Integrative analysis tools to dissect cell-type specific transcriptional programs

描述（由申请人提供）：细胞类型特异性基因表达程序如何建立和维持是分子生物学的一个基本问题。在哺乳动物细胞中，数百种序列特异性转录因子已被编目，它们以细胞类型特异性和组合占用模式结合其靶基因的调控区域。此外，产生不同细胞系的发育过程伴随着复杂的染色质重塑。越来越多的证据表明，细胞类型特异性基因的调控区域可能经常在发育的早期阶段被染色质标记建立，有时被“平衡”。然而，基因调控区域的详细特征-包括它们在早期祖细胞中的初始建立，它们的染色质状态的动力学以及多种转录因子对基因转录输出的组合控制-仅针对少数发育重要基因进行了研究。该项目的目标是开发新的综合计算方法，利用大量的下一代测序数据集，从根本上推进我们对细胞类型特异性转录程序的理解。我们将开发综合计算分析方法：(1)从ChIP-seq和dna -seq中学习转录因子结合的序列和染色质决定因素；(2)利用dna -seq在所有可用的细胞类型中绘制人类和小鼠基因组中所有调节区域的染色质可及性景观，剖析其早期祖细胞中染色质状态的变化，并提取控制其分化增益和损失的序列代码；(3)模拟细胞类型特异性基因表达程序作为染色质状态、转录因子结合和调控序列分析的函数。我们将把我们的计算方法开发与有针对性的实验验证结合起来，包括位点特异性和全基因组分析。

DESCRIPTION (provided by applicant): How cell-type specific gene expression programs are established and maintained is a fundamental question in molecular biology. In mammalian cells, hundreds of sequence-specific transcription factors have been catalogued, and they bind the regulatory regions of their target genes in cell-type specific and combinatorial occupancy patterns. Moreover, the developmental programs that generate different cell lineages are accompanied by complex chromatin remodeling. Increasing evidence suggests that the regulatory regions of cell-type specific genes may often be established and sometimes "poised" by chromatin marks at earlier stages in development. However, the detailed characterization of gene regulatory regions-including their initial establishment in earlier progenitor cells, the dynamics of their chromatin state, and the combinatorial control of gene transcriptional output by multiple transcription factors-has only been studied for a handful of developmentally important genes. The goal of this project is to develop new integrative computational methods that exploit massive next- generation sequencing data sets to fundamentally advance our understanding of cell-type specific transcriptional programs. We will develop integrative computational analysis methods for (1) learning the sequence and chromatin determinants of transcription factor binding from ChIP-seq and DNase-seq; (2) mapping the landscape of chromatin accessibility of all regulatory regions in the human and mouse genomes using DNase-seq across all available cell types, dissecting the poising of their chromatin state in earlier progenitor cells, and extracting the sequence code governing their gain and loss in differentiation; and (3) modeling cell-type specific gene expression programs as a function of chromatin state, transcription factor binding, and regulatory sequence analysis. We will couple our computational methods development with targeted experimental validation, including both locus-specific and genome-wide assays.