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A SCAN-box containing KRAB-ZFP maintains DNA methylation and inhibits gene expression [RRBS]

ABSTRACT: A SCAN-box containing KRAB-ZFP maintains DNA methylation and inhibits gene expression [RRBS]

PROVIDER: PRJNA970205 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24463500_1.fastq.gz	Fastqsanger.gz
	SRR24463500_2.fastq.gz	Fastqsanger.gz
	SRR24463501_1.fastq.gz	Fastqsanger.gz
	SRR24463501_2.fastq.gz	Fastqsanger.gz
	SRR24463502_1.fastq.gz	Fastqsanger.gz

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A SCAN-box containing KRAB-ZFP maintains DNA methylation and inhibits gene expression [RRBS]

Project description:DNA methylation is one of the most characteristic epigenetic modifications. In mammals, it is involved in a variety of biological processes, including transposable element silencing, gene expression regulation, genomic imprinting, and X chromosome inactivation. Here, through a medium-scale analysis of CpG islands loci coupled with ChIP-seq of Krüppel associated box zinc finger proteins (KRAB-ZFPs), we identified a murine ZFP, ZFP202, that bind to methylated CpG loci. We found that ZFP202 not only maintain CpG loci methylation, but also inhibit downstream gene expression in specific tissues. Disruption of ZFP202 in mouse led to genes upregulation in testis and placenta. Thus, our research identified a novel transcription factor that binding to methylated DNA and maintaining DNA methylation and promoting gene inhibition.

2025-05-01 | GSE231896 | GEO

A SCAN-box containing KRAB-ZFP maintains DNA methylation and inhibits gene expression

Project description:A SCAN-box containing KRAB-ZFP maintains DNA methylation and inhibits gene expression

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A SCAN-box containing KRAB-ZFP maintains DNA methylation and inhibits gene expression [ChIP-seq]

Project description:A SCAN-box containing KRAB-ZFP maintains DNA methylation and inhibits gene expression [ChIP-seq]

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A SCAN-box containing KRAB-ZFP maintains DNA methylation and inhibits gene expression [MeDIP-seq]

Project description:A SCAN-box containing KRAB-ZFP maintains DNA methylation and inhibits gene expression [MeDIP-seq]

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A SCAN-box containing KRAB-ZFP maintains DNA methylation and inhibits gene expression [RNA-seq]

Project description:A SCAN-box containing KRAB-ZFP maintains DNA methylation and inhibits gene expression [RNA-seq]

| PRJNA970204 | ENA

A SCAN-box containing KRAB-ZFP maintains DNA methylation and inhibits gene expression [MeDIP-seq]

2025-05-01 | GSE231893 | GEO

A SCAN-box containing KRAB-ZFP maintains DNA methylation and inhibits gene expression [ChIP-seq]

2025-05-01 | GSE231892 | GEO

A SCAN-box containing KRAB-ZFP maintains DNA methylation and inhibits gene expression [RNA-seq]

2025-05-01 | GSE231897 | GEO

Genome-wide analysis of differential transcription in KRAB-ZFP cluster knock-out ES cells and mouse tissues

Project description:Mammalian genomes encode several hundred Krüppel-associated box zinc finger proteins (KRAB-ZFPs) that bind DNA in a sequence-specific manner through tandem arrays of C2H2-type zinc fingers and repress transcription via KRAB-dependent recruitment of the silencing cofactor KAP1. The KRAB-ZFP family rapidly amplified and diversified in mammals by segmental gene duplications, mutations, and zinc finger rearrangements likely in response to continued transposable element invasions, but the biological functions and in vivo requirement of these proteins has gone largely unexplored. We determined the genomic binding sites of 61 murine KRAB-ZFPs and genetically deleted five large KRAB-ZFP gene clusters encoding more than 100 of the approximately 360 mouse KRAB-ZFPs. We demonstrate that most KRAB-ZFPs bind to specific retrotransposon families and that many of these retrotransposons are transcriptionally activated in KRAB-ZFP cluster KO ESCs, licensing retrotransposon-derived enhancers to activate nearby genes.

2019-06-27 | GSE115288 | GEO

Transposable elements and their KRAB-ZFP controllers regulate gene expression in adult tissues

Project description:The tetrapod-restricted KRAB-containing zinc finger proteins (KRAB-ZFPs) are essential early embryonic controllers of transposable elements (TEs), which they repress via their cofactor KAP1 and associated effectors through histone and DNA methylation, a process thought to result in irreversible silencing. Using a target-centered functional screen, we matched several murine TEs with their cognate KRAB-ZFP. This revealed an unexpected level of granularity in their interactions, with KRAB-ZFPs recognizing TEs from more than one subfamily, TEs recruiting more than one KRAB-ZFP, and spatially and temporally differential KRAB-ZFP-mediated regulation of TEs and nearby genes. Most importantly, we discovered that the KRAB/KAP1 system controls TEs in adult tissues, in cell culture and in vivo, where they partner up to regulate the expression of cellular genes. Therefore, TEs and KRAB-ZFPs establish widely active transcription networks that regulate not only development but probably also many physiological events. Given the high degree of species-specificity of both TEs and KRAB-ZFPs, these results have important implications for studying and understanding the biology of higher vertebrates, including humans. Analysis of transcriptional profiles of KAP1 or ZFP932/Gm15446 KO cells or tissues, and ZFP932 and Gm15446 ChIPseq in murine ES and C2C12 cells.

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