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RNAi and Epigenetic Control of Higher-Order Chromatin Assembly

高阶染色质组装的 RNAi 和表观遗传控制

基本信息

批准号：
7733067
负责人：
shivinder s grewal
金额：
$ 211.72万
依托单位：
DIVISION OF BASIC SCIENCES - NCI
依托单位国家：
美国
项目类别：
财政年份：
资助国家：
美国
起止时间：
至
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/7733067
关键词：
Amino Acids Binding Cell physiology Chromatin Chromatin Modeling Chromosome Structures Complex Deacetylase Defect Depth Development Disease Epigenetic Process Euchromatin Eukaryota Eukaryotic Cell Event Evolution Family Fission Yeast Fungal Genome Gene Expression Gene Expression Profile Genes Genome Genomics Heterochromatin Higher Order Chromatin Structure Histone Code Histone Deacetylation Histone H3 Histones Homologous Gene Human Biology Laboratories Large-Scale Sequencing Light Link Localized Location Lysine Maintenance Malignant Neoplasms Mammals Maps Measures Mediating Medical Surveillance Methylation Methyltransferase Modeling Modification Molecular Nucleosomes Pathway interactions Pattern Play Process Proteins RNA RNA Interference Range Recruitment Activity Regulation Research Resolution Retroelements Retrotransposon Role Site Small Interfering RNA Structure Tail Therapeutic Transcript Transposase Work cancer therapy centromere autoantigen 80K genetic regulatory protein human disease insight novel prevent promoter

项目摘要

Research in our laboratory is focused on the epigenetic control of higher-order chromatin assembly. The dynamic regulation of higher-order chromosome structure governs diverse cellular processes ranging from stable inheritance of gene expression patterns to other aspects of global chromosome structure essential for preserving genomic integrity. Our earlier studies revealed sequence of molecular events leading to the assembly of heterochromatic structures in the fission yeast Schizosaccharomyces pombe. We found that covalent modifications of histone tails by deacetylase and methyltransferase activities act in concert to establish the histone code essential for the assembly of heterochromatic structures. Moreover, we showed that distinct site-specific histone H3 methylation patterns dictate the organization of chromosomes into discrete structural and functional domains. Histone H3 methylated at lysine 9 is strictly localized to silent heterochromatic regions whereas H3 methylated at lysine 4, only a few amino acids away, is specific to the surrounding active euchromatic regions. We have continued to focus on the role of histone modifications and the factors that recognize specific histone modifications patterns (such as a chromodomain protein Swi6 that specifically binds histone H3 methylated at lysine 9) in the assembly of higher-order chromatin structures and have made significant progress in understanding the mechanism of higher-order chromatin assembly. More importantly, we provided evidence showing that RNA interference (RNAi), whereby double-stranded RNAs silence cognate genes, plays a critical role in targeting of heterochromatin complexes to specific locations in the genome. Our recent work has led to discovery of a self-enforcing loop mechanism though which RNAi machinery operates as a stable component of the heterochromatic domains (via tethering of RNAi complexes to heterochromatin marks) to destroy repeat transcripts that escape heterochromatin-mediated transcriptional silencing. In this loop mechanism, the processing of transcripts by RNAi machinery generate small interfering RNAs (siRNAs) that are utilized for further targeting of heterochromatin complexes, so the mechanism continues. In a comprehensive study, we have also developed a high-resolution map of the heterochromatin and euchromatin distribution across the entire fission yeast genome. These analyses together with mapping of RNAi components and large scale sequencing of siRNAs assocaited with an RNAi effector complex involved in heterochromatic silencing have yielded novel insights into the epigenetic profile of this model eukaryotic genome. Our work led to realization the heterochromatin serves as a dynamic platform of the genome involved in recruitment of diverse regulatory proteins (effectors) implicated in different chromosomal processes. Among other factors, these effectors include factors involved in deacetylation of histones and nucleosome remodeling proteins (such as SHREC complex described recently by our lab), which facilitate assembly of higher-order chromatin structures. The link between RNAi, heterochromatin, and chromatin-modifying factors is conserved in higher eukaryotes including mammals and has broad implications for human biology and disease including cancer. We have also uncovered a novel genome surveillance mechanism for retrotransposons by a family of transposase-derived CENP-B homologs. Retrotransposons are capable of exerting diverse effects on their hosts, profoundly influencing the organization, integrity and evolution of the host genome, and the host transcriptome. We discovered that CENP-Bs localize at and recruit histone deacetylases to silence retrotransposons. CENP-Bs also repress retrotransposon relics scattered throughout the fission yeast genome and often located near gene promoters to exert influence on expression of genes. Surprisingly, retroelements dispersed throughout the genome are clustered into specialized bodies, the organization of which depends on CENP-Bs. CENP-B-mediated surveillance is proactive, capable of preventing an extinct retrotransposon from reentering the host genome. These results reveal a likely ancient retrotransposon surveillance pathway important for host genome organization and maintenance of genomic integrity.

