Epigenetic regulation of stress responses in plants-2009

Available online at www.sciencedirect.com Epigenetic regulation of stress responses in plants Viswanathan Chinnusamy1and Jian-Kang Zhu2Gene expression driven by developmental and stress cues often depends on nucleosome histone post-translationalmodifications and sometimes on DNA methylation.A number of studies have shown that these DNA and histone modifications play a key role in gene expression and plant development under stress.Most of these stress-induced modifications are reset to the basal level once the stress is relieved,while some of the modifications may be stable,that is,may be carried forward as ‘stress memory’and may be inherited across mitotic or even meiotic cell divisions.Epigenetic stress memory may help plants more effectively cope with subsequent stresses. Comparative studies on stress-responsive epigenomes and transcriptomes will enhance our understanding of stress adaptation of plants.Addresses1Water Technology Centre,Indian Agricultural Research Institute,New Delhi110012,India2Department of Botany and Plant Sciences,Institute for Integrative Genome Biology,University of California,Riverside,CA92521,USACorresponding author:Zhu,Jian-Kang(jian-kang.zhu@ucr.edu)Current Opinion in Plant Biology2009,12:133–139This review comes from a themed issue onGenome studies and molecular geneticsEdited by Masahiro Yano and Roberto TuberosaAvailable online27th January20091369-5266/$–see front matter#2008Elsevier Ltd.All rights reserved.DOI10.1016/j.pbi.2008.12.006IntroductionInformation content of the genome(DNA sequence)and its expression in response to stress are crucial for the adaptability of a genotype.Expression of the genome is influenced by chromatin structure,which is governed by processes often associated with epigenetic regulation, namely histone variants,histone post-translational modi-fications,and DNA methylation.Developmental and environmental signals can induce epigenetic modifi-cations in the genome,and thus,the single genome in a plant cell gives rise to multiple epigenomes in response to developmental and environmental cues[1].Under-standing stress-induced epigenetic processes in stress tolerance of plants requires answers to the following questions:How much of the stress-induced gene expres-sion changes are associated with alterations in DNA methylation and histone modification marks?Are stress-induced DNA and histone modifications during acclimation or during thefirst experience of stress mem-orized and inherited mitotically and meiotically?What are the adaptive values of epigenetic stress memory?This review briefly describes epigenetic processes,and then focuses on recent data on the epigenetic regulation of stress responses and its heritability in plants. Epigenetic regulation of stress responses Retention of stress memory for short durations is well known in plants,as evident from acclimation responses [2,3].The stress memory can be retained for only short durations if the memory depends on the half-life of stress-induced proteins,RNAs,and metabolites,while the memory can last longer if it involves reprogramming in phenology and morphology of plants.Epigenetic processes,that is,stable or heritable DNA methylation and histone modifications,can also be a choice of retaining stress memory for longer times.Methods to decipher epigenetic changes are briefly described in Box1.Histone modificationsN-terminal regions of nucleosome core complex histones undergo various post-translational modifications.In addition,each histone has variants encoded by different genes.The combinations of histone variants and post-translational modifications can be considered a‘histone code’,which plays a key role in chromatin structure and thus determines the transcriptional state and expression level of genes.Some histone modifications,namely acety-lation,and certain phosphorylation and ubiquitination [4,5],enhance transcription,while biotinylation and sumoylation repress gene expression[6,7].Trimethyla-tion of H3K4activates transcription,while dimethylation of H3K9and H3K27represses transcription[5].Because several of the histone modifications are associated with changes in gene transcription in general,it is not surpris-ing that stress-induced gene regulation is associated with histone modifications in all cases that have been inves-tigated.Changes in histone variants,histone modifi-cations as well as DNA methylation are often referred to as epigenetic regulation.However,such changes may or may not be truly epigenetic in nature because common epigenetics definition requires mitotic or meiotic herit-ability.Drought induced the linker histone variant H1-S in tomato.H1-S appears to be involved in the negative regulation of stomatal conductance,because stomatal con-ductance and transpiration rates were higher in antisense transgenic H1-S tomato plants than in wild type(WT) plants[8].www.sciencedirect.com Current Opinion in Plant Biology2009,12:133–139