title: On the origin and evolutionary consequences of gene body DNA methylation.
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.
authors.affiliation: Department of Genetics, University of Georgia, Athens, GA 30602;
authors.forename: Adam J
authors.initials: AJ
authors.lastname: Bewick
authors.affiliation: Institute of Bioinformatics, University of Georgia, Athens, GA 30602;
authors.forename: Lexiang
authors.initials: L
authors.lastname: Ji
authors.affiliation: Department of Genetics, University of Georgia, Athens, GA 30602;
authors.forename: Chad E
authors.initials: CE
authors.lastname: Niederhuth
authors.affiliation: Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
authors.forename: Eva-Maria
authors.initials: EM
authors.lastname: Willing
authors.affiliation: Institute of Bioinformatics, University of Georgia, Athens, GA 30602;
authors.forename: Brigitte T
authors.initials: BT
authors.lastname: Hofmeister
authors.affiliation: Department of Genetics, University of Georgia, Athens, GA 30602;
authors.forename: Xiuling
authors.initials: X
authors.lastname: Shi
authors.affiliation: Department of Plant Biology, University of Georgia, Athens, GA 30602;
authors.forename: Li
authors.initials: L
authors.lastname: Wang
authors.affiliation: Department of Genetics, University of Georgia, Athens, GA 30602;
authors.forename: Zefu
authors.initials: Z
authors.lastname: Lu
authors.affiliation: Department of Genetics, University of Georgia, Athens, GA 30602;
authors.forename: Nicholas A
authors.initials: NA
authors.lastname: Rohr
authors.affiliation: Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
authors.forename: Benjamin
authors.initials: B
authors.lastname: Hartwig
authors.affiliation: Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
authors.forename: Christiane
authors.initials: C
authors.lastname: Kiefer
authors.affiliation: Department of Biology, Emory University, Atlanta, GA 30322;
authors.forename: Roger B
authors.initials: RB
authors.lastname: Deal
authors.affiliation: Hudson Alpha Genome Sequencing Center, Huntsville, AL 35806;
authors.forename: Jeremy
authors.initials: J
authors.lastname: Schmutz
authors.affiliation: Hudson Alpha Genome Sequencing Center, Huntsville, AL 35806;
authors.forename: Jane
authors.initials: J
authors.lastname: Grimwood
authors.affiliation: Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095;
authors.forename: Hume
authors.initials: H
authors.lastname: Stroud
authors.affiliation: Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095; Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095.
authors.forename: Steven E
authors.initials: SE
authors.lastname: Jacobsen
authors.affiliation: Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
authors.forename: Korbinian
authors.initials: K
authors.lastname: Schneeberger
authors.affiliation: Department of Plant Biology, University of Georgia, Athens, GA 30602;
authors.forename: Xiaoyu
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Department of Genetics, University of Georgia, Athens, GA 30602; schmitz@uga.edu.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Schmitz
mesh_terms: D004248:DNA (Cytosine-5-)-Methyltransferases / Q000502:physiology; D019175:DNA Methylation; D019143:Evolution, Molecular; D006657:Histones / Q000378:metabolism; D019684:Magnoliopsida / Q000235:genetics*
chemical_list: D006657:Histones; D004248:DNA (Cytosine-5-)-Methyltransferases; C112810:chromomethylase
keywords: CHROMOMETHYLASE 3; DNA methylation; epigenetics; gene body methylation; histone modifications