Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum

• Published in: Nature communications Vol. 4; no. 1; p. 2091
• Main Authors: Veluchamy, Alaguraj, Lin, Xin, Maumus, Florian, Rivarola, Maximo, Bhavsar, Jaysheel, Creasy, Todd, O’Brien, Kimberly, Sengamalay, Naomi A., Tallon, Luke J., Smith, Andrew D., Rayko, Edda, Ahmed, Ikhlak, Crom, Stéphane Le, Farrant, Gregory K., Sgro, Jean-Yves, Olson, Sue A., Bondurant, Sandra Splinter, Allen, Andrew E., Rabinowicz, Pablo D., Sussman, Michael R., Bowler, Chris, Tirichine, Leïla
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01.07.2013; Nature Publishing Group
• Subjects: 631/181; 631/208/176/1988; 631/326; Biochemistry, Molecular Biology; Chromosomes - genetics; Diatoms - genetics; DNA Methylation - genetics; DNA Transposable Elements - genetics; Gene Expression Profiling; Gene Expression Regulation; Genetic Loci - genetics; Genome - genetics; Genomics; Humanities and Social Sciences; Life Sciences; multidisciplinary; Repetitive Sequences, Nucleic Acid - genetics; Science; Science (multidisciplinary); drosophila-melanogaster; identification; rna; marine diatom; plants; arabidopsis-thaliana; reveals; 5-methylcytosine; evolution; sequences
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/ncomms3091

DNA cytosine methylation is a widely conserved epigenetic mark in eukaryotes that appears to have critical roles in the regulation of genome structure and transcription. Genome-wide methylation maps have so far only been established from the supergroups Archaeplastida and Unikont. Here we report the first whole-genome methylome from a stramenopile, the marine model diatom Phaeodactylum tricornutum . Around 6% of the genome is intermittently methylated in a mosaic pattern. We find extensive methylation in transposable elements. We also detect methylation in over 320 genes. Extensive gene methylation correlates strongly with transcriptional silencing and differential expression under specific conditions. By contrast, we find that genes with partial methylation tend to be constitutively expressed. These patterns contrast with those found previously in other eukaryotes. By going beyond plants, animals and fungi, this stramenopile methylome adds significantly to our understanding of the evolution of DNA methylation in eukaryotes. Genome-wide maps of DNA methylation have so far been restricted to plants, animals and fungi. Here, the authors report the first whole-genome methylome of a stramenopile, the diatom Phaeodactylum tricornatum , and provide insight into the evolution of DNA methylation in eukaryotes.