Expression and Impact of Interspersed Repeats

散布重复序列的表达和影响

• 批准号: 9816738
• 负责人: KATHLEEN H BURNS
• 金额: $ 32.75万
• 依托单位: JOHNS HOPKINS UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-07-24 至 2020-02-29
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9816738
• 关键词: Affect; Alleles; Amber; Area; Binding; Cells; Cellular biology; Complex; Conflict (Psychology); DNA; DNA Insertion Elements; DNA Methylation; DNA Transposable Elements; Data; Development; Disease; Disease model; Double-Stranded RNA; Elements; Embryo; Endogenous Retroviruses; Epigenetic Process; Experimental Models; Fertility; Gene Expression; Gene Expression Regulation; Gene Silencing; Genes; Genetic; Genetic Diseases; Genetic Transcription; Genome; Heterochromatin; Human; Immune response; Individual; Infectious Agent; Interferon Type II; Long Interspersed Elements; Measures; Messenger RNA; Modernization; Molecular; Mutagens; Mutation; Nuclear Export; Outcome; Pathway interactions; Phenotype; Proliferating; Proteins; Quantitative Trait Loci; RNA; RNA Editing; Regulation; Retroelements; Retrotransposition; Retrotransposon; Reverse Transcription; Role; SETDB1 gene; Short Interspersed Nucleotide Elements; Side; Signal Transduction; Site; Surveys; Testing; Tissues; Trans-Activators; Transcript; Transcriptional Regulation; Variant; Zinc Fingers; differential expression; genetic variant; genome editing; genome wide association study; human disease; human tissue; mRNA Export; pathogen; recruit; response; sensor; transcriptome sequencing

Summary Endogenous retroviruses and related transposable elements make up much of our genome, and active forms persist as long interspersed element-1 (LINE-1, L1) retrotransposons and the elements it mobilizes. These are self-propagating sequences which copy themselves through the reverse transcription of RNA intermediates. We have developed elaborate mechanisms to silence their transcription and limit their proliferation. However, a careful approach to RNAseq analysis reveals that that a subset of individual transposon loci (ITL) escape silencing and are transcriptionally active. In a survey of normal human cells, we identify both constitutive and variably expressed ITL. Our ability to measure these transcripts provides a unique opportunity to examine this host-pathogen relationship and its role in gene regulation. Here, we propose to test the hypothesis that retroelement expression (or lack thereof) is an indicator of specific regulatory mechanisms with cis-acting effects on neighboring genes. We propose to define the landscape of expressed retrotransposons in humans; demonstrate molecular mechanisms of transcriptional silencing and escape; and probe how these mechanisms affect gene expression in human ‘epigenetic’ diseases. We will use genome editing strategies to test whether altering ITL sequences affects neighboring gene expression. Finally, we will develop approaches to study prevalent, highly-expressed short interspersed elements (SINEs) to assess their potential for retrotransposition, determine whether they are targets of RNA editing or dsRNA sensing pathways, and test their interactions with cellular mRNAs in trans. These studies will be among the first to delve into the expression and function of a broad range of retrotransposon intermediates in human cells.

概括 内源性逆转录病毒和相关转座元件构成了我们基因组的大部分以及活性形式 作为长散布的 element-1 (LINE-1, L1) 反转录转座子及其动员的元件持续存在。这些都是 通过 RNA 中间体的逆转录自我复制的自我繁殖序列。 我们已经开发出复杂的机制来沉默它们的转录并限制它们的增殖。然而，一个 RNAseq 分析的仔细方法表明，单个转座子基因座 (ITL) 的一个子集逃逸 沉默并具有转录活性。在对正常人体细胞的调查中，我们识别了组成型和 可变表达的ITL。我们测量这些转录本的能力提供了一个独特的机会来检查这一点 宿主-病原体关系及其在基因调控中的作用。在这里，我们建议检验以下假设： 逆转录元件表达（或缺乏）是具有顺式作用的特定调节机制的指标 对邻近基因的影响。我们建议定义人类表达的逆转录转座子的概况； 展示转录沉默和逃逸的分子机制；并探讨这些机制如何 影响人类“表观遗传”疾病的基因表达。我们将使用基因组编辑策略来测试是否 改变 ITL 序列会影响邻近基因的表达。最后，我们将制定研究方法 普遍的、高表达的短散布元件（SINE）来评估它们的潜力 逆转录转座，确定它们是否是 RNA 编辑或 dsRNA 传感途径的目标，并测试 它们与反式细胞 mRNA 的相互作用。这些研究将是最先深入探讨这一问题的研究之一。 人类细胞中多种逆转录转座子中间体的表达和功能。