Zhao Ming-Tao, Shao Ning-Yi, Hu Shijun, Ma Ning, Srinivasan Rajini, Jahanbani Fereshteh, Lee Jaecheol, Zhang Sophia L, Snyder Michael P, Wu Joseph C
From the Stanford Cardiovascular Institute, Department of Medicine, Division of Cardiology, Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, CA (M.-T.Z., N.-Y.S., N.M., J.L., S.L.Z., J.C.W.); Department of Cardiovascular Surgery of the Frist Affiliated Hospital, Institute for Cardiovascular Science, Soochow University, Suzhou, Jiangsu, China (S.H.); Department of Chemical and Systems Biology, Stanford University School of Medicine, CA (R.S.); and Department of Genetics, Stanford University School of Medicine, CA (F.J., M.P.S.).
Circ Res. 2017 Nov 10;121(11):1237-1250. doi: 10.1161/CIRCRESAHA.117.311367. Epub 2017 Oct 13.
Regulatory DNA elements in the human genome play important roles in determining the transcriptional abundance and spatiotemporal gene expression during embryonic heart development and somatic cell reprogramming. It is not well known how chromatin marks in regulatory DNA elements are modulated to establish cell type-specific gene expression in the human heart.
We aimed to decipher the cell type-specific epigenetic signatures in regulatory DNA elements and how they modulate heart-specific gene expression.
We profiled genome-wide transcriptional activity and a variety of epigenetic marks in the regulatory DNA elements using massive RNA-seq (n=12) and ChIP-seq (chromatin immunoprecipitation combined with high-throughput sequencing; n=84) in human endothelial cells (CD31CD144), cardiac progenitor cells (Sca-1), fibroblasts (DDR2), and their respective induced pluripotent stem cells. We uncovered 2 classes of regulatory DNA elements: class I was identified with ubiquitous enhancer (H3K4me1) and promoter (H3K4me3) marks in all cell types, whereas class II was enriched with H3K4me1 and H3K4me3 in a cell type-specific manner. Both class I and class II regulatory elements exhibited stimulatory roles in nearby gene expression in a given cell type. However, class I promoters displayed more dominant regulatory effects on transcriptional abundance regardless of distal enhancers. Transcription factor network analysis indicated that human induced pluripotent stem cells and somatic cells from the heart selected their preferential regulatory elements to maintain cell type-specific gene expression. In addition, we validated the function of these enhancer elements in transgenic mouse embryos and human cells and identified a few enhancers that could possibly regulate the cardiac-specific gene expression.
Given that a large number of genetic variants associated with human diseases are located in regulatory DNA elements, our study provides valuable resources for deciphering the epigenetic modulation of regulatory DNA elements that fine-tune spatiotemporal gene expression in human cardiac development and diseases.
人类基因组中的调控DNA元件在胚胎心脏发育和体细胞重编程过程中，对于决定转录丰度和基因表达的时空特性起着重要作用。目前尚不清楚调控DNA元件中的染色质标记如何被调控，以在人类心脏中建立细胞类型特异性的基因表达。
我们旨在破译调控DNA元件中细胞类型特异性的表观遗传特征，以及它们如何调节心脏特异性基因表达。
我们使用大规模RNA测序（n = 12）和染色质免疫沉淀结合高通量测序（ChIP-seq；n = 84），分析了人类内皮细胞（CD31CD144）、心脏祖细胞（Sca-1）、成纤维细胞（DDR2）及其各自诱导多能干细胞中调控DNA元件的全基因组转录活性和多种表观遗传标记。我们发现了两类调控DNA元件：I类在所有细胞类型中均被鉴定为具有普遍存在的增强子（H3K4me1）和启动子（H3K4me3）标记，而II类则以细胞类型特异性方式富含H3K4me1和H3K4me3。I类和II类调控元件在给定细胞类型中对附近基因表达均表现出刺激作用。然而，无论远端增强子如何，I类启动子对转录丰度显示出更主要的调控作用。转录因子网络分析表明，人类诱导多能干细胞和心脏来源的体细胞选择了它们偏好的调控元件来维持细胞类型特异性基因表达。此外，我们在转基因小鼠胚胎和人类细胞中验证了这些增强子元件的功能，并鉴定出一些可能调控心脏特异性基因表达的增强子。
鉴于大量与人类疾病相关的遗传变异位于调控DNA元件中，我们的研究为破译调控DNA元件的表观遗传调控提供了宝贵资源，这些调控可在人类心脏发育和疾病中微调时空基因表达。
