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ZNF676 and ZNF728 ChIP-exo in HEK293T cells

ABSTRACT: Genome-wide binding profile of the primate-specific KRAB zinc finger proteins ZNF676 and ZNF728 in cell lines overexpressing the proteins.

ORGANISM(S): Homo sapiens

PROVIDER: GSE163540 | GEO | 2022/01/28

REPOSITORIES: GEO

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ZNF676 ChIP-seq in HEK293T and H1 cells

Project description:Genome-wide binding profile of the primate-specific KRAB zinc finger protein ZNF676 in cell lines overexpressing the protein.

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ZNF728 ChIP-seq in HEK293T cells

Project description:Genome-wide binding profile of the primate-specific KRAB zinc finger protein ZNF728 in a HEK293T cell line overexpressing the protein.

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ZNF676 and ZNF728 ChIP-exo in HEK293T cells

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ChIP-exo of human KRAB-ZNFs transduced in HEK 293T cells and KAP1 in hES H1 cells

Project description:Encoded in the hundreds by the human genome, KRAB-containing zinc finger proteins (KRAB-ZFPs) constitute a rapidly evolving family of transcription factors with largely undefined functions. Here, by a combination of phylogenetic and genomic approaches, we retrace the evolutionary history of KRAB-ZFP genes and define the genomic targets of their human products. Through in silico analysis of 207 vertebrate genomes and chromatin immunoprecipitation / deep sequencing characterization of 257 human KRAB-ZFPs, we identify the root of the family in an early Devonian ancestor of tetrapods, describe its diversity amongst these species, and reveal that the majority of its human members primarily recognize transposable elements. Furthermore, by dissecting the timeline and modalities of interactions between human KRAB-ZFPs and their targets, we provide evidence strongly suggesting that these proteins, rather than just engaged in an evolutionary arms race against transposable elements, exploit these invaders as regulatory platforms for the benefit of the host.

2017-03-06 | GSE78099 | 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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Human stem cell and mouse transchromosomic (hsa11) embryonic stem cell (with and without ectopic ZNF91 expression) ChIP-seq

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Genome-wide binding patterns of murine KRAB zinc finger proteins

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ChIP-exo of HH514-16 treated with NaB or left untreated

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2021-03-04 | GSE168239 | GEO

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