Physical and Functional Interactions of Cis Regulatory Modules

描述（由申请人提供）：序列特异性转录因子（TFs）通过与基因组中DNA序列的相互作用调节基因表达。这些相互作用控制着发育的关键步骤和对环境刺激的反应，它们的功能障碍可能导致各种疾病的进展。在这个项目中，作为我们的模型系统，我们将检查初级人类骨骼肌成肌细胞分化成肌管。在后生动物中，调控基序往往共同出现在非编码序列中，即调节附近基因表达的顺式调控模块（CRMs）。在这个项目中，我们将根据它们与邻近靶基因的相互作用及其对报告基因表达的影响来评估crm的物理和功能相互作用。特别是，我们将通过与更远的靶基因启动子的物理相互作用（“CRM- CRM相互作用”）以及对基因表达调节的潜在协同作用，研究CRM的远距离和潜在组合调节性质。这个项目的结果可能会揭示受调节的CRM调控但不与之相邻的基因有多远的趋势。这可能会对crm的调节作用的预测和实验研究产生重大影响，因为目前尚不清楚这种现象发生的频率。这个项目的结果可能还揭示了多个crm共同调节其靶基因的频率趋势，以及它们的综合效应是什么。这可能会对CRM的调节作用的预测和实验研究产生重大影响，因为目前的研究人员专注于寻找“[单一]CRM”，它赋予给定的表达模式，并将报告分析的结果分配给单独测试的CRM，并且很少不在另一个可能协同作用的候选CRM的背景下检查它。最后，该项目的结果可能揭示“分裂”crm是否发生（即，crm由物理分离的顺式调控区域组成，必须聚集在一起才能影响基因表达），并可能揭示“分裂”crm的不同“部分”如何在基因组中组织的趋势（即，“部分”的距离有多远，部分是在相同或不同的染色体上，等等）。这可能会对CRM的调控作用的预测和实验研究产生重大影响，包括我们对基因组调控元件进化的理解，并且需要在未来开发新的计算CRM预测算法，因为当前的算法认为CRM是作为独立调控单元的连续序列。

DESCRIPTION (provided by applicant): Sequence-specific transcription factors (TFs) regulate gene expression through their interactions with DNA sequences in the genome. These interactions control critical steps in development and responses to environmental stimuli, and their dysfunction can contribute to the progression of various diseases. In this project, as our model system we will examine primary human skeletal muscle myoblasts differentiating into myotubes. In metazoans, regulatory motifs tend to co-occur within stretches of noncoding sequence referred to as cis regulatory modules (CRMs) that regulate expression of the nearby gene(s). In this project, we will assess the physical and functional interactions of CRMs according to their interactions with their immediately adjacent target genes and their effects on reporter gene expression. In particular, we will examine the distant and potentially combinatorial regulatory nature of CRMs, through their physical interactions with the promoters of more distantly located target genes and with each other ('CRM- CRM interactions') and through potentially synergistic effects on regulation of gene expression. The results of this project may reveal trends in how far away are the genes that are regulated by but not adjacent to the regulating CRM. This could have major implications for the prediction and experimental study of the regulatory roles of CRMs, as it is currently unknown how often this phenomenon may occur. The results of this project may also reveal trends in how frequently multiple CRMs work together to regulate their target genes, and what their combined effects are. This could have major implications for the prediction and experimental study of the regulatory roles of CRMs, as currently investigators focus on finding "the [single] CRM" that confers a given expression pattern and assign the result of a reporter assay to the CRM tested on its own, and rarely do not examine it in the context of another candidate CRM with which it may synergize. Finally, the results of this project may reveal whether 'split' CRMs occur (i.e., CRMs composed of physically separated cis regulatory regions that must come together in order to affect gene expression), and may reveal trends in how the different 'parts' of the 'split' CRMs are organized in the genome (i.e., how far apart the 'parts' are, are the parts on the same or different chromosomes, etc.). This could have major implications for the prediction and experimental study of the regulatory roles of CRMs, including our understanding of the evolution of genomic regulatory elements, and would require new computational CRM prediction algorithms to be developed in the future since current algorithms consider CRMs to be contiguous stretches of sequence that function as independent regulatory units. PUBLIC HEALTH RELEVANCE: This project is focused on better understanding the genomic organization of DNA regulatory elements that regulate gene expression. In this project, we will examine differentiating skeletal muscle myoblasts, a biomedically important cell type. The findings from this project will provide a better understanding of gene regulatory mechanisms in these cell types.