Concerted Flexibility of Chromatin Structure, Methylome, and Histone Modifications Along with Plant Stress Responses

Overview

Journal Biology (Basel)

Publisher MDPI

Specialty Biology

Date 2017 Mar 10

PMID 28275209

Citations 11

Authors

Ana Paula Santos

Liliana J Ferreira

M Margarida Oliveira

Affiliations

Soon will be listed here.

Abstract

The spatial organization of chromosome structure within the interphase nucleus, as well as the patterns of methylome and histone modifications, represent intersecting layers that influence genome accessibility and function. This review is focused on the plastic nature of chromatin structure and epigenetic marks in association to stress situations. The use of chemical compounds (epigenetic drugs) or T-DNA-mediated mutagenesis affecting epigenetic regulators (epi-mutants) are discussed as being important tools for studying the impact of deregulated epigenetic backgrounds on gene function and phenotype. The inheritability of epigenetic marks and chromatin configurations along successive generations are interpreted as a way for plants to "communicate" past experiences of stress sensing. A mechanistic understanding of chromatin and epigenetics plasticity in plant response to stress, including tissue- and genotype-specific epigenetic patterns, may help to reveal the epigenetics contributions for genome and phenotype regulation.

Citing Articles

DNA methylation: an emerging paradigm of gene regulation under drought stress in plants.

Yadav S, Meena S, Kalwan G, Jain P Mol Biol Rep. 2024; 51(1):311.

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The Roles of Calcineurin B-like Proteins in Plants under Salt Stress.

Hunpatin O, Yuan G, Nong T, Shi C, Wu X, Liu H Int J Mol Sci. 2023; 24(23).

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Plant DNA Methylation: An Epigenetic Mark in Development, Environmental Interactions, and Evolution.

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Physiological, epigenetic, and proteomic responses in Pfaffia glomerata growth in vitro under salt stress and 5-azacytidine.

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Chromatin-Based Transcriptional Reprogramming in Plants under Abiotic Stresses.

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References

Silva M, Pereira H, Bento M, Santos A, Shaw P, Delgado M . Interplay of ribosomal DNA loci in nucleolar dominance: dominant NORs are up-regulated by chromatin dynamics in the wheat-rye system. PLoS One. 2008; 3(12):e3824. PMC: 2585015. DOI: 10.1371/journal.pone.0003824. View

Kovalchuk O, Burke P, Arkhipov A, Kuchma N, James S, Kovalchuk I . Genome hypermethylation in Pinus silvestris of Chernobyl--a mechanism for radiation adaptation?. Mutat Res. 2003; 529(1-2):13-20. DOI: 10.1016/s0027-5107(03)00103-9. View

Fuchs J, Houben A, Brandes A, Schubert I . Chromosome 'painting' in plants - a feasible technique?. Chromosoma. 1996; 104(5):315-20. DOI: 10.1007/BF00337219. View

McCLINTOCK B . The significance of responses of the genome to challenge. Science. 1984; 226(4676):792-801. DOI: 10.1126/science.15739260. View

Santos A, Abranches R, Stoger E, Beven A, Viegas W, Shaw P . The architecture of interphase chromosomes and gene positioning are altered by changes in DNA methylation and histone acetylation. J Cell Sci. 2002; 115(Pt 23):4597-605. DOI: 10.1242/jcs.00160. View

Rubbi C, Milner J . Disruption of the nucleolus mediates stabilization of p53 in response to DNA damage and other stresses. EMBO J. 2003; 22(22):6068-77. PMC: 275437. DOI: 10.1093/emboj/cdg579. View

Zhang C, Wang N, Zhang Y, Feng Q, Yang C, Liu B . DNA methylation involved in proline accumulation in response to osmotic stress in rice (Oryza sativa). Genet Mol Res. 2013; 12(2):1269-77. DOI: 10.4238/2013.April.17.5. View

Daniely Y, Dimitrova D, Borowiec J . Stress-dependent nucleolin mobilization mediated by p53-nucleolin complex formation. Mol Cell Biol. 2002; 22(16):6014-22. PMC: 133981. DOI: 10.1128/MCB.22.16.6014-6022.2002. View

Rao S, Huntley M, Durand N, Stamenova E, Bochkov I, Robinson J . A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014; 159(7):1665-80. PMC: 5635824. DOI: 10.1016/j.cell.2014.11.021. View

10.

Wada Y, Miyamoto K, Kusano T, Sano H . Association between up-regulation of stress-responsive genes and hypomethylation of genomic DNA in tobacco plants. Mol Genet Genomics. 2004; 271(6):658-66. DOI: 10.1007/s00438-004-1018-4. View

11.

Tsuji H, Saika H, Tsutsumi N, Hirai A, Nakazono M . Dynamic and reversible changes in histone H3-Lys4 methylation and H3 acetylation occurring at submergence-inducible genes in rice. Plant Cell Physiol. 2006; 47(7):995-1003. DOI: 10.1093/pcp/pcj072. View

12.

Lira-Medeiros C, Parisod C, Fernandes R, Mata C, Cardoso M, Ferreira P . Epigenetic variation in mangrove plants occurring in contrasting natural environment. PLoS One. 2010; 5(4):e10326. PMC: 2859934. DOI: 10.1371/journal.pone.0010326. View

13.

Li Q, Wang X, Sun H, Zeng J, Cao Z, Li Y . Regulation of Active DNA Demethylation by a Methyl-CpG-Binding Domain Protein in Arabidopsis thaliana. PLoS Genet. 2015; 11(5):e1005210. PMC: 4416881. DOI: 10.1371/journal.pgen.1005210. View

14.

Bickmore W, van Steensel B . Genome architecture: domain organization of interphase chromosomes. Cell. 2013; 152(6):1270-84. DOI: 10.1016/j.cell.2013.02.001. View

15.

Manuelidis L, Borden J . Reproducible compartmentalization of individual chromosome domains in human CNS cells revealed by in situ hybridization and three-dimensional reconstruction. Chromosoma. 1988; 96(6):397-410. DOI: 10.1007/BF00303033. View

16.

Kim J, To T, Ishida J, Matsui A, Kimura H, Seki M . Transition of chromatin status during the process of recovery from drought stress in Arabidopsis thaliana. Plant Cell Physiol. 2012; 53(5):847-56. DOI: 10.1093/pcp/pcs053. View

17.

Elliott T, Gregory T . What's in a genome? The C-value enigma and the evolution of eukaryotic genome content. Philos Trans R Soc Lond B Biol Sci. 2015; 370(1678):20140331. PMC: 4571570. DOI: 10.1098/rstb.2014.0331. View

18.

Leitch A, Mosgoller W, Shi M, Heslop-Harrison J . Different patterns of rDNA organization at interphase in nuclei of wheat and rye. J Cell Sci. 1992; 101 ( Pt 4):751-7. DOI: 10.1242/jcs.101.4.751. View

19.

Viegas-Pequignot E, Dutrillaux B . Segmentation of human chromosomes induced by 5-ACR (5-azacytidine). Hum Genet. 1976; 34(3):247-54. DOI: 10.1007/BF00295287. View

20.

Chen L, Luo M, Wang Y, Wu K . Involvement of Arabidopsis histone deacetylase HDA6 in ABA and salt stress response. J Exp Bot. 2010; 61(12):3345-53. PMC: 2905197. DOI: 10.1093/jxb/erq154. View