PreprintCited by 73Epigenetics and DNA MethylationPlant Molecular Biology ResearchPlant Stress Responses and Tolerance

The DOI matches its Crossref record.

Epigenomics of Plant’s Responses to Environmental Stress

Open access
Kumar, Suresh·2017·Epigenomes

Preprint — published as 10.3390/epigenomes2010006 · Paper page

Abstract

Genome-wide epigenetic changes in plants are being reported during the development and environmental stresses, which are often correlated with gene expression at the transcriptional level. Sum total of the biochemical changes in nuclear DNA, post-translational modifications in histone proteins and variations in the biogenesis of non-coding RNAs in a cell is known as epigenome. These changes are often responsible for variation in expression of the gene without any change in the underlying nucleotide sequence. The changes might also cause variation in chromatin structure resulting into the changes in function/activity of the genome. The epigenomic changes are dynamic with respect to the endogenous and/or environmental stimuli which affect phenotypic plasticity of the organism. Both, the epigenetic changes and variation in gene expression might return to the pre-stress state soon after withdrawal of the stress. However, a part of the epigenetic changes may be retained which is reported to play role in acclimatization, adaptation as well as in the evolutionary processes. Understanding epigenome-engineering for improved stress tolerance in plants has become essential for better utilization of the genetic factors. This review delineates the importance of epigenomics towards possible improvement of plant’s responses to environmental stresses for climate resilient agriculture.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.20944/preprints201710.0185.v2

Cites

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

No references could be resolved yet.

