seq) of testicular cell suspensions of adult wild-type and Hormad2-/-mice as well as mice where SYCP2 lacked the region that is predicted to bind HORMAD2 (Sycp2e16/e16 mutant). These datasets allowed us to resolve 17 distinct germ cell states spanning the full course of spermatogenesis. We observed that, unlike wild-type cells which transcriptionally progressed into mid-pachytene and beyond, neither Sycp2e16/e16 nor Hormad2-/- spermatocytes progressed beyond an early pachytene-like transcriptional state. We also saw clear evidence of impaired meiotic sex chromosome inactivation (MSCI) in the mutants. Specifically, sex-linked gene expression abnormally persisted in the mutants resulting in overexpression of Y-linked genes Zfy1 and Zfy2, whose high expression induces spermatocyte apoptosis in mid pachytene. Related experiment can be found in S-BSST1926
2026-06-18 | E-MTAB-16317 | biostudies-arrayexpress
Project description:In mammals and several other taxa, the ability of males to cope with the limited synapsis of the X and Y chromosomes during prophase I of meiosis relies on the process of meiotic sex chromosome inactivation (MSCI). Components of the somatic DNA damage response machinery, including ATR, TOPBP1, MDC1 and BRCA1 play key roles in MSCI, although how they establish XY silencing remains incompletely understood. In particular, it remains unclear how DDR factors coordinate XY silencing with DNA repair, chromosome synapsis and the formation of the sex body, a distinct phase-separated sub-nuclear structure formed during prophase I to house the unsynapsed XY bivalent. Here we report a mutant mouse (Topbp1B5/B5), harboring mutations in the BRCT5 domain of Topbp1, that shows impaired XY silencing but grossly normal sex body formation. While Topbp1B5/B5 mice are viable, without detectable somatic defects, males are completely infertile. Distinct from mice lacking ATR or TOPBP1 specifically during meiosis, Topbp1B5/B5 males exhibit normal chromosome synapsis and canonical markers of DNA repair in early prophase I. ATR signaling is mostly intact in Topbp1B5/B5 spermatocytes, although specific ATR-dependent events are disrupted, including localization of the RNA:DNA helicase Senataxin to chromatin loops of the XY. Strikingly, while Topbp1B5/B5 spermatocytes are able to initiate MSCI the completion of gene silencing is defective, with a subset of X chromosome genes displaying distinct patterns of transcriptional deregulation. These findings suggest a non-canonical role for the ATR-TOPBP1 signaling axis in XY silencing dynamics at advanced stages in pachynema. This is the first DDR mutant that separates XY silencing from sex body formation, as well as TOPBP1’s role in spermatogenesis from its roles in organismal viability.
2024-02-09 | PXD042199 | Pride
Project description:During meiosis, gene expression is silenced in aberrantly unsynapsed chromatin and in heterogametic sex chromosomes. Initiation of sex chromosome silencing is disrupted in meiocytes with sex chromosome-autosome translocations. To determine whether this is due to aberrant synapsis or loss of continuity of sex chromosomes, we engineered Caenorhabditis elegans with non-translocated, bisected X chromosomes. In early meiocytes of mutant males and hermaphrodites, X segments were enriched with euchromatin assembly markers and active RNA polymerase II staining, indicating active transcription. Analysis of RNA-seq data showed that genes from the X chromosome were upregulated in gonads of mutant worms. Contrary to previous models, which predicted that any unsynapsed chromatin is silenced during meiosis, our data indicate that unsynapsed X segments are transcribed. Therefore, our results suggest that sex chromosome chromatin has a unique character that facilitates its meiotic expression when its continuity is lost, regardless of whether or not it is synapsed.
