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Temporal Analyses of Cardiac Chromatin Accessibility, DNA Methylation and Epigenomic Structure Reveal Locus-Specific Regulation [RRBS]

ABSTRACT: Temporal Analyses of Cardiac Chromatin Accessibility, DNA Methylation and Epigenomic Structure Reveal Locus-Specific Regulation [RRBS]

PROVIDER: PRJNA785348 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12232101.fastq.gz	Fastqsanger.gz
	SRR12232102.fastq.gz	Fastqsanger.gz
	SRR12232103.fastq.gz	Fastqsanger.gz
	SRR12232104.fastq.gz	Fastqsanger.gz
	SRR12232105.fastq.gz	Fastqsanger.gz

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Temporal Analyses of Cardiac Chromatin Accessibility, DNA Methylation and Epigenomic Structure Reveal Locus-Specific Regulation [RRBS]

Project description:Heart failure can be induced or ameliorated by regulation of chromatin modifying enzymes. Because so many chromatin factors regulate gene expression, we used ATAC-seq to report the status of a given locus at any time—the sum total of all epigenetic modifiers—in a mouse model of pressure overload hypertrophy. Early compensation of pressure overload at 3 days was associated with widespread changes in chromatin accessibility and DNA methylation, the majority of which persisted to the decompensated phase (3 weeks), revealing the temporal nature of epigenomic compensation to pathologic stimuli. A cardiac-specific CTCF depletion model was used to examine how this protein maintains basal cardiac chromatin function and revealed that loss of CTCF causes widespread changes in accessibility and methylation that are distinct from those in pressure overload. Less than half of the gene expression changes occurring at either time point after pressure overload were explained by the actions of DNA methylation alone and accessibility was likewise an imperfect predictor of transcription. Distal enhancers were paired with genes based on chromatin structural data and the regulatory actions of these elements examined in the context of DNA methylation and accessibility: enhancer actions require specific combinations of transcription factors and histone modifications at different stages of disease and to execute a specific transcriptional event (methylation and accessibility alone were insufficient to predict the behavior). In summary, these studies characterize the logic employed at different coding, regulatory, and noncoding regions to regulate chromatin accessibility and transcription, providing a resource of epigenomic data at distinct temporal stages of heart failure.

2021-12-01 | GSE154520 | GEO

Temporal Analyses of Cardiac Chromatin Accessibility, DNA Methylation and Epigenomic Structure Reveal Locus-Specific Regulation [RNA-seq]

2021-12-01 | GSE154519 | GEO

Temporal Analyses of Cardiac Chromatin Accessibility, DNA Methylation and Epigenomic Structure Reveal Locus-Specific Regulation [ATAC-seq]

2021-12-01 | GSE154518 | GEO

Temporal Analyses of Cardiac Chromatin Accessibility, DNA Methylation and Epigenomic Structure Reveal Locus-Specific Regulation

Project description:Temporal Analyses of Cardiac Chromatin Accessibility, DNA Methylation and Epigenomic Structure Reveal Locus-Specific Regulation

| PRJNA647864 | ENA

Temporal Analyses of Cardiac Chromatin Accessibility, DNA Methylation and Epigenomic Structure Reveal Locus-Specific Regulation [RNA-seq]

Project description:Temporal Analyses of Cardiac Chromatin Accessibility, DNA Methylation and Epigenomic Structure Reveal Locus-Specific Regulation [RNA-seq]

| PRJNA647865 | ENA

Temporal Analyses of Cardiac Chromatin Accessibility, DNA Methylation and Epigenomic Structure Reveal Locus-Specific Regulation [ATAC-seq]

Project description:Temporal Analyses of Cardiac Chromatin Accessibility, DNA Methylation and Epigenomic Structure Reveal Locus-Specific Regulation [ATAC-seq]

| PRJNA785349 | ENA

Temporal Analyses of Cardiac Chromatin Accessibility, DNA Methylation and Epigenomic Structure Reveal Locus-Specific Regulation

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

2021-12-01 | GSE154521 | GEO

Temporal epigenomic and transcriptomic profiling of mesenchymal differentiation

Project description:Temporal epigenomic and transcriptomic profiling of mesenchymal differentiation

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Transcriptional Reprogramming And Epigenomic Landscape Dynamics During Grapevine Somatic Embryogenesis Process [RRBS]

Project description:Transcriptional Reprogramming And Epigenomic Landscape Dynamics During Grapevine Somatic Embryogenesis Process [RRBS]

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Temporal Analyses Reveal a Pivotal Role for Sense and Anti-sense Enhancer RNAs in Coordinate Immunoglobulin Lambda Locus Activation

Project description:Transcription enhancers are essential activators of V(D)J recombination that orchestrate non-coding transcription through complementary, unrearranged gene segments. How transcription is coordinately increased at spatially distinct promoters, however, remains poorly understood. Using the murine immunoglobulin lambda (Igλ) locus as model, we find that three enhancer-like elements in the 3’ Igλ domain, Eλ3-1, HSCλ1 and HSE-1, show strikingly similar transcription factor binding dynamics and close spatial proximity, suggesting that they form an active enhancer hub. Temporal analyses show coordinate recruitment of complementary V and J gene segments to this hub, with comparable transcription factor binding dynamics to that at enhancers. We find further that E2A, p300, Mediator and Integrator bind to enhancers as early events, whereas YY1 recruitment and eRNA synthesis occur later, corresponding to transcription activation. Remarkably, the interplay between sense and anti-sense enhancer RNA is central to both active enhancer hub formation and coordinate Igλ transcription: Antisense Eλ3-1 eRNA represses Igλ activation whereas temporal analyses demonstrate that accumulating levels of sense eRNA boost YY1 recruitment to stabilise enhancer hub/promoter interactions and lead to coordinate transcription activation. These studies therefore demonstrate for the first time a critical role for threshold levels of sense versus antisense eRNA in locus activation.

2023-08-28 | GSE239925 | GEO

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