Delineating Mechanisms of Signal-Induced RNA Polymerase II-Transcription

Abstract

Signal-induced transcriptional programs regulate critical biological processes through the precise spatio-temporal activation of inducible gene programs. Understanding the dynamics by which RNA Polymerase II precisely induces transcription to activate these programs is important for dissecting the basis for their role in cell fate responses and disease progression. Here, we utilize high-resolution genomic approaches coupled with temporal signal induction to characterize how individual transcription steps contribute to the gene expression cycle in signal-induced transcription activation. Our first story (chapter 2) utilizes acute depletion approaches to reveal that the KAP1 protein is a positive regulator of transcription of immediate early genes, a class of signal-induced genes that regulate diverse biological processes including cancer and development. Mechanistically, KAP1 negatively regulates elongation rate at the early stages of transcription, which allows for proper kinetic progression through the transcription cycle by bolstering new initiation and full activation of gene expression. Overall, this study is the first report to link KAP1 "repressive" control of transcription to a positive role in gene activation and has implications for transcription-induced cell fate responses. Our second story (chapter 3) centers on ligand-induced transcription activation of the HIV-1 provirus. Decades of research has shown that HIV-1 transcription is primarily activated through pause release and transcription elongation by the HIV-1 transactivator Tat. Here, we use a novel Tat depletion approach to show that Tat function in pause release is the catalyst that promotes sustained RNA Polymerase II recruitment to the HIV-1 promoter. This recruitment of RNA Polymerase II is the mechanism that robustly induces "logarithmic" HIV-1 expression and viral replication. These data reveals a new significance for Tat function in transcription initiation and explains how Tat can sustain extended levels of HIV-1 transcription for proviral fate. Overall, the two studies have provided important mechanistic insights for understanding transcription dynamics in gene expression programs that have implications for diverse biological phenomena and pathogenesis