Literature DB >> 34526697

Epigenome plasticity in plants.

James P B Lloyd1, Ryan Lister2.   

Abstract

Plant intra-individual and inter-individual variation can be determined by the epigenome, a set of covalent modifications of DNA and chromatin that can alter genome structure and activity without changes to the genome sequence. The epigenome of plant cells is plastic, that is, it can change in response to internal or external cues, such as during development or due to environmental changes, to create a memory of such events. Ongoing advances in technologies to read and write epigenomic patterns with increasing resolution, scale and precision are enabling the extent of plant epigenome variation to be more extensively characterized and functionally interrogated. In this Review, we discuss epigenome dynamics and variation within plants during development and in response to environmental changes, including stress, as well as between plants. We review known or potential functions of such plasticity and emphasize the importance of investigating the causality of epigenomic changes. Finally, we discuss emerging technologies that may underpin future research into plant epigenome plasticity.
© 2021. Springer Nature Limited.

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Year:  2021        PMID: 34526697     DOI: 10.1038/s41576-021-00407-y

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  131 in total

1.  Genome-wide analysis of DNA methylation in soybean.

Authors:  Qing-Xin Song; Xiang Lu; Qing-Tian Li; Hui Chen; Xing-Yu Hu; Biao Ma; Wan-Ke Zhang; Shou-Yi Chen; Jin-Song Zhang
Journal:  Mol Plant       Date:  2013-08-21       Impact factor: 13.164

Review 2.  DNA methylation landscapes: provocative insights from epigenomics.

Authors:  Miho M Suzuki; Adrian Bird
Journal:  Nat Rev Genet       Date:  2008-06       Impact factor: 53.242

3.  Epigenetics, cellular memory and gene regulation.

Authors:  Steven Henikoff; John M Greally
Journal:  Curr Biol       Date:  2016-07-25       Impact factor: 10.834

Review 4.  Associating cellular epigenetic models with human phenotypes.

Authors:  Tuuli Lappalainen; John M Greally
Journal:  Nat Rev Genet       Date:  2017-05-30       Impact factor: 53.242

5.  Covering your bases: inheritance of DNA methylation in plant genomes.

Authors:  Chad E Niederhuth; Robert J Schmitz
Journal:  Mol Plant       Date:  2013-11-22       Impact factor: 13.164

6.  A simple method for gene expression and chromatin profiling of individual cell types within a tissue.

Authors:  Roger B Deal; Steven Henikoff
Journal:  Dev Cell       Date:  2010-06-15       Impact factor: 12.270

7.  Unique cell-type-specific patterns of DNA methylation in the root meristem.

Authors:  Taiji Kawakatsu; Tim Stuart; Manuel Valdes; Natalie Breakfield; Robert J Schmitz; Joseph R Nery; Mark A Urich; Xinwei Han; Ryan Lister; Philip N Benfey; Joseph R Ecker
Journal:  Nat Plants       Date:  2016-04-29       Impact factor: 15.793

8.  Cell-type-specific transcriptome and histone modification dynamics during cellular reprogramming in the Arabidopsis stomatal lineage.

Authors:  Laura R Lee; Diego L Wengier; Dominique C Bergmann
Journal:  Proc Natl Acad Sci U S A       Date:  2019-10-08       Impact factor: 11.205

9.  Plants regenerated from tissue culture contain stable epigenome changes in rice.

Authors:  Hume Stroud; Bo Ding; Stacey A Simon; Suhua Feng; Maria Bellizzi; Matteo Pellegrini; Guo-Liang Wang; Blake C Meyers; Steven E Jacobsen
Journal:  Elife       Date:  2013-03-19       Impact factor: 8.140

10.  Widespread natural variation of DNA methylation within angiosperms.

Authors:  Chad E Niederhuth; Adam J Bewick; Lexiang Ji; Magdy S Alabady; Kyung Do Kim; Qing Li; Nicholas A Rohr; Aditi Rambani; John M Burke; Joshua A Udall; Chiedozie Egesi; Jeremy Schmutz; Jane Grimwood; Scott A Jackson; Nathan M Springer; Robert J Schmitz
Journal:  Genome Biol       Date:  2016-09-27       Impact factor: 13.583

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  12 in total

Review 1.  Machine learning: its challenges and opportunities in plant system biology.

Authors:  Mohsen Hesami; Milad Alizadeh; Andrew Maxwell Phineas Jones; Davoud Torkamaneh
Journal:  Appl Microbiol Biotechnol       Date:  2022-05-16       Impact factor: 4.813

2.  Four to the floor: Active DNA demethylation defines somatic epigenetic patterns and impacts quantitative traits.

Authors:  Matthias Benoit
Journal:  Plant Cell       Date:  2022-03-29       Impact factor: 11.277

Review 3.  Omics Technology for the Promotion of Nutraceuticals and Functional Foods.

Authors:  Deepu Pandita; Anu Pandita
Journal:  Front Physiol       Date:  2022-05-13       Impact factor: 4.755

4.  An efficient chromatin immunoprecipitation (ChIP) protocol for studying histone modifications in peach reproductive tissues.

Authors:  Monica Canton; Silvia Farinati; Cristian Forestan; Justin Joseph; Claudio Bonghi; Serena Varotto
Journal:  Plant Methods       Date:  2022-03-31       Impact factor: 4.993

Review 5.  CRISPR-Cas-mediated transcriptional control and epi-mutagenesis.

Authors:  Jason Gardiner; Basudev Ghoshal; Ming Wang; Steven E Jacobsen
Journal:  Plant Physiol       Date:  2022-03-28       Impact factor: 8.340

6.  The INDEPTH (Impact of Nuclear Domains on Gene Expression and Plant Traits) Academy: a community resource for plant science.

Authors:  Christophe Tatout; Guillaume Mougeot; Geraint Parry; Célia Baroux; Mónica Pradillo; David Evans
Journal:  J Exp Bot       Date:  2022-04-05       Impact factor: 6.992

Review 7.  Epigenome and Epitranscriptome: Potential Resources for Crop Improvement.

Authors:  Quancan Hou; Xiangyuan Wan
Journal:  Int J Mol Sci       Date:  2021-11-29       Impact factor: 5.923

Review 8.  Epigenome guided crop improvement: current progress and future opportunities.

Authors:  Yan Zhang; Haylie Andrews; Judith Eglitis-Sexton; Ian Godwin; Miloš Tanurdžić; Peter A Crisp
Journal:  Emerg Top Life Sci       Date:  2022-04-15

Review 9.  Moving Beyond DNA Sequence to Improve Plant Stress Responses.

Authors:  Faisal Saeed; Usman Khalid Chaudhry; Allah Bakhsh; Ali Raza; Yasir Saeed; Abhishek Bohra; Rajeev K Varshney
Journal:  Front Genet       Date:  2022-04-19       Impact factor: 4.772

10.  Differential regulation of flower transpiration during abiotic stress in annual plants.

Authors:  Ranjita Sinha; Sara I Zandalinas; Yosef Fichman; Sidharth Sen; Shuai Zeng; Aurelio Gómez-Cadenas; Trupti Joshi; Felix B Fritschi; Ron Mittler
Journal:  New Phytol       Date:  2022-05-12       Impact factor: 10.323

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