Research works printed but not linked: 101

  1. Cantara, W.A.; Crain, P.F.; Rozenski, J.; McCloskey, J.A.; Harris, K.A.; Zhang, X.; et al. The RNA modification database, RNAMDB: Nucleic Acids Res. 2011, 39, D195-D201.
  2. Squires, J.E.; Patel, H.R.; Nousch, M.; Sibbritt, T.; Humphreys, D.T.; Parker, B.J.; et al. Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA. Nucleic Acids Res. 2012, 40, 5023-5033.
  3. Agris, P.F. Bringing order to translation: the contributions of transfer RNA anticodon- domain modifications. EMBO Rep. 2008, 9, 629-635.
  4. Motorin, Y.; Helm, M. tRNA stabilization by modified nucleotides. Biochemistry 2010, 49, 4934-44.
  5. Schaefer, M.; Pollex, T.; Hanna, K.; Tuorto, F.; Meusburger, M.; Helm, M.; Lyko, F. RNA methylation by Dnmt2 protects transfer RNAs against stress-induced cleavage. Genes Dev. 2010, 24, 1590-1595.
  6. Laland, K.; Uller, T.; Feldman, M.; Sterelny, K.; Müller, G.B.; et al. Does evolutionary theory need a rethink? Nature 2014, 514, 161-164.
  7. Ho, W.C.; Zhang, J. The genotype-phenotype map of yeast complex traits: basic parameters and the role of natural selection. Mol. Biol. Evol. 2014, 31, 1568-1580.
  8. Kumar, S. Epigenetic control of apomixis: A new perspective of an old enigma. Adv. Plants Agric. Res. 2017, 7, 00243. doi:10.15406/apar.2017.07.00243 · DOI
  9. Skinner, M.K. Environmental epigenetics and a unified theory of the molecular aspects of evolution: a neo-Lamarckian concept that facilitates neo-Darwinian evolution. Genome Biol. Evol. 2015, 7, 1296-1302.
  10. Farias, N.; Ho, N.; Butler, S.; Delaney, L.; Morrison, J.; Shahrzad, S.; et al. The effects of folic acid on global DNA methylation and colonosphere formation in colon cancer cell lines. J. Nutr. Biochem. 2015, 26, 818-26.
  11. Wan, J.; Oliver, V.F.; Wang, G.; Zhu, H.; Zack, D.J.; Merbs, S.L.; et al. Characterization of tissue-specific differential DNA methylation suggests distinct modes of positive and negative gene expression regulation. BMC Genom. 2015, 16, 49.
  12. Chen, K.; Zhang, J.; Guo, Z.; Ma, Q.; Xu, Z.; Zhou, Y.; et al. Loss of 5- hydroxymethylcytosine is linked to gene body hypermethylation in kidney cancer. Cell Res. 2016, 26, 103-118.
  13. Delgado-Morales, R.; Agís-Balboa, R.C.; Esteller, M.; Berdasco, M. Epigenetic mechanisms during ageing and neurogenesis as novel therapeutic avenues in human brain disorders. Clinical Epigenetics 2017, 9, 67. doi:10.1186/s13148-017-0365-z · DOI
  14. Behera, P. Epigenetics changes in breast cancer: current aspects in India. J Bioengineer Biomedical Sci. 2017, 7, 223. doi:10.4172/2155-9538.1000223 · DOI
  15. Kumar, S.; Beena, A.S.; Awana, M.; Singh, A. Salt-induced tissue-specific cytosine methylation downregulates expression of HKT genes in contrasting wheat (Triticum aestivum L.) genotypes. DNA Cell Biol. 2017a, 36, 283-394. doi:10.1089/dna.2016.3505. · DOI
  16. Eichten, S.R.; Schmitz, R.J.; Springer, N.M. Epigenetics: beyond chromatin modifications and complex genetic regulation. Plant Physiol. 2014, 165, 933-947. doi:10.1104/pp.113.234211 · DOI
  17. Kumar, S.; Singh, A. Epigenetic regulation of abiotic stress tolerance in plants. Adv. Plants Agric. Res. 2016, 5, 00179. doi:10.15406/apar.2016.05.00179 · DOI
  18. Avramova, Z. Transcriptional "memory" of a stress: transient chromatin and memory (epigenetic) marks at stress-response genes. Plant J. 2015, 83, 149-159.
  19. Lauria, M.; Rossi, V. Epigenetic control of gene regulation in plants. Biochim. Biophys. Acta 2011, 1809, 369-378. doi:10.1016/j.bbagrm.2011.03.002 · DOI
  20. Pikaard, C.S.; MittelstenScheid, O. Epigenetic regulation in plants. Cold Spring Harb. Perspect. Biol. 2014, 6, a019315. doi:10.1101/cshperspect.a0 19315 · DOI · Paper page
  21. Gallusci, P.; Hodgman, C.; Teyssier, E.; Seymour, G.B. DNA Methylation and chromatin regulation during fleshy fruit development and ripening. Front. Plant Sci. 2016, 7, 807. doi:10.3389/fpls.2016.00807 · DOI
