Abstract 13286: Paused Promoter-Proximal RNA Polymerase II Plays A Major Regulatory Role During Cardiac Hypertrophy
The regulation of gene expression is fundamental to organogenesis and pathogenesis. While posttranscriptional regulation has recently attracted much attention we have very limited knowledge regarding the extent and mode of transcriptional regulation of the genes involved in cardiac hypertrophy. We hypothesized that by performing RNA polymerase II (pol II) chromatin immunoprecipitation followed by extensive sequencing (ChIP-Seq) in adult mice hearts, before and after transverse aortic constriction (TAC), that we would identify genes that are transcriptionally regulated and the mode of pol II regulation involved in global vs. specific gene enhancement. Left ventricles isolated from 1 day-old and 12 week-old mice before or after TAC, were subjected to RNA pol II ChIP-Seq using Illumina Genome Analyzer 2. For analysis, 36-nt of the sequencing reads (tags, >10 million) with no more than 2 mismatches are aligned to the genome using ELAND algorithm. To determine fragment density tags were extended (110-200 bp) in silico at their 3’end. The genome is then divided into 32 nt bins and the density of the fragments in each bin is determined. The results of this is stored in a binary analysis results file and viewed by Affymetrix’ Integrated Genome Browser. In addition to identifying genes that were upregulated by de novo RNA pol II recruitment to the promoter, we also revealed for the first time widespread promoter-proximal RNA pol II pausing in the adult versus the neonatal hearts (62% of expressed genes). Interestingly, TAC induced a synchronized release of paused pol II, similar to that observed in the neonatal heart. We have also uncovered a novel aspect of RNA pol II transcription in the form of stalling downstream of transcribed genes. The reduction in paused promoter-proximal pol II is associated with a commensurate increase in downstream pol II (∼30 % of total pol II). On the other hand, we were able to identify 4 % of transcribed genes that were upregulated (>2x) by pol II recruitment that did not exhibit promoter-proximal pol II pausing. These genes predominantly fell in the GO category of cardiac development and sarcomeric proteins. Thus, we reveal for the first time that promoter-proximal pausing of pol II plays a major regulatory role during cardiac hypertrophic growth.
- © 2011 by American Heart Association, Inc.