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.

总结 内源性逆转录病毒和相关的转座因子构成了我们基因组的大部分， 作为长散布元件-1（LINE-1，L1）反转录转座子和它动员的元件而持续存在。这些是 通过RNA中间体的逆转录自我复制的自繁殖序列。 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。但 仔细的RNAseq分析方法揭示了单个转座子基因座（ITL）的一个子集逃脱了 沉默并且是转录活性的。在对正常人体细胞的调查中，我们鉴定了组成型和 ITL表示。我们测量这些成绩单的能力提供了一个独特的机会来研究这一点 宿主-病原体关系及其在基因调控中的作用。在这里，我们提出测试的假设， 逆转录元件表达（或缺乏）是顺式作用的特定调节机制的指标 对邻近基因的影响。我们建议定义在人类表达反转录转座子的景观; 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，我们将开发研究方法， 普遍的，高表达的短散布元件（西内斯），以评估其对 逆转录转座，确定它们是否是RNA编辑或dsRNA传感途径的靶点，并测试 这些研究将是第一批深入研究细胞内mRNA相互作用的研究。 在人类细胞中广泛的反转录转座子中间体的表达和功能。