Low temperature triggers genome-wide hypermethylation of transposable elements and centromeres in maize

Abstract

telephone: +33 1 69 33 23 57. RUNNING TITLECold triggers hypermethylation of maize transposons ABSTRACT Characterizing the molecular processes developed by plants to respond to environmental cues is a major task to better understand local adaptation. DNA methylation is a chromatin mark involved in the transcriptional silencing of transposable elements (TEs) and gene expression regulation. While the molecular bases of DNA methylation regulation are now well described, involvement of DNA methylation in plant response to environmental cues remains poorly characterized. Here, using the TErich maize genome and analyzing methylome response to prolonged cold at the chromosome and feature scales, we investigate how genomic architecture affects methylome response to stress in a cold-sensitive genotype. Interestingly, we show that cold stress induces a genome-wide methylation increase through the hypermethylation of TE sequences and centromeres. Our work highlights a cytosine context-specific response of TE methylation that depends on TE types, chromosomal location and proximity to genes. The patterns observed can be explained by the parallel transcriptional activation of multiple DNA methylation pathways that methylate TEs in the various chromatin locations where they reside. Our results open new insights into the possible role of genome-wide DNA methylation in phenotypic response to stress. A B C

Grapevine cell response to carbon deficiency requires transcriptome and methylome reprogramming

“…We identified 165 DMRs within genes (Figure 9) among which 75 are located at intronic-TE. Our results are in accordance with literature where hyper-methylation of TEs across all chromosomes in response to stress has also been recently reported for the first time in maize (Achour et al, 2019), as well as in tomato suffering from phosphate starvation where CHH DMRs were enriched in intra/inter-genic TE (Tian et al, 2021). As TEs are targeted by repressive epigenetic marks as a preservation mechanism for genome integrity (Okamoto and Hirochika 2001), this response has been proposed to be related to the activity of the RdDM pathway in repressing transposons in accessible chromatin environments (Gent et al, 2014).…”

High-quality genome and methylomes illustrate features underlying evolutionary success of oaks

“…It is possible they are simply the result of the type of TEs found near gene boundaries. In valley oak (Figure 5), maize 60 , and Arabidopsis 61 , mCHH is influenced by TE family, proximity to genes, and chromosomal location. The strong enrichment of small, highly methylated TE families neargenes (Figure 5E and F) could be due to, for example, selection against large TEs in gene proximal regions.…”