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

Nature Communications

Volumn 4, Issue , 2013, Pages

  Veluchamy, Alaguraj ^a   Lin, Xin ^a,g   Maumus, Florian ^a,h   Rivarola, Maximo ^b,i   Bhavsar, Jaysheel ^b   Creasy, Todd ^b   O'Brien, Kimberly ^b   Sengamalay, Naomi A ^b   Tallon, Luke J ^b   Smith, Andrew D ^c   Rayko, Edda ^a   Ahmed, Ikhlak ^a   Crom, Stéphane Le ^a   Farrant, Gregory K ^a   Sgro, Jean Yves ^d   Olson, Sue A ^e   Bondurant, Sandra Splinter ^d   Allen, Andrew ^f   Rabinowicz, Pablo D ^b   Sussman, Michael R ^d   Bowler, Chris ^a   Tirichine, Leïla ^a   more..

^a PSL RESEARCH UNIVERSITY   (France)

^b UNIVERSITY OF MARYLAND SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^d UNIVERSITY OF WISCONSIN MADISON   (United States)

^e Roche NimbleGen Inc   (United States)

^f J CRAIG VENTER INSTITUTE   (United States)

^g XIAMEN UNIVERSITY   (China)

^h Centre de recherche de Versailles   (France)

ⁱ INSTITUTO NACIONAL DE TECNOLOGÍA AGROPECUARIA INTA   (Argentina)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; CYTOSINE; MESSENGER RNA;

DIATOM; DNA; ECOLOGICAL MODELING; EUKARYOTE; GENE EXPRESSION; GENOME; METHYLATION;

ARTICLE; BACTERIAL GENE; DNA LIBRARY; DNA METHYLATION; EUKARYOTE EVOLUTION; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE TRANSFER; HORIZONTAL GENE TRANSFER; NONHUMAN; PHAEODACTYLUM TRICORNUTUM; PROMOTER REGION; START CODON; STOP CODON; STRAMENOPILE; TRANSPOSON;

CHROMOSOMES; DIATOMS; DNA METHYLATION; DNA TRANSPOSABLE ELEMENTS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC LOCI; GENOME; REPETITIVE SEQUENCES, NUCLEIC ACID;

EID: 84880120526     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms3091     Document Type: Article

References (47)

