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Conservation and divergence of methylation patterning in plants and animals.

Cytosine DNA methylation is a heritable epigenetic mark present in many eukaryotic organisms. Although DNA methylation likely has a conserved role in gene silencing, the levels and patterns of DNA methylation appear to vary drastically among different organisms. Here we used shotgun genomic bisulfite sequencing (BS-Seq) to compare DNA methylation in eight diverse plant and animal genomes. We found that patterns of methylation are very similar in flowering plants with methylated cytosines detected in all sequence contexts, whereas CG methylation predominates in animals. Vertebrates have methylation throughout the genome except for CpG islands. Gene body methylation is conserved with clear preference for exons in most organisms. Furthermore, genes appear to be the major target of methylation in Ciona and honey bee. Among the eight organisms, the green alga Chlamydomonas has the most unusual pattern of methylation, having non-CG methylation enriched in exons of genes rather than in repeats and transposons. In addition, the Dnmt1 cofactor Uhrf1 has a conserved function in maintaining CG methylation in both transposons and gene bodies in the mouse, Arabidopsis, and zebrafish genomes.

Pubmed ID: 20395551

Authors

  • Feng S
  • Cokus SJ
  • Zhang X
  • Chen PY
  • Bostick M
  • Goll MG
  • Hetzel J
  • Jain J
  • Strauss SH
  • Halpern ME
  • Ukomadu C
  • Sadler KC
  • Pradhan S
  • Pellegrini M
  • Jacobsen SE

Journal

Proceedings of the National Academy of Sciences of the United States of America

Publication Data

May 11, 2010

Associated Grants

  • Agency: NCI NIH HHS, Id: 5F32CA126302
  • Agency: NIGMS NIH HHS, Id: GM60398
  • Agency: NIDDK NIH HHS, Id: R01 DK080789
  • Agency: NICHD NIH HHS, Id: R01 HD058530
  • Agency: NICHD NIH HHS, Id: R01 HD058530-04
  • Agency: NIDDK NIH HHS, Id: R01DK080789
  • Agency: NICHD NIH HHS, Id: R01HD058530
  • Agency: NIGMS NIH HHS, Id: R37 GM060398
  • Agency: Howard Hughes Medical Institute, Id:

Mesh Terms

  • Animals
  • Arabidopsis
  • DNA Methylation
  • Evolution, Molecular
  • Exons
  • Introns
  • Mutation
  • Oligonucleotide Array Sequence Analysis
  • Open Reading Frames
  • Phylogeny
  • Plants
  • Repetitive Sequences, Nucleic Acid
  • Trans-Activators
  • Zebrafish
  • Zebrafish Proteins