Research Project 3

研究项目3

• 批准号: 10090714
• 负责人: Miriam Kristine Konkel
• 金额: $ 26.84万
• 依托单位: CLEMSON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-02-10 至 2026-01-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10090714
• 关键词: Algorithms; Alu Elements; Back; Binding Sites; Biology; Birth; Centers of Research Excellence; Code; Codon Nucleotides; Complex; Custom; DNA Insertion Elements; DNA Polymerase II; DNA Polymerase III; DNA Sequence; DNA Transposable Elements; Data; Data Set; Diagnostic; Disease; Elements; Embryo; Enhancers; Evolution; Exons; Family; Foundations; Future; Gene Expression Regulation; Genes; Genetic; Genetic Diseases; Genetic Recombination; Genetic Transcription; Genetic Variation; Genome; Genomic Segment; Genomic approach; Genomics; Human; Human Genetics; Human Genome; Individual; Inherited; Investigation; Jumping Genes; Knowledge; Life; Light; Literature; Live Birth; Location; Longevity; Messenger RNA; Mutation; Nature; Output; Pan Genus; Phase; Play; Polymerase; Population; Primates; Proteins; RNA; RNA Splicing; Recording of previous events; Regulation; Regulator Genes; Repetitive Sequence; Research Project Grants; Resolution; Retrotransposition; Role; Site; Source; Structure; Tissues; Untranslated RNA; Variant; base; burden of illness; comparative; comparative genomics; contig; genome annotation; genome sequencing; human disease; human reference genome; improved; insertion/deletion mutation; mammalian genome; offspring; personalized approach; premature; prospective; reference genome; success; targeted sequencing; transcription factor; whole genome

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.

总结 转座因子（TE，也称为跳跃基因或移动的因子 包括人类在内的真核生物基因组多样性的贡献者。TE占人类的一半以上， 基因组中的蛋白质编码基因比蛋白质编码基因更常见，后者占人类基因组的1%。 基因组尽管它们丰富，但TE研究不足，其移动的元素生物学的主要方面 仍然难以捉摸由于它们在基因组内的随机插入，插入发生在基因间和基因组中。 区域（包括外显子）。由于逆转录正在进行中，每20例活产约有1例新插入， 人类群体中存在数百万个多态性TE，包括一些与疾病相关的TE。高度重复- 众所周知，序列区很难组装，重叠群末端的表达过多， 短读段测序读段（目前在生物医学环境中流行）。在目标I中，我们将改进 通过建立在人类基因组的基础上， 参考基因组和人类基因组结构变异联盟（提供对Illumina短- read和PacBio HiFi测序数据）。我们的重点之一将是改善短期阅读的TE调用 测序数据。我们将（a）将黑猩猩作为外群，以区分TE 包含TE序列插入和缺失;和（B）开发用于反式- 可造型元素后者将与全基因组测序相结合。我们的靶向测序 这种方法将提供更深的断点覆盖，改进对移动的元素的识别。我们还将 生成具有良好解析的末端分支的高分辨率子家族注释。最年轻的子家族 由于大小和很少的共同诊断突变，通常在较老的亚家族中崩溃。 在最近的历史中，对最年轻的亚家族的识别不足导致了TE的明显相对静止。 在目标I中TE注释改进的基础上，我们将研究TE以识别和表征PU。 典型的源元件（即能够产生后代插入的TE）。大多数TE插入都是在 到达并且不能创建后代TE。虽然识别活跃的L1相对容易， Alu和SVA扩张的驱动因素的确定要难以捉摸得多。一个精细尺度的TE亚族 包括最年轻的亚家族的分辨率将揭示最近的TE进化， 允许在最年轻的细胞中调查源元素（这些元素往往对其宿主有害）， 亚家族这使得最年轻的亚族成为综合源元素鉴定的主要目标 比较法。