Maize DNA Methylation in Response to Drought Stress Is Involved in Target Gene Expression and Alternative Splicing

Abstract

DNA methylation is important for plant growth, development, and stress response. To understand DNA methylation dynamics in maize roots under water stress (WS), we reanalyzed DNA methylation sequencing data to profile DNA methylation and the gene expression landscape of two inbred lines with different drought sensitivities, as well as two of their derived recombination inbred lines (RILs). Combined with genotyping-by-sequencing, we found that the inheritance pattern of DNA methylation between RILs and parental lines was sequence-dependent. Increased DNA methylation levels were observed under WS and the methylome of drought-tolerant inbred lines were much more stable than that of the drought-sensitive inbred lines. Distinctive differentially methylated genes were found among diverse genetic backgrounds, suggesting that inbred lines with different drought sensitivities may have responded to stress in varying ways. Gene body DNA methylation showed a negative correlation with gene expression but a positive correlation with exon splicing events. Furthermore, a positive correlation of a varying extent was observed between small interfering RNA (siRNA) and DNA methylation, which at different genic regions. The response of siRNAs under WS was consistent with the differential DNA methylation. Taken together, our data can be useful in deciphering the roles of DNA methylation in plant drought-tolerance variations and in emphasizing its function in alternative splicing.

DNA Methylation in Plant Responses and Adaption to Abiotic Stresses

“…Drought stress is also associated with changes in the methylation of the gene body of many genes, including those encoding transcription factors (TFs). A negative correlation between gene body methylation and gene expression was found in maize roots under water stress [29]. Changes of DNA methylation occurs in TEs as well.…”

“…Correlation analysis has shown that DNA methylation has multiple effects on gene expression under drought stress, indicating that it directly or indirectly affects gene ex-pression through multiple regulatory pathways. Drought-tolerant plants were found to have a more stable methylome under drought conditions, with differentially methylated regions (DMRs)-related genes mainly related to the stress response, programmed cell death, and other pathways in rice (Oryza sativa L.) [26], mulberry (Morus alba L.) [27], mungbean (Vigna radiata L.) [28], and maize (Zea mays L.) [29]. For example, an in-silico genome-wide DNA methylation (5mC) analysis was performed in rice (Oryza sativa cv.…”

DNA Methylation Changes and Its Associated Genes in Mulberry (Morus alba L.) Yu-711 Response to Drought Stress Using MethylRAD Sequencing

“…The ongoing development of high-throughput sequencing technologies and array-based methods allows studying DNA methylation patterns across entire genomes. DNA methylation is a significant epigenetic modification and has been widely implicated in plant development and stress responses [29]. MethylRAD sequencing is a powerful method that determines methylation patterns in plants [4].…”

Genome-Wide Profiling of Alternative Splicing and Gene Fusion during Rice Black-Streaked Dwarf Virus Stress in Maize (Zea mays L.)

“…AS events typically include signal transduction, growth, abiotic stresses, and circadian rhythms [ 41 , 42 ], and AS has recently been found to play a major role in these processes during stress events, such as drought, heat, and disease [ 43 , 44 , 45 , 46 , 47 ]. In maize, AS events were identified that responded to drought [ 48 , 49 ], development [ 29 ], and endosperm [ 25 ]. AS events can provide a novel strategy for plant response to virus stresses.…”