Strahl BD, Allis CD. The language of covalent histone modifications. Nature. 2000;403(6765):41.
Article
CAS
PubMed
Google Scholar
Donà M, Mittelsten SO. DNA damage repair in the context of plant chromatin. Plant Physiol. 2015;168(4):1206.
Article
PubMed
PubMed Central
Google Scholar
Sulli G, Di MR. D'Adda dFF: crosstalk between chromatin state and DNA damage response in cellular senescence and cancer. Nat Rev Cancer. 2012;12(10):709–20.
Article
CAS
PubMed
Google Scholar
Miller KM, Jackson SP. Histone marks: repairing DNA breaks within the context of chromatin. Biochem Soc Trans. 2012;40(2):370–6.
Article
CAS
PubMed
Google Scholar
Kouzarides T. Chromatin modifications and their function. Cell. 2007;128(4):693.
Article
CAS
PubMed
Google Scholar
Wurtele H, Verreault A. Histone post-translational modifications and the response to DNA double-strand breaks. Curr Opin Cell Biol. 2006;18(2):137–44.
Article
CAS
PubMed
Google Scholar
Altaf M, Saksouk N, Côté J. Histone modifications in response to DNA damage. Mutation Research/fundamental & Molecular Mechanisms of. Mutagenesis. 2007;618(1–2):81–90.
CAS
Google Scholar
Downs JA, Lowndes NF, Jackson SP. A role for Saccharomyces Cerevisiae histone H2A in DNA repair. Nature. 2000;408(6815):1001–4.
Article
CAS
PubMed
Google Scholar
Rogakou EP, Pilch DR, Orr AH, Ivanova VS, Bonner WM. DNA double-stranded breaks induce histone H2AX phosphorylation on serine 139. J Biol Chem. 1998;273(10):5858–68.
Article
CAS
PubMed
Google Scholar
Downs JA, Allard S, Jobin-Robitaille O, Javaheri A, Auger A, Bouchard N, Kron SJ, Jackson SP, Côté J. Binding of chromatin-modifying activities to phosphorylated histone H2A at DNA damage sites. Mol Cell. 2004;16(6):979–90.
Article
CAS
PubMed
Google Scholar
Shroff R, Arbeleden A, Pilch D, Ira G, Bonner WM, Petrini JH, Haber JE, Lichten M. Distribution and dynamics of chromatin modification induced by a defined DNA double-strand break. Current Biology Cb. 2004;14(19):1703–11.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tjeertes JV, Miller KM, Jackson SP. Screen for DNA-damage-responsive histone modifications identifies H3K9Ac and H3K56Ac in human cells. EMBO J. 2009, 1878;28(13)
Huyen Y, Zgheib O, Jr DR, Gorgoulis VG, Zacharatos P, Petty TJ, Sheston EA, Mellert HS, Stavridi ES, Halazonetis TD. Methylated lysine 79 of histone H3 targets 53BP1 to DNA double-strand breaks. Nature. 2004;432(7015):406–11.
Article
CAS
PubMed
Google Scholar
Sanders SL, Portoso M, Mata J, Bähler J, Allshire RC, Kouzarides T. Methylation of histone H4 lysine 20 controls recruitment of Crb2 to sites of DNA damage. Cell. 2004;119(5):603–14.
Article
CAS
PubMed
Google Scholar
Manova V, Gruszka D. DNA damage and repair in plants – from models to crops. Front Plant Sci. 2015;6:885.
Article
PubMed
PubMed Central
Google Scholar
Braszewska-Zalewska A, Tylikowska M, Kwasniewska J, Szymanowska-Pulka J. Epigenetic chromatin modifications in barley after mutagenic treatment. J Appl Genet. 2014;55(4):449.
Article
CAS
PubMed
PubMed Central
Google Scholar
Drury GE, Dowle AA, Ashford DA, Waterworth WM, Thomas J, West CE. Dynamics of plant histone modifications in response to DNA damage. Biochem J. 2012;445(3):393–401.
