长链非编码RNA染色质结合的机制研究

Pervasive transcription in the mammalian genome produces thousands of long noncoding RNAs (lncRNAs), which participated in multiple biological processes. Compared with protein-coding genes, lncRNAs are preferentially retained in the nucleus and associated with chromatin. However, the mechanism controlling the chromatin retention of lncRNAs remain elusive. We hypothesize that embedded RNA sequences and interacting proteins may be the cis and trans regulators governing RNA subcellular localization, respectively. To comprehensively identify the cis-regulatory elements of RNA transcript, in this funding, we have developed a high-throughput sequencing-based method named RNA element for subcellular localization by sequencing (REL-seq). Using this method, we identified RNA sequences contribute to the chromatin retention of lncRNAs. We will further solve the detailed mechanism of lncRNAs chromatin retention through the cis-regulatory elements and trans-interacting factors identified. Furthermore, we will explore the role of this regulatory mechanism in the function of lncRNAs, as well as its correlation with disease occurrence and potential pathogenic mechanism. The expected results of this study will solve the long-lived problem—how lncRNAs retained to chromatin. At the same time, this project will provide new methods and strategies for lncRNA function and mechanism studies. Elucidation of the mechanisms underlying RNA-chromatin association will shed a mechanistic insight into the functional roles of lncRNAs in modulating transcription and chromatin structure, and also facilitate an overall understanding of how noncoding portions of the genome contribute to cell-specific expression programs in development and disease.

长链非编码RNA（lncRNA）参与调控多种生命活动过程。相比于细胞质定位的蛋白编码基因，lncRNA更倾向定位于细胞核且结合于染色质，参与基因的表达及染色质高级结构的调控。然而，lncRNA的染色质结合的机制一直不明。基于此，本项目通过构建筛选参与lncRNA亚细胞定位的顺式调控元件的方法，鉴定出参与调控lncRNA染色质结合的关键顺式元件，通过该顺式元件鉴定其反式作用因子，进而解析lncRNA染色质结合的分子机制。在此基础上，我们将进一步探究这一调控机制对lncRNA功能发挥的作用，及其与疾病发生的相关性和潜在的致病机理。预期研究成果将解决lncRNA的染色质结合这一重大科学问题，弥补lncRNA亚细胞定位机制研究匮乏的不足。同时，该项目为lncRNA研究提供了新的研究方法和研究思路，对后续进一步探究lncRNA的作用机制及其在生命活动及疾病发生过程中的作用提供借鉴。

长链非编码RNA（lncRNA）参与调控多种生命活动过程。相比于细胞质定位的蛋白编码基因，lncRNA更倾向定位于细胞核且结合于染色质，参与基因的表达及染色质高级结构的调控。然而，lncRNA的染色质结合的机制一直不明。本项目通过建立筛选参与lncRNA亚细胞定位顺式调控元件的方法，并进一步鉴定关键顺式元件的反式识别因子，揭示了U1 snRNP广泛参与调控lncRNA的染色质结合。我们的数据表明，U1 snRNP参与调控了接近一半的在小鼠胚胎干细胞中表达的lncRNA，以及大部分染色质结合的，转录调控区域关联的不稳定转录本的染色质滞留。机制上，相比于细胞质定位的蛋白编码基因，lncRNA转录本具有更多的U1 snRNP识别基序以及更强的U1 snRNP的结合。U1 snRNP与lncRNA结合后通过与磷酸化的RNA聚合酶II互作将lncRNA滞留在染色质上。同时，U1 snRNP协同其下游的转录终止信号，促进了其所结合的RNA的降解。我们的工作一方面阐明了lncRNA结合于染色质的调控机制这一关键科学问题，另一方面也揭示了U1 snRNP这一被广泛研究的小核糖核蛋白粒子的新颖功能。相关研究成果最后发表于《Nature》杂志，项目负责人并被受邀在RNA领域经典杂志《RNA Biology》撰写综述论文。

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