Differential Acetylation of Histone H3 at the Regulatory Region of OsDREB1b Promoter Facilitates Chromatin Remodelling and Transcription Activation during Cold Stress

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.

A Land Plant-Specific Transcription Factor Directly Enhances Transcription of a Pathogenic Noncoding RNA Template by DNA-Dependent RNA Polymerase II

“…To pull down Pol II from N. benthamiana, we used the commercial mouse monoclonal antibody 8WG16, which was raised against the C-terminal domain of the largest subunit of Pol II that had been purified from a plant source (Thompson et al, 1989). The existence of highly conserved YSPTSPS repeats in the C-terminal domain of eukaryotic Pol II has allowed a broad use of this 8WG16 antibody for immunoblotting and immunoprecipitation experiments in various animals and plants, including Arabidopsis (Zheng et al, 2009), rice (Oryza sativa; Roy et al, 2014), and Nicotiana tabacum (Shin et al, 2014). We tested the specificity of 8WG16 for the largest subunit of Pol II in N. benthamiana.…”

ABI3 mediates dehydration stress recovery response in Arabidopsis thaliana by regulating expression of downstream genes

“…The bands corresponding to di-nucleosomal DNA and mono-nucleosomal DNA was excised and purified with gel extraction kit (Qiagen). To monitor the movement of nucleosomes in the promoter region(s) MNase accessibility assay was carried out as described in Chua et al [29] and Roy et al [29,37]. Nuclei from control, stressed and recovered seedlings were isolated, as discussed earlier, and subjected to digestion by MNase enzyme (5.5 units) for different time periods.…”

“…Recent evidences indicate that histone modifications like H3 K9, K14, K27 acetylation and H3 K4 methylation along with alterations in nucleosome positions and density occur during gene expression in response to abiotic stress and recovery [28][29][30]. Interestingly, Phaseolus vulgaris ABI3-like factor (PvALF), has been shown to facilitate chromatin remodeling along with histone modifications at the promoter region of its target ␤-phaseolin gene during transcription [31,32].…”

Stress-induced structural changes in plant chromatin

“…Often connected with dehydration is osmotic stress or salinity, also elucidating responses at the chromatin level [reviewed in 40]. Extreme temperatures induce specific responses affecting chromatin configurations: cold stress [41][42][43] and heat stress for higher plants [36,[44][45][46] and in algae [47,48]. Light deficiency induces chromatin changes, signaled by light perception factors [22,49,50].…”