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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.

2022-01-28 | GSE163541 | GEO

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.

2022-01-28 | GSE163542 | GEO

ZNF676 and ZNF728 ChIP-exo in HEK293T cells

Project description:ZNF676 and ZNF728 ChIP-exo in HEK293T cells

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Primate-restricted KRAB zinc finger proteins control gene expression in human brain

Project description:Primate-restricted KRAB zinc finger proteins control gene expression in human brain

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Adaptive evolution of gene promoters driven by primate-specific KRAB zinc finger proteins

Project description:Adaptive evolution of gene promoters driven by primate-specific KRAB zinc finger proteins

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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.

2019-06-27 | GSE115288 | GEO

Human stem cell and mouse transchromosomic (hsa11) embryonic stem cell (with and without ectopic ZNF91 expression) ChIP-seq

Project description:We compared the binding patterns in embryonic stem cells of KAP1 and KRAB Zinc Finger (KZNF) proteins as well as H3K4me3 DNA under several conditions. Native human stem cells. Mouse stem cells containing a transchromosomic copy of human chromosome 11, with and without the introduction of plasmids containing KRAB Zinc Finger sequences. We show that certain KZNFs are responsible for the repression of certain retrotransposons in embryonic stem cells, preventing their spread across the genome. ChIP-seq of HESCs and mouse TC11 ESCs with ZNF91 plasmids and with empty vector plasmids. ChIP of KAP1, ZNF486, H3K4me3. At least 2 replicates of each condition.

2014-09-29 | E-GEOD-60210 | biostudies-arrayexpress

Genome-wide binding patterns of murine KRAB zinc finger proteins

Project description: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

Project description:How Krüppel-associated box-domain zinc finger protein (KRAB-ZFP) transcriptional repressors recruit TRIM28/KAP1 to recognizes target sequences or foreign genomes is unclear. Here, we used Epstein-Barr virus-infected cells in which a KRAB-ZFP, SZF1, silences lytic/replicative-phase genes of the virus to determine how the ZFP-footprints on cell and viral genomes to target pericentromeric regions. We observed that it uses non-consensus sites to target viral genes. This heterochromatin machinery employed by the host silences and regulate an invader without deregulating itself.

2021-03-04 | GSE168239 | GEO

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