Date of Award

2021

Degree Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Graduate Group

Cell & Molecular Biology

First Advisor

Chi V. Dang

Abstract

The roles of lncRNAs, particularly those regulated by the circadian transcription factors BMAL1-CLOCK, in biological processes are poorly understood. We identified ADIRF-AS1 as a BMAL1-regulated high amplitude circadian lncRNA, whose loss (ADIRF-AS1 KO) affected rhythmicity of cell cycle genes and altered expression of genes associated with the extracellular matrix. Through proteomics analysis, all components of the tumor suppressive PBAF (PBRM1/BRG1) complex as bound to ADIRF-AS1. We found that a subset of PBAF rhythmic circadian target genes lost rhythmicity in ADIRF-AS1 KO cells. Thus, we sought to determine how ADIRF-AS1 regulates the PBAF complex and found that differentially expressed cell cycle and selected metabolic genes in ADIRF-AS1 KO 786O ccRCC cells could be rescued by loss of PBRM1. Consistent with regulation of the PBAF complex, loss of ADIRF-AS1 in the 786O ccRCC cell line did not affect in vitro growth, but in vivo tumorigenesis was absent. Tumorigenesis was partially rescued by concurrent loss of PBRM1 in the presence of Matrigel, accounting for PBAF dependent and independent functions of ADIRF-AS1. Further, ADIRF-AS1 is upregulated in human ccRCC and correlates with survival, particularly in PBRM1 wild-type tumors, using TCGA data. Our findings suggest that ADIRF-AS1 functions to antagonize the tumor suppressive effect of the PBAF complex and hence behaves as an unforeseen circadian-regulated, oncogenic lncRNA.

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