Visualization of the dynamic interaction between nucleosomal histone H3K9 tri-methylation and HP1α chromodomain in living cells

Kazuki Sasaki; Michihiro Suzuki; Takeshi Sonoda; Tilman Schneider-Poetsch; Akihiro Ito; Motoki Takagi; Shinya Fujishiro; Yoshihiro Sohtome; Kosuke Dodo; Takashi Umehara; Hiroyuki Aburatani; Kazuo Shin-Ya; Yoichi Nakao; Mikiko Sodeoka; Minoru Yoshida

doi:10.1016/j.chembiol.2022.05.006

Visualization of the dynamic interaction between nucleosomal histone H3K9 tri-methylation and HP1α chromodomain in living cells

Cell Chem Biol. 2022 Jul 21;29(7):1153-1161.e5. doi: 10.1016/j.chembiol.2022.05.006. Epub 2022 Jun 20.

Authors

Affiliations

¹ Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan. Electronic address: kzsasaki@riken.jp.
² Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; Department of Chemistry and Biochemistry, Waseda University, Shinjuku-ku, Tokyo 169-8555, Japan.
³ Drug Discovery Seed Compounds Exploratory Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan.
⁴ Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan.
⁵ Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan.
⁶ Japan Biological Informatics Consortium (JBIC), Koto-ku, Tokyo, 135-0064, Japan.
⁷ Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan.
⁸ Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan; Catalysis and Integrated Research Group, RIKEN Center for Sustainable Research Science, Wako, Saitama 351-0198, Japan.
⁹ Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
¹⁰ Genome Science & Medicine Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan.
¹¹ National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo 135-0064, Japan; Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.
¹² Department of Chemistry and Biochemistry, Waseda University, Shinjuku-ku, Tokyo 169-8555, Japan; Research Institute for Science and Engineering, Waseda University, Shinjuku-ku, Tokyo 169-8555, Japan.
¹³ Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; Drug Discovery Seed Compounds Exploratory Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan; Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan. Electronic address: yoshidam@riken.jp.

PMID: 35728598
DOI: 10.1016/j.chembiol.2022.05.006

Abstract

Histone lysine methylation is an epigenetic mark that can control gene expression. In particular, H3K9me3 contributes to transcriptional repression by regulating chromatin structure. Successful mitotic progression requires correct timing of chromatin structure changes, including epigenetic marks. However, spatiotemporal information on histone modifications in living cells remains limited. In this study, we created an FRET-based probe for live-cell imaging based on the HP1α chromodomain (HP1αCD), which binds to H3K9me3. The probe was incorporated into chromatin and the emission ratio decreased after treatment with histone methyltransferase inhibitors, indicating that it successfully traced dynamic changes in H3K9me3. Upon entry into mitosis, the probe's emission ratio transiently increased with a concomitant increase in H3K9me3, then exhibited a stepwise decrease, probably due to loss of HP1αCD binding caused by phosphorylation of H3S10 and demethylation of H3K9me3. This probe will be a useful tool for detecting dynamic changes in chromatin structure associated with HP1α.

Keywords: FRET; H3K9me3; H3S10p; HP1α chromodomain; chromatin; live-cell imaging; mitosis.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Chromatin
Chromobox Protein Homolog 5
Chromosomal Proteins, Non-Histone / metabolism
Histones* / metabolism
Methylation
Nucleosomes*
Transcription Factors / metabolism

Substances

Chromatin
Chromosomal Proteins, Non-Histone
Histones
Nucleosomes
Transcription Factors
Chromobox Protein Homolog 5