Divergent DNA Methylation Patterns Associated with Abiotic Stress in Hevea brasiliensis

Abstract

Cytosine methylation is a fundamental epigenetic mechanism for gene-expression regulation and development in plants. Here, we report for the first time the identification of DNA methylation patterns and their putative relationship with abiotic stress in the tree crop Hevea brasiliensis (source of 99% of natural rubber in the world). Regulatory sequences of four major genes involved in the mevalonate pathway (rubber biosynthesis pathway) and one general defense-related gene of three high-yielding popular rubber clones grown at two different agroclimatic conditions were analyzed for the presence of methylation. We found several significant variations in the methylation pattern at core DNA binding motifs within all the five genes. Several consistent clone-specific and location-specific methylation patterns were identified. The differences in methylation pattern observed at certain pivotal cis-regulatory sites indicate the direct impact of stress on the genome and support the hypothesis of site-specific stress-induced DNA methylation. It is assumed that some of the methylation patterns observed may be involved in the stress-responsive mechanism in plants by which they adapt to extreme conditions. The study also provide clues towards the existence of highly divergent phenotypic characters among Hevea clones despite their very similar genetic make-up. Altogether, the observations from this study prove beyond doubt that there exist epigenetic variations in Hevea and environmental factors play a significant role in the induction of site-specific epigenetic mutations in its genome.

In silico identification of transcription factors associated with the biosynthesis of carotenoids in corn ( Zea mays L. )

“…DNA methylation can be found on CpNpG islands and non-symmetrical trinucleotides in addition to cytosine of CpG islands (Pradhan et al, 1999;Lindroth et al, 2001;Cao and Jacobsen, 2002). Abiotic stress-induced methylation is thought to be associated with various biochemical pathways involved in plant adaptation and stress responses (Uthup et al, 2011). As demonstrated in this study, one CpG island is present in the promoter of GRMZM2G300348_T02, T03, T04 covering almost all promoter regions, suggesting an important role for DNA methylation in the transcriptional regulation of the expression of these transcripts.…”

Genetic and epigenetic variation in a cosmopolitan grass Poa annua from Antarctic and Polish populations

“…Thus, we tend to think, that al− though the population from Arctowski Station is less variable at the genetic level (possibly due to founder or bottleneck effects), the increase of epigenetic varia− tion in the Antarctic population may point out a response to external stress fac− tors. It could be induced by environmental stimuli (Chinnusamy and Zhu 2009;Boyko and Kovalchuk 2011;Uthup et al 2011) such as e.g. cold (Stewards et al 2002, water (Labra et al 2002), and/or osmotic (Tan 2010) stresses (Bruce et al 2007), commonly experienced by organisms under polar condition.…”

Identification and expression profiling of DNA methyltransferases during development and stress conditions in Solanaceae

“…Furthermore, binding sites for MADS-box transcription factor, RIN, one of the main ripening transcription factors, are frequently localized in the demethylated regions of the promoters of numerous ripening genes, and it is suggested that its binding to these sites occurs in concert with demethylation (Chen, et al 2015). Besides development, growing evidences have suggested a role of DNA methylation in the regulation of gene expression during abiotic stress responses (Chinnusamy and Zhu 2009, Dowen et al 2012, Garg et al 2015, Shaik and Ramakrishna 2012, Uthup et al 2011. Likewise, biotic stress such as pathogenic infection resulted in genome-wide hypermethylation, and resistance-related genes were hypomethylated in plants (Peng and Zhang 2009).…”