  22. Allis, C.D.; Jenuwein, T. The molecular hallmarks of epigenetic control. Nat. Rev. Genet. 2016, 17, 487-500.
  23. Lanciano, S.; Mirouze, M. DNA methylation in rice and relevance for breeding. Epigenomes 2017, 1, 1-13. doi:10.3390/epigenomes1020010 · DOI
  24. Li, Y.; Kumar, S.; Qian, W. Active DNA demethylation: mechanism and role in plant development. Plant Cell Rep. 2017, doi: 10.1007/s00299-017-2215-z · DOI
  25. Springer, N.M.; Schmitz, R.J. Exploiting induced and natural epigenetic variation for crop improvement. Nat Rev Genet. 2017, doi:10.1038/nrg.2017.45 · DOI
  26. Breiling, A.; Lyko, F. Epigenetic regulatory functions of DNA modifications: 5-methylcytosine and beyond. Epigenetics Chromatin 2015, 8, 24. doi:10.1186/s13072- 015-0016-6 · DOI
  27. Jones, P.A. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet. 2012, 13, 484-492.
  28. Lister, R.; O'Malley, R.C.; Tonti-Filippini, J.; Gregory, B.D.; Berry, C.C.; Millar, A.H.; Ecker, J.R. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 2008, 133, 523-536.
  29. Wang, X.; Li, Q.; Yuan, W.; Cao, Z.; Qi, B.; Kumar, S.; Li, Y.; Qian, W. The cytosolic Fe- S cluster assembly component MET18 is required for the full enzymatic activity of ROS1 in active DNA demethylation. Sci. Rep. 2016, 6, 26443. doi:10.1038/srep26443 · DOI
  30. Slotkin, R.K.; Vaughn, M.; Borges, F.; Tanurdzic, M.; Becker, J.D.; Feijo, J.A.; Martienssen, R.A. Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 2009, 136, 461-472.
  31. Zhang, H.; Zhu, J.-K. Active DNA demethylation in plants and animals. Cold Spring Harb Symp. Quant. Biol. 2012, 77, 161-173.
  32. Law, J.A.; Jacobsen, S.E. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat. Rev. Genet. 2010, 11, 204-20.
  33. Penterman, J.; Zilberman, D.; Huh, J.H.; Ballinger, T.; Henikoff, S.; Fischer, R.L. DNA demethylation in the Arabidopsis genome. Proc. Natl. Acad. Sci. USA 2007, 104, 6752-57.
  34. Zhu, J.K. Active DNA demethylation mediated by DNA glycosylases. Annu. Rev. Genet. 2009, 43, 143-166.
  35. Hsieh, T.F.; Ibarra, C.A.; Silva, P.; Zemach, A.; Eshed-Williams, L.; Fischer, R.L.; et al. Genome-wide demethylation of Arabidopsis endosperm. Science 2009, 324, 1451-54.
  36. Steward, N.; Ito, M.; Yamachuchi, Y.; Koizumi, N.; Sano, H. Periodic DNA methylation in maize nucleosomes and demethylation by environmental stress. J. Biol. Chem. 2002, 277, 37741-746.
  37. Kou, H.P.; Li, Y.; Song, X.X.; Ou, X.F.; Xing, S.C.; Ma, J.; et al. Heritable alteration in DNA methylation induced by nitrogen-deficiency stress accompanies enhanced tolerance by progenies to the stress in rice (Oryza sativa L.). J. Plant Physiol. 2011, 168, 1685-1693. doi:10.1016/j.jplph.2011.03.017 · DOI
  38. Kumar, S.; Beena, A.S.; Awana, M.; Singh, A. Physiological, biochemical, epigenetic and molecular analyses of wheat (Triticum aestivum) genotypes with contrasting salt tolerance. Front. Plant Sci. 2017b, 8, 1-20. doi: 10.3389/fpls.2017.01151 · DOI
  39. Jullien, P.E.; Mosquna, A.; Ingouff, M.; Sakata, T.; Ohad, N.; Berger, F. Retinoblastoma and its binding partner MSI1 control imprinting in Arabidopsis. PLoS Biol 2008, 6, e194.
  40. Tahiliani, M.; Koh, K.P.; Shen, Y.; Pastor, W.A.; Bandukwala, H.; Brudno, Y.; et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science. 2009, 324, 930-935.
  41. Ito, S.; D'Alessio, A.C.; Taranova, O.V.; Hong, K.; Sowers, L.C.; Zhang, Y. Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature 2010, 466, 1129-33.
  42. Penn, N.W.; Suwalski, R.; O'Riley, C.; Bojanowski, K.; Yura, R.; The presence of 5- hydroxymethylcytosine in animal deoxyribonucleic acid. Biochem J. 1972, 126, 781-90.
  43. Kriaucionis, S.; Heintz, N. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 2009, 324, 929-930.
  44. Globisch, D.; Munzel, M.; Muller, M.; Michalakis, S.; Wagner, M.; Koch, S.; et al. Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates. PLoS One 2010, 5, e15367.
  45. He, Y.F.; Li, B.Z.; Li, Z.; Liu, P.; Wang, Y.; Tang, Q.; et al. Tet-mediated formation of 5- carboxylcytosine and its excision by TDG in mammalian DNA. Science 2011, 333, 1303- 1307.
