GSBS Student Publications

Student Author(s)

Hsiuyi V. Chen

GSBS Program

Interdisciplinary Graduate Program

UMMS Affiliation

Department of Biochemistry and Molecular Pharmacology

Date

7-31-2012

Document Type

Article

Medical Subject Headings

Chromatin; Chromatin Assembly and Disassembly; Chromatin Immunoprecipitation; Diamide; Gene Expression Profiling; Gene Expression Regulation, Fungal; Genes, Fungal; Histone-Lysine N-Methyltransferase; Histones; Methylation; Nucleosomes; Phosphorylation; Repressor Proteins; Ribosomes; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Sequence Deletion; Stress, Physiological; Substrate Specificity; Time Factors; Time-Lapse Imaging; Transcription, Genetic

Disciplines

Biochemistry | Cell Biology | Cellular and Molecular Physiology | Genetics | Genomics

Abstract

Packaging of eukaryotic genomes into chromatin has wide-ranging effects on gene transcription. Curiously, it is commonly observed that deletion of a global chromatin regulator affects expression of only a limited subset of genes bound to or modified by the regulator in question. However, in many single-gene studies it has become clear that chromatin regulators often do not affect steady-state transcription, but instead are required for normal transcriptional reprogramming by environmental cues. We therefore have systematically investigated the effects of 83 histone mutants, and 119 gene deletion mutants, on induction/repression dynamics of 170 transcripts in response to diamide stress in yeast. Importantly, we find that chromatin regulators play far more pronounced roles during gene induction/repression than they do in steady-state expression. Furthermore, by jointly analyzing the substrates (histone mutants) and enzymes (chromatin modifier deletions) we identify specific interactions between histone modifications and their regulators. Combining these functional results with genome-wide mapping of several histone marks in the same time course, we systematically investigated the correspondence between histone modification occurrence and function. We followed up on one pathway, finding that Set1-dependent H3K4 methylation primarily acts as a gene repressor during multiple stresses, specifically at genes involved in ribosome biosynthesis. Set1-dependent repression of ribosomal genes occurs via distinct pathways for ribosomal protein genes and ribosomal biogenesis genes, which can be separated based on genetic requirements for repression and based on chromatin changes during gene repression. Together, our dynamic studies provide a rich resource for investigating chromatin regulation, and identify a significant role for the "activating" mark H3K4me3 in gene repression.

Rights and Permissions

Citation: PLoS Biol. 2012;10(7):e1001369. doi: 10.1371/journal.pbio.1001369. Epub 2012 Jul 31. Link to article on publisher's website

DOI of Published Version

10.1371/journal.pbio.1001369

Comments

Copyright: © Weiner et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Related Resources

Link to article in PubMed

Journal Title

PLoS biology

PubMed ID

22912562

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