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血管异常的顺式调控 SNP 的血管生成顺式调控元件的全基因组分析

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

机构信息

Department of Pediatric Cardiology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200092, China.

Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, 100081, China.

出版信息

Sci Data. 2024 May 8;11(1):467. doi: 10.1038/s41597-024-03272-6.

DOI:10.1038/s41597-024-03272-6
PMID:38719891
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11078952/
Abstract

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.

摘要

血管生成广泛参与胚胎发育，需要复杂的调控网络，其缺陷可导致多种血管异常。顺式调控元件在所有发育阶段控制基因表达，但它们在血管生成中尚未得到研究或描述。在这项研究中，我们利用了来自 VEGFA 刺激的体外血管生成模型的公共 DNase-seq 和 RNA-seq 数据集，并对整个过程中的转录组和染色质可及性进行了综合分析。总共，我们生成了一个包含 47125 个具有启动子（由 H3K4me3 标记）和/或增强子（由 H3K27ac 标记）活性的血管生成顺式调控元件的库。基序富集分析表明，这些血管生成顺式调控元件优先与 ETS 家族 TF 相互作用。使用我们的 TAPVC 的 WES 数据进行关联研究，我们发现 rs199530718 是与疾病风险相关的顺式调控 SNP。总之，这项研究生成了一个全基因组的血管生成顺式调控元件库，并说明了它在识别 TAPVC 的新型顺式调控 SNP 中的效用，为血管生成和血管异常遗传学开辟了新的视野。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0f0e/11078952/6a6de4359b5c/41597_2024_3272_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0f0e/11078952/c6fb1196f1bb/41597_2024_3272_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0f0e/11078952/487800372418/41597_2024_3272_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0f0e/11078952/3dbdf664d160/41597_2024_3272_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0f0e/11078952/70369e96ec2a/41597_2024_3272_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0f0e/11078952/a99e584e7c6d/41597_2024_3272_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0f0e/11078952/6a6de4359b5c/41597_2024_3272_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0f0e/11078952/c6fb1196f1bb/41597_2024_3272_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0f0e/11078952/487800372418/41597_2024_3272_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0f0e/11078952/3dbdf664d160/41597_2024_3272_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0f0e/11078952/70369e96ec2a/41597_2024_3272_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0f0e/11078952/a99e584e7c6d/41597_2024_3272_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0f0e/11078952/6a6de4359b5c/41597_2024_3272_Fig6_HTML.jpg

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