RT Journal Article
SR Electronic
T1 The evolution of CHROMOMETHYLASES and gene body DNA methylation in plants
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 054924
DO 10.1101/054924
A1 Adam J. Bewick
A1 Chad E. Niederhuth
A1 Ji Lexiang
A1 Nicholas A. Rohr
A1 Patrick T. Griffin
A1 Jim Leebens-Mack
A1 Robert J. Schmitz
YR 2017
UL http://biorxiv.org/content/early/2017/01/31/054924.abstract
AB Background The evolution of gene body methylation (gbM), its origins and its functional consequences are poorly understood. By pairing the largest collection of transcriptomes (>1000) and methylomes (77) across Viridiplantae we provide novel insights into the evolution of gbM and its relationship to CHROMOMETHYLASE (CMT) proteins.Results CMTs are evolutionary conserved DNA methyltransferases in Viridiplantae. Duplication events gave rise to what are now referred to as CMT1, 2 and 3. Independent losses of CMT1, 2 and 3 in eudicots, CMT2 and ZMET in monocots and monocots/commelinids, variation in copy number and non-neutral evolution suggests overlapping or fluid functional evolution of this gene family. DNA methylation within genes is widespread and is found in all major taxonomic groups of Viridiplantae investigated. Genes enriched with methylated CGs (mCG) were also identified in species sister to angiosperms. The proportion of genes and DNA methylation patterns associated with gbM are restricted to angiosperms with a functional CMT3 or ortholog. However, mCG-enriched genes in the gymnosperm Pinus taeda shared some similarities with gbM genes in Amborella trichopoda. Additionally, gymnosperms and ferns share a CMT homolog closely related to CMT2 and 3. Hence, the dependency of gbM on a CMT most likely extends to all angiosperms and possibly gymnosperms and ferns.Conclusions The resulting gene family phylogeny of CMT transcripts from the most diverse sampling of plants to date redefines our understanding of CMT evolution and its evolutionary consequences on DNA methylation. Future, functional tests of homologous and paralogous CMTs will uncover novel roles and consequences to the epigenome.