Uncovering origins of convergent enhancer activities

 描述（申请人提供）：超过98%的人类基因组含有非编码DNA，其中一些编码控制基因表达的顺式调控序列。这些顺式调节序列通过与转录因子（TF）结合而发挥功能。这些调控元件的突变以及与这些元件结合的转录因子会引起适应性表型变异和疾病。尽管它们很重要，但关于这些调控序列如何发挥作用和进化仍存在许多问题。迄今为止，研究顺式调控序列的进化主要集中在邻位非编码序列如何在功能上分化或保留其功能，尽管DNA序列的分歧。对于新的顺式调控序列如何进化，人们了解得更少.在这里，我建议调查两个增强子，独立地发展类似的活动，以确定similaritis和调节这些元素的TF集之间的差异。这项工作不仅提供了对顺式调节序列的灵活性的洞察，而且还提供了与它们相互作用的反式调节网络的灵活性。为了探索增强子活性如何来自非编码序列，我将比较调节具有会聚活性的一对增强子的TF的集合。同一组TF可以识别不同的序列，产生趋同的表型。或者，不同组的TF可以以产生趋同表型的方式识别不同的序列。双报告基因系统将用于鉴定调节驱动会聚表达的两个增强子的TF组。具体地说，我将研究黑腹果蝇和果蝇中黄色基因的特征性增强子。willistoni研究独立进化的增强子如何驱动相似的表达模式。最后，我将测试这些转录因子是否直接结合这些调控区作为这些表达模式的分子机制的测试。通过这些努力，我将深入了解产生相同表型的途径的多样性，新的顺式调控序列的起源，以及顺式调控DNA的语法。这些见解将告知我们的表型，如疾病和癌症，所产生的影响顺式调控序列的突变的理解。

 DESCRIPTION (provided by applicant): More than 98% of the human genome contains non-coding DNA, some of which encodes cis-regulatory sequences that control gene expression. These cis-regulatory sequences function by binding to transcription factors (TFs). Mutations to these regulatory elements-and the TFs that bind these elements-give rise to the adaptive phenotypic variation as well as disease. Despite their importance, many questions remain about how these regulatory sequences function and evolve. To date, studies investigating the evolution of cis-regulatory sequences have focused primarily on how orthologous non-coding sequences either diverge in function or retain their function despite DNA sequence divergence. Much less has been learned about how new cis- regulatory sequences evolve. Here, I propose to investigate two enhancers that independently evolved similar activity to identify the similaritis and differences between the sets of TFs regulating these elements. This work provides insight into not only the flexibility of cis-regulatory sequences, but also the flexibility of the trans- regulatory networks with which they interact. To explore how enhancer activity arises from non-coding sequences, I will compare the sets of TFs regulating a pair of enhancers with convergent activities. The same set of TFs may recognize distinct sequences, creating convergent phenotypes. Alternatively, different sets of TFs may recognize the distinct sequences in a manner that produces convergent phenotypes. A dual reporter gene system will be used to identify the sets of TFs regulating two enhancers driving convergent expression. Specifically, I will examine the well-characterized enhancers of the gene yellow in Drosophila melanogaster and D. willistoni to study how independently evolved enhancers drive similar expression patterns. Finally, I will test whether these transcription factors directly bind either of these regulatory regions as a test of the molecular mechanisms underlying these expression patterns. Through these efforts, I will gain insights into the diversity of pathways that produce identical phenotypes, the origin of new cis-regulatory sequences, and the syntax of cis-regulatory DNA. These insights will inform our understanding of phenotypes, such as disease and cancers, arising from mutations affecting cis-regulatory sequences.