Ding Haiping, Gao Jian, Qin Cheng, Ma Haixia, Huang Hong, Song Pan, Luo Xirong, Lin Haijian, Shen Ya'ou, Pan Guangtang, Zhang Zhiming
Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China.
Zunyi Academy of Agricultural Sciences, Zunyi 563102, China.
Int J Mol Sci. 2014 Dec 17;15(12):23537-54. doi: 10.3390/ijms151223537.
Plants adapt to adverse conditions through a series of physiological, cellular, and molecular processes, culminating in stress tolerance. However, little is known about the associated regulatory mechanisms at the epigenetic level in maize under lead (Pb) stress. Therefore, in this study, we aimed to compare DNA methylation profiles during the dynamic development of maize roots following Pb treatment to identify candidate genes involved in the response to Pb stress. Methylated DNA immunoprecipitation-sequencing (MeDIP-seq) was used to investigate the genome-wide DNA methylation patterns in maize roots under normal condition (A1) and 3 mM Pb(NO3)2 stress for 12 h (K2), 24 h (K3) and 48 h (K4). The results showed that the average methylation density was the highest in CpG islands (CGIs), followed by the intergenic regions. Within the gene body, the methylation density of the introns was higher than those of the UTRs and exons. In total, 3857 methylated genes were found in 4 tested samples, including 1805 differentially methylated genes for K2 versus A1, 1508 for K3 versus A1, and 1660 for K4 versus A1. Further analysis showed that 140 genes exhibited altered DNA methylation in all three comparisons, including some well-known stress-responsive transcription factors and proteins, such as MYB, AP2/ERF, bZIP, serine-threonine/tyrosine-proteins, pentatricopeptide repeat proteins, RING zinc finger proteins, F-box proteins, leucine-rich repeat proteins and tetratricopeptide repeat proteins. This study revealed the genome-scale DNA methylation patterns of maize roots in response to Pb exposure and identified candidate genes that potentially regulate root dynamic development under Pb stress at the methylation level.
植物通过一系列生理、细胞和分子过程适应逆境，最终实现胁迫耐受性。然而，关于铅（Pb）胁迫下玉米在表观遗传水平上的相关调控机制知之甚少。因此，在本研究中，我们旨在比较铅处理后玉米根动态发育过程中的DNA甲基化谱，以鉴定参与铅胁迫响应的候选基因。采用甲基化DNA免疫沉淀测序（MeDIP-seq）技术，研究正常条件下（A1）以及3 mM Pb(NO3)2胁迫12 h（K2）、24 h（K3）和48 h（K4）时玉米根的全基因组DNA甲基化模式。结果表明，平均甲基化密度在CpG岛（CGIs）中最高，其次是基因间区域。在基因体内，内含子的甲基化密度高于非翻译区（UTRs）和外显子。在4个测试样本中共发现3857个甲基化基因，其中K2与A1相比有1805个差异甲基化基因，K3与A1相比有1508个，K4与A1相比有1660个。进一步分析表明，在所有三个比较中，有140个基因的DNA甲基化发生了改变，包括一些众所周知的胁迫响应转录因子和蛋白质，如MYB、AP2/ERF、bZIP、丝氨酸-苏氨酸/酪氨酸蛋白、五肽重复蛋白、RING锌指蛋白、F-box蛋白、富含亮氨酸重复蛋白和四肽重复蛋白。本研究揭示了玉米根在铅暴露下的全基因组DNA甲基化模式，并鉴定了在甲基化水平上潜在调控铅胁迫下根动态发育的候选基因。
