Genome-wide chromatin modification targeting by endogenous small RNAs

描述（由申请人提供）：本申请涉及广泛的挑战领域（08）基因组学和特定的挑战主题08-CA-104：小RNA的调控功能。我们的目标是确定小RNA（smRNAs）作为组蛋白修饰酶的调节因子，介导与启动子和/或启动子近端区域中存在的非编码RNA的相互作用，并介导对基因表达的长期影响。这是一个新的模型，将基因组编码的小RNA，非编码RNA和组蛋白修饰的调节联系在一起，导致基因表达的长期调节。表观遗传修饰是以关键组蛋白残基的酶促操作或DNA序列中特定胞嘧啶的甲基化的形式对基因组的可遗传改变。致癌作用可能包括该途径的异常使用，从而导致转化细胞中基因表达的长期变化。事实上，表观遗传失调是许多癌症的标志，广泛影响组蛋白修饰的化合物作为癌症疗法受到严格审查。虽然这种策略可能是有效的，但我们相信，通过利用现有的RNAi机制，如几种smRNA和基因所证明的那样，有可能在治疗上靶向所选基因的表观遗传调节。该项目旨在了解小的非编码RNA序列和表观遗传组蛋白修饰之间的关系，并探索表观基因组修饰复合物可能被小RNA招募到其靶DNA序列的机制。通过基因组比对位点的深度测序在人类胚胎干细胞中鉴定的smRNAs与先前发表的关键组蛋白修饰的表观基因组数据的比较已经鉴定了这两个先前独立的途径之间的显著关联。在这个提议中，我们将测试smRNAs介导表观遗传标记放置的假设。具体而言，我们将（1）鉴定和表征与神经分化过程中人类ES细胞中特定染色质修饰相关的smRNA序列类别;（2）生物信息学预测尚未观察到的smRNA介导的表观遗传效应;（3）实验证实hESC中非编码小RNA与表观遗传修饰之间的功能相互作用。表观遗传标记是生物学和医学的下一个重大问题之一。我们认为内源性smRNAs是组蛋白修饰机制和个体基因组位点之间的关键联系。如果smRNAs确实指导表观遗传修饰，这可能代表了细胞能够进行转录调控的一种新机制。这将提供额外的治疗靶点，并增强对癌症期间改变的组蛋白修饰区域的疾病病因的理解。 公共卫生相关性：表观遗传失调是几种人类疾病和许多癌症的标志。组蛋白修饰代表了表观遗传调控的一种机制，其直接影响相邻基因组元件的转录可用性。该项目旨在确定小的非编码RNA序列与表观遗传组蛋白修饰之间的关系，并探索小RNA将表观基因组修饰复合物招募到其靶基因组区域的机制。小RNA与特定组蛋白修饰的关联提供了对疾病病因的理解，并提出了转录调节患者靶基因的机制。

DESCRIPTION (provided by applicant): This application addresses broad Challenge Area (08) Genomics, and specific Challenge Topic 08-CA-104: Regulatory functions of small RNAs. Our goal is to identify small RNAs (smRNAs) as regulators of histone modifying enzymes, mediating interactions with promoters and/or non-coding RNAs present in promoter proximal regions and mediating long-term effects on gene expression. This is a novel model that would tie together genome-encoded small RNAs, non-coding RNAs, and the regulation of histone modifications, leading to long-term modulation of gene expression. Epigenetic modifications are inheritable alterations to the genome in the form of enzymatic manipulations of key histone residues, or the methylation of specific cytosines in the DNA sequence. Carcinogenesis is likely to include aberrant use of this pathway to cause long-term changes in gene expression in transformed cells. In fact, epigenetic dysregulation is a hallmark of numerous cancers, and compounds which broadly affect histone modifications are under intense scrutiny as cancer therapies. While this strategy may be effective, we believe that it will be possible to therapeutically target epigenetic modulation of selected genes by exploiting the existing RNAi machinery, as demonstrated for several smRNAs and genes. This project aims to understand the relationship between small, non-coding RNA sequences and epigenetic histone modifications, and explore the mechanisms by which epigenome-modifying complexes may be recruited by small RNAs to their target DNA sequences. Comparison of smRNAs identified in human embryonic stem cells by deep sequencing with genomic alignment sites and previously published epigenomic data of key histone modifications has identified striking association between these two previously independent pathways. In this proposal we will test the hypothesis that smRNAs mediate the placement of epigenetic marks. Specifically, we will (1) identify and characterize classes of smRNA sequences associated with specific chromatin modifications in human ES Cells during neural differentiation; (2) bioinformatically predict as yet unobserved smRNA-mediated epigenetic effects; and (3) experimentally confirm the functional interaction between small non-coding RNAs and epigenetic modifications in hESC. Epigenetic marking is one of the next great questions in biology and medicine. We propose that endogenous smRNAs are the key link between histone modification mechanisms and individual genomic loci. If smRNAs do in fact direct epigenetic modifications, this may represent a novel mechanism by which cells are capable of transcriptional regulation. This will provide both additional therapeutic targets and enhanced understanding of disease etiologies for regions of altered histone modification during cancers. PUBLIC HEALTH RELEVANCE: Epigenetic dysregulation is a hallmark of several human disorders and numerous cancers. Histone modifications represent one mechanism of epigenetic regulation that directly affects the transcriptional availability of adjacent genomic elements. This project aims to identify the relationship between small, non-coding RNA sequences and epigenetic histone modifications, and explore the mechanisms by which epigenome modifying complexes may be recruited by small RNAs to their target genomic regions. The association of small RNAs with specific histone modifications provides understanding of disease etiologies and suggests mechanisms to transcriptionally regulate target genes in patients.