Roy Dipan, Paul Amit, Roy Adrita, Ghosh Ritesh, Ganguly Payel, Chaudhuri Shubho
Division of Plant Biology, Bose Institute (Centenary Campus), P-1/12, C.I.T. Scheme VII M, Kolkta-700054, West Bengal, India.
School of Biotechnology, Yeungnam University, Gyeongsan, Korea.
PLoS One. 2014 Jun 18;9(6):e100343. doi: 10.1371/journal.pone.0100343. eCollection 2014.
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 ∼ 700 bp 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.
水稻中DREB1的同源基因OsDREB1b受冷胁迫转录诱导，过表达OsDREB1b可提高对高盐和冻害胁迫的耐受性。OsDREB1b的这种时空表达之前，启动子和基因激活上游区域的染色质结构会发生变化。OsDREB1b基因的启动子和上游区域似乎排列成核小体阵列。对OsDREB1b上游约700 bp区域进行核小体定位，结果显示在-610至-258之间有两个定位核小体，在核心启动子和转录起始位点（TSS）处有一个定位较弱的核小体。冷胁迫时，上游区域的核小体排列发生显著变化，核心启动子顺式元件和TATA框附近的DNaseI超敏性或MNase消化增加。染色质免疫沉淀（ChIP）分析表明，整个基因座的组蛋白H3K9发生了超乙酰化，而在H3K14ac和H3K27ac中观察到区域特异性增加。此外，转录激活过程中启动子区域的RNA聚合酶II占有率增加。OsDREB1b基因座中的H3占有率没有显著变化，排除了冷胁迫期间核小体丢失的可能性。有趣的是，当受胁迫的植株恢复到正常温度时，冷诱导的OsDREB1b转录水平增强以及上游区域的组蛋白H3乙酰化减弱。结果表明，染色质构象变化对于OsDREB1b基因响应冷胁迫转录上调是绝对必要的。综合结果表明，在转录“关闭”状态下，OsDREB1b的上游和启动子区域存在封闭的染色质构象。冷胁迫期间，区域特异性组蛋白修饰标记的变化促进了染色质结构的改变，以利于转录机制的结合，从而实现正常的基因表达。