2021-05-24 | GSE171938 | GEO
Project description:Balanced constitutional reciprocal translocations are the most common structural chromosomal rearrangements identified in man and pigs. Carriers are generally phenotypically normal, but such rearrangements frequently lead to reproductive disorders. In reciprocal translocation heterozygotes, the homologous regions of the normal and derivative chromosomes involved in the rearrangement pair during the prophase of the first meiotic division, thanks to the synaptonemal complex (SC), and form a particular structure called quadrivalent. In some cases, chromosomal regions (within the quadrivalent) remain unsynapsed, especially around the breakpoints, which may trigger meiosis checkpoints leading to spermatogenesis arrest at the pachytene stage. Several hypotheses have been proposed to explain such effects of pairing failure on gametogenesis. The first one is an altered transcription of the genes located on the unpaired segments. Indeed, studies conducted in mice revealed a transcriptional repression of unpaired regions by a specific mechanism called “Meiotic Silencing of Unsynapsed Chromatin” (MSUC) in individuals with a partial or total spermatogenesis arrest (Turner et al., 2005). If some genes necessary for the proper course of meiosis are located in such unsynapsed genomic regions, MSUC may result in an arrest of the meiotic division. Secondly, associations between the “quadrivalent” and the XY bivalent which is transcriptionally silenced by a phenomenon known as meiotic sex chromosome inactivation (MSCI, (Turner, 2007) were also observed in individuals with altered semen parameters (azoospermic or oligospemic) (Oliver-Bonet et al., 2005; Sciurano et al., 2007a, 2012). Such an association could result in a partial reactivation of the XY body (XYB) leading to the expression of some genes located on the X chromosome (Lifschytz and Lindsley, 1972), or result in the spreading of the XYB inactivation towards the autosomal segments attached to the XYB, without reactivation of the latter (Jaafar et al., 1993). Beyond the potential spermatogenesis failure mentioned above, reciprocal translocations are systematically responsible for the production of genetically unbalanced gametes. Here we report the detailed analysis of the whole meiotic process (from spermatocytes to spermatozoa) in the case of a constitutional balanced reciprocal translocation responsible for severe oligoasthenoteratospermia.
2016-06-30 | GSE80693 | GEO
Project description:Balanced constitutional reciprocal translocations are the most common structural chromosomal rearrangements identiï¬ed in man and pigs. Carriers are generally phenotypically normal, but such rearrangements frequently lead to reproductive disorders. In reciprocal translocation heterozygotes, the homologous regions of the normal and derivative chromosomes involved in the rearrangement pair during the prophase of the first meiotic division, thanks to the synaptonemal complex (SC), and form a particular structure called quadrivalent. In some cases, chromosomal regions (within the quadrivalent) remain unsynapsed, especially around the breakpoints, which may trigger meiosis checkpoints leading to spermatogenesis arrest at the pachytene stage. Several hypotheses have been proposed to explain such effects of pairing failure on gametogenesis. The first one is an altered transcription of the genes located on the unpaired segments. Indeed, studies conducted in mice revealed a transcriptional repression of unpaired regions by a specific mechanism called âMeiotic Silencing of Unsynapsed Chromatinâ (MSUC) in individuals with a partial or total spermatogenesis arrest (Turner et al., 2005). If some genes necessary for the proper course of meiosis are located in such unsynapsed genomic regions, MSUC may result in an arrest of the meiotic division. Secondly, associations between the âquadrivalentâ and the XY bivalent which is transcriptionally silenced by a phenomenon known as meiotic sex chromosome inactivation (MSCI, (Turner, 2007) were also observed in individuals with altered semen parameters (azoospermic or oligospemic) (Oliver-Bonet et al., 2005; Sciurano et al., 2007a, 2012). Such an association could result in a partial reactivation of the XY body (XYB) leading to the expression of some genes located on the X chromosome (Lifschytz and Lindsley, 1972), or result in the spreading of the XYB inactivation towards the autosomal segments attached to the XYB, without reactivation of the latter (Jaafar et al., 1993). Beyond the potential spermatogenesis failure mentioned above, reciprocal translocations are systematically responsible for the production of genetically unbalanced gametes. Here we report the detailed analysis of the whole meiotic process (from spermatocytes to spermatozoa) in the case of a constitutional balanced reciprocal translocation responsible for severe oligoasthenoteratospermia. Total RNA was extracted in 3 replicates from testicular biopsies control animals, from testicular biopsy of an oligospermic boar and from testicular biopsy of a severe oligo-astheno-teratospermic boar carrier of the trcp(1;14) reciprocal translocation.
