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Proc Natl Acad Sci U S A. 2016 Aug 9;113(32):9111-6. doi: 10.1073/pnas.1604666113. Epub 2016 Jul 25.

On the origin and evolutionary consequences of gene body DNA methylation.

Author information

1
Department of Genetics, University of Georgia, Athens, GA 30602;
2
Institute of Bioinformatics, University of Georgia, Athens, GA 30602;
3
Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
4
Department of Plant Biology, University of Georgia, Athens, GA 30602;
5
Department of Biology, Emory University, Atlanta, GA 30322;
6
Hudson Alpha Genome Sequencing Center, Huntsville, AL 35806;
7
Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095;
8
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.
9
Department of Genetics, University of Georgia, Athens, GA 30602; schmitz@uga.edu.

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.

KEYWORDS:

CHROMOMETHYLASE 3; DNA methylation; epigenetics; gene body methylation; histone modifications

PMID:
27457936
PMCID:
PMC4987809
DOI:
10.1073/pnas.1604666113
[Indexed for MEDLINE]
Free PMC Article

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