Genome-associated RNA Polymerase II includes the dissociable Rpb4/7 subcomplex

Yeast RNA polymerase (Pol) II consists of a ten-subunit core enzyme and the Rpb4/7 subcomplex, which is dispensable for catalytic activity and dissociates in vitro. To investigate whether Rpb4/7 is an integral part of DNA-associated Pol II in vivo, we used chromatin immuno-precipitation coupled to high-resolution tiling microarray analysis. We show that the genome-wide occupancy profiles for Rpb7 and the core subunit Rpb3 are essentially identical. Thus, the complete Pol II associates with DNA in vivo, consistent with functional roles of Rpb4/7 throughout the transcription cycle. Keywords: ChIP-chip Comparison of Rpb3 vs. Rpb4/7 genome-wide occupancy profiles. Data obtained from independent ChIP-chip experiments on two yeast strains: S288C Rpb3TAP vs. Rpb7-TAP strain and W303 Rpb3-TAP vs. wild type strain (IP with the monoclonal antibody for Rpb4/7). Biological replicates W303 strains: 1 x Rpb3-TAP, 1 x wt with Rpb4/7 antibody, independently grown and harvested. Biological replicates S288C strains: 3 x Rpb3-TAP, 2 x Rpb7-TAP, independently grown and harvested. One replicate per array.