2016-06-30 | E-GEOD-80693 | biostudies-arrayexpress
Project description:Meiotic sex chromosome inactivation (MSCI) is an essential process in the male germline. While genetic experiments have established that the DNA damage response (DDR) pathway directs MSCI, due to limitations to the experimental systems available, mechanisms underlying MSCI remain largely unknown. Here we establish a system to study MSCI ex vivo, based on a short-term culture method, and demonstrate that active DDR signaling is required both to initiate and maintain MSCI via a dynamic and reversible process. DDR-directed MSCI follows two layers of modifications: active DDR-dependent reversible processes and irreversible histone post-translational modifications. Further, the DDR initiates MSCI independent of the downstream repressive histone mark H3K9 trimethylation (H3K9me3), thereby demonstrating that active DDR signaling is the primary mechanism of silencing in MSCI. By unveiling the dynamic nature of MSCI, and its governance by active DDR signals, our study highlights the sex chromosomes as an active signaling hub in meiosis.
2022-10-05 | GSE211519 | GEO
Project description:Meiotic sex chromosome inactivation (MSCI) is an essential event in meiotic progression in mammalian spermatogenesis. We found that La Ribonucleoprotein 7 (LARP7) is involved in MSCI. LARP7 plays a role in fetal germ cells to promote their proliferation, but is once abolished in postnatal gonocytes and re-expresses in spermatocytes at the onset of meiosis. In spermatocytes, LARP7 localizes to the XY body, a compartmentalized chromatin domain on sex chromosomes. This study aimed to elucidate a possible function of LARP7 in the XY body by using germline-specific Larp7-deficient mice.
2024-10-01 | GSE261526 | GEO
Project description:Argonaute proteins (AGO) are best known for their role in microRNA-mediated post-transcriptional gene silencing. Here, we demonstrate that AGO3 and AGO4, but not AGO2, localize to the sex chromatin of pachytene spermatocytes, where they are required for the transcriptional silencing of XY-linked genes that characterizes Meiotic Sex Chromosome Inactivation (MSCI). Previous findings showed that deletion of Ago4 (Ago4-/-) mildly impairs MSCI and normal spermatozoa production. By contrast, loss of Ago3 (Ago3-/-) does not produce these defects, while combined deletion of Ago1, Ago3, and Ago4 (Ago413-/-) leads to severely reduced fertility, accompanied by disrupted autosomal and sex chromosome gene regulation and altered chromatin accessibility in spermatocytes. In Ago413-/- mice, premature overexpression of spermiogenesis genes during prophase I results in reduced sperm production, abnormal sperm morphology, and impaired fertilization capacity. Together, AGO3 and AGO4 act during prophase I to ensure the timely expression of meiosis-related genes during prophase I while maintaining repression of spermiogenesis-associated genes. These results indicate that AGO3 and AGO4 act in a coordinated fashion in the male germline to orchestrate cell progression in spermatogenesis through temporal regulation of autosomal and sex chromosome genes.
2026-06-22 | GSE332917 | GEO
Project description:The switch from mitosis to meiosis is a major transition that takes place during germ cell development. The precise sequence and the different gene expression programs activated during this process are only partly known. Here, we applied single-cell mRNA sequencing to interrogate the transcriptional changes that occur during the early steps of male germ cell differentiation. We isolated single cells from testes using a Dazl-GFP reporter mouse, which allowed us to focus on germ cells undergoing the mitotic to meiotic transition. We identified 4 distinct meiotic stages with unique transcriptome profiles and reconstructed the timeline of the meiotic entry in silico, from spermatogonia up to the pachytene stage, identifying transcriptional changes with an unprecedented resolution. This allowed us to characterize 3 major transitions in the meiotic prophase 1 of the male germline: meiotic entry, the meiotic sex chromosome inactivation (MSCI), and concomitant pachytene transcriptional activation. Meiotic entry is initiated following the downregulation of a tightly connected set of pluripotency factors and accompanied by a global transcriptional silencing. In contrast, during subsequent sex chromosome inactivation at the zygotene stage, gene silencing proceeds in a defined order, related to gene function.
2021-05-22 | GSE114788 | GEO