NuA3 HAT contributes to the Rpd3 containing HDACs-mediated regulation of mRNA and lncRNA expression dynamics

In yeast, NuA3 histone acetyltransferase (NuA3 HAT) enhances H3K14 acetylation and transcription of a subset gene via interaction between the Yng1 PHD finger and H3K4me3. Although NuA3 HAT includes multiple chromatin binding modules with distinct specificities, their interdependencies and combinatorial actions in chromatin binding and transcription remain unknown. Modified peptide pulldown assays reveal that Yng1 n-terminal region is important for the integrity of NuA3 HAT by mediating interaction between core subunits and two methyl-binders, Yng1and Pdp3. We further uncover that NuA3 HAT contributes to both Rpd3S and Rpd3L HDACs-mediated regulation of mRNA and lncRNA expression dynamics. Yng1 n-terminal region, Nto1 PHD finger and Pdp3 PWWP domain are important for optimal induction of mRNA and cryptic transcription repressed by the Set2-Rpd3S HDAC pathway. In contrast, the Yng1 PHD finger-H3K4me3 interaction affects transcriptional repression memory (TREM) regulated by Rpd3L HDAC. These findings suggest that NuA3 HAT utilizes distinct chromatin readers to compete with two Rpd3 containing HDACs for optimal mRNA and lncRNA expression dynamics. Ananysis of gene expression dynamics in wild type and mutants for NuA3 HAT during carbon source shifts.