Population genetics and evolution of mobile elements

 描述(由申请人提供)： 移动元件(MES)构成了人类基因组的一半以上，它们的转座和重排直接导致了100多种遗传病。由于这些突变特性，MES是基因组进化和创新的重要驱动力，占人类基因组结构变异的20%-30%。然而，它们发挥作用的机制几乎完全不为人所知。在这一更新应用中，我们建议利用新的高通量测序技术来解决关于MES生物学及其基因组影响的一系列基本问题：ME插入发生的频率和时间，以及它们的活动在人类群体中如何变化(目标1)？MES如何以及在何种情况下通过非等位基因同源重组(Nahr)(目标2)创造结构基因组变异？MES如何促进人类内部和灵长类进化中基因表达的变化(目标3)？在目标1中，我们将评估来自多代犹他州家庭的3000个全基因组序列以及来自125个不同人类群体的300多个全基因组序列中的ME插入活性。(这些测序研究都是在每个基因组覆盖30-50倍的情况下进行的，已经在单独的资助机制下进行，我们可以免费获得这些序列。)这些基因组资源，结合1000基因组计划的序列数据，也将被用来确定现有最大的ME介导的Nahr事件集合，使我们能够确定促进或抑制MES介导的基因组不稳定性的基因组因素(目标2)。此外，我们将在上一个资助周期中开发的ME扫描技术应用于来自90名男性的精子和血细胞的收集，以首次评估精子发生过程中移动元素活动的时间。最后，在目标3中，我们将检验这一假设，即多态和谱系特异的MES分别对人类内部和灵长类物种之间的基因表达变化做出实质性贡献。将通过测试ME插入多态与421名人类的基因表达变异之间的关联来评估种内效应。为了探索种间效应，我们将利用代表所有主要类人灵长类物种的一组物种的相同细胞类型的比较RNA测序。特别是，这些数据将为我们提供一个前所未有的机会来评估MES在长非编码RNA的进化和调控中的作用，长非编码RNA已经成为一类丰富而重要的基因组调控因子。

 DESCRIPTION (provided by applicant): Mobile elements (MEs) compose more than half of the human genome, and their transposition and rearrangement have been directly implicated in causing more than 100 genetic diseases. Because of these mutagenic properties, MEs are important drivers of genome evolution and innovation, accounting for as much as 20-30% of structural variation in the human genome. However, the mechanisms through which they exert their effects are almost completely unknown. In this renewal application, we propose to exploit new high- throughput sequencing technologies to address a series of fundamental questions about the biology of MEs and their genomic impact: how often and when in development do ME insertions occur, and how does their activity vary among human populations (Aim 1)? How, and under which circumstances, do MEs create structural genomic variation through non-allelic homologous recombination (NAHR) (Aim 2)? How do MEs contribute to changes in gene expression within humans and in primate evolution (Aim 3)? In Aim 1, we will assess ME insertion activity in 3,000 whole-genome sequences sampled from multigenerational Utah families and in a set of more than 300 whole-genome sequences from individuals from 125 different worldwide human populations. (These sequencing studies, both carried out at 30-50x coverage per genome, are already under way under separate funding mechanisms, and the sequences are available to us at no cost.) These genomic resources, in combination with sequence data from the 1000 Genomes Project, will also be used to identify the largest existing collection of ME-mediated NAHR events, enabling us to identify the genomic factors that promote or inhibit the genomic instability mediated by MEs (Aim 2). In addition, we will apply the ME-Scan technology developed in our last funding cycle to a collection of sperm and blood cells from 90 males in order to assess, for the first time the timing of mobile element activity during spermatogenesis. Finally, in Aim 3, we will test the hypothesis that polymorphic and lineage-specific MEs make a substantial contribution to gene expression changes within humans and between primate species, respectively. Intraspecific effects will be assessed by testing for association between ME insertion polymorphisms and gene expression variation across 421 humans. To explore interspecific effects, we will capitalize on comparative RNA sequencing of the same cell types across a set of species representing all major anthropoid primate lineages. In particular, these data will provide us with an unprecedented opportunity to evaluate the role of MEs in the evolution and regulation of long noncoding RNAs, which have emerged as an abundant and important class of genomic regulators.