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Plant Epigenomics

Guest Editors: Nathan Springer and Claudia Köhler

Epigenetic modifications contribute to phenotypic variation at multiple levels, from gene regulation, to development, stress response, and population-level phenotypic diversity and evolution. As sessile organisms, plants are particularly dependent on epigenetic mechanisms to express diverse phenotypic responses from the same genome sequence. Technological advances that allow genome-wide analysis of DNA or histone modifications coupled with new opportunities for editing the epigenome have the potential to reveal the functions of epigenetic regulation in plants. Here, Genome Biology highlights advances in our understanding of the functions of epigenetic modifications, and the application of this knowledge.

Comment

EDITORIAL
Plant epigenomics—deciphering the mechanisms of epigenetic inheritance and plasticity in plants
Claudia Köhler and Nathan Springer

Genome Biology 2017 18:132
Published on: 6 July 2017

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COMMENT
An evolutionary case for functional gene body methylation in plants and animals
Methylation in the bodies of active genes is common in animals and vascular plants. Evolutionary patterns indicate homeostatic functions for this type of methylation.
Daniel Zilberman

Genome Biology 2017 18:87
Published on: 9 May 2017

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RESEARCH HIGHLIGHT
Epigenomics: dissecting hybridization and polyploidization
Epigenetic profiling in diploid, allopolyploid, and domesticated cotton shows that despite most DNA methylation being conserved and stably inherited, alterations likely due to hybridization and domestication a...
Scott A. Jackson

Genome Biology 2017 18:117
Published on: 19 June 2017

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RESEARCH HIGHLIGHT
Chromatin marks and ambient temperature-dependent flowering strike up a novel liaison
A distinct chromatin mark, H3K36me3, has been found to engage in temperature-dependent alternative splicing and ambient temperature-dependent flowering-time control in Arabidopsis.
Alexander Steffen and Dorothee Staiger

Genome Biology 2017 18:119
Published on: 19 June 2017

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RESEARCH HIGHLIGHT
Unreeling the chromatin thread: a genomic perspective on organization around the periphery of the Arabidopsis nucleus
The first genome-wide examination of the chromatin landscape at the periphery of the plant cell nucleus reveals substantial enrichment of heterochromatin and Polycomb-based repressive chromatin.
Fredy Barneche and Celia Baroux

Genome Biology 2017 18:97
Published on: 23 May 2017

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Review

REVIEW
Epigenetic and chromatin-based mechanisms in environmental stress adaptation and stress memory in plants
Plants frequently have to weather both biotic and abiotic stressors, and have evolved sophisticated adaptation and defense mechanisms. In recent years, chromatin modifications, nucleosome positioning, and DNA ...
Jörn Lämke and Isabel Bäurle

Genome Biology 2017 18:124
Published on: 27 June 2017

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REVIEW
Emerging roles of chromatin in the maintenance of genome organization and function in plants
Chromatin is not a uniform macromolecular entity; it contains different domains characterized by complex signatures of DNA and histone modifications. Such domains are organized both at a linear scale along the...
Zaida Vergara and Crisanto Gutierrez

Genome Biology 2017 18:96
Published on: 23 May 2017

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REVIEW
Developmental transitions: integrating environmental cues with hormonal signaling in the chromatin landscape in plants
Plant development is predominantly postembryonic and tuned in to respond to environmental cues. All living plant cells can be triggered to de-differentiate, assume different cell identities, or form a new orga...
Jun Xiao, Run Jin and Doris Wagner

Genome Biology 2017 18:88
Published on: 10 May 2017

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REVIEW
Methylome evolution in plants
Despite major progress in dissecting the molecular pathways that control DNA methylation patterns in plants, little is known about the mechanisms that shape plant methylomes over evolutionary time. Drawing on ...
Amaryllis Vidalis, Daniel Živković, René Wardenaar, David Roquis, Aurélien Tellier and Frank Johannes

Genome Biology 2016 17:264
Published on: 20 December 2016
The Erratum to this article has been published in Genome Biology 2017 18:41

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Research

RESEARCH
DNA methylation dynamics during early plant life
Cytosine methylation is crucial for gene regulation and silencing of transposable elements in mammals and plants. While this epigenetic mark is extensively reprogrammed in the germline and early embryos of mam...
Daniel Bouyer, Amira Kramdi, Mohamed Kassam, Maren Heese, Arp Schnittger, François Roudier and Vincent Colot

Genome Biology 2017 18:179
Published on: 25 September 2017

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RESEARCH

Dynamic DNA methylation reconfiguration during seed development and germination
Unlike animals, plants can pause their life cycle as dormant seeds. In both plants and animals, DNA methylation is involved in the regulation of gene expression and genome integrity. In animals, reprogramming ...
Taiji Kawakatsu, Joseph R. Nery, Rosa Castanon and Joseph R. Ecker

