Methylome-Transcriptome Interplay During Acquisition and Release From Seasonal Dormancy In Populus trichocarpa

Seasonal dormancy is a fundamental adaptation of perennial plants to their environment. To better understand the role of the epigenome in regulation of gene expression during dormancy, we compared transcriptome data (RNA-seq) with whole-genome DNA 5-methylcytosine (5mC) data (MeDIP-seq).  Lateral buds of field grown trees of genotype Nisqually-1 (reference Populus sequence) were collected in fall (paradormancy), winter (endormancy) and spring (ecodormancy) in western Oregon. We found that in fall and winter 30% of genes were expressed at low levels (FPKM 1-5), and 20% were highly expressed (FPKM >=10).  In contrast, in spring 71% of genes were expressed at low levels, and only 5% were highly expressed.  Pairwise comparisons identified the largest number of differentially-expressed (q<0.05) genes between winter and spring (4,766). Both gene promoter and gene body 5mC decreased from fall to winter, then increased in spring, although this trend was more pronounced in gene bodies. Lower gene body 5mC was associated with higher gene expression in winter, and higher gene body 5mC was associated with lower gene expression in spring. Surprisingly, promoter 5mC was not significantly correlated with gene expression at any stage. Gene Ontology (GO) categories enriched in winter-upregulated genes included abiotic stress response and carbohydrate metabolism.  Among the genes with decreased 5mC and increased expression during the fall-winter transition were WRKY11 and AP2/EREBP, transcription factors associated with dormancy transition in apical and axillary buds. We will also present results from other candidate genes for which epigenetic modifications may help to control dormancy.