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Uncovering origins of convergent enhancer activities

揭示收敛增强子活动的起源

基本信息

批准号：
9420767
负责人：
Jennifer Anna Lachowiec
金额：
$ 0.18万
依托单位：
UNIVERSITY OF MICHIGAN AT ANN ARBOR
依托单位国家：
美国
项目类别：
财政年份：
2016
资助国家：
美国
起止时间：
2016-09-01 至 2018-08-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9420767
关键词：
Affect Antibodies Automobile Driving Binding Biochemical Biological Assay Biological Models Collection Complement Confocal Microscopy DNA DNA Binding DNA Sequence Disease Drosophila genus Drosophila melanogaster Elements Enhancers Evolution Fluorescence Gene Expression Gene Expression Profile Genes Genome Goals Growth and Development function Homeostasis Human Genome Individual Insulator Elements Intergenic Sequence Introns Laboratories Lead Malignant Neoplasms Methods Molecular Mutation Nucleic Acid Regulatory Sequences Pathway interactions Pattern Phenotype Pigmentation physiologic function Process Proteins RNA Interference Regulator Genes Regulatory Element Reporter Reporter Genes Research Set protein Site System Testing Untranslated RNA Variant Wing Work activating transcription factor exhaustion flexibility genetic approach human disease in vivo insight overexpression prevent promoter public health relevance pyrosequencing response syntax tool transcription factor

项目摘要

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.

描述（由申请人提供）：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。这些顺式调控序列通过与转录因子 (TF) 结合发挥作用。这些调节元件以及结合这些元件的转录因子的突变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然存在许多问题。迄今为止，研究顺式调控序列进化的研究主要集中在直系同源非编码序列如何在功能上发生分歧或尽管DNA序列存在分歧但仍保留其功能。关于新的顺式调控序列如何进化，人们所知甚少。在这里，我建议研究两个独立进化出相似活性的增强子，以确定调节这些元素的转录因子组之间的相似性和差异。这项工作不仅提供了对顺式调控序列的灵活性的见解，而且还提供了与它们相互作用的反式调控网络的灵活性的见解。为了探索增强子活性如何从非编码序列中产生，我将比较调节一对具有收敛活性的增强子的转录因子组。同一组 TF 可以识别不同的序列，从而产生趋同的表型。或者，不同的转录因子组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趋同表达的两个增强子的转录因子组。具体来说，我将检查果蝇和 D. willistoni 中已充分表征的黄色基因增强子，以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域，以测试这些表达模式背后的分子机制。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、新顺式调控序列的起源以及顺式调控 DNA 的语法。这些见解将有助于我们理解由影响顺式调控序列的突变引起的表型，例如疾病和癌症。