Genome Biology 2017 18:171
Published on: 15 September 2017

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RESEARCH
Extensive transcriptomic and epigenomic remodelling occurs during Arabidopsis thaliana germination
Seed germination involves progression from complete metabolic dormancy to a highly active, growing seedling. Many factors regulate germination and these interact extensively, forming a complex network of input...
Reena Narsai, Quentin Gouil, David Secco, Akanksha Srivastava, Yuliya V. Karpievitch, Lim Chee Liew, Ryan Lister, Mathew G. Lewsey and James Whelan

Genome Biology 2017 18:172
Published on: 15 September 2017

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RESEARCH
Conservation and divergence of small RNA pathways and microRNAs in land plants
As key regulators of gene expression in eukaryotes, small RNAs have been characterized in many seed plants, and pathways for their biogenesis, degradation, and action have been defined in model angiosperms. Ho...
Chenjiang You, Jie Cui, Hui Wang, Xinping Qi, Li-Yaung Kuo, Hong Ma, Lei Gao, Beixin Mo and Xuemei Chen

Genome Biology 2017 18:158
Published on: 23 August 2017

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RESEARCH
Altered chromatin compaction and histone methylation drive non-additive gene expression in an interspecific Arabidopsis hybrid
The merging of two diverged genomes can result in hybrid offspring that phenotypically differ greatly from both parents. In plants, interspecific hybridization plays important roles in evolution and speciation...
Wangsheng Zhu, Bo Hu, Claude Becker, Ezgi Süheyla Doğan, Kenneth Wayne Berendzen, Detlef Weigel and Chang Liu

Genome Biology 2017 18:157
Published on: 22 August 2017

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RESEARCH
Stable inheritance of DNA methylation allows creation of epigenotype maps and the study of epiallele inheritance patterns in the absence of genetic variation
Differences in DNA methylation can arise as epialleles, which are loci that differ in chromatin state and are inherited over generations. Epialleles offer an additional source of variation that can affect phen...
Brigitte T. Hofmeister, Kevin Lee, Nicholas A. Rohr, David W. Hall and Robert J. Schmitz

Genome Biology 2017 18:155
Published on: 16 August 2017

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RESEARCH
Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize
While most cells in multicellular organisms carry the same genetic information, in each cell type only a subset of genes is being transcribed. Such differentiation in gene expression depends, for a large part,...
Rurika Oka, Johan Zicola, Blaise Weber, Sarah N. Anderson, Charlie Hodgman, Jonathan I. Gent, Jan-Jaap Wesselink, Nathan M. Springer, Huub C. J. Hoefsloot, Franziska Turck and Maike Stam

Genome Biology 2017 18:137
Published on: 21 July 2017

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RESEARCH
Inhibition of RNA polymerase II allows controlled mobilisation of retrotransposons for plant breeding
Retrotransposons play a central role in plant evolution and could be a powerful endogenous source of genetic and epigenetic variability for crop breeding. To ensure genome integrity several silencing mechanism...
Michael Thieme, Sophie Lanciano, Sandrine Balzergue, Nicolas Daccord, Marie Mirouze and Etienne Bucher

Genome Biology 2017 18:134
Published on: 7 July 2017

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RESEARCH
MAPK-triggered chromatin reprogramming by histone deacetylase in plant innate immunity
Microbial-associated molecular patterns activate several MAP kinases, which are major regulators of the innate immune response in Arabidopsis thaliana that induce large-scale changes in gene expression. Here, we ...
David Latrasse, Teddy Jégu, Huchen Li, Axel de Zelicourt, Cécile Raynaud, Stéphanie Legras, Andrea Gust, Olga Samajova, Alaguraj Veluchamy, Naganand Rayapuram, Juan Sebastian Ramirez-Prado, Olga Kulikova, Jean Colcombet, Jean Bigeard, Baptiste Genot, Ton Bisseling…

Genome Biology 2017 18:131
Published on: 6 July 2017

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RESEARCH
Stable centromere positioning in diverse sequence contexts of complex and satellite centromeres of maize and wild relatives
Paradoxically, centromeres are known both for their characteristic repeat sequences (satellite DNA) and for being epigenetically defined. Maize (Zea mays mays) is an attractive model for studying centromere posit...
Jonathan I. Gent, Na Wang and R. Kelly Dawe

Genome Biology 2017 18:121
Published on: 21 June 2017

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RESEARCH
The Arabidopsis SWI/SNF protein BAF60 mediates seedling growth control by modulating DNA accessibility
Plant adaptive responses to changing environments involve complex molecular interplays between intrinsic and external signals. Whilst much is known on the signaling components mediating diurnal, light, and tem...
Teddy Jégu, Alaguraj Veluchamy, Juan S. Ramirez-Prado, Charley Rizzi-Paillet, Magalie Perez, Anaïs Lhomme, David Latrasse, Emeline Coleno, Serge Vicaire, Stéphanie Legras, Bernard Jost, Martin Rougée, Fredy Barneche, Catherine Bergounioux, Martin Crespi, Magdy M. Mahfouz…

