Cooperative control of Polycomb Repressive Complexes by long noncoding RNAs, CpG island DNA, and RNA-binding proteins

长非编码 RNA、CpG 岛 DNA 和 RNA 结合蛋白对 Polycomb 抑制复合物的协同控制

• 批准号: 10343785
• 负责人: Joseph Mauro Calabrese
• 金额: $ 38.68万
• 依托单位: UNIV OF NORTH CAROLINA CHAPEL HILL
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-05-01 至 2024-02-29
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10343785
• 关键词: 3-Dimensional; Affect; Area; Binding; Binding Proteins; Biological Assay; Cell Nucleus; Cellular biology; Chromatin; Clustered Regularly Interspaced Short Palindromic Repeats; Code; Complex; CpG Islands; DNA; DNA Binding; DNA Sequence; Data; Deposition; Development; Disease; Elements; Epigenetic Process; Gene Expression; Genes; Genetic Transcription; Genome; Goals; Grant; Heat-Shock Response; Intellectual functioning disability; Intercistronic Region; Malignant Neoplasms; Measures; Mediating; Modeling; Modification; Mus; Nuclear; PRC1 Protein; Pattern; Polycomb; Proteins; RNA; RNA Binding; RNA Interference; RNA-Binding Proteins; Regulatory Element; Research Personnel; Role; SAFB gene; Series; Stress; Structure; Testing; Therapeutic; Time; Untranslated RNA; Work; biological systems; body system; developmental disease; histone modification; mRNA Precursor; recruit; trophoblast stem cell

ABSTRACT The goal of this grant is to determine the mechanisms through which long noncoding RNAs (lncRNAs) induce the spread of Polycomb Repressive Complexes (PRCs) over specific regions of the genome. Each of the two PRCs, PRC1 and PRC2, deposits histone modifications that repress transcription and simultaneously stimulate the activity of the other complex. PRCs are essential for the development of most major organ systems and their dysregulation causes a wide range of diseases. PRCs are unique amongst known epigenetic modifiers in that their spread over chromatin is induced by specific lncRNAs. However, despite decades of study, the field has not established how lncRNAs induce the spread of PRCs. Prominent models suggest that lncRNAs rely on 3- dimensional (3D) genome structure to spread PRCs indiscriminately across chromatin, without being influenced by the underlying sequence of DNA. Yet, these models cannot account for the extensive variability of PRC- dependent modifications in lncRNA target domains, and do not consider that outside of lncRNA target domains, DNA elements called CpG islands (CGIs) recruit PRCs to chromatin. Moreover, it remains unclear how many lncRNAs induce the spread of PRCs. While investigators originally proposed that thousands of lncRNAs have this function, the number of validated PRC-inducing lncRNAs remains close to ten. Our findings have begun to resolve these unknowns. For example, we discovered that in mouse trophoblast stem cells, the lncRNA Airn causes PRCs to spread outwards from CGIs that bind PRCs autonomously, prior to expression of Airn. Deletion of just one of these CGIs causes a multi-megabase loss of PRC-deposited modifications in the Airn domain. Moreover, we and others found specific RNA-binding proteins that associate with the PRCs, and at least two of these proteins appear to be required for lncRNAs to induce PRC spread. Thus, rather than spreading PRCs indiscriminately across chromatin, we hypothesize that lncRNAs associate with CGIs to spread PRCs from specific points of contact, and, that this association is mediated by RNA-binding proteins that bind lncRNAs and PRCs. Further, we hypothesize that any chromatin-bound RNA can induce the spread of PRCs, so long as it binds the necessary proteins. We now propose rigorous tests of these hypotheses: Under Aim 1, we will determine the role of CGIs and CGI-bound factors in the spread of PRCs induced by lncRNAs. Under Aim 2, we will determine the role of RNA-binding proteins in the spread of PRCs induced by lncRNAs. Under Aim 3, we will determine the roles of non-canonical RNAs in inducing the spread of PRCs. If successful, our work will demonstrate new roles for DNA regulatory elements, RNA-binding proteins, and RNAs in PRC function. Paradigms we establish should apply to broad areas in nuclear cell biology, and suggest multiple new avenues for controlling gene expression therapeutically.

抽象的 这笔赠款的目的是确定长期非编码RNA（LNCRNA）诱导的机制 多肉液抑制复合物（PRC）在基因组的特定区域的传播。两者中的每一个 PRCS，PRC1和PRC2沉积组蛋白修饰，抑制转录并同时刺激转录 另一个复合物的活性。 PRC对于大多数主要器官系统及其开发至关重要 失调会引起多种疾病。 PRC在已知的表观遗传修饰剂中是独一无二的 它们在染色质上的分布是由特定的lncRNA诱导的。但是，尽管研究了几十年，但该领域还是 没有确定LNCRNA如何诱导PRC的传播。著名模型表明lncrnas依赖3- 尺寸（3D）基因组结构，以不加选择地散布染色质，而不会受到影响 通过DNA的基础序列。但是，这些模型无法解释PRC-的广泛可变性 lncRNA目标域中的依赖性修改，并且不认为在lncRNA目标域之外， DNA元素称为CpG岛（CGIS）将PRC招募到染色质。而且，尚不清楚多少 LNCRNA诱导中国的传播。虽然调查人员最初提出成千上万的lncrnas 此功能，经过验证的PRC诱导LNCRNA的数量保持接近十。我们的发现开始 解决这些未知数。例如，我们发现在小鼠滋养细胞中，lncrna airn 导致PRC从CGI中向外散布，该CGI在表达AIRN之前自主结合PRC。删除 这些CGI中的一种只会导致在AIRN域中进行多个PRC沉积修饰的多个损失。 此外，我们和其他人发现与PRC相关的特定RNA结合蛋白，至少两个 这些蛋白质似乎是LNCRNA诱导PRC扩散所必需的。因此，而不是传播中国 在染色质上不加选择的情况下，我们假设LNCRNA与CGIS相关以将PRC从 特定的接触点，并且该关联是由结合lncRNA和的RNA结合蛋白介导的 中国。此外，我们假设任何染色质的RNA都可以诱导PRC的扩散，只要它 结合必要的蛋白质。现在，我们提出对这些假设的严格测试：在AIM 1下，我们将 确定CGI和CGI结合因子在LNCRNA诱导的PRC扩散中的作用。在AIM 2下，我们 将确定RNA结合蛋白在LNCRNA诱导的PRC扩散中的作用。在AIM 3下，我们将 确定非经典RNA在诱导PRC传播中的作用。如果成功，我们的工作将会 展示了DNA调节元件，RNA结合蛋白和RNA在PRC功能中的新作用。 我们建立的范例应适用于核细胞生物学的广泛领域，并建议多个新途径 用于治疗基因表达。