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：
10409704
负责人：
KATHLEEN H BURNS
金额：
$ 35.4万
依托单位：
DANA-FARBER CANCER INST
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 2023-05-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10409704
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

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

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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的转座元素构成了我们的大部分基因组，而活性形式是持续存在长时间散布的元素-1（LINE-1，L1）逆转座子及其动员的元素。这些都是通过RNA中间体的逆转录复制自身的自传播序列。我们已经开发出精心的机制来使其转录沉默并限制它们的增殖。但是，仔细的RNASEQ分析方法表明，单个转座基因座（ITL）逃脱的子集沉默并具有转录活性。在对正常人类细胞的调查中，我们确定了本构和可变表示ITL。我们测量这些成绩单的能力为研究这一点提供了独特的机会宿主病原体关系及其在基因调节中的作用。在这里，我们建议检验以下假设恢复表达（或缺乏）是特定调节机制的指标对相邻基因的影响。我们建议定义在人类中表达的逆转座子的景观。展示转录沉默和逃生的分子机制；并探测这些机制如何影响人类“表观遗传”疾病中的基因表达。我们将使用基因组编辑策略来测试是否改变ITL序列会影响相邻的基因表达。最后，我们将开发学习方法普遍，高表达的短散布元素（罪），以评估其潜力逆转录，确定它们是RNA编辑还是DSRNA感应途径的目标，然后测试它们与反式的细胞mRNA相互作用。这些研究将是最早深入研究的研究人类细胞中广泛的返回跨座子中间体的表达和功能。