Article
CAS
PubMed
Google Scholar
Amiard S, Charbonnel C, Allain E, Depeiges A, White CI, Gallego ME. Distinct roles of the ATR kinase and the Mre11-Rad50-Nbs1 complex in the maintenance of chromosomal stability in Arabidopsis. Plant Cell. 2010;22(9):3020–33.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lang J, Smetana O, Sanchez-Calderon L, Lincker F, Genestier J, Schmit AC, Houlne G, Chaboute ME. Plant gammaH2AX foci are required for proper DNA DSB repair responses and colocalize with E2F factors. New Phytol. 2012;194(2):353–63.
Article
CAS
PubMed
Google Scholar
Mah LJ, El-Osta A, Karagiannis TC. gammaH2AX: a sensitive molecular marker of DNA damage and repair. Leukemia. 2010;24(4):679–86.
Article
CAS
PubMed
Google Scholar
Sharma A, Singh K, Almasan A. Histone H2AX phosphorylation: a marker for DNA damage. Methods Mol Biol. 2012;920:613–26.
Article
CAS
PubMed
Google Scholar
van Attikum H, Gasser SM. The histone code at DNA breaks: a guide to repair? Nat Rev Mol Cell Biol. 2005;6(10):757–65.
Article
CAS
PubMed
Google Scholar
Karlic R, Chung HR, Lasserre J, Vlahovicek K, Vingron M. Histone modification levels are predictive for gene expression. Proc Natl Acad Sci U S A. 2010;107(7):2926–31.
Article
CAS
PubMed
PubMed Central
Google Scholar
Spencer VA, Davie JR. Role of covalent modifications of histones in regulating gene expression. Gene. 1999;240(1):1–12.
Article
CAS
PubMed
Google Scholar
Roudier F, Ahmed I, Bérard C, Sarazin A, Maryhuard T, Cortijo S, Bouyer D, Caillieux E, Duvernoisberthet E, Alshikhley L. Integrative epigenomic mapping defines four main chromatin states in Arabidopsis. Nat Publ Group. 2011;
Zhou VW, Goren A, Bernstein BE. Charting histone modifications and the functional organization of mammalian genomes. Nat Rev Genet. 2011;12(1):7–18.
Article
PubMed
Google Scholar
Liu T, Rechtsteiner A, Egelhofer TA, Vielle A, Latorre I, Cheung MS, Ercan S, Ikegami K, Jensen M, Kolasinskazwierz P. Broad chromosomal domains of histone modification patterns in C. Elegans. Genome Res. 2011;21(2):227.
Article
CAS
PubMed
PubMed Central
Google Scholar
Todaka D, Shinozaki K, Yamaguchi-Shinozaki K. Recent advances in the dissection of drought-stress regulatory networks and strategies for development of drought-tolerant transgenic rice plants. Front Plant Sci. 2015;6:84.
Article
PubMed
PubMed Central
Google Scholar
Gupta A, Sarkar AK, Senthil-Kumar M. Global transcriptional analysis reveals unique and shared responses in Arabidopsis Thaliana exposed to combined drought and pathogen stress. Front Plant Sci. 2016;7:686.
PubMed
PubMed Central
Google Scholar
Barah P, NM B, Jayavelu ND, Sowdhamini R, Shameer K, Bones AM. Transcriptional regulatory networks in Arabidopsis Thaliana during single and combined stresses. Nucleic Acids Res. 2016;44(7):3147–64.
Article
CAS
PubMed
Google Scholar
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(1–2):175–88.
Article
CAS
PubMed
Google Scholar
Wang D, Pan Y, Zhao X, Zhu L, Fu B, Li Z. Genome-wide temporal-spatial gene expression profiling of drought responsiveness in rice. BMC Genomics. 2011;12:149.
Article
PubMed
PubMed Central
Google Scholar
Kanno S, Hyodo M, Suzuki K, Ohkido M. Effect of DNA-damaging agents on DNA replication and cell-cycle progression of cultured mouse mammary carcinoma cells. Jpn J Cancer Res. 1985;76(4):289–96.
