The Antisense Transcriptome and the Epigenetics of Cancer.

反义转录组和癌症的表观遗传学。

• 批准号: 8257161
• 负责人: PETER K VOGT
• 金额: $ 30.58万
• 依托单位: SCRIPPS RESEARCH INSTITUTE, THE
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-08-01 至 2014-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8257161
• 关键词: Antisense RNA; Area; Biological Assay; Cancer Model; Cells; Chromatin; Chronic; Complex; Coupled; Data; Epigenetic Process; Exons; Functional RNA; Gene Expression; Gene Expression Profile; Genes; Genetic; Genetic Transcription; Human; Immunoprecipitation; Infection; Intervention; Link; Malignant Neoplasms; Mediating; Messenger RNA; MicroRNAs; Modeling; Modification; Mus; Oncogenes; Outcome; Process; Promoter Regions; Proteins; Protocols documentation; RNA Interference; Regulation; Signal Transduction; Small Interfering RNA; Specific qualifier value; System; Transcript; Transcription Coactivator; Transcription Repressor/Corepressor; Transcriptional Regulation; Validation; Work; cancer cell; chromatin modification; chromatin remodeling; developmental disease; genome-wide; novel; novel therapeutics; overexpression; promoter; public health relevance

DESCRIPTION (provided by applicant): Recent discoveries involving large, antisense RNAs that are distinct from other non-coding RNAs have prompted us to propose the existence of a novel, endogenous system of transcriptional regulation. We hypothesize that antisense transcripts mediate transcriptional silencing and activation by the recruitment of chromatin-modifying complexes to specific genetic loci. We envisage an excess of antisense transcripts to signal transcriptional silencing and low levels of antisense transcripts to activate transcription. In this application, we propose to investigate this hypothesis as applied to differential, epigenetically determined transcription seen in cancer. We will characterize the antisense transcriptome of cancer cells that show epigenetic changes in gene expression. We will also carry out genome-wide profiling of antisense transcripts on isogenic pairs of cells that differ by the expression of a single oncogene. We will then identify genetic loci involved in chromatin remodeling in these cells by double immunoprecipitation ChiP assays and deep sequencing and correlate these data with the antisense profiles, specifying genes that show significant antisense transcription coupled to chromatin modification. From that list, we will select cancer-relevant genes and characterize their antisense transcripts by targeted RT and 3' RACE. The transcriptional regulatory activity of specific antisense transcripts will be determined by overexpression and by interference with the function of antisense RNA using RNAi constructs. We expect to obtain decisive data that support or refute our core hypothesis and, independent of this outcome, to generate comprehensive information on antisense-associated transcriptional changes that are tied to the action of specific oncogenes and to genes that show epigenetically altered transcription in cancer. The transcriptional regulation mediated by non-coding RNAs is long-term, in contrast to the conventional regulation by transcriptional activator proteins and transcriptional repressors. The application of a new cell-endogenous system of transcriptional controls involving antisense RNAs that mediate chromatin remodeling challenges the current paradigm of transcriptional regulation. The validation of such a system would have a deep impact on our understanding of transcription. It would also reveal new therapeutic strategies for cancer, chronic infections and developmental disorders that involve epigenetic changes of transcription. PUBLIC HEALTH RELEVANCE: Numerous genes generate antisense transcripts. There is emerging evidence that these non-coding RNAs can regulate transcription by inducing epigenetic changes of the chromatin. The present application will examine antisense-dependent transcriptional regulation on a genome wide scale.

描述（由申请人提供）：最近涉及不同于其他非编码RNA的大反义RNA的发现促使我们提出存在一种新颖的内源性转录调控系统。我们假设反义转录本通过将染色质修饰复合物招募到特定的基因位点来介导转录沉默和激活。我们设想过量的反义转录本会发出转录沉默信号，而低水平的反义转录本会激活转录。在本申请中，我们建议研究这一假设，并将其应用于癌症中观察到的差异性、表观遗传决定的转录。我们将表征癌细胞的反义转录组，这些转录组显示基因表达的表观遗传变化。我们还将对因单个癌基因的表达而不同的同基因细胞对的反义转录物进行全基因组分析。然后，我们将通过双免疫沉淀 ChiP 测定和深度测序来识别这些细胞中参与染色质重塑的遗传位点，并将这些数据与反义图谱相关联，指定显示与染色质修饰相关的显着反义转录的基因。从该列表中，我们将选择癌症相关基因，并通过靶向 RT 和 3' RACE 表征其反义转录本。特定反义转录物的转录调节活性将通过过度表达和使用RNAi构建体干扰反义RNA的功能来确定。我们期望获得支持或反驳我们的核心假设的决定性数据，并且独立于这一结果，生成有关反义相关转录变化的全面信息，这些变化与特定癌基因的作用以及在癌症中显示表观遗传改变转录的基因有关。与转录激活蛋白和转录阻遏蛋白的常规调节相反，非编码RNA介导的转录调节是长期的。涉及介导染色质重塑的反义RNA的新型细胞内源性转录控制系统的应用挑战了当前的转录调控范式。这样一个系统的验证将对我们对转录的理解产生深远的影响。它还将揭示涉及转录表观遗传变化的癌症、慢性感染和发育障碍的新治疗策略。 公共健康相关性：许多基因都会产生反义转录本。越来越多的证据表明，这些非编码 RNA 可以通过诱导染色质的表观遗传变化来调节转录。本申请将在基因组范围内检查反义依赖性转录调控。