Dynamic Changes in Genome-Wide Histone H3 Changes Lysine 4 Methylation Patterns in Response to Dehydration Stress in Arabidopsis thaliana

Authors

Karin V. van Dijk, University of Nebraska - LincolnFollow
Yong Ding, University of Nebraska - LincolnFollow
Sridar Achary Malkaram, University of Nebraska - LincolnFollow
Jean-Jack Riethoven, University of Nebraska - LincolnFollow
Rong Liu, University of Nebraska - Lincoln
Jingyi Yang, University of Nebraska - Lincoln
Peter Laczko, University of Nebraska - Lincoln
Han Chen, University of Nebraska - LincolnFollow
Yuannan Xia, University of Nebraska - LincolnFollow
Istvan Ladunga, University of Nebraska at LincolnFollow
Zoya V. Avramova, University of Nebraska - LincolnFollow
Michael E. Fromm, University of Nebraska - LincolnFollow

ORCID IDs

Istvan Ladunga

Date of this Version

2010

Comments

Published in BMC Plant Biology (2010) 10: 238 (12 p.). http://www.biomedcentral.com/1471-2229/10/238. Copyright 2010, the authors, and PubMed Central. Used by permission.

Abstract

Background: The molecular mechanisms of genome reprogramming during transcriptional responses to stress are associated with specific chromatin modifications. Available data, however, describe histone modifications only at individual plant genes induced by stress. We have no knowledge of chromatin modifications taking place at genes whose transcription has been down-regulated or on the genome-wide chromatin modification patterns that occur during the plant’s response to dehydration stress. Results: Using chromatin immunoprecipitation and deep sequencing (ChIP-Seq) we established the wholegenome distribution patterns of histone H3 lysine 4 mono-, di- and tri-methylation (H3K4me1, H3K4me2, and H3K4me3, respectively) in Arabidopsis thaliana during watered and dehydration stress conditions. In contrast to the relatively even distribution of H3 throughout the genome, the H3K4me1, H3K4me2, and H3K4me3 marks are predominantly located on genes. About 90% of annotated genes carry one or more of the H3K4 methylation marks. The H3K4me1 and H3K4me2 marks are more widely distributed (80% and 84%, respectively) than the H3K4me3 marks (62%), but the H3K4me2 and H3K4me1 levels changed only modestly during dehydration stress. By contrast, the H3K4me3 abundance changed robustly when transcripts levels from responding genes increased or decreased. In contrast to the prominent H3K4me3 peaks present at the 5’-ends of most transcribed genes, genes inducible by dehydration and ABA displayed atypically broader H3K4me3 distribution profiles that were present before and after the stress. Conclusions: A higher number (90%) of annotated Arabidopsis genes carry one or more types of H3K4me marks than previously reported. During the response to dehydration stress the changes in H3K4me1, H3K4me2, and H3K4me3 patterns show different dynamics and specific patterns at up-regulated, down-regulated, and unaffected genes. The different behavior of each methylation mark during the response process illustrates that they have distinct roles in the transcriptional response of implicated genes. The broad H3K4me3 distribution profiles on nucleosomes of stress-induced genes uncovered a specific chromatin pattern associated with many of the genes involved in the dehydration stress response.