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CTCF-mediated 3D chromatin predetermines the gene expression program in the male germline

ABSTRACT: CTCF-mediated 3D chromatin predetermines the gene expression program in the male germline

PROVIDER: PRJNA1024383 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26287827_1.fastq.gz	Fastqsanger.gz
	SRR26287827_2.fastq.gz	Fastqsanger.gz
	SRR26287828_1.fastq.gz	Fastqsanger.gz
	SRR26287828_2.fastq.gz	Fastqsanger.gz
	SRR26287829_1.fastq.gz	Fastqsanger.gz

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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.

2024-12-13 | GSE244676 | GEO

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

2024-12-13 | GSE244675 | GEO

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.

2024-12-13 | GSE272432 | GEO

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

Project description:CTCF-mediated 3D chromatin predetermines the gene expression program in the male germline (ChIP-seq)

| PRJNA1024376 | ENA

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

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

| PRJNA1024380 | ENA

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

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

| PRJNA1136865 | ENA

CTCF-mediated 3D chromatin predetermines the gene expression program in the male germline.

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 contacts on autosomes pre-establish meiosis-specific super-enhancers (SE). 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.

| S-EPMC10705413 | biostudies-literature

CTCF-mediated 3D chromatin predetermines the gene expression program in the male germline

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-12-11 | GSE244681 | GEO

The mitotic STAG3-cohesin defines male germline nucleome

Project description:Cohesin is a tetrameric protein complex with a ring-like structure that entraps DNA to ensure sister chromatid cohesion and higher-order chromatin organization. The mechanism by which cohesin regulates chromatin structure and gene expression remains a fundamental question. In multicellular organisms, germ cells are unique in that they tailor chromatin organization toward generating totipotency. As part of this program, spermatogonial stem cells (SSCs) in mammals, the source for male gametes, acquire distinctive chromatin organization with exceptionally weak insulation, but the underlying mechanism is unknown. Here, we show that STAG3, exclusively known to form meiotic cohesins, contributes to a mitotic cohesin defining nucleome programming during male germline development. With slower loop extrusion and shorter chromatin residence, STAG3–cohesin attenuates topologically associating domains (TADs) demarcated by CCCTC-binding factor (CTCF), re-wires both enhancer–promoter and Polycomb-mediated repressive interactions, and creates finer and strengthened compartments, establishing a characteristic SSC nucleome. Moreover, STAG3–cohesin controls the balance between SSC self-renewal and differentiation for spermatogenesis. Notably, mitotic STAG3–cohesin is also highly expressed in human B cells and potentially involved in B-cell malignancies. Thus, mitotic STAG3–cohesin with its unique loop extrusion property elucidates a principle for male germline nucleome programming and, more broadly, may contribute to human malignancy.

2025-07-07 | PXD045854 | JPOST Repository

SNP array data for Wilms Tumor harboring de novo germline mutation in CTCF

Project description:SNP array was combined with next generation sequencing (NGS) to identify a unique de novo germline mutation in CTCF that became homozygous in the tumor. SNP array shows an LOH through chr16q where CTCF is located.

2022-01-11 | GSE193017 | GEO

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