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Meiotic cohesin RAD21L shapes 3D genome structure and transcription in the male germline [scRNA-seq]

ABSTRACT: The unique genome organization that chromosome acquired during meiosis is essential for fertility. Yet, the functional implications of the fine-scale spatial 3D genome folding during this process remain poorly understood. Here, we study the impact of RAD21L depletion, a meiosis-specific cohesin subunit, on the 3D genome architecture and gene expression in the male germ line. Employing fluorescence activated cell sorting, chromosome conformation capture and single cell RNA-seq, we found that the absence of RAD21L impairs chromatin organization during meiosis, leading to pronounced alterations of genome compartmentalization and inter- and intra-chromosomal interactions. This conspicuous genome remodelling also disrupts bouquet formation, resulting in increased telomeric interactions between heterologous chromosomes in primary spermatocytes. Importantly, genome remodelling was accompanied by detectable transcriptional dysregulation in spermatogonia and primary spermatocytes, mainly affecting sex chromosomes. Overall, we demonstrate how cohesin shapes the 3D genome reorganization genome-wide during spermatogenesis and influences its transcriptional landscape.

ORGANISM(S): Mus musculus

PROVIDER: GSE297601 | GEO | 2025/09/01

REPOSITORIES: GEO

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Meiotic cohesin RAD21L shapes 3D genome structure and transcription in the male germline [HiC]

Project description:The unique genome organization that chromosome acquired during meiosis is essential for fertility. Yet, the functional implications of the fine-scale spatial 3D genome folding during this process remain poorly understood. Here, we study the impact of RAD21L depletion, a meiosis-specific cohesin subunit, on the 3D genome architecture and gene expression in the male germ line. Employing fluorescence activated cell sorting, chromosome conformation capture and single cell RNA-seq, we found that the absence of RAD21L impairs chromatin organization during meiosis, leading to pronounced alterations of genome compartmentalization and inter- and intra-chromosomal interactions. This conspicuous genome remodelling also disrupts bouquet formation, resulting in increased telomeric interactions between heterologous chromosomes in primary spermatocytes. Importantly, genome remodelling was accompanied by detectable transcriptional dysregulation in spermatogonia and primary spermatocytes, mainly affecting sex chromosomes. Overall, we demonstrate how cohesin shapes the 3D genome reorganization genome-wide during spermatogenesis and influences its transcriptional landscape.

2025-09-01 | GSE297600 | GEO

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CTCF-mediated 3D chromatin predetermines the gene expression program in the male germline (RNA-Seq)

Project description:Spermatogenesis is a unidirectional differentiation process that generates haploid sperm, but how the gene expression program that directs this process is established is largely unknown. Here we determine the high-resolution 3D chromatin architecture of male germ cells during spermatogenesis and show that CTCF-mediated 3D chromatin predetermines the gene expression program required for spermatogenesis. In undifferentiated spermatogonia, CTCF-mediated chromatin interactions between meiosis-specific super-enhancers (SE) loci and target genes precede activation of meiosis-specific SEs on autosomes. These meiotic SE recruit the master transcription factor A-MYB in meiotic spermatocytes, which strengthens their 3D contacts and instructs a burst of meiotic gene expression. We also find that at the mitosis-to-meiosis transition, the germline-specific Polycomb protein SCML2 resolves chromatin loops that are specific to mitotic spermatogonia. Moreover, SCML2 and A-MYB establish the unique 3D chromatin organization of sex chromosomes during meiotic sex chromosome inactivation. We propose that CTCF-mediated 3D chromatin organization enforces epigenetic priming that directs unidirectional differentiation, thereby determining the cellular identity of the male germline.

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CTCF-mediated 3D chromatin predetermines the gene expression program in the male germline (Hi-C)

Project description:Spermatogenesis is a unidirectional differentiation process to produce haploid sperm. However, it remains largely unknown how the gene expression program is determined to direct a unidirectional differentiation. Here we unveil the high-resolution 3D chromatin architecture of male germ cells and show that CTCF-mediated 3D chromatin predetermines the gene expression program required for spermatogenesis. At the mitosis-to-meiosis transition, the germline-specific Polycomb protein SCML2 resolves chromatin loops specific to mitotic spermatogonia. On autosomes, CTCF-mediated 3D chromatin manifests the structural feature of meiosis-specific super-enhancer (meiotic SE) loci already in undifferentiated spermatogonia. In meiotic spermatocytes, the master transcription factor A-MYB is recruited to these meiotic SE loci to strengthen their 3D contacts to instruct the burst of meiotic gene expression. Further, SCML2 and A-MYB establish unique 3D chromatin of the sex chromosomes in meiotic sex chromosome inactivation. We propose that CTCF-mediated 3D chromatin underlines epigenetic priming to direct unidirectional differentiation, thereby determining the cellular identity of the male germline.

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