Figure 2.

Generation and assessment of anti-phosphorylated Ser2/Ser5 RNAPII antibodies. (a) RNAPII was categorized by the phosphorylation status of its C-terminal domain (CTD). (a) Free RNAPII was hypophosphorylated in its CTD residues, and recruited to the promoter, where TFIIH phosphorylates Ser5 residues. Ser5-phosphorylated RNAPII progresses to the pausing site, but it is halted by negative elongation factors. Phosphorylation of Ser2 allows active transcription. Recent evidence suggests that several pausing genes produce full-length transcripts at low levels. (b) Reactivity of different RNAPII antibodies against hyper- and hypophosphorylated RNAP2 was assessed by immunoblotting. (c) The average Ser2/Ser5 phosphorylated RNAP2 enrichment tags per one gene from ChIPseq data, normalized to input by Peakseq, were summed according to their shifted positions, with the definition that gene length was from 0 to 1. Where 0 represents the transcription start site and 1 represents the transcription end site.