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

Author

Listed:
  • 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
    Present address: State Key Laboratory of Marine Environmental Science, Xiamen University, China)

  • Florian Maumus

    (Environmental and Evolutionary Genomics Section, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR 8197 INSERM U1024
    Present address: Unité de Recherche en Génomique-Info, UR 1164, INRA Centre de Versailles-Grignon, route de Saint-Cyr 78,026 Versailles Cedex, France)

  • Maximo Rivarola

    (Institute for Genome Sciences (IGS), University of Maryland School of Medicine
    Present address: Instituto de Biotecnología, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA Castelar), CC 25, Castelar B1712WAA, Argentina)

  • 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)

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.

Suggested Citation

  • 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, 2013. "Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum," Nature Communications, Nature, vol. 4(1), pages 1-10, October.
    • Handle: RePEc:nat:natcom:v:4:y:2013:i:1:d:10.1038_ncomms3091
    DOI: 10.1038/ncomms3091
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