Understanding biological functions of repeat-containing noncoding RNAs

DNA传统上被认为通过编码许多具有不同酶功能、调节功能和结构功能的蛋白质来存储关于我们身体发育和功能的信息。然而，只有约2%的人类基因组实际用于这一目的，因为它产生的RNA信使随后被翻译成蛋白质。剩下的98%--通常被称为基因组的“暗物质”--中的很大一部分最近被证明产生了相对较长的非蛋白质编码RNA(LncRNAs)，但对其功能了解很少。值得注意的是，我们基因组的这一部分还富含重复的DNA序列，包括所谓的短串联重复序列(STR)。众所周知，由于基因突变而扩大的少数异常长的STR阵列的表达，通过将重要的RNA结合蛋白(RBPs)的多个副本招募到重复序列单元而导致毁灭性的退行性疾病。另一方面，大多数STR在健康人类基因组中的表达状况和可能的生物学功能还没有得到系统的研究。我们提出了一种假设，即含有STR的lncRNAs通过与相应的RBPs形成多个接触并控制它们的活性和细胞定位来发挥细胞RNA代谢的普遍调节作用。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-lncRNAs的数量，并询问这些分子如何对RBP调节做出贡献。为此，我们将使用计算和实验工具的创新组合，识别在生物医学重要样本-包括癌细胞和发育中的神经元-中表达的STR-lncRNAs。在第二个目标中，我们将专注于我们在前期工作中发现的一种特殊的STR-lncRNA，称为PNCTR。我们已经知道PNCTR在癌细胞中过度产生，在那里它集中了一种关键的RBP，多嘧啶结合蛋白(PTBP1)，在高级别和转移性肿瘤中呈点状图案。此外，PNCTR可能是细胞生存和增殖所必需的。我们将继续这一研究，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。总而言之，这些研究将极大地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的见解，并最终为疾病诊断和治疗开辟新的途径。

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.