Global Methylomic and Transcriptomic Analyses Reveal the Broad Participation of DNA Methylation in Daily Gene Expression Regulation of Populus trichocarpa

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.