Role of Negative Elongation Factor Complex in RNA polymerase II pausing and gene transcription in Heart

PROJECT SUMMARY/ABSTRACT Congestive heart failure is one of the leading cause of morbidity and mortality in the USA and the World. However, despite the major advancements in research and therapeutic developments, there has been no improvement in death rates over the years. This necessitates reinvestigating the basic mechanisms that govern the progression heart failure. Adaptation of gene expression is the earliest fundamental response during overload. We have shown the widespread regulatory influence of promoter-proximal RNA polymerase II (pol II) pausing on gene transcription in heart. However, the underlying mechanisms that control and synchronize the release of paused pol II for active transcription are unclear and conflicting, and its contribution to development of cardiac hypertrophy and failure still unknown. Negative elongation factors (Nelf), comprising of five subunits (NelfA to NelfE) has been implicated in pol II pausing, with NelfA subunit identified as an essential component for pausing. Our preliminary data shows increase in NelfA expression with cardiac hypertrophy, which is required for compensatory increase in gene expression in these hearts. Conversely, NelfA levels decline in failing hearts, suggesting downregulation of NelfA could be contributing to decompensation and progression of failure. Our genome-wide sequencing data shows widespread NelfA occupancy on active promoters including inducible and constitutively expressed essential genes. Interestingly, immunoprecipitation of chromatin bound NelfA shows association with chromatin remodelers and pre-mRNA processing proteins. In this study, we investigate the role of NelfA in pol II dynamics, chromatin remodeling and gene expression, and its impact on progression of heart failure. We have hypothesized that adaptation of gene expression during cardiac hypertrophy is achieved by phosphorylation dependent increase in the rate of clearance of paused pol II from essential gene promoters, and de novo recruitment of NelfA and assembly of paused complex at inducible promoters. Loss of NelfA results in disrupted paused complex, altered chromatin remodeling, inefficient transcript processing and inhibited gene expression that precipitates heart failure. We have proposed two robust specific aims to test our hypothesis – 1. To examine the mechanisms regulating NelfA -dependent pol II pausing in gene transcription during cardiac hypertrophy. 2. To investigate the effects of loss of NelfA on gene expression and progression of heart failure in conditional NelfA-KO model subjected to pressure overload.