GEO DataSets

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

Organism:

Drosophila melanogaster; Mus musculus; Homo sapiens

Type:

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

Platforms:

GPL19057 GPL19415 GPL25537

124 Samples

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(Submitter supplied) Transcription must be highly controlled to regulate gene expression and development. However, our understanding of the molecular mechanisms that influence transcription and how these are coordinated in cells to ensure normal gene expression remains rudimentary. Here, we reveal that actively transcribed CpG island-associated gene promoters recruit SET1 chromatin modifying complexes to enable gene expression. more...

Organism:

Drosophila melanogaster; Mus musculus

Type:

Other

Platform:

GPL25537

18 Samples

Download data: BW, CSV

(Submitter supplied) Transcription must be highly controlled to regulate gene expression and development. However, our understanding of the molecular mechanisms that influence transcription and how these are coordinated in cells to ensure normal gene expression remains rudimentary. Here, we reveal that actively transcribed CpG island-associated gene promoters recruit SET1 chromatin modifying complexes to enable gene expression. more...

Organism:

Drosophila melanogaster; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25537

46 Samples

Download data: BW, CSV

(Submitter supplied) Transcription must be highly controlled to regulate gene expression and development. However, our understanding of the molecular mechanisms that influence transcription and how these are coordinated in cells to ensure normal gene expression remains rudimentary. Here, we reveal that actively transcribed CpG island-associated gene promoters recruit SET1 chromatin modifying complexes to enable gene expression. more...

Organism:

Homo sapiens; Mus musculus; Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL25537 GPL19057 GPL19415

60 Samples

Download data: BED, BW, CSV

(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; Other

Platforms:

GPL19057 GPL17021 GPL13112

126 Samples

Download data

(Submitter supplied) Chromatin modifications and the promoter associated epigenome are thought to be important for the regulation of gene expression. However, the mechanisms by which chromatin modifying complexes are targeted to the appropriate gene promoters in vertebrates and how they influence gene expression have remained poorly defined. Here, using a combination of live cell imaging and functional genomics, we discover that the vertebrate SET1 complex is targeted to actively transcribed target gene promoters through CFP1 which engages in a unique form of multivalent chromatin reading that involves recognition of non-methylated DNA and histone H3 lysine 4 trimethylation (H3K4me3). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL19057

19 Samples

Download data: BW, TXT

(Submitter supplied) Chromatin modifications and the promoter associated epigenome are thought to be important for the regulation of gene expression. However, the mechanisms by which chromatin modifying complexes are targeted to the appropriate gene promoters in vertebrates and how they influence gene expression have remained poorly defined. Here, using a combination of live cell imaging and functional genomics, we discover that the vertebrate SET1 complex is targeted to actively transcribed target gene promoters through CFP1 which engages in a unique form of multivalent chromatin reading that involves recognition of non-methylated DNA and histone H3 lysine 4 trimethylation (H3K4me3). more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

74 Samples

Download data: BW

(Submitter supplied) Chromatin modifications and the promoter associated epigenome are thought to be important for the regulation of gene expression. However, the mechanisms by which chromatin modifying complexes are targeted to the appropriate gene promoters in vertebrates and how they influence gene expression have remained poorly defined. Here, using a combination of live cell imaging and functional genomics, we discover that the vertebrate SET1 complex is targeted to actively transcribed target gene promoters through CFP1 which engages in a unique form of multivalent chromatin reading that involves recognition of non-methylated DNA and histone H3 lysine 4 trimethylation (H3K4me3). more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19057 GPL17021 GPL13112

24 Samples

Download data: BED, BIGWIG, BW

(Submitter supplied) Chromatin modifications and the promoter associated epigenome are thought to be important for the regulation of gene expression. However, the mechanisms by which chromatin modifying complexes are targeted to the appropriate gene promoters in vertebrates and how they influence gene expression have remained poorly defined. Here, using a combination of live cell imaging and functional genomics, we discover that the vertebrate SET1 complex is targeted to actively transcribed target gene promoters through CFP1 which engages in a unique form of multivalent chromatin reading that involves recognition of non-methylated DNA and histone H3 lysine 4 trimethylation (H3K4me3). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL19057 GPL13112

9 Samples

Download data: BED, BW

(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:

GPL19057

176 Samples

Download data

(Submitter supplied) CpG islands (CGI) are associated with the majority of mammalian gene promoters and function to recruit chromatin modifying enzymes. It has therefore been proposed that CGIs regulate gene expression through chromatin-based mechanisms, however in most cases this has not been directly tested. Here, we reveal that the histone H3 lysine 36 (H3K36) demethylase activity of the CGI-binding KDM2 proteins contributes only modestly to the H3K36me2-depleted state at CGI-associated gene promoters and is dispensable for normal gene expression. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

