The evolution of CHROMOMETHYLASES and gene body DNA methylation in plants

Genome Biology
Adam J BewickRobert J Schmitz

Abstract

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. 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...Continue Reading

References

Jul 4, 2017·Nature Reviews. Genetics·Nathan Springer, Robert J Schmitz
Nov 7, 2018·Molecular Biology and Evolution·Aline Muyle, Brandon S Gaut
Feb 20, 2019·Nature Ecology & Evolution·Adam J BewickRobert J Schmitz
Nov 3, 2018·Journal of Integrative Plant Biology·Jin Cheng LongYan He
May 31, 2019·G3 : Genes - Genomes - Genetics·Adam J BewickRobert J Schmitz
Sep 1, 2019·Molecular Ecology·Thomas C MathersCock van Oosterhout
Nov 7, 2019·The Plant Journal : for Cell and Molecular Biology·Seydina Issa DiopPéter Szövényi
Jul 1, 2020·Plant Cell Reports·R Wambui MbichiTao Wan
Jul 18, 2018·BMC Genomics·José Luis Rodríguez LorenzoBoris Vyskot
Jul 14, 2019·BMC Plant Biology·Liuling PeiMaojun Wang
Nov 3, 2018·Ecology and Evolution·Katrin HeerStefan A Rensing
Oct 24, 2018·Frontiers in Plant Science·Katharina Bräutigam, Quentin Cronk
Jul 31, 2019·Nature Plants·Frank Johannes
Mar 8, 2020·Nature Communications·Zhengming Wang, David C Baulcombe
Dec 14, 2017·The Plant Journal : for Cell and Molecular Biology·Daniel LangStefan A Rensing
May 23, 2018·Nature Reviews. Molecular Cell Biology·Huiming ZhangJian-Kang Zhu
Mar 29, 2019·The New Phytologist·Adolfo Aguilar-CruzMario Alberto Arteaga-Vázquez
Feb 20, 2020·Proceedings of the National Academy of Sciences of the United States of America·Yinwen ZhangRobert J Schmitz
Oct 28, 2019·Essays in Biochemistry·Sunil K Kenchanmane RajuChad E Niederhuth
Oct 9, 2020·PLoS Genetics·Robert M Erdmann, Colette L Picard

Citations

Apr 29, 1997·Proceedings of the National Academy of Sciences of the United States of America·J W Stiller, B D Hall
Apr 5, 2000·Nature Biotechnology·C M McCallumSteven Henikoff
Sep 22, 2000·Plant Molecular Biology·E J Finnegan, K A Kovac
Nov 10, 2000·Science·M Lynch, J S Conery
Mar 19, 2002·Nature·James P JacksonSteven E Jacobsen
Sep 19, 2003·Nature·Charles H WellmanUzma Mohiuddin
Jan 26, 2005·Current Biology : CB·Robert K TranSteven Henikoff
May 8, 2007·Molecular Biology and Evolution·Ziheng Yang
Apr 18, 2009·Science·P SteemansCharles H Wellman
Apr 17, 2010·Science·Assaf ZemachDaniel Zilberman
Apr 17, 2010·Proceedings of the National Academy of Sciences of the United States of America·Suhua FengSteven E Jacobsen
Aug 25, 2010·The New Phytologist·C V RubinsteinP Steemans
Apr 12, 2011·Nature·Yuannian JiaoClaude W dePamphilis
Aug 5, 2011·Molecular Biology and Evolution·Shohei Takuno, Brandon S Gaut
Jan 11, 2013·Cold Spring Harbor Symposia on Quantitative Biology·S Inagaki, T Kakutani
Jan 16, 2013·Proceedings of the National Academy of Sciences of the United States of America·Shohei Takuno, Brandon S Gaut
Dec 18, 2013·Nature Structural & Molecular Biology·Hume StroudSteven E Jacobsen
Jan 24, 2014·Bioinformatics·Philip JonesSarah Hunter
Jul 16, 2014·Molecular Cell·Jiamu DuSteven E Jacobsen
Oct 31, 2014·Proceedings of the National Academy of Sciences of the United States of America·Norman J WickettJames Leebens-Mack
Dec 21, 2014·The Plant Cell·Qing LiNathan Springer
Dec 31, 2014·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Siavash MirarabTandy Warnow
Feb 19, 2015·Nature Protocols·Mark A UrichJoseph R Ecker
May 6, 2015·ELife·Adam J Bewick, Robert J Schmitz
Jun 2, 2015·Nature·Matthew D SchultzJoseph R Ecker
Aug 22, 2015·Nature Reviews. Molecular Cell Biology·Jiamu DuDinshaw J Patel
Sep 20, 2015·Proceedings of the National Academy of Sciences of the United States of America·Cody E HinchliffKaren A Cranston
Jun 2, 2016·Nature Plants·Shohei TakunoBrandon S Gaut
Jul 28, 2016·Proceedings of the National Academy of Sciences of the United States of America·Adam J BewickRobert J Schmitz
Sep 28, 2016·Genome Biology·Chad E NiederhuthRobert J Schmitz

Related Concepts

DNA Methylation [PE]
Patterns
Body Structure
Protein Methylation
Genome
Genes
KIF1B
Moniliformopses
Methylate
DNA Methylation

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Sexual Dimorphism in Neurodegeneration

There exist sex differences in neurodevelopmental and neurodegenerative disorders. For instance, multiple sclerosis is more common in women, whereas Parkinson’s disease is more common in men. Here is the latest research on sexual dimorphism in neurodegeneration

HLA Genetic Variation

HLA genetic variation has been found to confer risk for a wide variety of diseases. Identifying these associations and understanding their molecular mechanisms is ongoing and holds promise for the development of therapeutics. Find the latest research on HLA genetic variation here.

Super-resolution Microscopy

Super-resolution microscopy is the term commonly given to fluorescence microscopy techniques with resolutions that are not limited by the diffraction of light. Here are the latest discoveries pertaining to super-resolution microscopy.

Genetic Screens in iPSC-derived Brain Cells

Genetic screening is a critical tool that can be employed to define and understand gene function and interaction. This feed focuses on genetic screens conducted using induced pluripotent stem cell (iPSC)-derived brain cells.

Brain Lower Grade Glioma

Low grade gliomas in the brain form from oligodendrocytes and astrocytes and are the slowest-growing glioma in adults. Discover the latest research on these brain tumors here.

CD4/CD8 Signaling

Cluster of differentiation 4 and 8 (CD8 and CD8) are glycoproteins founds on the surface of immune cells. Here is the latest research on their role in cell signaling pathways.

Alignment-free Sequence Analysis Tools

Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences. Here is the latest research.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.