Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ACCESS DATA

Json Xml

Dataset's files

Source:

			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

Items per page:

1 - 5 of 77

Similar Datasets

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.

| S-EPMC7033740 | biostudies-literature

Enhancer transcription identifies cis-regulatory elements for photoreceptor cell types

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

2020-01-08 | GSE136565 | GEO

Enhancer Cis Elements Instruct Promoter-Enhancer Interaction, Promoter-Enhancer Insulation and Compartmental Segregation

Project description:Enhancers harbor instructions encoded for the interactions between cis-elements and transcription factors to orchestrate lineage specific gene programs. Here we developed a modified method for chromosome conformation capture (3C), named MID Hi-C, to reveal how in mouse embryonic stem cells differential cooperation of enhancers and the chromatin remodeler BAF, as instructed by the underlying transcription factor motifs, modulate enhancer-promoter communication. We show that BAF-dependent enhancers permit genomic interactions beyond enhancer boundaries. BAF-dependent enhancers do not dictate genomic interactions within enhancer-promoter loop domains but rather act to instruct remote enhancer-promoter communication. In contrast, BAF-independent enhancers interact with promoter regions within tightly insulated enhancer-promoter loop domains that are marked by promoter and enhancer boundary elements. In addition, enhancer activeness modulated by BAF enforces compartment segregation. Based on these observations, we propose that enhancer cis elements instruct with great precision BAF-induced enhancer-promoter communication and compartmental segregation.

2023-12-31 | GSE213501 | GEO

Enhancer Cis Elements Instruct Promoter-Enhancer Interaction, Promoter-Enhancer Insulation and Compartmental Segregation

Project description:Enhancer Cis Elements Instruct Promoter-Enhancer Interaction, Promoter-Enhancer Insulation and Compartmental Segregation

| PRJNA881254 | ENA

Cis-regulatory landscape of four cell types of the retina

Project description:The retina is composed of ~50 cell-types with specific functions for the process of vision. Identification of the cis-regulatory elements active in retinal cell-types is key to elucidate the networks controlling this diversity. Here, we combined transcriptome and epigenome profiling to map the regulatory landscape of four cell-types isolated from mouse retinas including rod and cone photoreceptors as well as rare inter-neuron populations such as horizontal and starburst amacrine cells. Integration of this information reveals sequence determinants and candidate transcription factors for controlling cellular specialization. Additionally, we refined parallel reporter assays to enable studying the transcriptional activity of large collection of sequences in individual cell-types isolated from a tissue. We provide proof of concept for this approach and its scalability by characterizing the transcriptional capacity of several hundred putative regulatory sequences within individual retinal cell-types. This generates a catalogue of cis-regulatory regions active in retinal cell types and we further demonstrate their utility as potential resource for cellular tagging and manipulation.

2017-10-25 | GSE84589 | GEO

Characterizing cis-regulatory elements associated with mammary gland function

Project description:The goal of this study is to improve the quality, efficiency, and sustainability of milk production by improving the understanding of the function of cis-regulatory elements in regulating the bovine mammary gland. To this end, we have characterized the non-lactating and lactating mammary gland transcriptomes by whole transcriptome shotgun sequencing (RNA-seq). We will identify cis-regulatory elements in the non-lactating and lactating bovine mammary gland genome-wide. Finally, we will annotate and characterize mammary gland cis-regulatory elements by computational analysis and identify high-resolution genome-wide in vivo footprints of diverse trans-acting-factors (TF), over-represented TF bindings sites and overlapping SNPs.

2021-04-06 | GSE116079 | GEO

CRISPRi proliferation dropout screen of EGFR cis-regulatory elements

Project description:CRISPRi proliferation dropout screen of EGFR cis-regulatory elements

| PRJNA579582 | ENA

High-throughput discovery of post-transcriptional cis-regulatory elements

Project description:High-throughput discovery of post-transcriptional cis-regulatory elements

| PRJNA302654 | ENA

Characterizing cis-regulatory elements associated with mammary gland function

Project description:Characterizing cis-regulatory elements associated with mammary gland function

| PRJNA476965 | ENA

Mapping cis-regulatory elements in the midgestation mouse placenta

Project description:Mapping cis-regulatory elements in the midgestation mouse placenta