CAS
PubMed
Google Scholar
Lindahl T. Instability and decay of the primary structure of DNA. Nature. 1993;362(6422):709.
Article
CAS
PubMed
Google Scholar
Majchrzak M, Bowater RP, Staczek P, Parniewski P. SOS repair and DNA supercoiling influence the genetic stability of DNA triplet repeats in Escherichia Coli. J Mol Biol. 2006;364(4):612.
Article
CAS
PubMed
Google Scholar
Sullivan JH, Muhammad D, Warpeha KM. Phenylalanine is required to promote specific developmental responses and prevents cellular damage in response to ultraviolet light in soybean (Glycine max) during the seed-to-seedling transition. PLoS One. 2014;9(12):e112301.
Article
PubMed
PubMed Central
Google Scholar
Zhao Y, Ai X, Wang M, Xiao L, Xia G. A putative pyruvate transporter TaBASS2 positively regulates salinity tolerance in wheat via modulation of ABI4 expression. BMC Plant Biol. 2016;16(1):109.
Article
PubMed
PubMed Central
Google Scholar
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(2):129.
Article
CAS
PubMed
Google Scholar
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 Physiology. 2006;47(7):995.
Article
CAS
Google Scholar
Chinnusamy JK. Epigenetic regulation of stress responses in plants. Curr Opin Plant Biol. 2009;12(2):133–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Van DK, Ding Y, Malkaram S, Riethoven JJ, Liu R, Yang J, Laczko P, Chen H, Xia Y, Ladunga I. Dynamic changes in genome-wide histone H3 lysine 4 methylation patterns in response to dehydration stress in Arabidopsis thaliana. BMC Plant Biology. 2010;24(1):3150–3153+3219.
Google Scholar
Wei Z, 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(1):175–88.
Google Scholar
Steward N, Ito M, Yamaguchi Y, Koizumi N, Sano H. Periodic DNA methylation in maize nucleosomes and demethylation by environmental stress. J Biol Chem. 2002;277(40):37741–6.
Article
CAS
PubMed
Google Scholar
Hu Y, Zhang L, Zhao L, Li J, He S, Zhou K, Yang F, Huang M, Jiang L, Li L. Trichostatin a selectively suppresses the cold-induced transcription of the ZmDREB1 gene in maize. PLoS One. 2012;6(7):e22132.
Article
Google Scholar
Chen LT, Luo M, Wang YY, Wu K. Involvement ofArabidopsis histone deacetylase HDA6 in ABA and salt stress response. J Exp Bot. 2010;61(12):3345–53.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ball AR Jr, Yokomori K. Damage site chromatin: open or closed? Curr Opin Cell Biol. 2011;23(3):277–83.
Article
CAS
PubMed
PubMed Central
Google Scholar
Papamichos-Chronakis M, Peterson CL. Chromatin and the genome integrity network. Nat Rev Genet. 2013;14(1):62–75.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hunt CR, Ramnarain D, Horikoshi N, Iyengar P, Pandita RK, Shay JW, Pandita TK. Histone modifications and DNA double-strand break repair after exposure to ionizing radiations. Radiat Res. 2013;179(4):383–92.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhu Q, Wani AA. Histone modifications: crucial elements for damage response and chromatin restoration. J Cell Physiol. 2010;223(2):283–8.
CAS
PubMed
PubMed Central
Google Scholar
Rossetto D, Truman AW, Kron SJ, Côté J. Epigenetic modifications in double strand break DNA damage signaling and repair. Clin Cancer Res. 2010;16(18):4543.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bannister AJ, Kouzarides T. Regulation of chromatin by histone modifications. Cell Res. 2011;21(3):381–95.
Article
CAS
PubMed
PubMed Central
Google Scholar
Peserico A, Simone C. Physical and functional HAT/HDAC interplay regulates protein acetylation balance. J Biomed Biotechnol. 2011;2011:371832.
