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，以及特定的挑战主题08-CA-104：小RNA的调节功能。我们的目标是确定小RNA(SmRNAs)是组蛋白修饰酶的调节者，介导与启动子和/或存在于启动子近端的非编码RNA的相互作用，并介导对基因表达的长期影响。这是一种新的模型，它将基因组编码的小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操纵或DNA序列中特定胞嘧啶甲基化的形式对基因组进行的可遗传改变。癌变很可能包括异常使用这一途径，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，而广泛影响组蛋白修饰的化合物正作为癌症疗法受到严格审查。虽然这一策略可能是有效的，但我们相信，通过利用现有的RNAi机制，如对几个smRNA和基因所展示的那样，将有可能从治疗上针对选定基因的表观遗传调节。该项目旨在了解小的、非编码的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体可能被小RNA招募到其目标DNA序列的机制。通过与基因组比对位点和先前发表的关键组蛋白修饰的表观基因组数据进行比较，通过深度测序在人类胚胎干细胞中鉴定出的smRNAs发现了这两条先前独立的途径之间的显著关联。在这项提案中，我们将检验smRNAs介导表观遗传标记放置的假设。具体地说，我们将(1)鉴定和表征与人类ES细胞神经分化过程中特定染色质修饰相关的几类smRNA序列；(2)从生物信息上预测尚未观察到的smRNA介导的表观遗传效应；以及(3)通过实验证实hESC中小的非编码RNA和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是组蛋白修饰机制与单个基因组位点之间的关键环节。如果smRNA确实直接进行表观遗传修饰，这可能代表了一种新的机制，通过这种机制，细胞能够进行转录调控。这将为癌症过程中改变的组蛋白修饰区域提供额外的治疗靶点和增强对疾病病因的理解。 与公共卫生相关：表观遗传失调是几种人类疾病和许多癌症的标志。组蛋白修饰是表观遗传调控的一种机制，直接影响相邻基因组元件的转录可获得性。该项目旨在确定小的、非编码的RNA序列与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体可能被小RNA招募到其目标基因组区域的机制。小RNA与特异组蛋白修饰的关联提供了对疾病病因的理解，并提示了从转录上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.