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New Phytol. 2020 Jan;225(1):234-249. doi: 10.1111/nph.16125. Epub 2019 Sep 27.

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

Author information

1
Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.
2
Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao, China.
3
Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China.
4
College of Life Science, Dezhou University, Dezhou, 253023, China.
5
Shandong Key Laboratory of Biophysics, Dezhou University, Dezhou, 253023, China.
6
Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
7
University of Chinese Academy of Sciences, Shenzhen, China.
8
Department of Molecular, Cell and Developmental Biology, Institute for Genomics and Proteomics, University of California, Los Angeles, CA, 90095, USA.
9
Biological Sciences, Flinders University, GPO Box 2100, Adelaide, SA, 5001, Australia.
10
State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Sciences, Xiamen University, Xiamen, China.
11
CNRS UMR 6286, Faculté des Sciences et des Techniques, Université de Nantes, 2 rue de la Houssinière, 44322, Nantes, France.
12
School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.

Abstract

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.

KEYWORDS:

BS-PCR; DNA methylation; DNMT2; MeDIP-seq; WGBS-seq; brown algae; gene expression; life-cycle stages

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