The Dynamics of DNA Methylation in Maize Roots under Pb Stress
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...
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doaj-c68d67691f8a4ea0b7455d365728317f2020-11-24T23:55:29ZengMDPI AGInternational Journal of Molecular Sciences1422-00672014-12-011512235372355410.3390/ijms151223537ijms151223537The Dynamics of DNA Methylation in Maize Roots under Pb StressHaiping Ding0Jian Gao1Cheng Qin2Haixia Ma3Hong Huang4Pan Song5Xirong Luo6Haijian Lin7Ya'ou Shen8Guangtang Pan9Zhiming Zhang10Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, ChinaMaize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, ChinaZunyi Academy of Agricultural Sciences, Zunyi 563102, ChinaMaize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, ChinaMaize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, ChinaMaize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, ChinaZunyi Academy of Agricultural Sciences, Zunyi 563102, ChinaMaize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, ChinaMaize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, ChinaMaize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, ChinaMaize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, ChinaPlants 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.http://www.mdpi.com/1422-0067/15/12/23537maize (Zea mays L.)methylated DNA immunoprecipitation-sequencing (MeDIP-seq)Pb stressdifferentially methylated genes (DMG) |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Haiping Ding Jian Gao Cheng Qin Haixia Ma Hong Huang Pan Song Xirong Luo Haijian Lin Ya'ou Shen Guangtang Pan Zhiming Zhang |
spellingShingle |
Haiping Ding Jian Gao Cheng Qin Haixia Ma Hong Huang Pan Song Xirong Luo Haijian Lin Ya'ou Shen Guangtang Pan Zhiming Zhang The Dynamics of DNA Methylation in Maize Roots under Pb Stress International Journal of Molecular Sciences maize (Zea mays L.) methylated DNA immunoprecipitation-sequencing (MeDIP-seq) Pb stress differentially methylated genes (DMG) |
author_facet |
Haiping Ding Jian Gao Cheng Qin Haixia Ma Hong Huang Pan Song Xirong Luo Haijian Lin Ya'ou Shen Guangtang Pan Zhiming Zhang |
author_sort |
Haiping Ding |
title |
The Dynamics of DNA Methylation in Maize Roots under Pb Stress |
title_short |
The Dynamics of DNA Methylation in Maize Roots under Pb Stress |
title_full |
The Dynamics of DNA Methylation in Maize Roots under Pb Stress |
title_fullStr |
The Dynamics of DNA Methylation in Maize Roots under Pb Stress |
title_full_unstemmed |
The Dynamics of DNA Methylation in Maize Roots under Pb Stress |
title_sort |
dynamics of dna methylation in maize roots under pb stress |
publisher |
MDPI AG |
series |
International Journal of Molecular Sciences |
issn |
1422-0067 |
publishDate |
2014-12-01 |
description |
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. |
topic |
maize (Zea mays L.) methylated DNA immunoprecipitation-sequencing (MeDIP-seq) Pb stress differentially methylated genes (DMG) |
url |
http://www.mdpi.com/1422-0067/15/12/23537 |
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