Integrative transcriptional and epigenomic modeling of xenobiotic-activated gene regulatory networks

项目总结/摘要 环境污染物2，3，7，8-四氯二苯并-对-二恶英（TCDD）是一种最有效的， 已知的持久性毒物。TCDD和其他二恶英类化学物质主要通过食物摄入， 引起各种不良反应，从免疫抑制到肝毒性和发育毒性。 改变。尽管环境和身体负担逐渐减少， 特别关注子宫内、母乳喂养的婴儿以及以当地捕捞的鱼类为食物的特定人群 与野生动物.芳烃受体（AHR）是一种配体诱导型转录因子， 二恶英的毒性作用。AHR被发现近40年后，它仍然是一个神秘的分子 除了作为环境传感器的功能外，还具有多种内源性作用。我们最近对 小鼠肝脏中AHR信号传导网络显示AHR直接结合启动子中的同源序列 靶基因的区域仅解释了约10%的TCDD诱导的基因扰动。此外，尚不清楚 为什么人类对TCDD的反应远不如啮齿类动物敏感。我们知识上的这些差距 很难估计人类接触二恶英的风险。我们的首要假设是组织和 AHR激活诱导的基因表达的物种特异性改变，这反过来又导致二恶英毒性， 由局部染色质可及性、基因调控区中的AHR结合和 AHR介导的长距离染色质相互作用。我们建议使用创新的功能组合， 基因组实验，计算建模和靶向表观基因组编辑（CRISPRi），以开发一种 AHR介导的组织和物种特异性基因调控的预测模型，并重建AHR 在人类与小鼠肝脏和B细胞中的转录调控网络。我们将借鉴AHR的具体 该项目产生的数据，以及NIH ENCODE和Roadmap表观基因组学项目， 从400多个人类细胞系中总共获得了10，000多个基因组和表观基因组数据集 和组织类型。在目标1中，我们将比较小鼠和人类的全基因组染色质可及性， 肝细胞和B细胞在不存在和存在TCDD的情况下。在目标2中，一种新的预测模型， 全基因组AHR结合将基于ChIP-Seq、染色质可及性和组蛋白 修改数据。在目标3中，我们将鉴定和预测AHR靶基因在大肠杆菌中的差异表达。 小鼠和人类从AHR结合位点的调节DNA和AHR介导的远程相互作用。的 我们的模型的总体影响将提高对组织和物种特异性基因的机制理解， AHR以前所未有的全基因组细节进行调控。我们的长期目标是开发一个基因组- 对核心转录失调的化学品进行人类风险评估的定量框架 调控途径。

PROJECT SUMMARY/ABSTRACT The environmental contaminant 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is one of the most potent and persistent toxicants known. TCDD and other dioxin-like chemicals are primarily ingested through food, and can cause various adverse effects ranging from immune suppression to hepatotoxicity and developmental alterations. Despite gradually decreasing environmental and body burdens, dioxin exposure remains of particular concern in utero, in breastfed infants, and specific populations reliant for food on locally caught fish and wildlife. The aryl hydrocarbon receptor (AHR), a ligand-inducible transcription factor, mediates virtually all of the toxic effects of dioxins. Nearly four decades after its discovery, the AHR remains an enigmatic molecule with a variety of endogenous roles in addition to its function as an environmental sensor. Our recent analysis of the AHR signaling network in mouse liver showed that direct AHR binding to cognate sequences in promoter regions of target genes explains only about 10% of TCDD-induced gene perturbations. In addition, it is unclear why humans are much less sensitive in responses to TCDD than rodents. These gaps in our knowledge make it difficult to estimate the risks of human exposure to dioxins. Our overarching hypothesis is that tissue- and species-specific alterations in gene expression induced by AHR activation, which in turn lead to dioxin toxicity, are determined by a combination of local chromatin accessibility, AHR binding in gene regulatory regions, and AHR-mediated long-range chromatin interactions. We propose to use an innovative combination of functional genomic experiments, computational modeling, and targeted epigenome editing (CRISPRi) to develop a predictive model for AHR-mediated tissue- and species-specific gene regulation, and to reconstruct the AHR transcriptional regulatory network in human vs. mouse liver and B cells. We will draw on both AHR-specific data generated in this project, and the NIH ENCODE and Roadmap Epigenomics projects, which have collectively made available 10,000+ genomic and epigenomic data sets from more than 400 human cell lines and tissue types. In Aim 1, we will compare genome-wide chromatin accessibility of mouse and human hepatocytes and B cells in the absence and presence of TCDD. In Aim 2, a novel predictive model for genome-wide AHR binding will be developed based on ChIP-Seq, chromatin accessibility and histone modification data. In Aim 3, we will identify and predict the differential expression of AHR target genes in mouse and human from AHR binding sites in regulatory DNA and AHR-mediated long-range interactions. The overall impact of our model will be improved mechanistic understanding of tissue-and species-specific gene regulation by the AHR in unprecedented genome-wide detail. Our long-term goal is to develop a genome- based quantitative framework for human risk assessment of chemicals that dysregulate core transcriptional regulatory pathways.