GEO DataSets

(Submitter supplied) Transposable elements (TEs) are major contributors of genetic material in mammalian genomes. These often include binding sites for architectural proteins, including the multifarious master protein, CTCF, which shapes the 3D genome by creating loops, domains, compartment borders and RNA-DNA interactions, all of which play a role in the compact packaging of DNA and have the potential to facilitate regulatory function. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL18573

9 Samples

Download data: BEDGRAPH, BIGWIG, HIC

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

Organism:

Homo sapiens

Type:

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

Platform:

GPL24676

87 Samples

Download data

(Submitter supplied) Mammalian genomes harbour a large number of transposable elements (TEs) and their remnants. Most TEs are incapable of retrotransposition, however, they have evolved as cis-regulatory elements (CREs), enabling them to recruit host-encoded factors. Understanding the contribution of TEs in the regulation of the mammalian genome is an active area of research. Here we show that the male-specific lethal (MSL) complex-mediated acetylation of histone H4 lysine 16 (H4K16ac) regulates the transcription of TEs. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

8 Samples

Download data: BW

(Submitter supplied) Mammalian genomes harbour a large number of transposable elements (TEs) and their remnants. Most TEs are incapable of retrotransposition, however, they have evolved as cis-regulatory elements (CREs), enabling them to recruit host-encoded factors. Understanding the contribution of TEs in the regulation of the mammalian genome is an active area of research. Here we show that the male-specific lethal (MSL) complex-mediated acetylation of histone H4 lysine 16 (H4K16ac) regulates the transcription of TEs. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

69 Samples

Download data

(Submitter supplied) Mammalian genomes harbour a large number of transposable elements (TEs) and their remnants. Most TEs are incapable of retrotransposition, however, they have evolved as cis-regulatory elements (CREs), enabling them to recruit host-encoded factors. Understanding the contribution of TEs in the regulation of the mammalian genome is an active area of research. Here we show that the male-specific lethal (MSL) complex-mediated acetylation of histone H4 lysine 16 (H4K16ac) regulates the transcription of TEs. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

10 Samples

Download data: BW

(Submitter supplied) Transposable elements (TE) have been shown to contrain functional transcription factor (TF) binding sites for long, but the extent to which TEs contribute TF binding sites is not well know. Here, we comprehensively mapped binding sites for 26 pairs of orthologous TFs, in two pairs of human and mouse cell lines (i.e., leukemia, and lymphoblast), along with epigenomic profiles representing DNA methylation and six histone modifications. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL15103

4 Samples

Download data: BIGWIG

(Submitter supplied) Transposable elements (TE) have been shown to contrain functional transcription factor (TF) binding sites for long, but the extent to which TEs contribute TF binding sites is not well know. Here, we comprehensively mapped binding sites for 26 pairs of orthologous TFs, in two pairs of human and mouse cell lines (i.e., leukemia, and lymphoblast), along with epigenomic profiles representing DNA methylation and six histone modifications. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL15433

4 Samples

Download data: BIGWIG

(Submitter supplied) Co-option of transposable elements maintains conserved 3D genome structures via CTCF binding site turnover in human and mouse.

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL15520 GPL18573 GPL22790

32 Samples

Download data: HIC

(Submitter supplied) The goal of this study is to analyze the contribution of transposable elements (TEs) tocis-regulation in CD8+ T cells. Using a combination of NGS techniques we show that specific subfamilies of TEs are enriched, and distributed in a lineage-specific fashion in core and boundary domains of CD8+T cell enhancers.This study represents the first detailed analysis of the topology and the enhancer domain-associated putative functions of distinct TE types.

Organism:

Mus musculus

Type:

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

Platform:

GPL17021

23 Samples

Download data: BW, WIG

(Submitter supplied) Transposable elements (TEs) are key to the evolutionary turnover of regulatory sequences. How they can play such an essential role in spite of their genotoxic potential is unknown. Here, we demonstrate that KRABcontaining zinc finger proteins control the timely and pleiotropic engagement of TE-derived cis-regulators of transcription. We first observed that evolutionary recent TEs of the SVA, HERVK and HERVH subgroups are major contributors to chromatin opening during human embryonic genome activation and act as KLF-stimulated enhancers in naïve embryonic stem cells. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

10 Samples

Download data: BED

(Submitter supplied) Transposable elements (TEs) are key to the evolutionary turnover of regulatory sequences. How they can play such an essential role in spite of their genotoxic potential is unknown. Here, we demonstrate that KRABcontaining zinc finger proteins control the timely and pleiotropic engagement of TE-derived cis-regulators of transcription. We first observed that evolutionary recent TEs of the SVA, HERVK and HERVH subgroups are major contributors to chromatin opening during human embryonic genome activation and act as KLF-stimulated enhancers in naïve embryonic stem cells. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

