Authors and Affiliations

Authors and Affiliations

Bo Bae Lee^1,†, Ahyoung Choi^1,†, Ji Hyun Kim¹, Yukyung Jun¹, Hyeonju Woo¹, So Dam Ha¹, Chae Young Yoon¹, Jin-Taek Hwang², Lars Steinmetz³, Stephen Buratowski⁴, Sanghyuk Lee¹, Hye Young Kim^5,* and TaeSoo Kim<sup>1,*

1</sup>Department 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.

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.