Abstract

Sequential waves of modifications of the RNA polymerase II (Pol II) carboxyl‐terminal domain (CTD) coordinate the stage‐specific association and release of cellular machines that participate in RNA biogenesis. We examined the genome‐wide distributions of the “early” (phospho‐serine 5), “mid” (phospho‐serine 7) and “late” (phospho‐serine 2) marks of the CTD. We observed gene‐class specific patterns and found a surprising degree of co‐occurrence of the CTD marks. In particular, contrary to its role in 3′ processing of non‐coding RNA, the Ser7‐P marks are placed early and retained until transcription termination at all Pol II‐dependent genes. Chemical‐genomic analysis reveals that the promoter‐distal Ser7‐P marks are not remnants of early phosphorylation events, but are placed anew by Bur1, a CTD kinase that associates with the elongating Pol II. Consistent with the ability of Bur1 to facilitate transcription elongation, high levels of Ser7‐P are observed at highly transcribed genes. This pattern of Ser7‐P enrichment could serve as a shared signal for cellular machines that process functional non‐coding RNA and enhance transcription elongation through protein‐coding genes.

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