On the origin and evolutionary consequences of gene body DNA methylation

• Type of Material: Article
• Authors: Adam J. Bewick, University of Georgia; Lexiang Ji, University of Georgia; Chad E. Niederhuth, University of Georgia; Eva-Maria Willing, Max Planck Institute for Plant Breeding Research; Brigitte T. Hofmeister, University of Georgia; Xiuling Shi, University of Georgia; Li Wang, University of Georgia; Zefu Lu, University of Georgia; Nicholas A. Rohr, University of Georgia; Benjamin Hartwig, Max Planck Institute for Plant Breeding Research; Christiane Kiefer, Max Planck Institute for Plant Breeding Research; Roger Deal, Emory University; Jeremy Schmutz, Hudson Alpha Genome Sequencing Ctr; Jane Grimwood, Hudson Alpha Genome Sequencing Ctr; Hume Stroud, University of California Los Angeles; Steven E. Jacobsen, University of California Los Angeles; Korbinian Schneeberger, Max Planck Institute for Plant Breeding Research; Xiaoyu Zhang, University of Georgia; Robert J. Schmitz, University of Georgia
• Language: English
• Date: 2016-08-09
• Publisher: United States National Academy of Sciences
• Publication Version: Final Published Version
• Copyright Statement: © 2016 National Academy of Sciences.
• Final Published Version (URL): http://dx.doi.org/10.1073/pnas.1604666113
• Title of Journal or Parent Work: PNAS
• Volume: 113
• Issue: 32
• Start Page: 9111
• End Page: 9116
• Grant/Funding Information: This work was supported by the National Institutes of Health (R00GM100000), Pew Charitable Trusts, and the Office of the Vice President of Research at UGA (R.J.S.). C.E.N. was supported by National Science Foundation (NSF) Postdoctoral Fellowship IOS-1402183. Research in the X.Z. laboratory was supported by the NSF (MCB-0960425).; H.S. was a Howard Hughes Medical Institute (HHMI) Fellow of the Damon Runyon Cancer Research Foundation (DRG-2194-14).; S.E.J. is an Investigator of the Howard Hughes Medical Institute.; B.T.H. was supported by a Scholars of Excellence graduate fellowship from the University of Georgia (UGA).
• Keywords: Chromomethylase 3; Science & Technology; JMJC Domain; Binding; Science & Technology - Other Topics; Protein; Multidisciplinary Sciences; Reveals; Arabidopsis thaliana; Expression; DNA methylation; histone modifications; gene body methylation; Alignment; epigenetics; Transcripts
• Research Categories: Biology, Genetics; Biology, Cell; Biology, Bioinformatics; Biology, Molecular; Agriculture, Plant Culture

Abstract

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.