Transcription of mammalian cis-regulatory elements is restrained by actively enforced early termination [ChIP-Seq]. Mus musculus

Upon recruitment to active enhancers and promoters, RNA polymerase II (Pol_II) generates short non-coding transcripts of unclear function. The mechanisms that control the length and the amount of ncRNAs generated by cis-regulatory elements are largely unknown. Here, we show that the adapter protein WDR82 and its associated complexes actively limit such non-coding transcription. WDR82 targets the SET1/COMPASS H3K4 methyltransferase and the nuclear Protein Phosphatase 1 (PP1) complexes to the initiating Pol_II. WDR82 and PP1 also interact with components of the transcriptional termination and RNA processing machineries. Depletion of WDR82, SET1 or the PP1 subunit required for its nuclear import caused distinct but overlapping transcription termination defects at highly expressed genes, active enhancers and promoters, thus enabling the increased synthesis of unusually long ncRNAs. These data indicate that transcription initiated from cis-regulatory elements is tightly coordinated with termination mechanisms that impose the synthesis of short RNAs. Overall design: Chromatin immunoprecipitations of H3 lysine 4 tri- or mono-methylated, H3 lysine 27 acetylated, H3 lysine 36 tri-methylated, total or CTD-serine 2 phosphorylated RNA polymerase II followed by multiparallel sequencing performed in murine bone marrow-derived macrophages (BMDMs). Experiments were carried out in cells containing either a short hairpin targeting Wdr82 or the empty vector (LMP) or a scrambled as a control. BMDMs were either untreated or treated for 4 hrs with lipopolysaccharide (LPS).