Genome Biology 2017 18:114
Published on: 15 June 2017

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RESEARCH
Histone H3 lysine 36 methylation affects temperature-induced alternative splicing and flowering in plants
Global warming severely affects flowering time and reproductive success of plants. Alternative splicing of pre-messenger RNA (mRNA) is an important mechanism underlying ambient temperature-controlled responses...
Pajoro, E. Severing, G. C. Angenent and R. G. H. Immink

Genome Biology 2017 18:102
Published on: 1 June 2017

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RESEARCH
The developmental regulator PKL is required to maintain correct DNA methylation patterns at RNA-directed DNA methylation loci
The chromodomain helicase DNA-binding family of ATP-dependent chromatin remodeling factors play essential roles during eukaryote growth and development. They are recruited by specific transcription factors and...
Rong Yang, Zhimin Zheng, Qing Chen, Lan Yang, Huan Huang, Daisuke Miki, Wenwu Wu, Liang Zeng, Jun Liu, Jin-Xing Zhou, Joe Ogas, Jian-Kang Zhu, Xin-Jian He and Heng Zhang

Genome Biology 2017 18:103
Published on: 31 May 2017

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RESEARCH
Epigenomic and functional analyses reveal roles of epialleles in the loss of photoperiod sensitivity during domestication of allotetraploid cottons
Polyploidy is a pervasive evolutionary feature of all flowering plants and some animals, leading to genetic and epigenetic changes that affect gene expression and morphology. DNA methylation changes can produc...
Qingxin Song, Tianzhen Zhang, David M. Stelly and Z. Jeffrey Chen

Genome Biology 2017 18:99
Published on: 31 May 2017

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RESEARCH
The histone H3 variant H3.3 regulates gene body DNA methylation in Arabidopsis thaliana
Gene bodies of vertebrates and flowering plants are occupied by the histone variant H3.3 and DNA methylation. The origin and significance of these profiles remain largely unknown. DNA methylation and H3.3 enri...
Heike Wollmann, Hume Stroud, Ramesh Yelagandula, Yoshiaki Tarutani, Danhua Jiang, Li Jing, Bhagyshree Jamge, Hidenori Takeuchi, Sarah Holec, Xin Nie, Tetsuji Kakutani, Steven E. Jacobsen and Frédéric Berger

Genome Biology 2017 18:94
Published on: 18 May 2017

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SOFTWARE
EpiTEome: Simultaneous detection of transposable element insertion sites and their DNA methylation levels
The genome-wide investigation of DNA methylation levels has been limited to reference transposable element positions. The methylation analysis of non-reference and mobile transposable elements has only recentl...
Josquin Daron and R. Keith Slotkin

Genome Biology 2017 18:91
Published on: 12 May 2017

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RESEARCH
Epistatic and allelic interactions control expression of ribosomal RNA gene clusters in Arabidopsis thaliana
Ribosomal RNA (rRNA) accounts for the majority of the RNA in eukaryotic cells, and is encoded by hundreds to thousands of nearly identical gene copies, only a subset of which are active at any given time. In Arab...
Fernando A. Rabanal, Terezie Mandáková, Luz M. Soto-Jiménez, Robert Greenhalgh, David L. Parrott, Stefan Lutzmayer, Joshua G. Steffen, Viktoria Nizhynska, Richard Mott, Martin A. Lysak, Richard M. Clark and Magnus Nordborg

Genome Biology 2017 18:75
Published on: 3 May 2017

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RESEARCH
The evolution of CHROMOMETHYLASES and gene body DNA methylation in plants
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 Viridipl...
Adam J. Bewick, Chad E. Niederhuth, Lexiang Ji, Nicholas A. Rohr, Patrick T. Griffin, Jim Leebens-Mack and Robert J. Schmitz

Genome Biology 2017 18:65
Published on: 1 May 2017

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RESEARCH
Proximal methylation features associated with nonrandom changes in gene body methylation
Gene body methylation at CG dinucleotides is a widely conserved feature of methylated genomes but remains poorly understood. The Arabidopsis thaliana strain Cvi has depleted gene body methylation relative to the ...
Colette L. Picard and Mary Gehring

Genome Biology 2017 18:73
Published on: 26 April 2017

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RESEARCH
H2A monoubiquitination in Arabidopsis thaliana is generally independent of LHP1 and PRC2 activity
Polycomb group complexes PRC1 and PRC2 repress gene expression at the chromatin level in eukaryotes. The classic recruitment model of Polycomb group complexes in which PRC2-mediated H3K27 trimethylation recrui...
Yue Zhou, Francisco J. Romero-Campero, Ángeles Gómez-Zambrano, Franziska Turck and Myriam Calonje

Genome Biology 2017 18:69
Published on: 12 April 2017

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