Understanding biological functions of repeat-containing noncoding RNAs

了解含有重复序列的非编码 RNA 的生物学功能

• 批准号: BB/R001049/1
• 负责人: Eugene Makeyev
• 金额: $ 63.05万
• 依托单位: King's College London
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2018
• 资助国家: 英国
• 起止时间: 2018 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FR001049%2F1
• 关键词: Understanding; biological; functions; repeat; containing

DNA has been traditionally thought to store information about development and function of our body by encoding numerous proteins with distinct enzymatic, regulatory and structural functions. Yet, only ~2% of the human genome is actually used for this purpose by producing RNA messengers subsequently translated into proteins. A large fraction of the remaining 98% - often referred to as genome's "dark matter" - has been recently shown to give rise to relatively long non-protein-coding RNAs (lncRNAs) with poorly understood functions. Notably, this part of our genome is also enriched in repeated DNA sequences including so-called short tandem repeats (STRs). Expression of a few aberrantly long STR arrays expanded as a result of genetic mutations is known to lead to devastating degenerative diseases by recruiting multiple copies of important RNA-binding proteins (RBPs) to the repeated sequence units. On the other hand, the expression status and possible biological functions of most STRs encoded in healthy human genomes have not been investigated systematically.We propose to test the hypothesis that STR-containing lncRNAs function as pervasive regulators of cellular RNA metabolism by forming multiple contacts with corresponding RBPs and controlling their activity and cellular localization. We will develop our program by pursuing two interrelated objectives.In the first objective, we will estimate the number of STR-lncRNAs encoded in the genome and ask how these molecules can contribute to RBP regulation. For this purpose, we will identify STR-lncRNAs expressed in biomedically important samples - including cancer cells and developing neurons - by using an innovative combination of computational and experimental tools. The most interesting examples of the newly discovered STR-lncRNAs will be examined for their RBP interaction properties, localization, and possible role in shaping cellular gene expression.In the second objective, we will focus on a specific STR-lncRNA called PNCTR that we uncovered in our preliminary work. We already know that PNCTR is over-produced in cancer cells where it focuses a critical RBP, polypyrimidine tract-binding protein (PTBP1), in a dot-like pattern characteristic of high-grade and metastatic tumors. Moreover, PNCTR might be required for cell survival and proliferation. We will continue this line of research by elucidating the mechanisms controlling PNCTR expression and underlying its functional contributions to cancer biology.All in all, these studies should substantially improve our understanding of the "dark matter" of the human genome, provide fundamental insights into regulation of RNA metabolism, and ultimately open up new avenues in disease diagnosis and treatment.

传统上认为，DNA通过编码具有不同酶、调节和结构功能的许多蛋白质来存储有关我们身体发育和功能的信息。然而，只有约2%的人类基因组实际上用于此目的，通过产生RNA信使，随后翻译成蛋白质。剩下的98%中的一大部分-通常被称为基因组的“暗物质”-最近已被证明会产生相对较长的非蛋白质编码RNA（lncRNA），其功能知之甚少。值得注意的是，我们基因组的这一部分也富含重复的DNA序列，包括所谓的短串联重复序列（STR）。已知由于基因突变而扩增的一些异常长的STR阵列的表达通过将重要的RNA结合蛋白（RBP）的多个拷贝募集到重复序列单元而导致破坏性的退行性疾病。另一方面，在健康人类基因组中编码的大多数STR的表达状态和可能的生物学功能还没有被系统地调查，我们建议测试的假设，STR-含有lncRNA作为普遍的调节细胞RNA代谢形成多个接触相应的RBP和控制他们的活动和细胞定位。我们将通过追求两个相互关联的目标来发展我们的计划。在第一个目标中，我们将估计基因组中编码的STR-lncRNA的数量，并询问这些分子如何有助于RBP调节。为此，我们将通过使用计算和实验工具的创新组合来识别在生物医学上重要的样品中表达的STR-lncRNA-包括癌细胞和发育中的神经元。最有趣的例子，新发现的STR-lncRNA将检查其RBP相互作用的性质，定位，并在塑造细胞基因expression.In第二个目标，我们将集中在一个特定的STR-lncRNA称为PNCTR，我们发现在我们的初步工作中的可能作用。我们已经知道，PNCTR在癌细胞中过度产生，它以高级别和转移性肿瘤的点状模式特征集中了一种关键的RBP，多嘧啶片段结合蛋白（PTBP 1）。此外，PNCTR可能是细胞存活和增殖所必需的。我们将通过阐明PNCTR表达的控制机制及其对癌症生物学的潜在功能贡献来继续这一研究路线。总之，这些研究将大大提高我们对人类基因组“暗物质”的理解，为RNA代谢的调控提供基本见解，并最终为疾病诊断和治疗开辟新的途径。

项目成果

Functional Annotation of Custom Transcriptomes.

自定义转录组的功能注释。

• DOI: 10.1007/978-1-0716-2521-7_9
• 发表时间: 2022
• 期刊: Methods in molecular biology (Clifton, N.J.)
• 作者: Hamid F

Mutant Muscle LIM Protein C58G causes cardiomyopathy through protein depletion.

• DOI: 10.1016/j.yjmcc.2018.07.248
• 发表时间: 2018-08
• 期刊: Journal of molecular and cellular cardiology
• 影响因子: 5
• 作者: Ehsan M;Kelly M;Hooper C;Yavari A;Beglov J;Bellahcene M;Ghataorhe K;Poloni G;Goel A;Kyriakou T;Fleischanderl K;Ehler E;Makeyev E;Lange S;Ashrafian H;Redwood C;Davies B;Watkins H;Gehmlich K
• 通讯作者: Gehmlich K

A conserved role for the ALS-linked splicing factor SFPQ in repression of pathogenic cryptic last exons.

• DOI: 10.1038/s41467-021-22098-z
• 发表时间: 2021-03-26
• 期刊: Nature communications
• 影响因子: 16.6
• 作者: Gordon PM;Hamid F;Makeyev EV;Houart C
• 通讯作者: Houart C