Transcriptional regulation patterns revealed by high resolution chromatin immunoprecipitation during cardiac hypertrophy.

Cardiac hypertrophy is characterized by a generalized increase in gene expression that is commensurate with the increase in myocyte size and mass, on which is superimposed more robust changes in the expression of specialized genes. Both transcriptional and posttranscriptional mechanisms play fundamental roles in these processes; however, genome-wide characterization of the transcriptional changes has not been investigated. Our goal was to identify the extent and modes, RNA polymerase II (pol II) pausing versus recruitment, of transcriptional regulation underlying cardiac hypertrophy. We used anti-pol II and anti-histone H3K9-acetyl (H3K9ac) chromatin immunoprecipitation-deep sequencing to determine the extent of pol II recruitment and pausing, and the underlying epigenetic modifications, respectively, during cardiac growth. The data uniquely reveal two mutually exclusive modes of transcriptional regulation. One involves an incremental increase (30-50%) in the elongational activity of preassembled, promoter-paused, pol II, and encompasses ∼25% of expressed genes that are essential/housekeeping genes (e.g. RNA synthesis and splicing). Another involves a more robust activation via de novo pol II recruitment, encompassing ∼5% of specialized genes (e.g. contractile and extracellular matrix). Moreover, the latter subset has relatively shorter 3'-UTRs with fewer predicted targeting miRNA, whereas most miRNA targets fall in the former category, underscoring the significance of posttranscriptional regulation by miRNA. The results, for the first time, demonstrate that promoter-paused pol II plays a role in incrementally increasing housekeeping genes, proportionate to the increase in heart size. Additionally, the data distinguish between the roles of posttranscriptional versus transcriptional regulation of specific genes.