  46. Ito, S.; Shen, L.; Dai, Q.; Wu, S.C.; Collins, L.B.; Swenberg, J.A.; et al. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 2011a, 333, 1300-3.
  47. Erdmann, R.M.; Souza, A.L.; Clish, C.B.; Gehring, M. 5-Hydroxymethylcytosine is not present in appreciable quantities in Arabidopsis DNA. Genes Genome Genetics 2015, 5, 1-8. doi:10.1534/g3.114.014670 · DOI
  48. Casadesus, J.; Low, D. Epigenetic gene regulation in the bacterial world. Microbiol. Mol. Biol. Rev. 2006, 70, 830-56.
  49. Ratel, D.; Ravanat, J.L.; Berger, F.; Wion, D. N6-methyladenine: the other methylated base of DNA. BioEssays 2006, 28, 309-315.
  50. Greer, E.L.; Blanco, M.A.; Gu, L.; Sendinc, E.; Liu, J.; Aristizabal-Corrales, D.; et al. DNA Methylation on N-Adenine in C. elegans. Cell 2015, 161, 868-78.
  51. Zhang, G.; Huang, H.; Liu, D.; Cheng, Y.; Liu, X.; Zhang, W.; et al. N-methyladenine DNA modification in Drosophila. Cell 2015, 161, 893-906.
  52. Fu, Y.; Luo, G.Z.; Chen, K.; Deng, X.; Yu, M.; Han, D. et al. N-Methyldeoxyadenosine marks active transcription start sites in Chlamydomonas. Cell 2015, 161, 879-892.
  53. Huang, W.; Xiong, J.; Yang, Y.; Liu, S.M.; Yuan, B.F.; Feng, Y.Q. Determination of DNA adenine methylation in genomes of mammals and plants by liquid chromatography/mass spectrometry. Royal Society Chem. Adv. 2015, 5, 64046-54.
  54. Bartholomew, B. Regulating the chromatin landscape: structural and mechanistic perspectives. Annu. Rev. Biochem. 2014, 83, 671-696.
  55. Spruijt, C.G.; Vermeulen, M. DNA methylation: old dog, new tricks? Nat. Struct. Mol. Biol. 2014, 21, 949-954.
  56. Baubec, T.; Colombo, D.F.; Wirbelauer, C.; Schmidt, J.; Burger, L.; Krebs, A.R.; et al. Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation. Nature 2015, 520, 243-247.
  57. Bhaumik, S.R.; Smith, E.; Shilatifard, A. Covalent modifications of histones during development and disease pathogenesis. Nat. Struct. Mol. Biol. 2007, 14, 1008-1016.
  58. Benayoun, B.A.; Pollina, E.A.; Brunet, A. Epigenetic regulation of ageing: linking environmental inputs to genomic stability. Nat. Rev. Mol. Cell Biol. 2015, 16, 593-610.
  59. Seong, K.H.; Li, D.; Shimizu, H.; Nakamura, R.; Ishii, S. Inheritance of stress-induced, ATF-2-dependent epigenetic change. Cell 2011, 145, 1049-1061.
  60. Zemach, A.; Kim, M.Y.; Silva, P.; Rodrigues, J.A.; Dotson, B.; et al. Local DNA hypomethylation activates genes in rice endosperm. Proc. Natl. Acad. Sci. USA 2010, 107, 18729-734.
  61. Zilberman, D.; Gehring, M.; Tran, R.K.; Ballinger, T.; Henikoff, S. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat. Genet. 2007, 39, 61-69. doi:10.1038/ng1929 · DOI
  62. Earley, K.; Lawrence, R.J.; Pontes, O.; Reuther, R.; Enciso, A.J.; Silva, M.; et al. Erasure of histone acetylation by Arabidopsis HDA6 mediates large-scale gene silencing in nucleolar dominance. Genes Dev. 2006, 20, 1283-1293
  63. Rossi, V.; Locatelli, S.; Varotto, S.; Donn, G.; Pirona, R.; Henderson, D.A.; Hartings, H.; Motto, M. Maize histone deacetylase hda101 is involved in plant development, gene transcription, and sequence-specific modulation of histone modification of genes and repeats. Plant Cell. 2007, 19, 1145-1162.
  64. Chinnusamy, V.; Zhu, J.K. Epigenetic regulation of stress responses in plants. Curr. Opin. Plant Biol. 2009, 12, 133-139.
  65. Millar, C.B.; Grunstein, M. Genome-wide p patterns of histone modifications in yeast. Nat. Rev. Mol. Cell Biol. 2006, 7, 657-666.
  66. Shlyueva, D.; Stampfel, G.; Stark, A. Transcriptional enhancers: from properties to genome-wide predictions. Nat Rev Genet. 2014, 15, 272-86.
  67. Sims, III, R.J.; Nishioka, K.; Reinberg, D. Histone lysine methylation: A signature for chromatin function. Trends Genet. 2003, 19, 629-639.
  68. Kouzarides, T. Chromatin modifications and their function. Cell 2007, 128, 693-705.
