Functional elucidation of the sequence-encoded regulatory activity of enhancers in vivo in the brain

大脑体内增强子序列编码调节活性的功能阐明

基本信息

批准号：
10330886
负责人：
Alexander Nord
金额：
$ 45.13万
依托单位：
UNIVERSITY OF CALIFORNIA AT DAVIS
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 2026-12-31
项目状态：
未结题

项目摘要

SUMMARY Once considered junk, non-coding regions of the genome have emerged as central components of evolution, development, and disease. The most common non-coding regulatory elements in the human genome are enhancers, which ensure expression of target genes at the right time in the right cells by controlling their activation. Perturbation to enhancer function is widely accepted as a major, but still poorly understood, component of human brain evolution and disease. There have been major and continuing advances in annotating enhancers and predicting activity of these elements in cells and tissues, including the brain. Despite these advances, predicting the sequence-encoded function of enhancers remains a major challenge. Further, the dynamic and context-dependent chromosomal interactions, epigenetic modifications, and transcription factor activity that ultimately determine enhancer-mediated gene regulation generally remain poorly understood. This represents a significant barrier in understanding the function of enhancers and in interpreting the effect of enhancer sequence variation on human brain development, evolution and disease. As such, there is critical need to determine the relationship between sequence and function for regulatory DNA, and to define the determinants of enhancer activity and gene regulation in the brain. In the initial early stage investigator MIRA funding, we established a productive research program focused elucidating enhancer- mediated gene regulatory wiring in the mammalian brain. We paired functional assays with genetic and genomic approaches to model the function of enhancers, transcription factors, and chromatin remodeling proteins in normal and pathogenic brain development. The overarching goals of our MIRA research program are to: 1) Extend and apply methods to define sequence-encoded enhancer activity in the mammalian brain, 2) Determine the molecular mechanisms of enhancer-mediated gene regulation and transcriptional programming in the brain, and 3) Characterize the consequences of regulatory sequence variation to understand the role of enhancer DNA in the development, evolution, and disorders of the mammalian brain. In the renewal period, we will apply integrative genetic, genomic, and neuroscience methods to address key gaps in the understanding of sequence-encoded enhancer function and to answer fundamental questions regarding gene regulation in the brain. Our work will address basic and translationally-relevant questions regarding the sufficiency and necessity of enhancers for neurodevelopmental gene regulation, and will advance the emerging field of enhancer-based tools for labeling and manipulation of cell types in the brain. Overall, our contributions will help to decipher how transcriptional control is encoded at the genetic and epigenetic level and to illuminate the gene regulatory circuitry of the mammalian brain.

概括一旦被认为是垃圾，基因组的非编码区域已成为进化的中心成分，发育和疾病。人类基因组中最常见的非编码调节元件是增强子，通过控制靶基因在右细胞中确保靶基因的表达激活。对增强子功能的扰动已被广泛接受为主要，但仍然知之甚少，人脑进化和疾病的组成部分。在注释增强子并预测这些元素在包括大脑在内的细胞和组织中的活性。尽管这些进步，预测增强子的序列编码功能仍然是一个重大挑战。更远，动态和上下文依赖性染色体相互作用，表观遗传修饰和转录最终确定增强子介导的基因调节的因子活性通常保持较差理解。这代表了理解增强剂和解释功能的重大障碍增强子序列变化对人脑发育，进化和疾病的影响。这样，那里确定调节性DNA的序列与函数之间的关系是至关重要的，以及定义大脑增强子活性和基因调节的决定因素。在最初的早期阶段调查员Mira资助，我们建立了一项富有成效的研究计划，以阐明增强剂的阐明哺乳动物大脑中介导的基因调节布线。我们将功能分析与遗传和基因组方法来建模增强剂，转录因子和染色质重塑的功能正常和致病性脑发育中的蛋白质。 MIRA研究计划的总体目标为：1）扩展和应用方法来定义哺乳动物大脑中序列编码的增强子活性，2）确定增强子介导的基因调节和转录编程的分子机制在大脑中，3）表征调节序列变化的后果，以了解哺乳动物大脑的发育，进化和疾病中增强剂DNA。在续签时期，我们将应用综合遗传，基因组和神经科学方法来解决理解中的关键差距序列编码的增强子功能，并回答有关基因调节的基本问题脑。我们的工作将解决有关足够和翻译的基本和翻译问题的问题需要增强神经发育基因调节的增强子，并将推进新兴领域基于增强剂的工具，用于标记和操纵大脑细胞类型的工具。总体而言，我们的贡献将有所帮助破译转录控制如何在遗传和表观遗传水平上编码并照亮基因哺乳动物大脑的调节电路。