1. Kato, M., Miura, A., Bender, J., Jacobsen, S. E. & Kakutani, T. Role of CG and non-CG methylation in immobilization of transposons in Arabidopsis. Curr. Biol. 13, 421-426 (2003). (Pubitemid 36280461)
2. Bird, A. P. CpG-rich islands and the function of DNA methylation. Nature 321, 209-213 (1986). (Pubitemid 16016411)
3. Feil, R. & Berger, F. Convergent evolution of genomic imprinting in plants and mammals. Trends. Genet. 23, 192-199 (2007). (Pubitemid 46509542)
4. Zilberman, D., Gehring, M., Tran, R. K., Ballinger, T. & Henikoff, S. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat. Genet. 39, 61-69 (2007). (Pubitemid 46026502)
5. Cokus, S. J. et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452, 215-219 (2008). (Pubitemid 351380251)
6. Feng, S. et al. Conservation and divergence of methylation patterning in plants and animals. Proc. Natl Acad. Sci. USA 107, 8689-8694 (2010).
7. Lister, R. et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462, 315-322 (2009).
8. Lyko, F. et al. The honey bee epigenomes: differential methylation of brain DNA in queens and workers. PLoS Biol. 8, e1000506 (2010).
9. Xiang, H. et al. Single base-resolution methylome of the silkworm reveals a sparse epigenomic map. Nat. Biotechnol. 28, 516-520 (2010).
10. Zemach, A., McDaniel, I. E., Silva, P. & Zilberman, D. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 328, 916-919 (2010).
11. Su, Z., Han, L. & Zhao, Z. Conservation and divergence of DNA methylation in eukaryotes: new insights from single base-resolution DNA methylomes. Epigenetics 6, 134-140 (2010).
12. Proffitt, J. H., Davie, J. R., Swinton, D. & Hattman, S. 5-Methylcytosine is not detectable in Saccharomyces cerevisiae DNA. Mol. Cell. Biol. 4, 985-988 (1984). (Pubitemid 14051817)
13. Simpson, V. J., Johnson, T. E. & Hammen, R. F. Caenorhabditis elegans DNA does not contain 5-methylcytosine at any time during development or aging. Nucleic Acids Res. 14, 6711-6719 (1986).
14. Urieli-Shoval, S., Gruenbaum, Y., Sedat, J. & Razin, A. The absence of detectable methylated bases in Drosophila melanogaster DNA. FEBS Lett. 146, 148-152 (1982).
15. Lyko, F., Ramsahoye, B. H. & Jaenisch, R. DNA methylation in Drosophila melanogaster. Nature 408, 538-540 (2000).
16. Cock, J. M. et al. The Ectocarpus genome and the independent evolution of multicellularity in brown algae. Nature 465, 617-621 (2010).
17. Cavalier-Smith, T. The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. Int. J. Syst. Evol. Microbiol. 52, 297-354 (2002). (Pubitemid 34262632)
18. Bowler, C., Vardi, A. & Allen, A. E. Oceanographic and biogeochemical insights from diatom genomes. Ann. Rev. Mar. Sci. 2, 333-365 (2010).
19. Moustafa, A. et al. Genomic footprints of a cryptic plastid endosymbiosis in diatoms. Science 324, 1724-1726 (2009).
20. Bowler, C. et al. The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature 456, 239-244 (2008).
21. Bowler, C., De Martino, A. & Falciatore, A. Diatom cell division in an environmental context. Curr. Opin. Plant. Biol. 13, 623-630 (2010).
22. Maumus, F., Rabinowicz, P., Bowler, C. & Rivarola, M. Stemming epigenetics in marine Stramenopiles. Curr. Genomics 12, 357-370 (2011).
23. Lippman, Z., Gendrel, A. V., Colot, V. & Martienssen, R. Profiling DNA methylation patterns using genomic tiling microarrays. Nat. Methods 2, 219-224 (2005). (Pubitemid 41122130)
24. Maumus, F. et al. Potential impact of stress activated retrotransposons on genome evolution in a marine diatom. BMC Genomics 10, 624 (2009).
25. Maheswari, U. et al. Digital expression profiling of novel diatom transcripts provides insight into their biological functions. Genome Biol. 11, R85 (2010).
26. Ahmed, I., Sarazin, A., Bowler, C., Colot, V. & Quesneville, H. Genome-wide evidence for local DNA methylation spreading from small RNA-targeted sequences in Arabidopsis. Nucleic Acids Res. 39, 6919-6931 (2011).
27. Barry, C., Faugeron, G. & Rossignol, J. L. Methylation induced premeiotically in Ascobolus: coextension with DNA repeat lengths and effect on transcript elongation. Proc. Natl Acad. Sci. USA 90, 4557-4561 (1993). (Pubitemid 23148944)
28. Maheswari, U., Mock, T., Armbrust, E. V. & Bowler, C. Update of the Diatom EST Database: a new tool for digital transcriptomics. Nucleic Acids Res. 37, D1001-D1005 (2009).
29. Paul, J. H., Jeffrey, W. H. & DeFlaun, M. F. Dynamics of extracellular DNA in the marine environment. Appl. Environ. Microbiol. 53, 170-179 (1987). (Pubitemid 17226632)
30. Bao, Z. & Eddy, S. R. Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res. 12, 1269-1276 (2002). (Pubitemid 41264428)
31. Benson, G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27, 573-580 (1999). (Pubitemid 29210025)
32. Jarvis, E. E., Dunahay, T. G. & Brown, L. M. DNA nucleoside composition and methylation in several species of microalgae. J. Phycol. 28, 356-362 (1992).
33. Suzuki, M. M. & Bird, A. DNA methylation landscapes: provocative insights from epigenomics. Nat. Rev. Genet. 9, 465-476 (2008). (Pubitemid 351693975)
34. Wang, W. et al. High rate of chimeric gene origination by retroposition in plant genomes. Plant Cell 18, 1791-1802 (2006). (Pubitemid 44260178)
35. Goll, M. G. et al. Methylation of tRNAAsp by the DNA methyltransferase homolog Dnmt2. Science 311, 395-398 (2006). (Pubitemid 43132667)
36. Ponger, L. & Li, W. H. Evolutionary diversification of DNA methyltransferases in eukaryotic genomes. Mol. Biol. Evol. 22, 1119-1128 (2005). (Pubitemid 40471424)
37. De Riso, V. et al. Gene silencing in the marine diatom Phaeodactylum tricornutum. Nucleic Acids Res. 37, e96 (2009).
38. Mette, M. F., Aufsatz, W., van der Winden, J., Matzke, M. A. & Matzke, A. J. Transcriptional silencing and promoter methylation triggered by double-stranded RNA. EMBO J. 19, 5194-5201 (2000).
39. Teixeira, F. K. et al. A role for RNAi in the selective correction of DNA methylation defects. Science 323, 1600-1604 (2009).
40. Wassenegger, M., Heimes, S., Riedel, L. & Sanger, H. L. RNA-directed de novo methylation of genomic sequences in plants. Cell 76, 567-576 (1994). (Pubitemid 24064176)
41. Norden-Krichmar, T. M., Allen, A. E., Gaasterland, T. & Hildebrand, M. Characterization of the small RNA transcriptome of the diatom, Thalassiosira pseudonana. PLoS One 6, e22870 (2011).
42. Huang, A., He, L. & Wang, G. Identification and characterization of microRNAs from Phaeodactylum tricornutum by high-throughput sequencing and bioinformatics analysis. BMC Genomics 12, 337 (2011).
43. You, W. et al. Atypical DNA methylation of genes encoding cysteine-rich peptides in Arabidopsis thaliana. BMC Plant Biol. 12, 51 (2012).
44. De Martino, A. et al. Physiological and molecular evidence that environmental changes elicit morphological interconversion in the model diatom Phaeodactylum tricornutum. Protist 162, 462-481 (2011).
45. De Martino, A., Meichenein, A., Shi, J., Pan, K. & Bowler, C. Genetic and phenotypic characterization of Phaeodactylum tricornutum (Bacillariophyceae) accessions. J. Phycol. 43, 992-1009 (2007). (Pubitemid 47493105)
46. Toedling, J. et al. Ringo-an R/Bioconductor package for analyzing ChIP-chip readouts. BMC Bioinform. 8, 221 (2007).
47. Krzywinski, M. et al. Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639-1645 (2009).