NuA3 HAT antagonizes the Rpd3S and Rpd3L HDACs to optimize mRNA and lncRNA expression dynamics

Ji Hyun Kim, Chae Young Yoon, Yukyung Jun, Bo Bae Lee, Ji Eun Lee, So Dam Ha, Hyeonju Woo, Ahyoung Choi, Sanghyuk Lee, Woojin Jeong, Ji Hyung Kim, Tae Soo Kim

Research output: Contribution to journalArticlepeer-review

9 Scopus citations


In yeast, NuA3 histone acetyltransferase (NuA3 HAT) promotes acetylation of histone H3 lysine 14 (H3K14) and transcription of a subset of genes through interaction between the Yng1 plant homeodomain (PHD) finger and H3K4me3. Although NuA3 HAT has multiple chromatin binding modules with distinct specificities, their interdependence and combinatorial actions in chromatin binding and transcription remain unknown. Modified peptide pulldown assays reveal that the Yng1 N-terminal region is important for the integrity of NuA3 HAT by mediating the interaction between core subunits and two methyl-binding proteins, Yng1 and Pdp3. We further uncover that NuA3 HAT contributes to the regulation of mRNA and lncRNA expression dynamics by antagonizing the histone deacetylases (HDACs) Rpd3S and Rpd3L. The Yng1 N-terminal region, the Nto1 PHD finger and Pdp3 are important for optimal induction of mRNA and lncRNA transcription repressed by the Set2-Rpd3S HDAC pathway, whereas the Yng1 PHD finger-H3K4me3 interaction affects transcriptional repression memory regulated by Rpd3L HDAC. These findings suggest that NuA3 HAT uses distinct chromatin readers to compete with two Rpd3-containing HDACs to optimize mRNA and lncRNA expression dynamics.

Original languageEnglish
Pages (from-to)10753-10767
Number of pages15
JournalNucleic Acids Research
Issue number19
StatePublished - 4 Nov 2020

Bibliographical note

Funding Information:
National Research Foundation [NRF-2017M3A9B506088 7, NRF-2017M3A9G7073033, NRF-2017M3C9A502998 0, NRF-2019R1A5A6099645 to T.K; NRF-2019R1A6A 3A01095423 to J.H.K]. Funding for open access charge: National Research Foundation.

Publisher Copyright:
© 2020 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research.


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