Abstract
SummaryTranscriptional fidelity depends on accurate promoter selection and initiation from the correct sites. In yeast, H3K36me3-mediated recruitment of the Rpd3S HDAC complex to gene bodies suppresses spurious transcription initiation. Here we describe an equivalent pathway in metazoans. PWWP2A/B is an H3K36me3 reader that forms a stable complex with HDAC1/2. We used CAGE-seq to profile all transcription initiation sites in wild-type mESCs and cells lacking PWWP2A/B. Loss of PWWP2A/B enhances spurious initiation from intragenic sites present in wild-type mESCs, and this effect is associated with increased levels of initiating Pol-II and histone acetylation. Spurious initiation events in Pwwp2a/b DKO mESCs do not overlap in genomic location or chromatin features with spurious sites that arise in Dnmt3b KO mESCs, previously reported to function in the suppression of intragenic transcriptional initiation, suggesting these pathways function cooperatively in maintaining the fidelity of transcription initiation in metazoans.
Highlights
Trimethylation of lysine 36 on histone H3 (H3K36me3) is a highly conserved posttranslational histone modification in eukaryotic organisms and is enriched over the bodies of actively transcribed genes (Bannister et al, 2005)
Loss of PWWP2A/B enhances spurious initiation from intragenic sites present in wild-type mouse embryonic stem cells (mESCs), and this effect is associated with increased levels of initiating Pol-II and histone acetylation
CAGE-seq using the nuclear RNA fraction as input was performed in triplicate for wild-type and Pwwp2a/b double knockout (DKO) C7 and in duplicate for DKO A1 (Figure 1A), and the biological replicates were merged owing to high reproducibility (Figure S1A)
Summary
Trimethylation of lysine 36 on histone H3 (H3K36me3) is a highly conserved posttranslational histone modification in eukaryotic organisms and is enriched over the bodies of actively transcribed genes (Bannister et al, 2005). H3K36me is recognized by the PWWP domain, a motif that is present in many chromatinmodifying complexes (Dhayalan et al, 2010; Qin and Min, 2014; Tian et al, 2019; van Nuland et al., 2013; Wen et al, 2014; Xu et al, 2008) These readers are involved in a variety of biological processes, including intragenic DNA methylation, transcription elongation, DNA repair, alternative splicing, and repression of spurious transcription initiation (as reviewed in Huang and Zhu, 2018; Wagner and Carpenter, 2012). H3K36me3-mediated recruitment of effectors from two different epigenetic pathways, DNA methylation and histone deacetylation, has been linked to the suppression of spurious intragenic transcription initiation in actively transcribed genes. We uncover a newly described PWWP2A/B-HDAC complex in mammalian cells that suppresses transcription initiation from the gene bodies of actively transcribed genes
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