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

Alaguraj Veluchamy, Xin Lin, Florian Maumus, Maximo Rivarola, Jaysheel Bhavsar, Todd Creasy, Kimberly O’Brien, Naomi A. Sengamalay, Luke J. Tallon, Andrew D. Smith, Edda Rayko, Ikhlak Ahmed, Stéphane Le Crom, Gregory K. Farrant, Jean-Yves Sgro, Sue A. Olson, Sandra Splinter Bondurant, Andrew E. Allen, Pablo D. Rabinowicz, Michael R. Sussman, Chris Bowler and Leïla Tirichine ()
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Alaguraj Veluchamy: Environmental and Evolutionary Genomics Section, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR 8197 INSERM U1024
Xin Lin: Environmental and Evolutionary Genomics Section, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR 8197 INSERM U1024
Florian Maumus: Environmental and Evolutionary Genomics Section, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR 8197 INSERM U1024
Maximo Rivarola: Institute for Genome Sciences (IGS), University of Maryland School of Medicine
Jaysheel Bhavsar: Institute for Genome Sciences (IGS), University of Maryland School of Medicine
Todd Creasy: Institute for Genome Sciences (IGS), University of Maryland School of Medicine
Kimberly O’Brien: Institute for Genome Sciences (IGS), University of Maryland School of Medicine
Naomi A. Sengamalay: Institute for Genome Sciences (IGS), University of Maryland School of Medicine
Luke J. Tallon: Institute for Genome Sciences (IGS), University of Maryland School of Medicine
Andrew D. Smith: University of Southern California
Edda Rayko: Environmental and Evolutionary Genomics Section, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR 8197 INSERM U1024
Ikhlak Ahmed: Environmental and Evolutionary Genomics Section, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR 8197 INSERM U1024
Stéphane Le Crom: Plateforme Génomique, Institut de Biologie de l’École Normale Supérieure (IBENS), CNRS UMR 8197 INSERM U1021
Gregory K. Farrant: Environmental and Evolutionary Genomics Section, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR 8197 INSERM U1024
Jean-Yves Sgro: Gene Expression Center Facility, Biotechnology Center, University of Wisconsin-Madison
Sue A. Olson: Roche NimbleGen Inc. Production Bioinformatics
Sandra Splinter Bondurant: Gene Expression Center Facility, Biotechnology Center, University of Wisconsin-Madison
Andrew E. Allen: J. Craig Venter Institute
Pablo D. Rabinowicz: Institute for Genome Sciences (IGS), University of Maryland School of Medicine
Michael R. Sussman: Biotechnology Center, 425 Henry Mall, University of Wisconsin
Chris Bowler: Environmental and Evolutionary Genomics Section, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR 8197 INSERM U1024
Leïla Tirichine: Environmental and Evolutionary Genomics Section, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR 8197 INSERM U1024

Nature Communications, 2013, vol. 4, issue 1, 1-10

Abstract: Abstract 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.

Date: 2013
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DOI: 10.1038/ncomms3091

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