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: 10570834
• 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 2025-02-28
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10570834
• 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; gene repression; 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.

摘要 这项资助的目的是确定长链非编码RNA（lncRNA）诱导细胞凋亡的机制。 多梳抑制复合物（PRCs）在基因组特定区域的扩散。每两 PRCs，PRC 1和PRC 2，沉积组蛋白修饰，抑制转录，同时刺激 另一个复合体的活动。PRC对于大多数主要器官系统的发育及其 失调会导致多种疾病。PRC在已知的表观遗传修饰剂中是独特的， 它们在染色质上的扩散是由特异性lncRNA诱导的。然而，尽管经过几十年的研究，该领域 还没有确定lncRNA是如何诱导PRCs扩散的。突出的模型表明lncRNA依赖于3- 三维（3D）基因组结构，使PRC不受影响地不加选择地分布在染色质上， DNA的基本序列。然而，这些模型不能解释PRC的广泛变异性- lncRNA靶向结构域中依赖性修饰，而不考虑lncRNA靶向结构域之外， 称为CpG岛（CGI）的DNA元件将PRC招募到染色质中。此外，目前还不清楚有多少人 lncRNA诱导PRC的扩散。虽然研究人员最初提出数千种lncRNA 在这种功能中，验证的PRC诱导lncRNA的数量保持接近10个。我们的发现已经开始 解决这些未知数。例如，我们发现在小鼠滋养层干细胞中，lncRNA Airn 导致PRC在Airn表达之前从自主结合PRC的CGI向外扩散。删除 这些CGI中的仅仅一个的缺失导致Airn域中PRC沉积的修饰的数百万次的损失。 此外，我们和其他人发现了与PRCs相关的特异性RNA结合蛋白， 这些蛋白质似乎是lncRNA诱导PRC扩散所必需的。因此，与其传播PRC， 不加区别地跨越染色质，我们假设lncRNA与CGIs相关， 特定的接触点，并且这种结合是由结合lncRNA的RNA结合蛋白介导的， PRC。此外，我们假设任何染色质结合的RNA都可以诱导PRCs的扩散，只要它 结合必要的蛋白质。我们现在提出对这些假设的严格测试：在目标1下，我们将 确定CGI和CGI结合因子在由lncRNA诱导的PRC扩散中的作用。根据目标2，我们 将确定RNA结合蛋白在lncRNA诱导的PRC扩散中的作用。根据目标3，我们将 确定非典型RNA在诱导PRCs扩散中的作用。如果成功，我们的工作将 证明了DNA调控元件，RNA结合蛋白和RNA在PRC功能中的新作用。 我们建立的范例应该适用于核细胞生物学的广泛领域，并提出多种新途径 用于治疗性地控制基因表达。