  69. Pandey, R.; Muller, A.; Napoli, C.A.; Selinger, D.A.; Pikaard, C.S.; Richards, E.J.; et al. Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes. Nucleic Acids Res. 2002, 30, 5036-5055.
  70. Pontvianne, F.; Blevins, T.; Pikaard, C.S. Arabidopsis histone lysine methyltransferases. Adv. Bot. Res. 2010, 53, 1-22. doi: 10.1016/S0065-2296(10)53001-5 · DOI
  71. Zhang, K.; Sridhar, V.V.; Zhu, J.; Kapoor, A.; Zhu, J.-K. Distinctive core histone post- translational modification patterns in Arabidopsis thaliana. PLoS ONE 2007, 2, e1210. doi:10.1371/journal.pone.0001210 · DOI
  72. Camporeale, G.; Oommen, A.M.; Griffin, J.B.; Sarath, G.; Zempleni, J. K12-biotinylated histone H4 marks heterochromatin in human lymphoblastoma cells. J. Nutr. Biochem. 2007, 18, 760-768.
  73. Sani, E.; Herzyk, P.; Perrella, G.; Colot, V.; Amtmann, A. Hyperosmotic priming of Arabidopsis seedlings establishes a long-term somatic memory accompanied by specific changes of the epigenome. Genome Biol. 2013, 14, R59.
  74. Wang, Z.; Casas-Mollano, J.A.; Xu, J.; Riethoven, J.-J.M.; Zhang, C.; Cerutti, H. Osmotic stress induces phosphorylation of histone H3 at threonine 3 in pericentromeric regions of Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 2015, 112, 8487-8492.
  75. Zheng, Y.; Ding, Y.; Sun, X.; Xie, S.; Wang, D.; Liu, X.; et al. Histone deacetylase HDA9 negatively regulates salt and drought stress responsiveness in Arabidopsis. J. Exp. Bot. 2016, 67, 1703-713. doi:10.1093/jxb/erv562 · DOI
  76. Borsani, O.; Zhu, J.; Verslues, P.E.; Sunkar, R.; Zhu, J.K. Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 2005, 123, 1279-1291.
  77. Fang, H.; Liu, X.; Thorn, G.; Duan, J.; Tian L. Biochemical and biophysical research communications expression analysis of histone acetyltransferases in rice under drought stress. Biochem. Biophys. Res. Commun. 2014, 443, 400-405. doi:10.1016/j.bbrc.2013.11.102 · DOI
  78. Li, Q.; Eichten, S.R.; Hermanson, P.J.; Zaunbrecher, V.M.; Song, J.; Wendt, J.; et al. Genetic perturbation of the maize methylome. Plant Cell 2014, 26, 4602-16.
  79. Su, L.-C.; Deng, B.; Liu, S.; Li, L.-M.; Hu, B.; Zhong, Y.-T.; et al. Isolation and characterization of an osmotic stress and ABA induced histone deacetylase in Arachis hypogaea. Front. Plant Sci. 2015, 6, 512. doi:10.3389/fpls.2015.00512 · DOI
  80. 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, 3345-3353. doi:10.1093/jxb/erq154 · DOI
  81. Luo, M.; Liu, X.; Singh, P.; Cui, Y.; Zimmerli, L.; Wu, K. Chromatin modifications and remodeling in plant abiotic stress responses. Biochim. Biophys. Acta 2012, 1819, 129-136. doi:10.1016/j.bbagrm.2011.06.008 · DOI
  82. González, R.M.; Ricardi, M.M.; Iusem, N.D. Epigenetic marks in an adaptive water stress- responsive gene in tomato roots under normal and drought conditions. Epigenetics 2013, 8, 864-872. doi:10.4161/epi.25524 · DOI
  83. Bocchini, M.; Bartucca, M.L.; Ciancaleoni, S.; Mimmo, T.; Cesco. S.; Pii, Y.; et al. Iron deficiency in barley plants: phytosiderophore release, iron translocation, and DNA methylation. Front. Plant Sci. 2015, 6, 514. doi:10.3389/fpls.2015.00514 · DOI
  84. Kim, J.-M.; Sasaki, T.; Ueda, M.; Sako, K.; Seki, M. Chromatin changes in response to drought, salinity, heat, and cold stresses in plants. Front. Plant Sci. 2015, 6, 114. doi:10.3389/fpls.2015.00114 · DOI
  85. Liu, R.; How-Kit, A.; Stammitti, L.; Teyssier, E.; Rolin, D.; Mortain-Bertrand, A.; et al. A DEMETER-like DNA demethylase governs tomato fruit ripening. Proc. Natl Acad. Sci. USA 2015, 112, 10804-09.
  86. Dijk, K.; Van Ding, Y.; Malkaram, S.; Riethoven, J.M.; Liu, R.; Yang, J.; et al. Dynamic changes in genome-wide histone H3 lysine 4 methylation patterns in response to dehydration stress in Arabidopsis thaliana. BMC Plant Biol. 2010, 10, 238. doi:10.1186/1471-2229-10-238 · DOI
  87. Zong, W.; Zhong, X.; You, J.; Xiong, L. Genome-wide profiling of histone H3K4-tri- methylation and gene expression in rice under drought stress. Plant Mol. Biol. 2013, 81, 175-188. doi:10.1007/s11103-012-9990-2 · DOI
