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Genome-wide enhancer-gene regulatory maps link causal variants to target genes underlying human colorectal cancer risk [H3K27ac ChIP-seq]

ABSTRACT: Genome-wide enhancer-gene regulatory maps link causal variants to target genes underlying human colorectal cancer risk [H3K27ac ChIP-seq]

PROVIDER: PRJNA923341 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23069451_1.fastq.gz	Fastqsanger.gz
	SRR23069451_2.fastq.gz	Fastqsanger.gz
	SRR23069452_1.fastq.gz	Fastqsanger.gz
	SRR23069452_2.fastq.gz	Fastqsanger.gz
	SRR23069453_1.fastq.gz	Fastqsanger.gz

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Genome-wide enhancer-gene regulatory maps link causal variants to target genes underlying human colorectal cancer risk [H3K27ac ChIP-seq]

2023-01-17 | GSE222768 | GEO

Genome-wide enhancer-gene regulatory maps link causal variants to target genes underlying human colorectal cancer risk [RNA-seq]

Project description:Although GWASs have identified thousands of variants associated with human complex traits, most of which reside in the non-coding regions, especially enhancers, and biological mechanisms remain unclear. To created enhancer-gene maps to determine causal variant of CRC risk, we performed multi-omics analyses of ATAC-seq, H3K27ac ChIP-seq and RNA-seq with high quality from our 10 CRC tissues. By computationally integrating these multi-omics data, we identified 34,130 enhancer-gene connections involving 15,121 unique enhancers and 12,351 expressed genes. We demonstrated an ABC regulatory variant rs4810856 that is significantly associated with an increased CRC risk with large-scale population study and biological experiments. Our study provides regulation maps linking enhancers to genes, providing new insights into colorectal cancer etiology.

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Genome-wide enhancer-gene regulatory maps link causal variants to target genes underlying human colorectal cancer risk [ATAC-seq]

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Genome-wide enhancer-gene regulatory maps link causal variants to target genes underlying human colorectal cancer risk

Project description:Genome-wide enhancer-gene regulatory maps link causal variants to target genes underlying human colorectal cancer risk

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Genome-wide enhancer-gene regulatory maps link causal variants to target genes underlying human colorectal cancer risk [ATAC-seq]

Project description:Genome-wide enhancer-gene regulatory maps link causal variants to target genes underlying human colorectal cancer risk [ATAC-seq]

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Genome-wide enhancer-gene regulatory maps link causal variants to target genes underlying human colorectal cancer risk [RNA-seq]

Project description:Genome-wide enhancer-gene regulatory maps link causal variants to target genes underlying human colorectal cancer risk [RNA-seq]

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Genome-wide enhancer-gene regulatory maps link causal variants to target genes underlying human cancer risk.

Project description:Genome-wide association studies have identified numerous variants associated with human complex traits, most of which reside in the non-coding regions, but biological mechanisms remain unclear. However, assigning function to the non-coding elements is still challenging. Here we apply Activity-by-Contact (ABC) model to evaluate enhancer-gene regulation effect by integrating multi-omics data and identified 544,849 connections across 20 cancer types. ABC model outperforms previous approaches in linking regulatory variants to target genes. Furthermore, we identify over 30,000 enhancer-gene connections in colorectal cancer (CRC) tissues. By integrating large-scale population cohorts (23,813 cases and 29,973 controls) and multipronged functional assays, we demonstrate an ABC regulatory variant rs4810856 associated with CRC risk (Odds Ratio = 1.11, 95%CI = 1.05-1.16, P = 4.02 × 10-5) by acting as an allele-specific enhancer to distally facilitate PREX1, CSE1L and STAU1 expression, which synergistically activate p-AKT signaling. Our study provides comprehensive regulation maps and illuminates a single variant regulating multiple genes, providing insights into cancer etiology.

| S-EPMC10520073 | biostudies-literature

Genome-wide enhancer-gene regulatory maps link causal variants to target genes underlying human colorectal cancer risk

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

2023-01-17 | GSE222770 | GEO

Human iPSC-derived retinal pigment epithelium: a model system for identifying and functionally characterizing causal variants at AMD risk loci

Project description:We evaluate whether human induced pluripotent stem cell-derived retinal pigment epithelium (iPSC-RPE) cells can be used to prioritize and functionally characterize causal variants at age-related macular degeneration (AMD) risk loci. We generated iPSC-RPE from six subjects and show that they have morphological and molecular characteristics similar to native RPE. We generated RNA-seq, ATAC-seq, and H3K27ac ChIP-seq data and observe high similarity in gene expression and enriched transcription factor motif profiles between iPSC-RPE and human fetal-RPE. We performed fine-mapping of AMD risk loci by integrating molecular data from the iPSC-RPE, adult retina, and adult RPE, which identified rs943080 as the probable causal variant at VEGFA. We show that rs943080 is associated with altered chromatin accessibility of a distal ATAC-seq peak, decreased overall gene expression of VEGFA, and allele specific expression of a non-coding transcript. These results provide insight into the mechanism underlying the association of the VEGFA locus with AMD. Raw data requires controlled access and is deposited at dbGaP http://www.ncbi.nlm.nih.gov/gap/?term=phs000924

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Genome-wide enhancer maps link risk variants to disease genes.

Project description:Genome-wide association studies (GWAS) have identified thousands of noncoding loci that are associated with human diseases and complex traits, each of which could reveal insights into the mechanisms of disease1. Many of the underlying causal variants may affect enhancers2,3, but we lack accurate maps of enhancers and their target genes to interpret such variants. We recently developed the activity-by-contact (ABC) model to predict which enhancers regulate which genes and validated the model using CRISPR perturbations in several cell types4. Here we apply this ABC model to create enhancer-gene maps in 131 human cell types and tissues, and use these maps to interpret the functions of GWAS variants. Across 72 diseases and complex traits, ABC links 5,036 GWAS signals to 2,249 unique genes, including a class of 577 genes that appear to influence multiple phenotypes through variants in enhancers that act in different cell types. In inflammatory bowel disease (IBD), causal variants are enriched in predicted enhancers by more than 20-fold in particular cell types such as dendritic cells, and ABC achieves higher precision than other regulatory methods at connecting noncoding variants to target genes. These variant-to-function maps reveal an enhancer that contains an IBD risk variant and that regulates the expression of PPIF to alter the membrane potential of mitochondria in macrophages. Our study reveals principles of genome regulation, identifies genes that affect IBD and provides a resource and generalizable strategy to connect risk variants of common diseases to their molecular and cellular functions.

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