Abstract
Changes in DNA methylation patterns in different tissues, at various developmental stages, and under environmental stimuli have been investigated in plants. However, the involvement of DNA methylation in daily gene expression regulation and the plant circadian clock have not been reported. Here, we investigated DNA methylomes and mRNA transcriptomes from leaves of P. trichocarpa over 24 h by high-throughput sequencing. We found that approximately 15.63–19.50% of the genomic cytosine positions were methylated in mature poplar leaves, with approximately half being in the form of asymmetric CHH sites. Repetitive sequences and transposable elements (TEs) were heavily methylated, and the hAT and CMC-EnSpm transposons were more heavily methylated than other TEs. High methylation levels were observed upstream and downstream of the transcribed region, medium in exon and intron, low in untranslated region (5′-UTR and 3′-UTR) of genic regions. In total, about 53,689 differentially methylated regions (DMRs) were identified and CHH context was the most abundant type among daily DNA methylation changes. The DMRs overlapped with over one third of the total poplar genes, including plant defense genes. In addition, a positive correlation between expression levels and DNA methylation levels in the gene body region were observed in DMR overlapping genes. About 1,895 circadian regulated genes overlapped with DMRs, with 871 hypermethylated genes with down-regulated expression levels and 881 hypomethylated genes with up-regulated expression levels, indicating the possible regulation of DNA methylation on the daily rhythmic expression of these genes. But rhythmic DNA methylation changes were not detected in any oscillator component genes controlling the plant circadian clock. Our results suggest that DNA methylation participates widely in daily gene expression regulation, but is not the main mechanism modulating the plant circadian clock.
Highlights
DNA methylation is an epigenetic modification that plays an important role in plant development and environmental adaption (Gehring, 2013; Bilichak and Kovalchuk, 2016)
The mechanisms responsible for the establishment and maintenance of plant DNA methylation have been clarified for Arabidopsis. de novo DNA methylation is mediated by RNA-directed DNA methylation pathways established by DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2), while maintenance of DNA methylation in CG and CHG contexts is catalyzed by DNA METHYLTRANSFERASE 1 (MET1) and CHROMOMETHYLASE 3 (CMT3), respectively, and maintenance of DNA methylation in CHH is carried out by DRM2 and CHROMOMETHYLASE 2 (CMT2) (Law and Jacobsen, 2010; Stroud et al, 2014; Zhang et al, 2018)
Most studies on plant stress responses found obvious changes in DNA methylation patterns after exposure to environmental stimuli (Raj et al, 2011; Yaish et al, 2011; Dowen et al, 2012; Rico et al, 2014; Eichten and Springer, 2015; Ohama et al, 2017), and some studies on plants indicated that DNA methylation changes can occur rapidly
Summary
DNA methylation is an epigenetic modification that plays an important role in plant development and environmental adaption (Gehring, 2013; Bilichak and Kovalchuk, 2016). Active demethylation was reported in plants, indicating that DNA methylation is dynamic rather than static (Agius et al, 2006; Penterman et al, 2007; Zhu, 2009; Kim and Zilberman, 2014). Due to these dynamic characteristics, changes in genomic DNA methylation patterns have been reported in plant stress responses, environmental adaption, and different developmental stages (Raj et al, 2011; Yaish et al, 2011; Dowen et al, 2012; Vining et al, 2012)
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