Differential acetylation of histone H3 at the regulatory region of OsDREB1b promoter facilitates chromatin remodelling and transcription activation during cold stress.

Dipan Roy,Amit Paul,Payel Ganguly,Ritesh Ghosh,Adrita Roy,Shubho Chaudhuri,Kristin C Scott

doi:10.1371/journal.pone.0100343

Abstract

The rice ortholog of DREB1, OsDREB1b, is transcriptionally induced by cold stress and over-expression of OsDREB1b results in increase tolerance towards high salt and freezing stress. This spatio-temporal expression of OsDREB1b is preceded by the change in chromatin structure at the promoter and the upstream region for gene activation. The promoter and the upstream region of OsDREB1b genes appear to be arranged into a nucleosome array. Nucleosome mapping of ∼700bp upstream region of OsDREB1b shows two positioned nucleosomes between −610 to −258 and a weakly positioned nucleosome at the core promoter and the TSS. Upon cold stress, there is a significant change in the nucleosome arrangement at the upstream region with increase in DNaseI hypersensitivity or MNase digestion in the vicinity of cis elements and TATA box at the core promoter. ChIP assays shows hyper-acetylation of histone H3K9 throughout the locus whereas region specific increase was observed in H3K14ac and H3K27ac. Moreover, there is an enrichment of RNA PolII occupancy at the promoter region during transcription activation. There is no significant change in the H3 occupancy in OsDREB1b locus negating the possibility of nucleosome loss during cold stress. Interestingly, cold induced enhanced transcript level of OsDREB1b as well as histone H3 acetylation at the upstream region was found to diminish when stressed plants were returned to normal temperature. The result indicates absolute necessity of changes in chromatin conformation for the transcription up-regulation of OsDREB1b gene in response to cold stress. The combined results show the existence of closed chromatin conformation at the upstream and promoter region of OsDREB1b in the transcription “off” state. During cold stress, changes in region specific histone modification marks promote the alteration of chromatin structure to facilitate the binding of transcription machinery for proper gene expression.

Highlights

The highly complex structure of chromatin imparts resistance to several nuclear processes including transcription [1,2]
Our results indicate that hyperacetylation at the promoter and upstream region of DREB1b gene promotes the alteration in the chromatin structure during transcription
RNA was isolated from 17 days old rice seedlings (Oryza sativa Indica, var IR 64) treated at cold temperature (4uC) for different time periods and the blot was hybridised with probes generated from the 39 terminal of Dehydration responsive element binding proteins (DREBs) genes (Figure 1)

Summary

Introduction

The highly complex structure of chromatin imparts resistance to several nuclear processes including transcription [1,2]. Dynamic changes in histone modifications has been reported in Tobacco BY2 and Arabidopsis cell lines where transient upregulation of H3 phosphoacetylation (S10&K14) followed by histone H4 acetylation occur in response to high salinity, cold stress and ABA [10]. It was found for cold responsive genes COR15a and AtGLOS3 that there was a decrease in H3K27me mark (transcription repression) for the transcription, in response to cold stress [11]. These findings suggest that rapid alteration of epigenetic marks and there reversibility with a potential to keep a memory to give plants the flexibility to respond to environmental stress

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Conclusion