Date of Award

Spring 2021

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Department

Molecular, Cellular, and Developmental Biology

First Advisor

Dimitrova, Nadya

Abstract

The tumor suppressor protein p53 plays a central role in sensing and responding to cellular stress, and loss of normal p53 activity is a feature of most human cancers. P53, functioning as a transcription factor, regulates a wide network of genes that coalesce to drive many diverse tumor suppressive cellular processes. Despite three decades of extensive study, it is unclear which p53 targets are most critical for these tumor suppressive functions and under which biological contexts. More recent studies have revealed that the p53 network is not solely comprised of protein coding genes but also includes many long noncoding RNAs (lncRNAs), which are an abundant but poorly characterized class of heterogenous RNA molecules. This work aimed to expand our understanding of the role of lncRNAs in the p53 transcriptional network and the importance of these diverse RNAs in various p53-regulated processes and/or tumor suppression.  We focused on characterizing the p53 response to stress generated by hyperactive oncogenes (i.e. oncogenic stress), which is an important but understudied facet of p53-mediated tumor suppression. By performing genome-wide analysis of p53 regulation across a panel of cancer cell lines established from a genetically-engineered mouse model of p53-driven lung adenocarcinoma, sarcoma, and lymphoma, we uncovered oncogenic stress-specific, tumor type-specific, and p53 outcome-specific patterns of p53 gene activation and repression, including the activation of several novel and previously described lncRNAs. We interrogated the contributions of many of these lncRNAs to p53 pathway function, using a number of locus-specific genetic and molecular approaches to down- or upregulate lncRNA expression in vitro. These characterization efforts revealed that local gene regulation, also known as cis-regulation, is the dominant mode of action for lncRNAs within the p53 network, in contrast to most previous reports on individual p53-regulated lncRNAs. We show that this regulation is largely in the positive direction, suggesting that lncRNAs do not significantly contribute to p53-mediated gene repression, and demonstrate that lncRNA cis-regulation can be important for p53-dependent growth arrest in certain tumor contexts. Altogether, this work provides novel insights into the p53 response across different cellular contexts and clarifies the contributions of lncRNAs to the p53 tumor suppressor network. Namely, we propose that lncRNAs primarily serve as an important fine-tuning regulatory mechanism. As such, this work has broader implications on the mechanisms by which lncRNAs as a class may influence other complex transcriptional networks important in human health and disease.

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