IOCAS-IR
Single-base methylome profiling of the giant kelp Saccharina japonica reveals significant differences in DNA methylation to microalgae and plants
Fan, Xiao1,2,3; Han, Wentao1; Teng, Linhong1,4,5; Jiang, Peng6; Zhang, Xiaowen1; Xu, Dong1; Li, Chang7; Pellegrini, Matteo8; Wu, Chunhui6; Wang, Yitao1; Kaczurowski, Michelle Joyce Slade9; Lin, Xin10; Tirichine, Leila11; Mock, Thomas12; Ye, Naihao1,2
2019-09-27
Source PublicationNEW PHYTOLOGIST
ISSN0028-646X
Pages16
Corresponding AuthorMock, Thomas(t.mock@uea.ac.uk) ; Ye, Naihao(yenh@ysfri.ac.cn)
AbstractBrown algae have convergently evolved plant-like body plans and reproductive cycles, which in plants are controlled by differential DNA methylation. This contribution provides the first single-base methylome profiles of haploid gametophytes and diploid sporophytes of a multicellular alga. Although only c. 1.4% of cytosines in Saccharina japonica were methylated mainly at CHH sites and characterized by 5-methylcytosine (5mC), there were significant differences between life-cycle stages. DNA methyltransferase 2 (DNMT2), known to efficiently catalyze tRNA methylation, is assumed to methylate the genome of S. japonica in the structural context of tRNAs as the genome does not encode any other DNA methyltransferases. Circular and long noncoding RNA genes were the most strongly methylated regulatory elements in S. japonica. Differential expression of genes was negatively correlated with DNA methylation with the highest methylation levels measured in both haploid gametophytes. Hypomethylated and highly expressed genes in diploid sporophytes included genes involved in morphogenesis and halogen metabolism. The data herein provide evidence that cytosine methylation, although occurring at a low level, is significantly contributing to the formation of different life-cycle stages, tissue differentiation and metabolism in brown algae.
Keywordbrown algae BS-PCR DNA methylation DNMT2 gene expression life-cycle stages MeDIP-seq WGBS-seq
DOI10.1111/nph.16125
Indexed BySCI
Language英语
Funding ProjectNational key research and development program of China[2018YFD0900703] ; National key research and development program of China[2018YFD0901503-8] ; National key research and development program of China[2016YFC1402102] ; National Natural Science Foundation of China[41676145] ; Shandong key Research and Development Plan[2018GHY115010] ; Qingdao Municipal Science and Technology plan project[17-1-1-96-jch] ; Special Scientific Research Funds for Central Non-Profit Institutes, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences[20603022019006] ; Special Scientific Research Funds for Central Non-Profit Institutes, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences[20603022016001] ; Youth Talent Program - Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao)[2018-MFS-01] ; China Agriculture Research System[CARS-50] ; Marine S&T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology (Qingdao)[2018SDKJ0406-3] ; Ministry of Agriculture and Rural Affairs, China[NFZX2018] ; Taishan Scholars Funding ; Talent Projects of Distinguished Scientific Scholars in Agriculture ; Natural Environment Research Council, UK[NE/R000883/1] ; School of Environmental Sciences at the University of East Anglia, UK ; Region Pays de la Loire ; Nantes Metropole
WOS Research AreaPlant Sciences
WOS SubjectPlant Sciences
WOS IDWOS:000487841400001
PublisherWILEY
Citation statistics
Cited Times:3[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.qdio.ac.cn/handle/337002/162993
Collection中国科学院海洋研究所
Corresponding AuthorMock, Thomas; Ye, Naihao
Affiliation1.Chinese Acad Fishery Sci, Yellow Sea Fisheries Res Inst, Qingdao, Shandong, Peoples R China
2.Funct Lab Marine Fisheries Sci & Food Prod Proc, Qingdao, Shandong, Peoples R China
3.Shanghai Ocean Univ, Minist Educ, Key Lab Explorat & Utilizat Aquat Genet Resources, Shanghai 201306, Peoples R China
4.Dezhou Univ, Coll Life Sci, Dezhou 253023, Peoples R China
5.Dezhou Univ, Shandong Key Lab Biophys, Dezhou 253023, Peoples R China
6.Chinese Acad Sci, Inst Oceanol, Qingdao 266071, Shandong, Peoples R China
7.Univ Chinese Acad Sci, Shenzhen, Peoples R China
8.Univ Calif Los Angeles, Inst Genom & Prote, Dept Mol Cell & Dev Biol, Los Angeles, CA 90095 USA
9.Flinders Univ S Australia, Biol Sci, GPO Box 2100, Adelaide, SA 5001, Australia
10.Xiamen Univ, Coll Ocean & Earth Sci, State Key Lab Marine Environm Sci, Xiamen, Fujian, Peoples R China
11.Univ Nantes, Fac Sci & Tech, CNRS, UMR 6286, 2 Rue Houssiniere, F-44322 Nantes, France
12.Univ East Anglia, Sch Environm Sci, Norwich Res Pk, Norwich NR4 7TJ, Norfolk, England
Recommended Citation
GB/T 7714
Fan, Xiao,Han, Wentao,Teng, Linhong,et al. Single-base methylome profiling of the giant kelp Saccharina japonica reveals significant differences in DNA methylation to microalgae and plants[J]. NEW PHYTOLOGIST,2019:16.
APA Fan, Xiao.,Han, Wentao.,Teng, Linhong.,Jiang, Peng.,Zhang, Xiaowen.,...&Ye, Naihao.(2019).Single-base methylome profiling of the giant kelp Saccharina japonica reveals significant differences in DNA methylation to microalgae and plants.NEW PHYTOLOGIST,16.
MLA Fan, Xiao,et al."Single-base methylome profiling of the giant kelp Saccharina japonica reveals significant differences in DNA methylation to microalgae and plants".NEW PHYTOLOGIST (2019):16.
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