Statistical and high-throughput models of enhancer function and evolution

项目总结 增强子是一类重要的非编码区，在基因表达调控中发挥着重要作用。 调节不同的表型和疾病状态。然而，我们对增强剂在 表型进化是有限的，我们缺乏对序列之间关系的详细了解 物种内和物种间的变化，表观遗传状态和增强子功能的变化。此外，我们有 很少有统计模型允许研究人员将增强子序列的进化变化与 以及物种之间的表型差异，而我们往往不能明确地确定 观察到增强子的进化速度沿谱系的变化。最后，大多数对增强剂的研究 到目前为止，进化只研究了少量的增强子和全基因组的增强子分析。 变异和功能很少见。在这里，我们建议开发统计模型，将人类的系统发育模式 具有物种间表型差异的增强子进化，并利用物种内差异 多物种--“比较种群基因组学”--解开观察到的速率变化的根源 在不同物种的增强剂中。我们还将大规模测试不同的增强器，使用 作为发育和基因表达模式的飞翔和不会飞的鸟类的前肢和后肢的发育。 具体地说，在目标1中，我们将扩展最近开发的用于检测率的贝叶斯系统发育模型 通过加入随机基因树，改变非编码DNA，PhyloAcc，以提高其生物现实性 异质性和将序列变化与二元和连续性状相关联的能力。在基础上建设 跨多个物种的比较基因表达和染色质状态的新数据集 在发育阶段，我们还将开发方法将染色质状态的全基因组变异联系起来 在具有二元和连续特征的物种之间。在目标2中，我们将开发其他统计模型来 利用物种内序列变异的信息来更好地理解进化力量 导致观察到的物种间非编码DNA的速率差异。在AIMS 1中开发的模型 和2将经过改进，并以用户友好的格式提供给更广泛的社区，以便在各种 系统和物种。在目标3中，我们将从功能上验证在 目标1和目标2在发育过程中进化出新的功能或发现染色质状态发生变化-- 飞翔的不会飞的鸟的后肢。我们将在鸡肉、麋鹿和其他禽类中使用高通量检测 研究增强子的种内和种间序列变异与其能力的关系 来驱动基因的表达。综合起来，这些目标将提供一些工具，使 研究人员使用比较基因组学来了解基因型和表型之间的联系，并将 扩展表型特征和基因组签名的种类，这将成为这一新兴范式的基础。

PROJECT SUMMARY Enhancers are an important class of noncoding loci regulating gene expression and play important roles in modulating diverse phenotypes and disease states. However, our understanding of the role of enhancers in phenotypic evolution is limited and we lack a detailed understanding of the relationship between sequence change within and between species, epigenetic states and variation in enhancer function. Moreover, we have few statistical models that allow researchers to connect evolutionary changes in enhancer sequences within and between species to phenotypic variation, and we often cannot unambiguously determine the causes of observed changes in evolutionary rate of enhancers along lineages. Finally, most studies of enhancer evolution thus far have studied only small numbers of enhancers and genome-wide assays of enhancer variation and function are rare. Here we propose to develop statistical models linking phylogenetic patterns of enhancer evolution with phenotypic variation between species, and to leverage within-species variation across multiple species – “comparative population genomics” – to disentangle the sources of rate changes observed in enhancers across species. We will also functionally test diverse enhancers on a large-scale, using the developing fore- and hindlimb of volant and flightless birds as a model of development and gene expression. Specifically, in Aim 1 we will extend a recently developed Bayesian phylogenetic model for detecting rate changes in noncoding DNA, phyloAcc, to improve its biological realism by incorporating stochastic gene tree heterogeneity and the ability to associate sequence change with both binary and continuous traits. Building on a novel data set of comparative gene expression and chromatin states across multiple species and developmental stages, we will also develop methods to associate genome-wide variation in chromatin states between species with binary and continuous traits. In Aim 2 we will develop additional statistical models to leverage information from sequence variation within species to better understand the evolutionary forces contributing to rate variation in noncoding DNA observed between species. The models developed in Aims 1 and 2 will be refined and made available to the broader community in a user-friendly format for use on diverse systems and species. In Aim 3 we will functionally validate large numbers of candidate enhancers identified in Aims 1 and 2 as having evolved new functions or found in altered chromatin states in the developing fore- and hindlimb of volant and flightless birds. Using high-throughput assays in chicken, emu and other birds we will study the relationship between within- and between-species sequence variation of enhancers and their ability to drive gene expression. Together these aims will provide a number of tools that will benefit the community of researchers using comparative genomics to understand links between genotype and phenotype, and will extend the kinds of phenotypic traits and genomic signatures that will inform this emerging paradigm.