title: Transcriptome-wide high-throughput deep m(6)A-seq reveals unique differential m(6)A methylation patterns between three organs in Arabidopsis thaliana.
abstract: BACKGROUND
  m(6)A is a ubiquitous RNA modification in eukaryotes. Transcriptome-wide m(6)A patterns in Arabidopsis have been assayed recently. However, differential m(6)A patterns between organs have not been well characterized.
  
  
  RESULTS
  Over two-third of the transcripts in Arabidopsis are modified by m(6)A. In contrast to a recent observation of m(6)A enrichment in 5' mRNA, we find that m(6)A is distributed predominantly near stop codons. Interestingly, 85 % of the modified transcripts show high m(6)A methylation extent compared to their transcript level. The 290 highly methylated transcripts are mainly associated with transporters, stress responses, redox, regulation factors, and some non-coding RNAs. On average, the proportion of transcripts showing differential methylation between two plant organs is higher than that showing differential transcript levels. The transcripts with extensively higher m(6)A methylation in an organ are associated with the unique biological processes of this organ, suggesting that m(6)A may be another important contributor to organ differentiation in Arabidopsis. Highly expressed genes are relatively less methylated and vice versa, and different RNAs have distinct m(6)A patterns, which hint at mRNA fate. Intriguingly, most of the transposable element transcripts maintained a fragmented form with a relatively low transcript level and high m(6)A methylation in the cells.
  
  
  CONCLUSIONS
  This is the first study to comprehensively analyze m(6)A patterns in a variety of RNAs, the relationship between transcript level and m(6)A methylation extent, and differential m(6)A patterns across organs in Arabidopsis.
authors.affiliation: State Key Lab Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China. wyz689@hotmail.com.|Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA. wyz689@hotmail.com.
authors.forename: Yizhen
authors.initials: Y
authors.lastname: Wan
authors.affiliation: Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA.
authors.forename: Kai
authors.initials: K
authors.lastname: Tang
authors.affiliation: Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
authors.forename: Dayong
authors.initials: D
authors.lastname: Zhang
authors.affiliation: Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA.|Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
authors.forename: Shaojun
authors.initials: S
authors.lastname: Xie
authors.affiliation: Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA.|Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
authors.forename: Xiaohong
authors.initials: X
authors.lastname: Zhu
authors.affiliation: College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, China.
authors.forename: Zegang
authors.initials: Z
authors.lastname: Wang
authors.affiliation: Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA. lang.zhaobo@foxmail.com.|Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China. lang.zhaobo@foxmail.com.
authors.forename: Zhaobo
authors.initials: Z
authors.lastname: Lang
mesh_terms: D000241:Adenosine / Q000031:analogs & derivatives* / Q000032:analysis; D017360:Arabidopsis / Q000235:genetics*; D004251:DNA Transposable Elements; D035264:Flowers / Q000235:genetics; D020869:Gene Expression Profiling; D059014:High-Throughput Nucleotide Sequencing; D008745:Methylation; D018515:Plant Leaves / Q000235:genetics; D018517:Plant Roots / Q000235:genetics; D018749:RNA, Plant / Q000737:chemistry* / Q000378:metabolism; D017423:Sequence Analysis, RNA
chemical_list: D004251:DNA Transposable Elements; D018749:RNA, Plant; C010223:N-methyladenosine; D000241:Adenosine