Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Enhancer RNA transcriptomics-wide association study reveals an atlas of pan-cancer susceptibility eRNAs

ABSTRACT: Enhancer RNA transcriptomics-wide association study reveals an atlas of pan-cancer susceptibility eRNAs

PROVIDER: PRJNA1013097 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR25915800_1.fastq.gz	Fastqsanger.gz
	SRR25915800_2.fastq.gz	Fastqsanger.gz
	SRR25915801_1.fastq.gz	Fastqsanger.gz
	SRR25915801_2.fastq.gz	Fastqsanger.gz
	SRR25915802_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

Enhancer RNA transcriptomics-wide association study reveals an atlas of pan-cancer susceptibility eRNAs

Project description:Increasing evidence has demonstrated that enhancer RNAs (eRNAs) play essential roles in human diseases. However, the complete identification of disease-related subsets of eRNAs remains a major challenge. Here, we construct an atlas of common and rare genetic variants influencing the expression of enhancer RNAs across 49 human tissues. We identify 11,757 eRNA quantitative trait loci (eRNA-QTLs) associated with the expression of 89.75% annotated eRNAs. Mechanically, eRNA-QTLs frequently altered the binding motifs of transcription factors and were further experimentally validated by CRISPR-based base editing. We also observed that 28.48% of cancer signals were co-localized with eRNA-QTLs. Utilizing our newly developed eRNA transcriptome-wide association study (eRNA-TWAS) model, we have effectively identified 259 cancer susceptibility eRNAs spanning 23 distinct cancer types. Notably, among the identified eRNAs, these eRNA-linked cancer susceptibility genes exhibit significant dependence across various cancer cell lines. Interestingly, cancer risk can be significantly influenced by rare functional variants that are linked to eRNAs with transcriptomic outliers. Additionally, we develop a comprehensive and flexible data portal for exploring the genetic underpinnings of eRNAs. Overall, this study reveals a systematic landscape of genetic dependencies on eRNAs across pan-cancers and significantly expands the pool of disease-associated eRNAs.

2025-02-13 | GSE242322 | GEO

Chromatin association sites of KSHV and RRV PAN RNA

Project description:Chromatin association sites of KSHV and RRV PAN RNA

| PRJNA496580 | ENA

Chromatin association sites of KSHV and RRV PAN RNA

Project description:During lytic replication of Kaposi’s sarcoma-associated herpesvirus (KSHV), a nuclear viral long noncoding RNA known as PAN RNA becomes the most abundant polyadenylated transcript in the cell. Knockout or knockdown of KSHV PAN RNA results in loss of late lytic viral gene expression and, consequently, reduction of progeny virion release from the cell. We studied KSHV and RRV PAN RNA homologs using capture hybridization analysis of RNA targets (CHART) and observed their reproducible associations with host chromatin, but the loci differ between PAN RNA homologs.

2018-10-17 | GSE121268 | GEO

Functional Importance of eRNAs for Estrogen-dependent Gene Transcriptional Activation

Project description:The functional importance of gene enhancers in regulated gene expression is well established. In addition to widespread transcription of long non-coding RNA (ncRNA) transcripts in mammalian cells, bidirectional ncRNAs referred to as eRNAs are present on enhancers. However, it has remained unclear whether these eRNAs are functional, or merely a reflection of enhancer activation. Here, we report that 17 ?-estradiol (E2)-bound estrogen receptor alpha (ER?) on enhancers causes a global increase in eRNA transcription on enhancers adjacent to E2 upregulated coding genes. These induced eRNAs, as functional transcripts, appear to exert important roles for the observed ligand-dependent induction of target coding genes, causing an increased strength of specific enhancer:promoter looping initiated by ER? binding. Cohesin, present on many ER?-regulated enhancers even prior to ligand treatment, apparently contributes to E2-dependent gene activation by stabilizing E2/ER?/eRNA-induced enhancer:promoter looping. Our data indicate that eRNAs are likely to exert important functions in many regulated programs of gene transcription. The ChIP-seqs in this study measure the binding landscape of master transcription regulator of estrogen signaling - ER?, together with common histone marks including H3K27ac and H3K4me1 in MCF7 cells. These data serve as the basis to understand the enhancer map and subsequent analysis of eRNA expression using GRO-seq. The GRO-seq measures the trancription of nascent RNAs in the genome. From MCF7 cells treated with veichle or estrodial, we could identify estrogen-regulated eRNAs and subsequently could study their functions.

2013-06-04 | E-GEOD-45822 | biostudies-arrayexpress

A joint linkage/association strategy to interrogate AMD genetic susceptibility

Project description:A joint linkage/association strategy to interrogate AMD genetic susceptibility

| PRJNA390212 | ENA

Epigenome-wide Association Study of Obesity Susceptibility in Human Twins

Project description:Epigenome-wide Association Study of Obesity Susceptibility in Human Twins

| PRJNA903217 | ENA

An Exome-Wide Association Study Identifies New Susceptibility Loci for the Risk of Nicotine Dependence in European-American Populations

Project description:Cigarette smoking is one of the largest causes of preventable death worldwide. Smoking behaviors, including age at smoking initiation (ASI), smoking dependence (SD), and smoking cessation (SC), are all complex phenotypes determined by both genetic and environmental factors as well as their interactions. To identify susceptibility loci for each smoking phenotype, numerous studies have been conducted, with approaches including genome-wide linkage scans, candidate gene-based association analysis, and genome-wide association study (GWAS). Therefore, we conducted an exome-wide association study to identify new susceptibility loci for the risk of nicotine dependence in European-American populations.

2020-04-18 | GSE148812 | GEO

An Exome-Wide Association Study Identifies New Susceptibility Loci for the Risk of Nicotine Dependence in African-American Populations

2020-04-10 | GSE148375 | GEO

Functional Importance of eRNAs for Estrogen-dependent Gene Transcriptional Activation

2013-06-04 | GSE45822 | GEO

Transcriptome-wide association study to identify susceptibility genes for colorectal cancer

Project description:Transcriptome-wide association study to identify susceptibility genes for colorectal cancer

| PRJNA807047 | ENA