UNDERSTANDING THE RULES OF LIFE - Regulation of cellular stress responses by long noncoding RNAs

人类细胞不断暴露在外部和内部应激源中，对细胞及其基因组造成损害。为了应对不同的环境变化，确保有机体的生存，细胞制定了不同的应激适应策略。虽然细胞应激通常会导致正常细胞的程序性死亡，但癌细胞可以绕过生长限制检查点，从而导致肿瘤细胞存活。长非编码RNA(LncRNAs)是包括应激反应在内的多种生理和病理过程的关键调节因子。然而，在大多数研究案例中，lncRNA指导的应激反应调控的分子基础仍然是个谜。Shkumatava实验室最近发现了一种与癌症相关的lncRNA，它可以缓冲细胞压力。LncRNA的遗传失活导致P53途径持续上调，P53途径作为DNA损伤的细胞传感器和基因组的守护者。我们发现，该lncRNA通过其保守的RNA序列基序与关键的DNA损伤蛋白结合。我们现在的目标是定义这些高度保守的RNA元件的功能，并揭示它们与DNA损伤机制的关联如何有助于调节细胞应激反应和维持细胞完整性。为了实现我们的目标，我们采用了最先进的技术，包括相关哺乳动物细胞系的基因组编辑、高分辨率成像、全基因组测序方法(RNA-SEQ、CHIP-SEQ、ATAC-SEQ)、各种细胞和分子方法，包括我们新颖的高通量incPRINT RNA-蛋白质相互作用技术。学生将在上述所有学科中发展特定技能。该项目将由RNA生物学专家Shkumatava博士和基因组稳定性和DNA损伤反应专家Buonomo博士共同监督。此外，我们还与生物信息学家合作进行数据分析。

Human cells are constantly exposed to external and internal stressors causing damage to the cell and its genome. To cope with diverse environmental changes and ensure the survival of the organism, cells developed diverse stress adaptation strategies. Whereas cellular stress usually leads to programmed cell death in normal cells, cancer cells can by-pass growth-limiting checkpoints resulting in tumor cell survival. Long noncoding RNAs (lncRNAs) have emerged as key regulators of diverse physiological and pathological processes including stress response. However, the molecular basis of the lncRNA-directed regulation of stress responses remains enigmatic in the majority of studied cases. The Shkumatava laboratory has recently identified a cancer-associated lncRNA that buffers cellular stress. Genetic inactivation of the lncRNA leads to constant upregulation of the p53 pathway, which acts as a cellular sensor of DNA damage and a guardian of the genome. We found that this lncRNA engages with key DNA damage proteins via its conserved RNA sequence motifs. Our goal is now to define the function of these deeply conserved RNA elements and reveal how their association with the DNA damage machinery contributes to regulation of the cellular stress response and maintenance of the cell integrity. To achieve our goals, we employ state-of-the-art of technologies including genome editing in relevant mammalian cell lines, high resolution imaging, genome-wide sequencing approaches (RNA-seq, ChIP-seq, ATAC-seq), diverse cellular and molecular approaches including our novel high throughput incPRINT RNA-protein interaction technology. The student will develop specific skills in all mentioned above disciplines. The project will be jointly supervised by Dr Shkumatava who is an expert in RNA biology and Dr Buonomo who is an expert in genome stability and DNA damage response. In addition, we collaborate with bioinformaticians for data analyses.