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Enhancer transcription identifies cis-regulatory elements for photoreceptor cell types

ABSTRACT: Enhancer transcription identifies cis-regulatory elements for photoreceptor cell types

PROVIDER: PRJNA562691 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10030400.fastq.gz	Fastqsanger.gz
	SRR10030401.fastq.gz	Fastqsanger.gz
	SRR10030402.fastq.gz	Fastqsanger.gz
	SRR10030403.fastq.gz	Fastqsanger.gz
	SRR10030404.fastq.gz	Fastqsanger.gz

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Enhancer transcription identifies <i>cis</i>-regulatory elements for photoreceptor cell types.

Project description:Identification of cell type-specific cis-regulatory elements (CREs) is crucial for understanding development and disease, although identification of functional regulatory elements remains challenging. We hypothesized that context-specific CREs could be identified by context-specific non-coding RNA (ncRNA) profiling, based on the observation that active CREs produce ncRNAs. We applied ncRNA profiling to identify rod and cone photoreceptor CREs from wild-type and mutant mouse retinas, defined by presence or absence, respectively, of the rod-specific transcription factor (TF) Nrl Nrl-dependent ncRNA expression strongly correlated with epigenetic profiles of rod and cone photoreceptors, identified thousands of candidate rod- and cone-specific CREs, and identified motifs for rod- and cone-specific TFs. Colocalization of NRL and the retinal TF CRX correlated with rod-specific ncRNA expression, whereas CRX alone favored cone-specific ncRNA expression, providing quantitative evidence that heterotypic TF interactions distinguish cell type-specific CRE activity. We validated the activity of novel Nrl-dependent ncRNA-defined CREs in developing cones. This work supports differential ncRNA profiling as a platform for the identification of cell type-specific CREs and the discovery of molecular mechanisms underlying TF-dependent CRE activity.

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Enhancer transcription identifies cis-regulatory elements for photoreceptor cell types

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