Single-base methylome profiling of the giant kelp Saccharina japonica reveals significant differences in DNA methylation to microalgae and plants

doi:10.1111/nph.16125

IOCAS-IR

	Single-base methylome profiling of the giant kelp Saccharina japonica reveals significant differences in DNA methylation to microalgae and plants
	Fan, Xiao 1,2,3; Han, Wentao 1; Teng, Linhong 1,4,5; Jiang, Peng 6; Zhang, Xiaowen 1; Xu, Dong 1; Li, Chang 7; Pellegrini, Matteo 8; Wu, Chunhui6 ; Wang, Yitao 1; Kaczurowski, Michelle Joyce Slade 9; Lin, Xin 10; Tirichine, Leila 11; Mock, Thomas 12; Ye, Naihao 1,2
	2019-09-27
发表期刊	NEW PHYTOLOGIST
ISSN	0028-646X
页码	16
通讯作者	Mock, Thomas(t.mock@uea.ac.uk) ; Ye, Naihao(yenh@ysfri.ac.cn)
摘要	Brown 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.
关键词	brown algae BS-PCR DNA methylation DNMT2 gene expression life-cycle stages MeDIP-seq WGBS-seq
DOI	10.1111/nph.16125
收录类别	SCI
语种	英语
资助项目	National 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 ; National 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研究方向	Plant Sciences
WOS类目	Plant Sciences
WOS记录号	WOS:000487841400001
出版者	WILEY
引用统计	被引频次：27[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.qdio.ac.cn/handle/337002/162993
专题	中国科学院海洋研究所
通讯作者	Mock, Thomas; Ye, Naihao
作者单位	1.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
推荐引用方式 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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