Regulation and Role of Aryl Hydrocarbon Receptor in Human Embryonic Stem Cells and Their Differentiating Counterparts [RNA-Seq]

Aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor, which mediates the effects of various environmental contaminants, like polycyclic and halogenated aromatic hydrocarbons, including the most potent agonist 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), in multiple tissues. Recent advances in AHR biology have underlined its importance in cells with high developmental potency, including pluripotent stem cells. Nonetheless, there is little data on AHR expression and its role during the initial stages of stem cell differentiation. The purpose of this study was to investigate the temporal pattern of AHR expression during directed differentiation of human embryonic stem cells (hESC) into neural progenitor, early mesoderm and definitive endoderm cells. Additionally, we studied the effect of AHR agonist 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) on gene expression profile in hESCs and differentiated cells by RNA-seq, accompanied by identification of AHR binding sites by ChIP-seq and epigenetic landscape analysis by ATAC-seq. . We show that AHR is differentially regulated in distinct lineages, provide evidence that TCDD impairs differentiation of hESCs and identify novel potential AHR target genes which expand our understanding on the role of this protein in different cell types. Overall design: ATAC-seq profiles of hESC H9 cells pre-treated with DMSO (control) or 10 nM TCDD in mTESRTM1 medium for 3 days in three biological replicates

芳基烃受体（aryl hydrocarbon receptor, AHR）是一种配体激活型转录因子，可介导多种环境污染物的生物学效应，包括多环芳烃与卤代芳烃类化合物，其中活性最强的激动剂为2,3,7,8-四氯二苯并对二噁英（2,3,7,8-tetrachlorodibenzo-p-dioxin, TCDD），其作用遍及多种组织。近年来AHR生物学领域的研究进展凸显了其在高发育潜能细胞（包括多能干细胞）中的重要性，但目前关于AHR的表达及其在干细胞分化初始阶段的作用的相关数据仍较为匮乏。本研究旨在探究人胚胎干细胞（human embryonic stem cells, hESC）定向分化为神经前体细胞、早期中胚层细胞与定型内胚层细胞过程中，AHR表达的时序模式。此外，本研究通过RNA测序（RNA-seq）分析了AHR激动剂TCDD对hESC及分化细胞的基因表达谱的影响，并辅以染色质免疫沉淀测序（ChIP-seq）鉴定AHR结合位点，同时通过转座酶可及性测序（ATAC-seq）开展表观遗传景观分析。本研究发现AHR在不同细胞谱系中存在差异性调控，证实TCDD会损害hESC的分化过程，并鉴定出若干新型潜在AHR靶基因，从而拓展了我们对该蛋白在不同细胞类型中作用的认知。整体实验设计：在mTESRTM1培养基中，用二甲基亚砜（DMSO，对照组）或10 nM TCDD处理人胚胎干细胞H9细胞3天，设置3个生物学重复，随后进行ATAC-seq检测。