title: High-resolution chromatin dynamics during a yeast stress response.
abstract: Covalent histone modifications are highly conserved and play multiple roles in eukaryotic transcription regulation. Here, we mapped 26 histone modifications genome-wide in exponentially growing yeast and during a dramatic transcriptional reprogramming-the response to diamide stress. We extend prior studies showing that steady-state histone modification patterns reflect genomic processes, especially transcription, and display limited combinatorial complexity. Interestingly, during the stress response we document a modest increase in the combinatorial complexity of histone modification space, resulting from roughly 3% of all nucleosomes transiently populating rare histone modification states. Most of these rare histone states result from differences in the kinetics of histone modification that transiently uncouple highly correlated marks, with slow histone methylation changes often lagging behind the more rapid acetylation changes. Explicit analysis of modification dynamics uncovers ordered sequences of events in gene activation and repression. Together, our results provide a comprehensive view of chromatin dynamics during a massive transcriptional upheaval.
authors: School of Computer Science and Engineering, The Hebrew University, Jerusalem 9190401, Israel; Institute of Life Sciences, The Hebrew University, Jerusalem 9190401, Israel.
authors: Assaf
authors: A
authors: Weiner
authors: Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
authors: Tsung-Han S
authors: TH
authors: Hsieh
authors: School of Computer Science and Engineering, The Hebrew University, Jerusalem 9190401, Israel; Institute of Life Sciences, The Hebrew University, Jerusalem 9190401, Israel.
authors: Alon
authors: A
authors: Appleboim
authors: Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
authors: Hsiuyi V
authors: HV
authors: Chen
authors: School of Computer Science and Engineering, The Hebrew University, Jerusalem 9190401, Israel; Institute of Life Sciences, The Hebrew University, Jerusalem 9190401, Israel.
authors: Ayelet
authors: A
authors: Rahat
authors: Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel.
authors: Ido
authors: I
authors: Amit
authors: Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA. Electronic address: oliver.rando@umassmed.edu.
authors: Oliver J
authors: OJ
authors: Rando
authors: School of Computer Science and Engineering, The Hebrew University, Jerusalem 9190401, Israel; Institute of Life Sciences, The Hebrew University, Jerusalem 9190401, Israel. Electronic address: nir@cs.huji.ac.il.
authors: Nir
authors: N
authors: Friedman
mesh_terms: D002843:Chromatin / Q000235:genetics* / Q000378:metabolism; D042002:Chromatin Assembly and Disassembly / Q000187:drug effects; D003958:Diamide / Q000494:pharmacology*; D015966:Gene Expression Regulation, Fungal; D016681:Genome, Fungal; D006657:Histones / Q000378:metabolism; D008969:Molecular Sequence Data; D012441:Saccharomyces cerevisiae / Q000187:drug effects / Q000235:genetics* / Q000502:physiology; D014158:Transcription, Genetic
chemical_list: D002843:Chromatin; D006657:Histones; D003958:Diamide