Identifying enhancers with human-specific developmental functions

识别具有人类特异性发育功能的增强子

基本信息

批准号：
7945680
负责人：
James P Noonan
金额：
$ 63.17万
依托单位：
YALE UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2010
资助国家：
美国
起止时间：
2010-08-01 至 2015-07-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/7945680
关键词：
Acceleration Affinity Chromatography Alzheimer&apos s Disease Anterior Behavioral Binding Binding Sites Biochemical Biological Assay Brain Clinic Complement Complementary DNA Conserved Sequence Coupled Data Data Set Deposition Development Developmental Gene Disease E1A-associated p300 protein EP300 gene Elements Embryo Enhancers Event Evolution Gel Gene Expression Profile Gene Expression Regulation Gene Targeting Genes Genetic Genome Genomics Goals Health Heart Diseases Human Human Biology Human Development Human Genome In Situ Hybridization In Vitro Indium Infection LacZ Genes Language Light Limb Development Limb structure Macaca mulatta Malaria Maps Mass Spectrum Analysis Measures Metabolic Methods Mission Modeling Modification Molecular Molecular Profiling Morphology Multiple Sclerosis Mus Mutation Orthologous Gene Pan Genus Pattern Phenotype Phylogenetic Analysis Policies Primates Psychotic Disorders Public Health Publishing Recording of previous events Recruitment Activity Regulatory Element Relative (related person)Reporter Reporter Genes Research Research Personnel Research Proposals Role Skin Cancer Source Statistical Methods Talents Technology Testing Thumb structure Time Transgenic Mice Transgenic Organisms United States National Institutes of Health Vocabulary Walking Wrist base brain size embryo tissue experimental analysis gain of function genetic analysis genome database genome sequencing genome-wide homologous recombination human disease improved in vivo insertion/deletion mutation insight mouse development mouse genome novel positional cloning postnatal public health relevance research study spatiotemporal stem tool trait transcription factor web site

项目摘要

DESCRIPTION (provided by applicant): As a species, we are distinguished from other primates by our capacity for language, our ability to walk upright, and our talent for inventing and using sophisticated tools. These traits originated in physical adaptations, such as increased brain size and changes in the morphology of the limbs, which required changes in development. Although it has long been thought that changes in gene regulation drove the evolution of uniquely human traits, in vivo evidence for human-specific developmental regulatory functions remains elusive. Moreover, despite intensive efforts to annotate functional elements in the genome, such as the ENCODE project, there is no parallel effort to annotate uniquely human cis-regulatory functions. The goal of this study is to identify and characterize developmental enhancers with human-specific functions in vivo and examine their role in human evolution. The aims of our proposal are based on extensive preliminary data. We have developed a novel computational approach to identify noncoding, potentially regulatory sequences that are highly conserved across vertebrate species, but that changed substantially during human evolution. Using a mouse transgenic enhancer assay, we have identified eight of these "human-accelerated" conserved noncoding sequences (HACNSs) that function as enhancers during development. Of particular relevance for the aims of this proposal, we have also shown that the most rapidly evolving element in our dataset, HACNS1, is a developmental enhancer that has gained a robust limb expression domain relative to the orthologous elements from chimpanzee and rhesus macaque. This domain includes the presumptive anterior wrist and proximal thumb. Here we will build on these previous studies to generate more sophisticated maps of human-specific sequence acceleration in noncoding elements, including transcription factor binding site data and ChIP-seq data generated by genome-wide efforts to annotate regulatory function. We will use these data in conjunction with computational and experimental filters, such as extreme evolutionary constraint and recruitment of p300, to predict enhancers and mouse transgenic technologies to identify and characterize enhancers with human-specific activities. We will use synthetic enhancers and biochemical approaches to determine how human-specific sequence change alters enhancer function. Finally, we will use a reverse genetic strategy to study the evolutionary relevance of the human-specific functional change in HACNS1, by using gene targeting to replace the mouse ortholog of HACNS1 with the human enhancer and evaluating the effect of this genetic change on mouse development. The results from these studies will complement and extend current efforts to functionally annotate the human genome and will begin to reveal the precise molecular evolutionary events that produced modern humans. PUBLIC HEALTH RELEVANCE: Understanding the genetic basis of human morphology and development is central to the public health mission of the NIH. Beyond the fundamental question of human origins, studying human evolutionary history is directly relevant to human health, as many common human diseases may in part be due to the effects of sequence changes that were advantageous early in our evolution but are now harmful. Evidence for this hypothesis stems from human and chimpanzee comparisons: many prevalent human diseases with a genetic component, including skin cancers, heart disease, malaria infection, Alzheimer disease, multiple sclerosis and major psychoses, appear to be uncommon, different or absent in chimpanzees. Our research may thus shed light on the genetic and evolutionary basis of diseases that are unique to our species.

描述（由申请人提供）：作为一种物种，我们与其他灵长类动物的区别在于我们的语言能力，直立行走的能力以及发明和使用复杂工具的才能。这些特征源于身体适应，例如增加大脑的大小和四肢形态的变化，这需要发育的变化。尽管长期以来一直认为基因调节的变化推动了独特的人类特征的演变，但人类特异性发育调节功能的体内证据仍然难以捉摸。此外，尽管大力努力注释基因组中的功能元素，例如编码项目，但没有平行的努力来注释独特的人类顺式调节功能。这项研究的目的是识别和表征通过体内人类特异性功能的发育增强子，并检查其在人类进化中的作用。我们提案的目的是基于广泛的初步数据。我们已经开发了一种新型的计算方法，以识别脊椎动物物种高度保守的非编码，潜在的调节序列，但在人类进化过程中这种序列发生了很大变化。使用小鼠转基因增强剂测定法，我们已经确定了其中八个“人类加速”保守的非编码序列（HACNS），它们在发育过程中起增强子的功能。与该提案的目的特别相关，我们还表明，数据集中最快发展的元素HACNS1是一种发展性增强子，相对于来自黑猩猩和恒河猕猴的直系同源元素而获得了强大的肢体表达域。该领域包括推定的前手腕和近端拇指。在这里，我们将基于这些先前的研究，以生成非编码元素中人类特异性序列加速度的更复杂的地图，包括转录因子结合位点数据以及由全基因组范围努力产生的chip-seq数据，以注释调节功能。我们将使用这些数据与计算和实验过滤器（例如极端进化约束和p300募集）一起预测增强剂和小鼠转基因技术，以识别和表征具有人类特异性活动的增强剂。我们将使用合成增强剂和生化方法来确定人类特异性序列如何改变增强子功能。最后，我们将使用反向遗传策略来研究HACNS1中人类特异性功能变化的进化相关性，通过使用基因靶向替代人类增强剂的HACNS1的小鼠直系同源物，并评估这种遗传变化对小鼠发育的影响。这些研究的结果将补充并扩大当前的努力，以便在功能上注释人类基因组，并将开始揭示产生现代人类的精确分子进化事件。公共卫生相关性：了解人类形态和发展的遗传基础对于NIH的公共卫生使命至关重要。除了人类起源的基本问题之外，研究人类进化史与人类健康直接相关，因为许多常见的人类疾病可能部分是由于序列变化的影响，这些变化在我们的进化早期是有利的，但现在是有害的。该假设的证据源于人类和黑猩猩的比较：许多患有遗传成分的流行性人类疾病，包括皮肤癌，心脏病，疟疾感染，阿尔茨海默氏病，多发性硬化症和主要心理作用，似乎是不稳定的，在黑猩猩中不同或不存在。因此，我们的研究可能阐明了我们物种独有的疾病的遗传和进化基础。