Genome-wide profiling of angiogenic cis-regulatory elements unravels cis-regulatory SNPs for vascular abnormality

Angiogenesis is extensively involved in embryonic development and requires complex regulation networks, whose defects can cause a variety of vascular abnormalities. Cis -regulatory elements control gene expression at all developmental stages, but they have not been studied or profiled in angiogenesi...

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Bibliographic Details
Published in:Scientific data 2024-05, Vol.11 (1), p.467-467, Article 467
Main Authors: Jin, Lihui, Han, Zhenyuan, Mao, Xiaotong, Lu, Jieru, Yan, Bingqian, Lu, Yiwen, Liang, Lili, Wang, Lin, Yu, Yu, Sun, Kun
Format: Article
Language:English
Subjects:
631/114/2164
631/136/16
631/208/135
Analysis
Angiogenesis
Chromatin
Deoxyribonuclease
Developmental stages
Embryogenesis
Gene expression
Genome-Wide Association Study
Genomes
Humanities and Social Sciences
Humans
multidisciplinary
Neovascularization, Pathologic - genetics
Polymorphism, Single Nucleotide
Regulatory sequences
Regulatory Sequences, Nucleic Acid
Science
Science (multidisciplinary)
Single-nucleotide polymorphism
Transcriptomes
Vascular Endothelial Growth Factor A - genetics
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Summary:Angiogenesis is extensively involved in embryonic development and requires complex regulation networks, whose defects can cause a variety of vascular abnormalities. Cis -regulatory elements control gene expression at all developmental stages, but they have not been studied or profiled in angiogenesis yet. In this study, we exploited public DNase-seq and RNA-seq datasets from a VEGFA-stimulated in vitro angiogenic model, and carried out an integrated analysis of the transcriptome and chromatin accessibility across the entire process. Totally, we generated a bank of 47,125 angiogenic cis -regulatory elements with promoter (marker by H3K4me3) and/or enhancer (marker by H3K27ac) activities. Motif enrichment analysis revealed that these angiogenic cis -regulatory elements interacted preferentially with ETS family TFs. With this tool, we performed an association study using our WES data of TAPVC and identified rs199530718 as a cis -regulatory SNP associated with disease risk. Altogether, this study generated a genome-wide bank of angiogenic cis -regulatory elements and illustrated its utility in identifying novel cis -regulatory SNPs for TAPVC, expanding new horizons of angiogenesis as well as vascular abnormality genetics.
ISSN:2052-4463
2052-4463
DOI:10.1038/s41597-024-03272-6