Literature DB >> 28258985

Gene body DNA methylation in plants.

Adam J Bewick1, Robert J Schmitz2.   

Abstract

The type, amount, and location of DNA methylation within a gene provides pivotal information on the enzymatic pathway by which it was achieved and its functional consequences. In plants (angiosperms specifically), gene body methylation (gbM) refers to genes with an enrichment of CG DNA methylation within the transcribed regions and depletion at the transcriptional start and termination sites. GbM genes often compose the bulk of methylated genes within angiosperm genomes and are enriched for housekeeping functions. Contrary to the transcriptionally repressive effects of other chromatin modifications within gene bodies, gbM genes are constitutively expressed. GbM has intrigued researchers since its discovery, and much effort has been placed on identifying its functional role. Here, we highlight the recent findings on the evolutionary origin and molecular mechanism of gbM and synthesize studies describing the possible roles for this enigmatic epigenetic phenotype.
Copyright © 2017 Elsevier Ltd. All rights reserved.

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Year:  2017        PMID: 28258985      PMCID: PMC5413422          DOI: 10.1016/j.pbi.2016.12.007

Source DB:  PubMed          Journal:  Curr Opin Plant Biol        ISSN: 1369-5266            Impact factor:   7.834


  47 in total

1.  Conservation and divergence of methylation patterning in plants and animals.

Authors:  Suhua Feng; Shawn J Cokus; Xiaoyu Zhang; Pao-Yang Chen; Magnolia Bostick; Mary G Goll; Jonathan Hetzel; Jayati Jain; Steven H Strauss; Marnie E Halpern; Chinweike Ukomadu; Kirsten C Sadler; Sriharsa Pradhan; Matteo Pellegrini; Steven E Jacobsen
Journal:  Proc Natl Acad Sci U S A       Date:  2010-04-15       Impact factor: 11.205

2.  Body-methylated genes in Arabidopsis thaliana are functionally important and evolve slowly.

Authors:  Shohei Takuno; Brandon S Gaut
Journal:  Mol Biol Evol       Date:  2011-08-02       Impact factor: 16.240

Review 3.  RNA-directed DNA methylation: an epigenetic pathway of increasing complexity.

Authors:  Marjori A Matzke; Rebecca A Mosher
Journal:  Nat Rev Genet       Date:  2014-05-08       Impact factor: 53.242

4.  Evolutionary patterns of genic DNA methylation vary across land plants.

Authors:  Shohei Takuno; Jin-Hua Ran; Brandon S Gaut
Journal:  Nat Plants       Date:  2016-01-25       Impact factor: 15.793

5.  Control of genic DNA methylation by a jmjC domain-containing protein in Arabidopsis thaliana.

Authors:  Hidetoshi Saze; Akiko Shiraishi; Asuka Miura; Tetsuji Kakutani
Journal:  Science       Date:  2008-01-25       Impact factor: 47.728

6.  Mechanism of DNA methylation-directed histone methylation by KRYPTONITE.

Authors:  Jiamu Du; Lianna M Johnson; Martin Groth; Suhua Feng; Christopher J Hale; Sisi Li; Ajay A Vashisht; James A Wohlschlegel; Dinshaw J Patel; Steven E Jacobsen
Journal:  Mol Cell       Date:  2014-07-10       Impact factor: 17.970

7.  Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions.

Authors:  Taiji Kawakatsu; Shao-Shan Carol Huang; Florian Jupe; Eriko Sasaki; Robert J Schmitz; Mark A Urich; Rosa Castanon; Joseph R Nery; Cesar Barragan; Yupeng He; Huaming Chen; Manu Dubin; Cheng-Ruei Lee; Congmao Wang; Felix Bemm; Claude Becker; Ryan O'Neil; Ronan C O'Malley; Danjuma X Quarless; Nicholas J Schork; Detlef Weigel; Magnus Nordborg; Joseph R Ecker
Journal:  Cell       Date:  2016-07-14       Impact factor: 66.850

8.  RNAi, DRD1, and histone methylation actively target developmentally important non-CG DNA methylation in arabidopsis.

Authors:  Simon W-L Chan; Ian R Henderson; Xiaoyu Zhang; Govind Shah; Jason S-C Chien; Steven E Jacobsen
Journal:  PLoS Genet       Date:  2006-06-02       Impact factor: 5.917