Article
PubMed
Google Scholar
Miller KM, Tjeertes JV, Coates J, Legube G, Polo SE, Britton S, Jackson SP. Human HDAC1 and HDAC2 function in the DNA-damage response to promote DNA nonhomologous end-joining. Nat Struct Mol Biol. 2010;17(9):1144.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nagarajan S, Benito E, Fischer A, Johnsen SA. H4K12ac is regulated by estrogen receptor-alpha and is associated with BRD4 function and inducible transcription. Oncotarget. 2015;6(9):7305–17.
Article
PubMed
PubMed Central
Google Scholar
Vieweg M, Dvorakova-Hortova K, Dudkova B, Waliszewski P, Otte M, Oels B, Hajimohammad A, Turley H, Schorsch M, Schuppe HC, et al. Methylation analysis of histone H4K12ac-associated promoters in sperm of healthy donors and subfertile patients. Clin Epigenetics. 2015;7:31.
Article
PubMed
PubMed Central
Google Scholar
Paradowska AS, Miller D, Spiess AN, Vieweg M, Cerna M, Dvorakova-Hortova K, Bartkuhn M, Schuppe HC, Weidner W, Steger K. Genome wide identification of promoter binding sites for H4K12ac in human sperm and its relevance for early embryonic development. Epigenetics. 2012;7(9):1057–70.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu N, M F, Avramova Z. H3K27me3 and H3K4me3 chromatin environment at super-induced dehydration stress memory genes of Arabidopsis Thaliana. Mol Plant. 2014;7(3):502–13.
Article
CAS
PubMed
Google Scholar
Yang H, Howard M, Dean C. Antagonistic roles for H3K36me3 and H3K27me3 in the cold-induced epigenetic switch at Arabidopsis FLC. Curr Biol. 2014;24(15):1793–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kwon YI, Abe K, Endo M, Osakabe K, Ohtsuki N, Nishizawa-Yokoi A, Tagiri A, Saika H, Toki S. DNA replication arrest leads to enhanced homologous recombination and cell death in meristems of rice OsRecQl4 mutants. BMC Plant Biol. 2013;13:62.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang W, Lee HR, Koo DH, Jiang J. Epigenetic modification of centromeric chromatin: hypomethylation of DNA sequences in the CENH3-associated chromatin in Arabidopsis Thaliana and maize. Plant Cell. 2008;20(1):25–34.
Article
PubMed
PubMed Central
Google Scholar
Miao C, Tang D, Zhang H, Wang M, Li Y, Tang S, Yu H, Gu M, Cheng Z. Central region component1, a novel synaptonemal complex component, is essential for meiotic recombination initiation in rice. Plant Cell. 2013;25(8):2998–3009.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wu Z, Ji J, Tang D, Wang H, Shen Y, Shi W, Li Y, Tan X, Cheng Z, Luo Q. OsSDS is essential for DSB formation in rice meiosis. Front Plant Sci. 2015;6:21.
PubMed
PubMed Central
Google Scholar
Zhang W, Wu Y, Schnable JC, Zeng Z, Freeling M, Crawford GE, Jiang J. High-resolution mapping of open chromatin in the rice genome. Genome res. Genome Res. 2011;22(1):151–62.
Article
CAS
PubMed
Google Scholar
Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009;25(9):1105–11.
Article
CAS
PubMed
PubMed Central
Google Scholar
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010;28(5):511–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Du Z, Zhou X, Ling Y, Zhang Z, Su Z. agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res. 2010;38(Web Server issue):64–70.
Article
Google Scholar
Supek F, Bošnjak M. N Š, T Š: REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS One. 2011;6(7):e21800.
Article
CAS
PubMed
PubMed Central
Google Scholar
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):R25.
Article
PubMed
PubMed Central
Google Scholar
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.
Article
PubMed
PubMed Central
Google Scholar
Xu H, Wei CL, Lin F, Sung WK. An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data. Bioinformatics. 2008;24(20):2344.
Article
CAS
PubMed
Google Scholar
Ernst J, Kellis M. ChromHMM: automating chromatin-state discovery and characterization. Nat Methods. 2012;9(3):215–6.
Article
CAS
PubMed
PubMed Central
Google Scholar