Dual roles of the Arabidopsis PEAT complex in histone H2A deubiquitination and H4K5 acetylation [ChIP-seq]

Histone H2A monoubiquitination is associated with transcriptional repression and needs to be removed by deubiquitinases to facilitate gene transcription in eukaryotes. However, the deubiquitinase responsible for genome-wide H2A deubiquitination in plants has yet to be identified. We found that UBP5, an ubiquitin-specific protease, interacts with a previously identified PEAT (PWWP-EPCR-ARID-TRB) complex to form a larger version of PEAT complex in Arabidopsis thaliana. UBP5 functions as an H2A deubiquitinase in a nucleosome substrate-dependent manner in vitro and mediates H2A deubiquitination at the whole-genome level in vivo. Moreover, our results indicated that the histone acetyltransferases HAM1 and HAM2 (HAM1/2), catalytic subunits of the NuA4 histone acetyltransferase complex, are also part of the PEAT complex at PEAT target genomic loci. Within the PEAT complex, the PWWP components (PWWP1, PWWP2 and PWWP3) directly interact with UBP5 and are necessary for UBP5-mediated H2A deubiquitination, while the EPCR components (EPCR1 and EPCR2) directly interact with HAM1/2 and are required for HAM1/2-mediated H4K5 acetylation. This study identifies previously unknown regulators of H2A deubiquitination and H4K5 acetylation and illustrates how these processes collaborate at the whole-genome level. Examination of protein binding levels in transgenic plants; Examination of H4K5Ac, H2Aub level in wild type and mutants; Examination of H3K27me3 level in wild type.