CCG-1423-derived compounds reduce global RNA synthesis and inhibit transcriptional responses (ChIP-seq)

Myocardin-related transcription factors (MRTFs) are coactivators of serum response factor (SRF), and thereby regulate cytoskeletal gene expression in response to actin dynamics. MRTFs have also been implicated in heat shock protein (hsp) transcription in fly ovaries, but the mechanisms remain unclear. Here we demonstrate that in mammalian cells, MRTFs are dispensable for hsp gene induction. However, the widely used small molecule inhibitors of MRTF/SRF transcription pathway, derived from CCG-1423, efficiently inhibit hsp gene transcription in both fly and mammalian cells also in absence of MRTFs. Quantifying RNA synthesis and RNA polymerase distribution demonstrates that CCG-1423-derived compounds have a genome-wide effect on transcription. Indeed, tracking nascent transcription at nucleotide resolution reveals that CCG-1423-derived compounds reduce RNA polymerase II elongation, and severely dampen the transcriptional response to heat shock. The effects of CCG-1423-derived compounds therefore extend beyond the MRTF/SRF pathway into nascent transcription, opening novel opportunities for their use in transcription research. Chromatin immunoprecipitationfollowed by deep sequencing (ChIP-seq) in NIH3T3 cells of Pol II phosphorylated at serine 5 (Pol II S5P) and MAL (AC-74), and Pol II phosphorylated at serine 5 (Pol II S5P) in S2R+ cells culture. Drug treatment was done for allocated timepoints (10 mins with the inhibitors at NH condition) followed by heat shock for 20 mins either in 37°C waterbath (S2R+ cells) or 42°C waterbath (NIH 3T3 cells). Normal mouse IgG was used as negative control.