TCF21 and AP-1 interact through epigenetic modifications to regulate coronary artery disease gene expression

Quanyi Zhao,Clint L Miller,Manabu Nagao,Trieu Nguyen,Robert Wirka,Milos Pjanic,Thomas Quertermous,Paul Cheng,Juyong Brian Kim

doi:10.1186/s13073-019-0635-9

Abstract

BackgroundGenome-wide association studies have identified over 160 loci that are associated with coronary artery disease. As with other complex human diseases, risk in coronary disease loci is determined primarily by altered expression of the causal gene, due to variation in binding of transcription factors and chromatin-modifying proteins that directly regulate the transcriptional apparatus. We have previously identified a coronary disease network downstream of the disease-associated transcription factor TCF21, and in work reported here extends these studies to investigate the mechanisms by which it interacts with the AP-1 transcription complex to regulate local epigenetic effects in these downstream coronary disease loci.MethodsGenomic studies, including chromatin immunoprecipitation sequencing, RNA sequencing, and protein-protein interaction studies, were performed in human coronary artery smooth muscle cells.ResultsWe show here that TCF21 and JUN regulate expression of two presumptive causal coronary disease genes, SMAD3 and CDKN2B-AS1, in part by interactions with histone deacetylases and acetyltransferases. Genome-wide TCF21 and JUN binding is jointly localized and particularly enriched in coronary disease loci where they broadly modulate H3K27Ac and chromatin state changes linked to disease-related processes in vascular cells. Heterozygosity at coronary disease causal variation, or genome editing of these variants, is associated with decreased binding of both JUN and TCF21 and loss of expression in cis, supporting a transcriptional mechanism for disease risk.ConclusionsThese data show that the known chromatin remodeling and pioneer functions of AP-1 are a pervasive aspect of epigenetic control of transcription, and thus, the risk in coronary disease-associated loci, and that interaction of AP-1 with TCF21 to control epigenetic features, contributes to the genetic risk in loci where they co-localize.

Highlights

Genome-wide association studies have identified over 160 loci that are associated with coronary artery disease
We have investigated the interaction of transcription factors TCF21 and activated protein-1 (AP-1) at loci identified by genome-wide association studies (GWAS) to regulate risk for the coronary artery disease (CAD) phenotype, focusing on 15q22.33 and 9p21.3
To investigate the specific roles of AP-1 and TCF21 in regulating CAD gene transcription, we first focused our investigation on two candidate causal genes, CDKN2BAS and SMAD3 [33, 38]. siRNA knockdown of JUN in human coronary artery smooth muscle cells (HCASMC) was associated with decreased expression levels of CDKN2BAS and SMAD3 (Fig. 1a, c, Additional file 1: Figure S1A)

Summary

Introduction

Genome-wide association studies have identified over 160 loci that are associated with coronary artery disease. As with other complex human diseases, risk in coronary disease loci is determined primarily by altered expression of the causal gene, due to variation in binding of transcription factors and chromatin-modifying proteins that directly regulate the transcriptional apparatus. We have previously identified a coronary disease network downstream of the disease-associated transcription factor TCF21, and in work reported here extends these studies to investigate the mechanisms by which it interacts with the AP-1 transcription complex to regulate local epigenetic effects in these downstream coronary disease loci. In the context of atherosclerosis, an important feature of TCF21 biology is the fact that it regulates fundamental cellular differentiation events in the developing epicardium, serving as a determining factor for the divergence between coronary vascular smooth muscle cell (SMC) and cardiac fibroblast lineages [15, 16]. TCF21 downstream target regions are enriched for known CAD risk loci, suggesting that TCF21 plays a central role in regulating risk in other loci to effect the biology of atherosclerotic plaques [23]

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