GEO DataSets

(Submitter supplied) We report a retrotransposon-specific loss of CpG methylation in chromosome 4 KRAB-ZFP cluster (Chr4-cl) KO ES cells that are cultivated in conditions that induce DNA hypomethylation. The retrotransposon groups with the strongest DNA methylation loss are the main targets of the KRAB-ZFPs within the deleted gene cluster indicating that these KRAB-ZFPs prevent complete DNA demethylation at retrotransposons during global DNA demethylation.

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL21493 GPL17021

4 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL17021 GPL21493

280 Samples

Download data: BED, BIGWIG, TXT

(Submitter supplied) 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. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL21493

61 Samples

Download data: BIGWIG

(Submitter supplied) 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. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21493 GPL17021

74 Samples

Download data: BIGWIG, TXT

(Submitter supplied) We have shown that many mouse KRAB-ZFPs target retrotransposons which are generally marked by H3K9me3 and KAP1 in ES cells. To test whether these KRAB-ZFPs are require to establish and maintain repressive chromatin marks at these elements, we performed ChIP-seq with antibodies against KAP1 (2 KRAB-ZFP cluster KOs) and H3K9me3 (5 KRAB-ZFP cluster KOs). We show that KRAB-ZFP targeted retrotransposons show reduced KAP1 binding and H3K9me3 in these KO ES cells. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17021 GPL21493

54 Samples

Download data: BIGWIG

(Submitter supplied) Genetic deletion of a large KRAB-ZFP gene cluster on chromosome 4 (Chr4-cl) leads to transcriptional reactivation of retrotransposons (mainly ETn elements) in ES cells. We therefore wanted to test whether ETn elements retrotranspose in Chr4-cl KO mice at higher frequency. For this we purified genomic DNA from WT and KO mice, enriched gDNA libraries using ETn capture probes and sequenced those libraries as paire-end reads. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL17021

87 Samples

Download data: BED

(Submitter supplied) 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. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

41 Samples

Download data: BED, BW, TXT, XML

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL24676 GPL30173

18 Samples

Download data: BW

(Submitter supplied) We used ChIP-seq to assess how abolition of KRAB binding by KAP1 (through structure-guided mutations in the KAP1-KRAB binding interface) changed the distribution of KAP1 on chromatin genome-wide.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

7 Samples

Download data: BW

(Submitter supplied) We used CUT&RUN to assess how abolition of KRAB binding by KAP1 (through structure-guided mutations in the KAP1-KRAB binding interface) changed the distribution of H3K9me3 epigenetic mark genome-wide.

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL24676 GPL30173

11 Samples

Download data: BW

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Macaca mulatta; Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL14954 GPL11154 GPL13112

25 Samples

Download data

(Submitter supplied) 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.

Organism:

Mus musculus; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13112 GPL11154

15 Samples

Download data: XLSX

(Submitter supplied) We compared the expression in embryonic stem cells of KRAB ZNF proteins and retrotransposon elements in the human genome 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.

Organism:

Mus musculus; Macaca mulatta; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL14954 GPL11154 GPL13112

10 Samples

Download data: XLSX

(Submitter supplied) Transposable element (TE) invasions have shaped vertebrate genomes over the course of evolution. They have contributed an extra layer of species-specific gene regulation by providing novel transcription factor binding sites. In humans, SVA elements are one of three still active TE families, and approximately 2800 SVA insertions exist in the human genome, half of which are human-specific. TEs are often silenced by KRAB zinc finger (KZNF) proteins recruiting co-repressor proteins that establish a repressive chromatin state. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21697 GPL20301 GPL11154

26 Samples

Download data: CSV, NARROWPEAK, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

80 Samples

Download data: BW

(Submitter supplied) This work describes the function and targets of a maternal KRAB-Zinc finger protein, ZFP708, which specifically mediates maintenance of DNA-methylation at a subset of LTR retrotransposons during embryonic epigenetic reprogramming.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

61 Samples

Download data: XLSX

(Submitter supplied) This work describes the function and targets of a maternal KRAB-Zinc finger protein, ZFP708, which specifically mediates maintenance of DNA-methylation at a subset of LTR retrotransposons during embryonic epigenetic reprogramming.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

19 Samples

Download data: BW

(Submitter supplied) Krüppel-associated box (KRAB) domain-containing zinc finger proteins (KZFPs) are one of the largest groups of transcription factors encoded by tetrapods, with 378 members in human alone. KZFP genes are often grouped in clusters reflecting amplification by gene and segment duplication since the gene family first emerged more than 400 million years ago. Previous work has revealed that many KZFPs recognize transposable element (TE)-embedded sequences as genomic targets, and that KZFPs facilitate the co-option of the regulatory potential of TEs for the benefit of the host. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL16791 GPL20301

139 Samples

Download data: BED

(Submitter supplied) Kruppel-associated box (KRAB)-containing zinc-finger proteins (KZFPs) represent the largest family of transcription factors encoded by higher vertebrates. Together with their heterochromatin-inducing cofactor KAP1, many act as repressors of endogenous retroelements (EREs) during early embryonic genome reprogramming, yet their widespread expression in adult tissues and enrichment at other genetic loci indicate additional roles. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL16791 GPL18573

30 Samples

Download data: BED

(Submitter supplied) Mobile elements are important evolutionary forces that challenge genomic integrity. Long interspersed element-1 (L1, also known as LINE-1) is the only autonomous transposon still active in the human genome. It displays an unusual pattern of evolution, with at any given time a single active L1 lineage amplifying to thousands of copies before getting replaced by a new lineage likely under pressure of host restriction factors, which act notably by silencing L1 expression during early embryogenesis. more...

Organism:

Homo sapiens; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL11154 GPL13112

10 Samples

Download data: BED, TXT