Research Project 3

摘要 转座元件(TES，也被称为跳跃基因或移动元件)是非常特殊的 真核生物基因组多样性的贡献者，包括人类。TES占人类总数的50%以上 它们比蛋白质编码基因更常见，蛋白质编码基因约占人类总数的1% 基因组。尽管它们丰富，但它们的移动元素生物学的主要方面还没有得到充分的研究 仍然难以捉摸。由于它们在基因组中的随机插入，插入既发生在基因间也发生在基因内 区域(包括外显子)。由于逆转位正在进行中，每20个活产中约有1个新插入，有 在人类群体中有数百万的多态TE，包括一些与疾病相关的TES。高度反响- 众所周知，活动区域很难组装，在重叠群末端表示过多，并且注释不足 短读测序读数(目前在生物医学环境中很普遍)。在AIM I中，我们将改进 通过建立在人类的基础上对人类移动组(基因组的整个移动元素内容)的注释 参考基因组和人类基因组结构变异联盟(提供访问Illumina Short- 读取和PacBio高保真测序数据)。我们的部分重点将是改进短文阅读的TES调用 测序数据。我们将(A)将黑猩猩作为一个外类群来实现，以区分TE 包含TE序列的插入和缺失；以及(B)开发一种针对反式-DNA测序的方法 可能的元素。后者将与全基因组测序相结合。我们的定向测序 方法将提供更深层次的断点覆盖，改进对移动元素的识别。我们还将 使用解析良好的末端支管生成高分辨率子族注释。最年轻的亚家族 在较老的亚家族中通常会崩溃，因为其大小和很少有共同的诊断突变。 缺乏对最年轻亚家族的识别，导致了近代史上TES明显的相对平静。 在AIM I中TE注释改进的基础上，我们将调查TES以识别和表征PU- 可预测的源元素(即能够生成后代插入的TE)。大多数TE插入都是无效的 到达并不能产生后代的胚胎。虽然识别活动的L1相对容易，但 识别ALU和SVA扩张的驱动因素要难得多。一个小规模的TE子家族 包括最年轻的子家族的解决方案将揭示最新的TE进化，以及 允许调查最年轻的源元素(往往对宿主有害) 子族。这使得最年轻的子家族成为综合来源元素识别的主要目标 比较法。

SUMMARY Transposable elements (TEs, also referred to as jumping genes or mobile elements) are extraordinary contributors to eukaryotic genome diversity, including in humans. TEs make up more than 50% of the human genome and are far more common than protein coding genes, which comprise about 1% of the human genome. Despite their abundance, TEs are understudied and major aspects of their mobile element biology remain elusive. Due to their random insertion within the genome, insertions occur both in intergenic and genic regions (including in exons). As retrotransposition is ongoing, with ~1 new insertion per 20 live births, there are millions of polymorphic TEs within the human population, including some associated with disease. Highly repe- titive regions are notoriously difficult to assemble, overrepresented at contig ends, and under-annotated from short-read sequencing reads (presently prevalent in biomedical settings). In Aim I, we will improve the annotation of the human mobilome (the genome’s entire mobile element content) by building upon the human reference genome and the Human Genome Structural Variation consortium (providing access to Illumina short- read and PacBio HiFi sequencing data). Part of our focus will be on improved calling of TEs from short-read sequencing data. We will (a) implement chimpanzee as an outgroup in order to distinguish between TE insertions and deletions containing TE sequence; and (b) develop a targeted-sequencing approach for trans- posable elements. The latter will be combined with whole genome sequencing. Our targeted sequencing approach will provide deeper coverage of breakpoints, improving identification of mobile elements. We will also generate a high-resolution subfamily annotation with well-resolved end-branches. The youngest subfamilies are commonly collapsed within older subfamilies because of size and few shared diagnostic mutations. Underidentifying the youngest subfamilies leads to an apparent relative quiescence of TEs in recent history. Building upon the TE annotation improvement in Aim I, we will investigate TEs to identify and characterize pu- tative source elements (i.e. TEs capable of generating offspring insertions). Most TE insertions are dead upon arrival and not able to create offspring TEs. While the identification of active L1s is relatively easy, the identification of the drivers of Alu and SVA expansion has been far more elusive. A fine-scale TE subfamily resolution that includes the youngest subfamilies will both shed light on the most recent TE evolution, and allow investigation of source elements (which tend to be deleterious to their host) within the youngest subfamilies. This makes the youngest subfamilies a prime target for an integrative source element identification comparative approach.