Expression and Impact of Interspersed Repeats

散布重复序列的表达和影响

基本信息

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
项目类别：
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

项目摘要

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。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。 RNAseq 分析的仔细方法表明，单个转座子基因座 (ITL) 的一个子集逃逸在对正常人类细胞的调查中，我们识别出组成型和转录活性。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。在这里，我们建议检验以下假设：宿主-病原体关系及其在基因调控中的作用。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我们建议定义人类表达的逆转录转座子的景观；展示转录沉默和逃逸的分子机制；并探讨这些机制是如何发生的；我们将使用基因组编辑策略来测试是否会影响人类“表观遗传”疾病的基因表达。最后，我们将开发研究方法。普遍的、高表达的短散布元件（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 的相互作用是最先深入研究的研究之一。人类细胞中多种逆转录转座子中间体的表达和功能。