Actin associates with actively elongating genes
Nuclear actin has been demonstrated to be essential for optimal transcription, but the molecular mechanisms and direct binding partner for actin in the RNA polymerase complex have remained unknown. By using purified proteins in several biochemical assays, we demonstrate a direct and specific interaction between monomeric actin and Cdk9, the kinase subunit of the positive transcription elongation factor b (P-TEFb) required for RNA polymerase II (Pol II) pause-release. This interaction is not dependent on kinase activity of Cdk9 and is not involved with releasing P-TEFb from its inhibitor 7SK snRNP complex. Supporting the specific role for actin in the elongation phase of transcription, chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) reveals that actin interacts with genes only upon their active transcription elongation. This study therefore provides novel insights into the mechanisms by which actin facilitates the transcription process. Overall design: chromatin immunoprecipitationfollowed by deep sequencing (ChIP-seq) of actin (AC-74) and Pol II phosphorylated at serine 5 (Pol II S5P) in S2R+  cells culture at room temperature (non-heat shock; NHS) or heat shocked for 20 min at 37°C (HS). Normal mouse IgG and input were used as negative controls