Skip to main content


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.

Articles in this collection will be published throughout May and June.

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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