35 Samples

Download data: BED

(Submitter supplied) Transposable elements (TEs) are key to the evolutionary turnover of regulatory sequences. How they can play such an essential role in spite of their genotoxic potential is unknown. Here, we demonstrate that KRABcontaining zinc finger proteins control the timely and pleiotropic engagement of TE-derived cis-regulators of transcription. We first observed that evolutionary recent TEs of the SVA, HERVK and HERVH subgroups are major contributors to chromatin opening during human embryonic genome activation and act as KLF-stimulated enhancers in naïve embryonic stem cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

34 Samples

Download data: TAB

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

Organism:

Homo sapiens

Type:

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

Platform:

GPL16791

79 Samples

Download data: BED, TAB

(Submitter supplied) Chromatin accessibility and modification is a hallmark of regulatory DNA, which has led to the discovery of cis-regulatory elements (CREs). Here, we characterize chromatin accessibility, histone modifications and sequence conservation in 13 plant species. We identified thousands of putative CREs and revealed that distal CREs are prevalent in plants especially in species with large and complex genomes. more...

Organism:

Arabidopsis thaliana; Phaseolus vulgaris; Sorghum bicolor; Zea mays; Spirodela polyrhiza; Oryza sativa; Brachypodium distachyon; Populus trichocarpa; Glycine max; Hordeum vulgare; Setaria viridis; Asparagus officinalis; Eutrema salsugineum

Type:

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

13 related Platforms

170 Samples

Download data: BW

(Submitter supplied) The zebrafish has been widely used for the study of human disease and development, as ~70% of the protein-coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome, however, has lagged behind that of other model systems such as mouse and Drosophila. Based on multi-omics approaches taken in the ENCODE and Roadmap Epigenomics projects, we performed RNA-seq, ATAC-seq, ChIP-seq and Hi-C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. more...

Organism:

Danio rerio

Type:

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

4 related Platforms

204 Samples

Download data: BED, BW, HIC, NARROWPEAK, TXT

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

Organism:

Symphalangus syndactylus; Hylobates lar; Hylobates muelleri; Nomascus gabriellae; Nomascus leucogenys; Hylobates moloch; Hylobates pileatus; Hoolock leuconedys

Type:

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

15 related Platforms

60 Samples

Download data: TXT

(Submitter supplied) Co-option of transposable elements (TEs) to become part of existing or new enhancers is an important mechanism for evolution of gene regulation. However, contributions of lineage-specific TE insertions to recent regulatory adaptations remain poorly understood. Gibbons present a suitable model to study these contributions as they have evolved a lineage-specific TE called LAVA (LINE-AluSz-VNTR-AluLIKE), which is still active in the gibbon genome. more...

Organism:

Symphalangus syndactylus; Nomascus gabriellae; Hylobates lar; Hylobates pileatus; Nomascus leucogenys; Hylobates muelleri; Hylobates moloch; Hoolock leuconedys

Type:

Other

14 related Platforms

23 Samples

Download data: XLSX

(Submitter supplied) Co-option of transposable elements (TEs) to become part of existing or new enhancers is an important mechanism for evolution of gene regulation. However, contributions of lineage-specific TE insertions to recent regulatory adaptations remain poorly understood. Gibbons present a suitable model to study these contributions as they have evolved a lineage-specific TE called LAVA (LINE-AluSz-VNTR-AluLIKE), which is still active in the gibbon genome. more...

Organism:

Nomascus leucogenys

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25055 GPL24727

9 Samples

Download data: TXT

(Submitter supplied) Co-option of transposable elements (TEs) to become part of existing or new enhancers is an important mechanism for evolution of gene regulation. However, contributions of lineage-specific TE insertions to recent regulatory adaptations remain poorly understood. Gibbons present a suitable model to study these contributions as they have evolved a lineage-specific TE called LAVA (LINE-AluSz-VNTR-AluLIKE), which is still active in the gibbon genome. more...

Organism:

Nomascus leucogenys

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27430

4 Samples

Download data: BEDGRAPH, TXT, XLSX

(Submitter supplied) Co-option of transposable elements (TEs) to become part of existing or new enhancers is an important mechanism for evolution of gene regulation. However, contributions of lineage-specific TE insertions to recent regulatory adaptations remain poorly understood. Gibbons present a suitable model to study these contributions as they have evolved a lineage-specific TE called LAVA (LINE-AluSz-VNTR-AluLIKE), which is still active in the gibbon genome. more...

Organism:

Nomascus leucogenys

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL25055 GPL24727

24 Samples

Download data: BEDGRAPH