我们实验室的研究重点是高阶染色质组装的表观遗传控制。高阶染色体结构的动态调节控制着多种细胞过程，从基因表达模式的稳定遗传到保持基因组完整性所必需的全局染色体结构的其他方面。我们早期的研究揭示了导致裂殖酵母裂殖酵母异染色质结构组装的分子事件序列。我们发现，脱乙酰酶和甲基转移酶活性对组蛋白尾部的共价修饰协同作用，建立了异染色质结构组装所必需的组蛋白密码。此外，我们发现不同的位点特异性组蛋白 H3 甲基化模式决定染色体组织成离散的结构和功能域。在第 9 位赖氨酸甲基化的组蛋白 H3 严格定位于沉默异染色质区域，而在仅几个氨基酸之外的第 4 位赖氨酸甲基化的 H3 则特定于周围活跃的常染色质区域。我们持续关注组蛋白修饰和识别特定组蛋白修饰模式的因素（例如特异性结合赖氨酸 9 甲基化的组蛋白 H3 的染色质结构域蛋白 Swi6）在高阶染色质结构组装中的作用，并在理解高阶染色质组装机制方面取得了重大进展。更重要的是，我们提供的证据表明，RNA 干扰 (RNAi)，即双链 RNA 沉默同源基因，在将异染色质复合物靶向基因组中的特定位置方面发挥着关键作用。我们最近的工作发现了一种自我执行的循环机制，通过该机制，RNAi 机制作为异染色质结构域的稳定组成部分（通过将 RNAi 复合物束缚到异染色质标记）来破坏逃避异染色质介导的转录沉默的重复转录本。在这种循环机制中，RNAi 机器对转录本的处理会产生小干扰 RNA (siRNA)，这些小干扰 RNA 可用于进一步靶向异染色质复合物，因此该机制仍在继续。在一项综合研究中，我们还开发了整个裂殖酵母基因组中异染色质和常染色质分布的高分辨率图谱。这些分析连同 RNAi 成分的图谱和与参与异染色质沉默的 RNAi 效应复合物相关的 siRNA 的大规模测序，已经对该模型真核基因组的表观遗传谱产生了新的见解。我们的工作使我们认识到异染色质作为基因组的动态平台，参与不同染色体过程中涉及的多种调节蛋白（效应物）的招募。除其他因素外，这些效应物包括参与组蛋白和核小体重塑蛋白脱乙酰化的因素（例如我们实验室最近描述的 SHREC 复合物），这些因素促进高阶染色质结构的组装。 RNAi、异染色质和染色质修饰因子之间的联系在包括哺乳动物在内的高等真核生物中是保守的，并且对人类生物学和包括癌症在内的疾病具有广泛的影响。我们还通过转座酶衍生的 CENP-B 同源物家族发现了一种新的逆转录转座子基因组监视机制。逆转录转座子能够对其宿主产生多种影响，深刻影响宿主基因组和宿主转录组的组织、完整性和进化。我们发现 CENP-B 定位并招募组蛋白脱乙酰酶来沉默逆转录转座子。 CENP-B 还抑制分散在裂殖酵母基因组中的逆转录转座子遗迹，这些遗迹通常位于基因启动子附近，以对基因表达产生影响。令人惊讶的是，分散在整个基因组中的逆转录元件聚集成专门的体，其组织取决于 CENP-B。 CENP-B 介导的监视是主动的，能够防止灭绝的逆转录转座子重新进入宿主基因组。这些结果揭示了一个可能古老的逆转录转座子监视途径，对于宿主基因组组织和基因组完整性的维护很重要。