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: 8117311
• 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/8117311
• 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）：涉及与其他非编码RNA不同的大型反义RNA的最新发现促使我们提出了一种新型的内源性转录调控系统。我们假设反义转录物通过募集染色质修饰复合物介导转录沉默和激活，从而介导特定的遗传基因座。我们设想过量的反义转录本，以信号转录沉默和低水平的反义转录本以激活转录。在此应用中，我们建议研究该假设，该假设适用于癌症中观察到的差异，表观遗传确定的转录。我们将表征显示基因表达表观遗传变化的癌细胞的反义转录组。我们还将在单个癌基因表达的等源性细胞对上进行反义转录物的全基因组分析。然后，我们将通过双重免疫沉淀芯片分析和深层测序来鉴定这些细胞中染色质重塑涉及的遗传基因座，并将这些数据与反义谱相关联，并指定了与染色质修饰的明显反义转录相关的基因。从该列表中，我们将选择与癌症相关的基因，并通过目标RT和3'种族来表征其反义转录本。特异性反义转录本的转录调节活性将通过过表达和干扰RNAi构建体干扰反义RNA的功能。我们期望获得支持或反驳我们的核心假设的决定性数据，并且与这种结果无关，以产生有关反义相关转录变化的全面信息，这些信息与特定的癌基因的作用以及与表现出表观遗传改变癌症转录的基因相关的。由非编码RNA介导的转录调节长期是长期的，与转录激活蛋白和转录阻遏物的常规调节相反。涉及介导染色质重塑的反义RNA的新的转录控制细胞内源系统的应用挑战了当前的转录调控范式。这种系统的验证将对我们对转录的理解产生深远的影响。它还将揭示有关涉及转录表观遗传变化的癌症，慢性感染和发育障碍的新的治疗策略。 公共卫生相关性：许多基因产生反义转录本。有新兴的证据表明，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。本应用将在基因组大规模上检查反义依赖性转录调节。