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

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

PROVIDER: PRJNA970204 | ENA |

REPOSITORIES: ENA

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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 [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

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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 [RNA-seq]

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

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

2025-05-01 | GSE231898 | 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.

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