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

项目摘要/摘要 环境污染物2，3，7，8-四氯二苯并-对二恶英(TCDD)是目前危害最大的环境污染物之一。 已知的持久性毒物。TCDD和其他类似二恶英的化学物质主要通过食物摄入，可以 引起各种不良反应，从免疫抑制到肝毒性和发育 改装。尽管环境和身体负担逐渐减少，但接触二恶英仍然是 特别关注子宫内、母乳喂养的婴儿和依赖当地捕捞的鱼作为食物的特定人群 和野生动物。芳香烃受体(AHR)是一种配体诱导的转录因子，几乎介导了所有 二恶英的毒性作用。在发现近40年后，AHR仍然是一个谜一样的分子 除了作为环境传感器的功能外，它还具有各种内源性作用。我们最近对 小鼠肝脏AHR信号网络显示AHR直接与启动子中的同源序列结合 靶基因的区域只能解释大约10%的TCDD诱导的基因扰动。此外，目前还不清楚 为什么人类对TCDD的反应比啮齿动物低得多。我们知识中的这些差距使我们 很难估计人类接触二恶英的风险。我们最重要的假设是组织-和 AHR激活诱导的基因表达的物种特异性变化，进而导致二恶英毒性， 由局部染色质可及性、基因调节区中的AHR结合以及 AHR介导的长程染色质相互作用。我们建议使用创新的功能组合 基因组实验、计算建模和有针对性的表观基因组编辑(CRISPRi)以开发 AHR介导的组织和物种特异性基因调控的预测模型和AHR的重建 人与小鼠肝脏和B细胞的转录调控网络。我们将利用两个特定于AHR的 在这个项目中产生的数据，以及NIH ENCODE和Roadmap Eigenome项目，它们已经 总共提供了来自400多个人类细胞系的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全基因组染色质的可及性 肝细胞和B细胞在没有和存在TCDD的情况下。在目标2中，提出了一种新的预测模型 全基因组AHR结合将基于芯片序列、染色质可及性和组蛋白 修改数据。在目标3中，我们将识别和预测AHR靶基因在 小鼠和人的AHR结合位点在调节DNA和AHR介导的长距离相互作用中起作用。这个 我们模型的总体影响将是提高对组织和物种特定基因的机械性理解 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种基因组- 基于定量框架的人类对核心转录失调化学物质的风险评估 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.