A variant NuRD complex containing PWWP2A/B excludes MBD2/3 and directs HDAC activity to regulate histone acetylation and RNA Pol II dynamics

Transcriptional regulation by chromatin is a highly dynamic process directed through the recruitment and coordinated action of epigenetic modifiers and readers of these modifications. Using an unbiased proteomic approach to find interactors of H3K36me3, a modification enriched on active chromatin, here we identify PWWP2A and HDAC2 among the top interactors. PWWP2A and its paralog PWWP2B form a stable complex with NuRD subunits MTA1/2/3:HDAC1/2:RBBP4/7, but not with MBD2/3, p66α/β, and CHD3/4. PWWP2A competes with MBD3 for binding to MTA1, thus defining a new variant NuRD complex that is mutually exclusive with the MBD2/3-containing NuRD. In mESCs, PWWP2A/B is most enriched at highly transcribed genes. Loss of PWWP2A/B leads to increases in histone acetylation predominantly at highly expressed genes, accompanied by decreases in Pol II elongation. Collectively, these findings suggest a role for PWWP2A/B in regulating transcription through the fine-tuning of histone acetylation dynamics at actively transcribed genes. ChIP-seq analysis of chromatin epigenetics changes between wildtype and PWWP2A/B double knockout mouse embryonic stem cells. Conventional ChIP methods were applied for PWWP2A/B and derived truncated proteins. Calibrated ChIP-seq were applied for investigating the NuRD-variant complex recruitment (HDAC1 and MTA2), acetylation alterations (H3K27ac and H3K9ac), and RNA Polymerase II dynamics.