Transcriptional regulation by long noncoding RNAs

为了产生多样化的组织并对其环境做出反应，细胞需要以精致的特异性激活和抑制特定基因的表达。这一过程涉及多种蛋白质的活性，如转录因子和染色质修饰物，它们以协调的方式调节基因组。在过去的十年里，我们已经意识到细胞产生数以万计的长RNA，称为lncRNAs，不编码蛋白质。目前正在出现一种模型，其中许多lncRNAs被认为通过与染色质和蛋白质相互作用而参与调控基因的表达，并通过充当支架帮助它们组装成复合体、介导它们招募到特定位点或通过抑制它们的结合和活性来影响它们的功能。然而，破译哪些lncRNA能够直接调控基因表达被证明是具有挑战性的，而且对于lncRNA如何完成这些任务的机制理解仍然难以捉摸。这就提出了一些有趣的问题，比如在lncRNAs中是否存在调节它们与转录因子或染色质修饰物相互作用的功能结构域，以及如何发现和表征它们。它还需要应用允许探测和操纵lncRNA活性的新技术。利用一种新的基于CRISPR的方法，我们最近发现了一种当直接拴在定义的基因座上时能够激活表达的lncRNA。这具有重要的意义，并表明了一种依赖于RNA的转录调节功能，在这种功能中，lncRNA可能相互作用并帮助招募特定的蛋白质来靶向基因。在这个项目中，我们想通过识别那些具有转录调节活性的LncRNAs来定义LncRNAs的调节原理，直接测试它们的功能，解剖特定的RNA结构域以及相互作用的蛋白质伙伴来调节它们的功能。该项目的结果将为更好地理解这些神秘的RNA如何影响基因组调控提供有价值的见解，并有助于确定是否存在模块化的RNA序列依赖效应和调节基因表达的lncRNAs亚群。该项目还将能够建立一种通用的方法来识别和表征其他哺乳动物的ncRNA结构域，并指导旨在控制基因表达的新工具的设计。

In order to generate a diversity of tissues and respond to their environment, cells need to activate and repress the expression of defined genes with exquisite specificity. This process involves the activity of multiple proteins, such as transcription factors and chromatin modifiers, that act to regulate the genome in a coordinated fashion. Over the last decade, we've come to realize that cells produce tens of thousands of long RNAs, termed lncRNAs, that do not encode proteins. A model is now emerging whereby many of these lncRNAs are thought to be involved in regulating gene expression by interacting with chromatin and proteins and influence their function either by acting as a scaffold to help their assembly into complexes, mediating their recruitment to specific loci, or by inhibiting their binding and activity. However, deciphering which lncRNAs are able to directly regulate gene expression has proven challenging and a mechanistic understanding of how lncRNAs could accomplish these tasks has remained elusive. This raises interesting questions such as whether there are functional domains within lncRNAs that mediate their interaction with transcription factors or chromatin modifiers and how to find and characterize them. It also requires applying new technologies allowing to probe and manipulate lncRNA activity. Using a novel CRISPR-based approach, we recently found a lncRNA able to activate expression when directly tethered to a defined locus. This has important implications and suggests an RNA-dependent transcriptional regulatory function, where the lncRNA likely interacts and helps recruit specific proteins to target genes. In this project, we want to define the regulatory principles of lncRNAs by identifying those with transcriptional regulatory activity, directly test their function and dissecting the specific RNA domains as well as interacting protein partners that mediate their function. Results from this project will provide valuable insight to better understand how these enigmatic RNAs can affect genome regulation and help determine whether there are modular RNA sequence-dependent effects and subgroups of lncRNAs that regulate gene expression. This project will also enable the establishment of a general approach to identify and characterize other mammalian ncRNA domains and guide the design of novel tools aimed at controlling gene expression.