  88. Widiez, T.; Symeonidi, A.; Luo, C.; Lam, E.; Lawton, M.; Rensing, S.A. The chromatin landscape of the moss Physcomitrella patens and its dynamics during development and drought stress. Plant J. 2014, 79, 67-81. doi:10.1111/tpj.12542 · DOI
  89. Maxwell, P.H.; Burhans, W.C.; Curcio, M.J. Retrotransposition is associated with genome instability during chronological aging. Proc. Natl Acad. Sci. USA 2011, 108, 20376-20381.
  90. Ito, H.; Gaubert, H.; Bucher, E.; Mirouze, M.; Vaillant, I.; Paszkowski, J. An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress. Nature 2011b, 472, 115-119.
  91. Verhoeven, K.J.F.; VanGurp, T.P.; Transgenerational effects of stress exposure on offspring phenotypes in apomictic dandelion. PloS One 2012, 7, e38605.
  92. Pellegrini, M.; Wang, G.; Meyers, B.C.; Fellowship, D.Y. Plants regenerated from tissue culture contain stable epigenome changes in rice. eLife 2013, 2, e00354.
  93. Luna, E.; Bruce, T.J.A.; Roberts, M.R.; Flors, V.; Ton, J. Next-generation systemic acquired resistance. Plant Physiol. 2012, 158, 844-853.
  94. Luna, E.; Ton, J. The epigenetic machinery controlling transgenerational systemic acquired resistance. Plant Signal. Behav. 2012, 7, 615-618.
  95. Becker, C.; Hagmann, J.; Müller, J.; Koenig, D.; Stegle, O.; Borgwardt, K.; Weigel, D. Spontaneous epigenetic variation in the Arabidopsis thaliana methylome. Nature 2011, 480, 245-249. doi: 10.1038/nature10555 · DOI
  96. Schmitz, R.J.; Schultz, M.D.; Lewsey, M.G.; O'Malley, R.C.; Urich, M.A.; Libiger, O.; Schork, N.J.; Ecker, J.R. Transgenerational epigenetic instability is a source of novel methylation variants. Science 2011, 334, 369-373. doi: 10.1126/science.1212959 · DOI
  97. Havecker, E.R.; Wallbridge, L.M.; Fedito, P.; Hardcastle, T.J.; Baulcombe, D.C. Metastable differentially methylated regions within Arabidopsis inbred populations are associated with modified expression of non-coding transcripts. PloS One 2012, 7, e45242.
  98. Ni, Z.; Kim, E.D.; Ha, M.; Lackey, E.; Liu, J.; Zhang, Y.; et al. Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids. Nature 2009, 457, 327-331.
  99. Shivaprasad, P.V.; Dunn, R.M.; Santos, B.A.; Bassett, A.; Baulcombe, D.C. Extraordinary transgressive phenotypes of hybrid tomato are influenced by epigenetics and small silencing RNAs. EMBO J. 2012, 31, 257-266. 100. Zheng, X.; Chen, L.; Xia, H.; Wei, H.; Lou, Q.; Li, M.; Li, T.; Luo, L. Transgenerational epimutations induced by multi-generation drought imposition mediate rice plant's adaptation to drought condition. Sci. Rep. 2017, 7, 39843. doi: 10.1038/srep39843 101. · DOI
  100. Richards, E.J. Inherited epigenetic variation -revisiting soft inheritance. Nat. Rev. Genet. 2006, 7, 395-401. 102. Hauben, M.; Haesendonckx, B.; Standaert, E.; Kelen, K.; VanDerAzmi, A.; Breusegem, F.; et al. Energy use efficiency is characterized by an epigenetic component that can be directed. Proc. Natl. Acad. Sci. USA 2009, 106, 20109-20114. doi:10.1073/pnas.0908755106 103. Buck-Koehntop, B.A.; Defossez, P.A. On how mammalian transcription factors recognize methylated DNA. Epigenetics 2013, 8, 131-137. 104. Cong, L.; Ran, F.A.; Cox, D.; Lin, S.; Barretto, R.; Habib, N.; et al. Multiplex genome engineering using CRISPR/Cas systems. Science 2013, 339, 819-823. 105. Xu, X.; Tao, Y.; Gao, X.; Zhang, L.; Li, X.; Zou, W.; Ruan, K.; Wang, F.; Xu, G.; Hu, R. A CRISPR-based approach for targeted DNA demethylation. Cell Discovery 2016, 2, 1600. 106. Kumar, S.; Arul, L.; Talwar, D.; Raina, S.K. PCR amplification of minimal gene expression cassette: an alternative, low cost and easy approach to 'clean DNA' transformation. Curr. Sci. 2006, 91, 930-934. 107. Kumar, S.; Chandra, A.; Pandey, K.C. Bacillus thuringiensis (Bt) transgenic crop: An environment friendly insect-pest management strategy. J. Environ. Biol. 2008, 29, 641- 653. 108. · DOI
  101. Stricker, S.H.; Köferle, A.; Beck, S. From profiles to function in epigenomics. Nat. Rev. Genet. 2017, 18, 51-66. doi:10.1038/nrg.2016.138 · DOI

