Vernalization treatment induces site-specific DNA hypermethylation at the VERNALIZATION-A1 (VRN-A1) locus in hexaploid winter wheat

Abstract

BackgroundCertain temperate species require prolonged exposure to low temperature to initiate transition from vegetative growth to flowering, a process known as vernalization. In wheat, winter cultivars require vernalization to initiate flowering, making vernalization requirement a trait of key importance in wheat agronomy. The genetic bases of vernalization response have been largely studied in wheat, leading to the characterization of a regulation pathway that involves the key gene VERNALIZATION1 (VRN1). While previous studies in wheat and barley have revealed the functional role of histone modification in setting VRN1 expression, other mechanisms might also be involved. Here, we were interested in determining whether the cold-induced expression of the wheat VRN-A1 gene is associated with a change in DNA methylation.ResultsWe provide the first DNA methylation analysis of the VRN-A1 gene, and describe the existence of methylation at CG but also at non CG sites. While CG sites show a bell-shape profile typical of gene-body methylation, non CG methylation is restricted to the large (8.5 kb) intron 1, in a region harboring fragments of transposable elements (TEs). Interestingly, cold induces a site-specific hypermethylation at these non CG sites. This increase in DNA methylation is transmitted through mitosis, and is reset to its original level after sexual reproduction.ConclusionsThese results demonstrate that VRN-A1 has a particular DNA methylation pattern, exhibiting rapid shift within the life cycle of a winter wheat plant following exposure to particular environmental conditions. The finding that this shift occurs at non CG sites in a TE-rich region opens interesting questions onto the possible consequences of this type of methylation in gene expression.

DNA Methylation within Transcribed Regions

“…A relationship between non-CpG methylation in the intronic region and transcription also occurs in maize, where non-CpG methylation at exon-intron junctions inhibits alternative splicing (Regulski et al, 2013). In winter wheat (Triticum aestivum), cold treatment for induction of vernalization induces non-CpG methylation at TEs present in the intron of the VARNALIZATION-A1 gene, which is associated with the transcriptional activation of the gene (Khan et al, 2013). Thus, repressive epigenetic modifications on repeats and TEs in intronic regions might have a role in regulation of gene activation, beyond the silencing of TEs.…”

Immediate and Transgenerational Regulation of Plant Stress Response through DNA Methylation

“…In response to cold treatment (vernalization), site specific DNA hypermethylation has been recently reported (Khan et al, 2013). In this study, the DNA methylation profile of VRN-A1 gene was studied in winter wheat and differential pattern of methylation at non-CG sites was reported.…”

“…They can rather be called as non-heritable chromatin modifications. As supported by many examples, the heritable chromatin modifications (epigenetic modifications) can be classified into mitotically transmissible modifications (reset in the next generation) and meioticallytransgenerational chromatin modifications (inherited/transmitted to the generations) (Cubas et al, 1999;Khan et al, 2013;Lauria et al, 2004;Manning et al, 2006;Zemach et al, 2010a).…”

Flexible shift on gene body methylation and transcription of LpCYP72A161 exposed to temperature stress in perennial ryegrass

“…The accuracy of bisulfite sequencing in these experiments largely depend on the numbers of clone analyzed, making this a cost-and labor-effective method. PCR products obtained from bisulfite treated DNA were also sequenced directly without cloning, and this method has also been reported in several other studies (Gervin et al, 2011;Khan et al, 2013). The DNA methylation level of cytosine sites were estimated by chromatogram quantification using VarDetect to quantify the sanger sequence trace peaks (Ngamphiw et al, 2008).…”

“…Asr1 (abscisic acid stress and ripening gene) in tomato is a 1199-bp gene with two exons and one intron, and is demethylated in the gene body and up-regulated in mRNA levels under drought stress (Gonzalez et al, 2011). Interestingly, VRN-A1 (VERNALIZATION1) in Triticum aestivum has a large intron (8.5 kb) that harbors fragments of transposable elements (TEs), and this large intron is hypermethylated under cold stress, leading to the up-regulation of VRN-A1 in cold-treated individuals (Khan et al, 2013). These two examples highlight the complexity of gene body methylation, where gene body methylation levels may be positively or negatively correlated with the expression level of gene.…”