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Int. J. Mol. Sci. 2014, 15(12), 23537-23554; doi:10.3390/ijms151223537

The Dynamics of DNA Methylation in Maize Roots under Pb Stress

1
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
2
Zunyi Academy of Agricultural Sciences, Zunyi 563102, China
These authors contributed equally to this work.
*
Authors to whom correspondence should be addressed.
Received: 21 August 2014 / Revised: 1 December 2014 / Accepted: 2 December 2014 / Published: 17 December 2014
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Abstract

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. View Full-Text
Keywords: maize (Zea mays L.); methylated DNA immunoprecipitation-sequencing (MeDIP-seq); Pb stress; differentially methylated genes (DMG) maize (Zea mays L.); methylated DNA immunoprecipitation-sequencing (MeDIP-seq); Pb stress; differentially methylated genes (DMG)
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Ding, H.; Gao, J.; Qin, C.; Ma, H.; Huang, H.; Song, P.; Luo, X.; Lin, H.; Shen, Y.; Pan, G.; Zhang, Z. The Dynamics of DNA Methylation in Maize Roots under Pb Stress. Int. J. Mol. Sci. 2014, 15, 23537-23554.

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