Cited by

Sorted by citations

See all 73

Metadata

Authors
Kumar, S.
Affiliations
Indian Agricultural Research Institute (IN)
Corresponding author
Kumar, Suresh
Venue
Epigenomes
Publisher
MDPI AG
Published
2017-11-23
Volume
2
Issue
1
Pages
6-6
ISSN
2075-4655 (ISSN-L)
OpenAlex
W2791555312
Cited by
73
References
0
Citations by year
2026: 6 · 2025: 9 · 2024: 8 · 2023: 6 · 2022: 8 · 2021: 8 · 2020: 14 · 2019: 11 · 2018: 3
FWCI
3.20
Type
journal article
Language
en
Open access
Locations
  • Epigenomes (publishedVersion, cc-by)
  • Preprints.org (acceptedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Molecular Biology Research
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Stress Responses and Tolerance
Keywords
environmental stress, histone modifications, chromatin structure, phenotypic plasticity, stress memory, acclimatization, stress tolerance, climate-resilient agriculture

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

How to cite

Cite CoChat for the checks on this page, and the paper for its own findings.

This page
CoChat. (2026). Citation check: Epigenomics of Plant’s Responses to Environmental Stress. https://app.cochat.ai/papers/10.20944/preprints201710.0185.v2
The paper
Kumar, S. (2017). Epigenomics of Plant’s Responses to Environmental Stress. Epigenomes. https://doi.org/10.20944/preprints201710.0185.v2