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.
Highlights
Plants have developed the ability to adapt to environment changes that adversely affect growth, development and reproduction through various biochemical and physiological processes
Four maize roots tissues were used to generate one pooled DNA sample for each group, including a mock-treated group (A1) and those exposed to Pb1000 stress for 12 h (K2), 24 h (K3), and 48 h (K4)
The proportions of reads uniquely mapped to CpG islands (CGIs) in A1, K2, K3, and K4 were approximately 71.16%, 66.55%, 68.95%, and 63.81%, respectively (Table S1)
Summary
Plants have developed the ability to adapt to environment changes that adversely affect growth, development and reproduction through various biochemical and physiological processes. Some plants have evolved detoxification mechanisms that result in a natural tolerance to heavy metals [3] These species can accumulate an inordinate amount of heavy metals and inhabited heavy metal-enriched or -contaminated soil, extracting large concentrations of heavy metal. Pb concentrations were measured in the roots and above-ground parts of 19 inbred lines of maize seedlings [5]. Among these lines, line 9782 lacked the ability to hyperaccumulate Pb and showed increased tolerance to Pb stress in the roots and above-ground parts following growth in soil contaminated with 750 mg·kg−1 Pb, precluding the threat of Pb entry into the food chain [5]. Protein catabolic-related genes and transcription factor families, such as bZIP, ERF and GARP, accumulated predominantly in the maize roots during development in response to Pb stress as shown by RNA-seq [6]
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