title: Stable methylation of a non-coding RNA gene regulates gene expression in response to abiotic stress in Populus simonii.
abstract: DNA methylation plays important roles in responses to environmental stimuli. However, in perennial plants, the roles of DNA methylation in stress-specific adaptions to different abiotic stresses remain unclear. Here, we present a systematic, comparative analysis of the methylome and gene expression in poplar under cold, osmotic, heat, and salt stress conditions from 3h to 24h. Comparison of the stress responses revealed different patterns of cytosine methylation in response to the four abiotic stresses. We isolated and sequenced 1376 stress-specific differentially methylated regions (SDMRs); annotation revealed that these SDMRs represent 1123 genes encoding proteins, 16 miRNA genes, and 17 long non-coding RNA (lncRNA) genes. The SDMR162 region, consisting of Psi-MIR396e and PsiLNCRNA00268512, is regulated by epigenetic pathways and we speculate that PsiLNCRNA00268512 regulates miR396e levels by acting as a target mimic. The ratios of methylated cytosine declined to ~35.1% after 1 month of recovery from abiotic stress and to ~15.3% after 6 months. Among methylated miRNA genes, only expression of the methylation-regulated gene MIRNA6445a showed long-term stability. Our data provide a strong basis for future work and improve our understanding of the effect of epigenetic regulation of non-coding RNA expression, which will enable in-depth functional analysis.
authors.affiliation: National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China.
authors.forename: Yuepeng
authors.initials: Y
authors.lastname: Song
authors.affiliation: National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China.
authors.forename: Dong
authors.initials: D
authors.lastname: Ci
authors.affiliation: National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China.
authors.forename: Min
authors.initials: M
authors.lastname: Tian
authors.affiliation: National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China DeqiangZhang@bjfu.edu.cn.
authors.forename: Deqiang
authors.initials: D
authors.lastname: Zhang
mesh_terms: D003596:Cytosine / Q000378:metabolism; D019175:DNA Methylation / Q000235:genetics*; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018745:Genome, Plant; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D016366:Open Reading Frames / Q000235:genetics; D032107:Populus / Q000235:genetics* / Q000502:physiology*; D062085:RNA, Long Noncoding / Q000235:genetics* / Q000378:metabolism; D015203:Reproducibility of Results; D013312:Stress, Physiological / Q000235:genetics*
chemical_list: D035683:MicroRNAs; D062085:RNA, Long Noncoding; D003596:Cytosine
keywords: DNA methylation; Populus simonii; abiotic stress; non-coding RNA; transcriptome changes.