9.  Evolution of DNA methylation patterns in the Brassicaceae is driven by differences in genome organization.

Authors:  Danelle K Seymour; Daniel Koenig; Jörg Hagmann; Claude Becker; Detlef Weigel
Journal:  PLoS Genet       Date:  2014-11-13       Impact factor: 5.917

10.  The evolution of CHROMOMETHYLASES and gene body DNA methylation in plants.

Authors:  Adam J Bewick; Chad E Niederhuth; Lexiang Ji; Nicholas A Rohr; Patrick T Griffin; Jim Leebens-Mack; Robert J Schmitz
Journal:  Genome Biol       Date:  2017-05-01       Impact factor: 13.583

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  86 in total

1.  Natural variation in DNA methylation homeostasis and the emergence of epialleles.

Authors:  Yinwen Zhang; Jered M Wendte; Lexiang Ji; Robert J Schmitz
Journal:  Proc Natl Acad Sci U S A       Date:  2020-02-18       Impact factor: 11.205

2.  Role of gene body methylation in acclimatization and adaptation in a basal metazoan.

Authors:  Groves Dixon; Yi Liao; Line K Bay; Mikhail V Matz
Journal:  Proc Natl Acad Sci U S A       Date:  2018-12-07       Impact factor: 11.205

Review 3.  Exploiting induced and natural epigenetic variation for crop improvement.

Authors:  Nathan M Springer; Robert J Schmitz
Journal:  Nat Rev Genet       Date:  2017-07-03       Impact factor: 53.242

4.  Heritable Epigenomic Changes to the Maize Methylome Resulting from Tissue Culture.

Authors:  Zhaoxue Han; Peter A Crisp; Scott Stelpflug; Shawn M Kaeppler; Qing Li; Nathan M Springer
Journal:  Genetics       Date:  2018-05-30       Impact factor: 4.562

Review 5.  EvoChromo: towards a synthesis of chromatin biology and evolution.

Authors:  Ines A Drinnenberg; Frédéric Berger; Simon J Elsässer; Peter R Andersen; Juan Ausió; Wendy A Bickmore; Alexander R Blackwell; Douglas H Erwin; James M Gahan; Brandon S Gaut; Zachary H Harvey; Steven Henikoff; Joyce Y Kao; Siavash K Kurdistani; Bernardo Lemos; Mia T Levine; Karolin Luger; Harmit S Malik; José M Martín-Durán; Catherine L Peichel; Marilyn B Renfree; Kinga Rutowicz; Peter Sarkies; Robert J Schmitz; Ulrich Technau; Joseph W Thornton; Tobias Warnecke; Kenneth H Wolfe
Journal:  Development       Date:  2019-09-26       Impact factor: 6.868

6.  Expression and DNA methylation of SERK, BBM, LEC2 and WUS genes in in vitro cultures of Boesenbergia rotunda (L.) Mansf.

Authors:  Rezaul Karim; Yew Seong Tan; Pooja Singh; Norzulaani Khalid; Jennifer Ann Harikrishna
Journal:  Physiol Mol Biol Plants       Date:  2018-06-28

Review 7.  Epigenetic perspectives on the evolution and domestication of polyploid plant and crops.

Authors:  Mingquan Ding; Z Jeffrey Chen
Journal:  Curr Opin Plant Biol       Date:  2018-03-07       Impact factor: 7.834

Review 8.  DNA Methylation: Shared and Divergent Features across Eukaryotes.

Authors:  Robert J Schmitz; Zachary A Lewis; Mary G Goll
Journal:  Trends Genet       Date:  2019-08-06       Impact factor: 11.639

Review 9.  DNA methylation analysis in plants: review of computational tools and future perspectives.

Authors:  Jimmy Omony; Thomas Nussbaumer; Ruben Gutzat
Journal:  Brief Bioinform       Date:  2020-05-21       Impact factor: 11.622

Review 10.  Opportunities and limitations of reduced representation bisulfite sequencing in plant ecological epigenomics.

Authors:  Ovidiu Paun; Koen J F Verhoeven; Christina L Richards
Journal:  New Phytol       Date:  2018-08-19       Impact factor: 10.151

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