6102–6112 Nucleic Acids Research, 2016, Vol. 44, No. 13 Published online 25 March 2016 doi: 10.1093/nar/gkw193 Chromatin condensation and recruitment of PHD finger proteins to histone H3K4me3 are mutually exclusive Jovylyn Gatchalian1,†, Carmen Mora Gallardo2,†, Stephen A. Shinsky3, Ruben Rosas Ospina1, Andrea Mansilla Liendo2, Krzysztof Krajewski3, Brianna J. Klein1, Forest H. Andrews1, Brian D. Strahl3, Karel H. M. van Wely2,* and Tatiana G. Kutateladze1,*
1Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA, 2Department of Immunology and Oncology, Centro Nacional de Biotecnolog´ıa/CSIC, 28049 Madrid, Spain and 3Department of Biochemistry & Biophysics, The University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
Received January 06, 2016; Revised March 12, 2016; Accepted March 15, 2016
ABSTRACT modifications (PTMs), including acetylation and methyla- tion of lysine, methylation of arginine, and phosphorylation Histone post-translational modifications, and spe- of serine and threonine. Over 500 histone PTMs have been cific combinations they create, mediate a wide range identified by mass spectrometry analysis, and a number of of nuclear events. However, the mechanistic bases these modifications, or epigenetic marks, have been shown for recognition of these combinations have not been to modulate chromatin structure and cell cycle specific pro- elucidated. Here, we characterize crosstalk between cesses (1). H3T3 and H3T6 phosphorylation, occurring in mito- Methylation of histone H3 at lysine 4 is one of the canon- sis, and H3K4me3, a mark associated with active ical PTMs (2–4). The trimethylated species (H3K4me3), transcription. We detail the molecular mechanisms which is found primarily in active promoters, is impli- by which H3T3ph/K4me3/T6ph switches mediate ac- cated in transcriptional regulation (5). Methylation of lysine tivities of H3K4me3-binding proteins, including those residues in histones in general, and H3K4me3 in particular, is considered to be a stable mark compared to other PTMs containing plant homeodomain (PHD) and double Tu- (6,7). The H3K4me3 level remains fairly high and persists dor reader domains. Our results derived from nu- throughout the cell cycle owing to coordinating activities clear magnetic resonance chemical shift perturba- of K4-specific methyltransferases, such as the /KMT2 SET1 tion analysis, orthogonal binding assays and cell flu- family, and demethylases, such as the KDM5 family, though orescence microscopy studies reveal a strong anti- gene-specific alterations during mitosis have also been ob- correlation between histone H3T3/T6 phosphoryla- served. A set of epigenetic readers, including a plant home- tion and retention of PHD finger proteins in chro- odomain (PHD) finger, a double tudor domain (DTD) and matin during mitosis. Together, our findings uncover a double chromodomain (DCD), recognizes the H3K4me3 the mechanistic rules of chromatin engagement for mark by enclosing K4me3 in an aromatic cage-like bind- H3K4me3-specific readers during cell division. ing pocket (8). Preservation of H3K4me3 allows cells to re- cruit transcription complexes and resume normal gene ex- pression patterns soon after mitosis completion via bind- INTRODUCTION ing of epigenetic readers, present in these complexes, to H3K4me3-enriched promoters. Chromatin undergoes extensive reorganization throughout In contrast to lysine methylation, phosphorylation of ser- the cell cycle, transitioning from a relatively relaxed state ine and threonine residues in histone H3 fluctuates substan- in interphase to a highly condensed state in mitosis and tially throughout the cell cycle, rising sharply when cells en- returning back to the interphase state after cell division is ter mitosis (9). Phosphorylation of H3T3 (H3T3ph) is gen- completed. Cell cycle progression is highly regulated and erated, or written, by the kinase Haspin early in prophase correlates with alterations in the structure and dynamics of and is gradually erased by the PP1␥/Repo-Man phos- the nucleosome, the core building block of chromatin. Nu- phatase complex in anaphase (10,11). The H3T3ph mark cleosomal histone proteins are subject to post-translational
*To whom correspondence should be addressed. Tel: +1 303 724 3593; Fax: +1 303 724 3663; Email: [email protected] Correspondence may also be addressed to Karel H. M. van Wely. Tel: +34 91 5854537; Fax: +34 91 3720493; Email: [email protected] †These authors contributed equally to the paper as first authors.