Application of transcriptomics, computational modeling, and evolutionary analysis to investigate the regulation of transcription elongation factors

Between transcription initiation and termination, RNA Polymerase II (RNAPII) associates with a variety of transcription elongation factors. These proteins modulate RNAPII elongation rate, RNAPII processivity, and the activity of enzymes that co-transcriptionally process RNA. The evolutionarily conserved Paf1 complex (Paf1C), consisting of Paf1, Ctr9, Rtf1, Cdc73, and Leo1, associates with elongating RNAPII and has been implicated in a variety of co-transcriptional processes. Defects in Paf1C have been associated with disease states and misregulation of co-transcriptional events. Therefore, an understanding of how Paf1C functions in transcription elongation is paramount to understanding how these functions impact human health. Thus, for my dissertation, I investigated Paf1C and other transcription elongation factors to advance understanding of the fundamental processes underlying gene expression. Herein I describe my progress in characterizing the roles of Paf1C and other transcription elongation factors through multiple approaches. Through one investigation, I elucidate the direct and indirect contributions of Paf1C subunits to chromatin and transcription regulation using multi-omic and computational approaches. This work uncovers subunit-specific functions of Paf1C regulating transcription elongation processivity and an indirect role of Paf1C in modulating transcript processing through splicing. I have additionally developed a model of transcription elongation dynamics (TED) to predict how RNAPII elongation is altered in the short- and long-term absence of Paf1C. Furthermore, I interrogate the contributions of Paf1C-dependent histone modifications towards Paf1C-dependent transcriptional phenotypes. This work comprehensively analyzes both the immediate and extended roles of each Paf1C subunit in transcription elongation and transcript regulation. I also describe my contributions to another study characterizing the phylogenetics of core transcription elongation factors including Paf1C across the tree of life. In collaboration with Aakash Grover, we uncovered patterns of apparent reductive evolution which may render some transcription elongation factors disposable in select clades. This work reveals flexibility in the composition of the transcription elongation machinery across species. Together, this work advances our understanding of the fundamental biological processes regulating transcription in a model eukaryote and across all domains of life.