Rpd3L HDAC links H3K4me3 to transcriptional repression memory
 Authors and Affiliations
 Authors and Affiliations
Bo Bae Lee1,†, Ahyoung Choi1,†, Ji Hyun Kim1, Yukyung Jun1, Hyeonju Woo1, So Dam Ha1, Chae Young Yoon1, Jin-Taek Hwang2, Lars Steinmetz3, Stephen Buratowski4, Sanghyuk Lee1, Hye Young Kim5,* and TaeSoo Kim1,*
1Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea, 2Korea Food Research Institute, Wanju 55365, Korea, 3Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, and Stanford Genome Technology Center and Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA, 4Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA and 5Department of Biomedical Sciences and Medical Science, Seoul National University College of Medicine, Seoul 03080, Korea
*To whom correspondence should be addressed. Correspondence may also be addressed to Hye Young Kim.
†The authors wish it to be known that, in their opinion, the first two authors should be regarded as Joint First Authors.
Abstract Transcriptional memory is critical for the faster reactivation of necessary genes upon environmental changes and requires that the genes were previously in an active state. However, whether transcriptional repression also displays ‘memory’ of the prior transcriptionally inactive state remains unknown. In this study, we show that transcriptional repression of ∼540 genes in yeast occurs much more rapidly if the genes have been previously repressed during carbon source shifts. This novel transcriptional response has been termed transcriptional repression memory (TREM). Interestingly, Rpd3L histone deacetylase (HDAC), targeted to active promoters induces TREM. Mutants for Rpd3L exhibit increased acetylation at active promoters and delay TREM significantly. Surprisingly, the interaction between H3K4me3 and Rpd3L via the Pho23 PHD finger is critical to promote histone deacetylation and TREM by Rpd3L. Therefore, we propose that an active mark, H3K4me3 enriched at active promoters, instructs Rpd3L HDAC to induce histone deacetylation and TREM.
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