52 Samples

Download data: BW, TXT

(Submitter supplied) CpG islands (CGI) are associated with the majority of mammalian gene promoters and function to recruit chromatin modifying enzymes. It has therefore been proposed that CGIs regulate gene expression through chromatin-based mechanisms, however in most cases this has not been directly tested. Here, we reveal that the histone H3 lysine 36 (H3K36) demethylase activity of the CGI-binding KDM2 proteins contributes only modestly to the H3K36me2-depleted state at CGI-associated gene promoters and is dispensable for normal gene expression. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

98 Samples

Download data: BW

(Submitter supplied) CpG islands (CGI) are associated with the majority of mammalian gene promoters and function to recruit chromatin modifying enzymes. It has therefore been proposed that CGIs regulate gene expression through chromatin-based mechanisms, however in most cases this has not been directly tested. Here, we reveal that the histone H3 lysine 36 (H3K36) demethylase activity of the CGI-binding KDM2 proteins contributes only modestly to the H3K36me2-depleted state at CGI-associated gene promoters and is dispensable for normal gene expression. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

26 Samples

Download data: TXT

(Submitter supplied) We profiled CpG methylation for human T cells and compared this pattern with public T cell nucleosome (H2A.Z) and polymerase II profiles (SRA000234). Focusing on DNA regions surrounding the start codon and stop codon, instead of the transcription start and end sites, we discovered a very intriguing pattern, namely methylation and nucleosomal peaks at those regions, more prominent than peaks near transcript boundaries. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL9052

1 Sample

Download data: BED

(Submitter supplied) There are thousands of unstable non-coding (nc) RNAs in humans, but their transcriptional regulation is poorly characterized compared to protein-coding transcripts. We recently identified a restrictor complex containing ZC3H4 and WDR82, which terminates non-coding transcription. Here we show that the ncRNA termination factor, ARS2, and the nuclear exosome targeting complex (NEXT) are part of this complex.ARS2/NEXT and WDR82 contact different parts of ZC3H4, which are required for its transcription regulatory function. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

4 Samples

Download data: BW

(Submitter supplied) There are thousands of unstable non-coding (nc) RNAs in humans, but their transcriptional regulation is poorly characterized compared to protein-coding transcripts. We recently identified a restrictor complex containing ZC3H4 and WDR82, which terminates non-coding transcription. Here we show that the ncRNA termination factor, ARS2, and the nuclear exosome targeting complex (NEXT) are part of this complex.ARS2/NEXT and WDR82 contact different parts of ZC3H4, which are required for its transcription regulatory function. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

8 Samples

Download data: BW

(Submitter supplied) There are thousands of unstable non-coding (nc) RNAs in humans, but their transcriptional regulation is poorly characterized compared to protein-coding transcripts. We recently identified a restrictor complex containing ZC3H4 and WDR82, which terminates non-coding transcription. Here we show that the ncRNA termination factor, ARS2, and the nuclear exosome targeting complex (NEXT) are part of this complex.ARS2/NEXT and WDR82 contact different parts of ZC3H4, which are required for its transcription regulatory function. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: BW

(Submitter supplied) There are thousands of unstable non-coding (nc) RNAs in humans, but their transcriptional regulation is poorly characterized compared to protein-coding transcripts. We recently identified a restrictor complex containing ZC3H4 and WDR82, which terminates non-coding transcription. Here we show that the ncRNA termination factor, ARS2, and the nuclear exosome targeting complex (NEXT) are part of this complex.ARS2/NEXT and WDR82 contact different parts of ZC3H4, which are required for its transcription regulatory function. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

2 Samples

Download data: BW

(Submitter supplied) There are thousands of unstable non-coding (nc) RNAs in humans, but their transcriptional regulation is poorly characterized compared to protein-coding transcripts. We recently identified a restrictor complex containing ZC3H4 and WDR82, which terminates non-coding transcription. Here we show that the ncRNA termination factor, ARS2, and the nuclear exosome targeting complex (NEXT) are part of this complex.ARS2/NEXT and WDR82 contact different parts of ZC3H4, which are required for its transcription regulatory function. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

4 Samples

Download data: BW

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

Organism:

Homo sapiens

Type:

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

Platform:

GPL24676

76 Samples

Download data: BED