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KDM2 proteins constrain transcription from CpG island gene promoters independently of their histone demethylase activity

ABSTRACT: KDM2 proteins constrain transcription from CpG island gene promoters independently of their histone demethylase activity

PROVIDER: PRJNA523563 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8601920_1.fastq.gz	Fastqsanger.gz
	SRR8601920_2.fastq.gz	Fastqsanger.gz
	SRR8601930_1.fastq.gz	Fastqsanger.gz
	SRR8601930_2.fastq.gz	Fastqsanger.gz
	SRR8601940_1.fastq.gz	Fastqsanger.gz

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KDM2 proteins constrain transcription from CpG island gene promoters independently of their histone demethylase activity [ATAC-seq]

Project description: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. Instead, we discover that KDM2 proteins play a widespread and demethylase-independent role in constraining gene expression from CGI-associated gene promoters. We further show that KDM2 proteins shape RNA Polymerase II occupancy but not chromatin accessibility at CGI-associated promoters. Together this reveals a demethylase-independent role for KDM2 proteins in transcriptional repression and uncovers a new function for CGIs in constraining gene expression.

2019-07-03 | GSE126863 | GEO

KDM2 proteins constrain transcription from CpG island gene promoters independently of their histone demethylase activity [ChIP-seq]

2019-07-03 | GSE126862 | GEO

KDM2 proteins constrain transcription from CpG island gene promoters independently of their histone demethylase activity [RNA-seq]

2019-07-03 | GSE126861 | GEO

KDM2 proteins constrain transcription from CpG island gene promoters independently of their histone demethylase activity.

Project description:CpG islands (CGIs) 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. Instead, we discover that KDM2 proteins play a widespread and demethylase-independent role in constraining gene expression from CGI-associated gene promoters. We further show that KDM2 proteins shape RNA Polymerase II occupancy but not chromatin accessibility at CGI-associated promoters. Together this reveals a demethylase-independent role for KDM2 proteins in transcriptional repression and uncovers a new function for CGIs in constraining gene expression.

| S-EPMC6753492 | biostudies-literature

KDM2 proteins constrain transcription from CpG island gene promoters independently of their histone demethylase activity [ATAC-seq]

Project description:KDM2 proteins constrain transcription from CpG island gene promoters independently of their histone demethylase activity [ATAC-seq]

| PRJNA523566 | ENA

KDM2 proteins constrain transcription from CpG island gene promoters independently of their histone demethylase activity [ChIP-seq]

Project description:KDM2 proteins constrain transcription from CpG island gene promoters independently of their histone demethylase activity [ChIP-seq]

| PRJNA523568 | ENA

KDM2 proteins constrain transcription from CpG island gene promoters independently of their histone demethylase activity [RNA-seq]

Project description:KDM2 proteins constrain transcription from CpG island gene promoters independently of their histone demethylase activity [RNA-seq]

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KDM2 proteins constrain transcription from CpG island gene promoters independently of their histone demethylase activity

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-07-03 | GSE126864 | GEO

Bacillus velezensis isolate:KDM2

Project description:Bacillus velezensis isolate:KDM2 Genome sequencing

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CpG-island promoters drive transcription of human telomeres.

Project description:The longstanding dogma that telomeres, the heterochromatic extremities of linear eukaryotic chromosomes, are transcriptionally silent was overturned by the discovery that DNA-dependent RNA polymerase II (RNAPII) transcribes telomeric DNA into telomeric repeat-containing RNA (TERRA). Here, we show that CpG dinucleotide-rich DNA islands, shared among multiple human chromosome ends, promote transcription of TERRA molecules. TERRA promoters sustain cellular expression of reporter genes, are located immediately upstream of TERRA transcription start sites, and are bound by active RNAPII in vivo. Finally, the identified promoter CpG dinucleotides are methylated in vivo, and cytosine methylation negatively regulates TERRA abundance. The existence of subtelomeric promoters, driving TERRA transcription from independent chromosome ends, supports the idea that TERRA exerts fundamental functions in the context of telomere biology.

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