On the origin and evolutionary consequences of gene body DNA methylation

Adam J. Bewick, Lexiang Ji, Chad E. Niederhuth, Eva Maria Willing, Brigitt T. Hofmeister, Xiuling Shi, Li Wang, Zefu Lu, Nicholas A. Rohr, Benjamin Hartwig, Christiane Kiefer, Roger B. Deal, Jeremy Schmutz, Jane Grimwood, Hume Stroud, Steven E. Jacobsen, Korbinian Schneeberger, Xiaoyu Zhang, Robert J. Schmitza

Research output: Contribution to journalArticlepeer-review

199 Scopus citations


In plants, CG DNA methylation is prevalent in the transcribed regions of many constitutively expressed genes (gene body methylation; gbM), but the origin and function of gbM remain unknown. Here we report the discovery that Eutrema salsugineum has lost gbM from its genome, to our knowledge the first instance for an angiosperm. Of all known DNA methyltransferases, only CHROMOMETHYLASE 3 (CMT3) is missing from E. salsugineum. Identification of an additional angiosperm, Conringia planisiliqua, which independently lost CMT3 and gbM, supports that CMT3 is required for the establishment of gbM. Detailed analyses of gene expression, the histone variant H2A.Z, and various histone modifications in E. salsugineum and in Arabidopsis thaliana epigenetic recombinant inbred lines found no evidence in support of any role for gbM in regulating transcription or affecting the composition and modification of chromatin over evolutionary timescales.

Original languageEnglish (US)
Pages (from-to)9111-9116
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number32
StatePublished - Aug 9 2016
Externally publishedYes


  • DNA methylation|gene body methylation|epigenetics
  • Histone modifications

ASJC Scopus subject areas

  • General


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