Epigenetic control of gene expression in alcoholic brain

描述(申请人提供)：慢性酒精会导致人类和动物模型中大脑基因表达的广泛变化，其中一些会导致酒精成瘾和酒精依赖。最近的研究指出，染色质修饰在控制酒精诱导的基因表达和行为变化方面发挥着核心作用，通常被称为表观遗传变化。为了了解染色质修饰如何调节酒精脑中基因表达的变化，在基因组水平上整合染色质和转录数据是必要的。在这里，我们将检验一个假设，即长期酗酒通过染色质状态的长期变化来改变基因表达。我们将首先使用染色质免疫沉淀和DNA测序(CHIP-SEQ)来测量慢性酒精中毒患者和对照组死后大脑中两个染色质标记的基因组差异。然后，我们将使用一种新的系统方法，探索在同一样本中通过RNA-Seq测量的染色质修饰和基因表达之间的全基因组关系。这种方法将使我们能够将基因组变异划分为具有生物学意义的模式，并识别ChIP-Seq和RNA-Seq数据集之间的稳健相关性，我们将使用这些相关性来提出染色质标记和基因表达之间的机制联系。这种方法还将根据单个基因在基因网络中的重要性以及与染色质标记的相关性来确定它们的优先顺序，我们将使用这一策略来选择几个中枢基因进行验证。我们将用芯片验证几个HUB基因的染色质标记，然后用qRT-PCR验证它们的表达水平。总体而言，该提案旨在开发一种系统方法，该方法将检测CHIP-SEQ和RNA-SEQ数据集之间的稳健协变。我们将确定慢性酒精滥用对基因表达调控至关重要的表观遗传成分，并为人类酒精中毒的药物开发提供新的靶点。此外，这种方法可以作为分析现有和新出现的基因组数据的财富的原型。

DESCRIPTION (provided by applicant): Chronic alcohol causes widespread changes in brain gene expression in humans and animal models, some of which contribute to alcohol addiction and alcohol dependence. Recent studies point to a central role of chromatin modifications, often referred to as epigenetic changes, in controlling alcohol- induced changes in gene expression and behavior. To understand how chromatin modifications mediate changes in gene expression in alcoholic brain, an integration of chromatin and transcriptional data at the genome level is required. Here we will test the hypothesis that chronic alcohol abuse changes gene expression via long-lasting changes in chromatin states. We will first measure genomic differences at two chromatin marks in postmortem brains of chronic alcoholics and control cases using chromatin immunoprecipitation followed by DNA sequencing (ChIP-Seq). We will then explore the genome-wide relationships between chromatin modifications and gene expression measured in the same samples by RNA-Seq using a novel systems approach. This approach will allow us to partition genomic variance into biologically meaningful patterns and identify robust correlations between ChIP- Seq and RNA-Seq data sets, which we will use to propose mechanistic links between chromatin marks and gene expression. This approach will also prioritize individual genes based on their importance in gene networks and correlations with chromatin marks and we will use this strategy to select several hub genes for validation. We will validate chromatin marks of several hub genes with ChIP followed by qRT- PCR and their expression levels with qRT-PCR. Overall, this proposal aims to develop a systems approach that will detect robust co-variation between ChIP-Seq and RNA-Seq data sets. We will identify epigenetic components critical for regulation of gene expression by chronic alcohol abuse and provide new targets for medication development for human alcoholism. In addition, this approach may serve as a prototype for analysis of the wealth of existing and emerging genomic data.