Skip to main content
SpringerLink
Log in

Genome-wide changes in histone H3 lysine 27 trimethylation associated with bud dormancy release in peach

  • Original Paper
  • Published:
Tree Genetics & Genomes Aims and scope Submit manuscript

Abstract

Bud dormancy is an evolutionary adaptation of perennial plants to the seasonal fluctuation of temperatures in temperate climates, affected by intrinsic and environmental signals. Recent investigations point to a relevant role of epigenetic mechanisms in the regulation of bud dormancy. We have performed a chromatin immunoprecipitation sequencing (ChIP-seq) analysis of histone H3 lysine-27 trimethylation (H3K27me3), a chromatin mark associated with stable gene silencing, in dormant (D) and dormancy-released (ND) buds of peach (Prunus persica). H3K27me3 regions were more abundant in gene-rich euchromatic zones of chromosomes and associated with gene bodies. The dormancy regulators DORMANCY-ASSOCIATED MADS-box (DAM)1, DAM4, DAM5 and DAM6 were found significantly enriched in H3K27me3 in ND samples, in close agreement with their dormancy-specific expression. The DAM locus was modified at specific short regions, allowing the uneven regulation of distinct DAM genes. Additional regulatory factors related to meristem activity and flowering genes from Arabidopsis thaliana were differentially H3K27 trimethylated, which suggests that meristem reactivation and flower development could be also epigenetically regulated in reproductive buds of peach. A (GA)n motif and CACTA-type transposon-related sequences were found over-represented in H3K27me3 regions.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8

Similar content being viewed by others

References

  • Aarts MG, Keijzer CJ, Stiekema WJ, Pereira A (1995) Molecular characterization of the CER1 gene of Arabidopsis involved in epicuticular wax biosynthesis and pollen fertility. Plant Cell 7:2115–2127

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Adli M, Bernstein BE (2011) Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq. Nat Protoc 6:1656–1668

    Article  CAS  PubMed  Google Scholar 

  • Allona I, Ramos A, Ibáñez C, Contreras A, Casado R, Aragoncillo C (2008) Molecular control of winter dormancy establishment in trees. Span J Agric Res 6:201–210

    Article  Google Scholar 

  • Anders S, Pyl PT, Huber W (2015) HTSeq-a python framework to work with high-throughput sequencing data. Bioinformatics 31:166–169

    Article  PubMed Central  PubMed  Google Scholar 

  • Arora R, Rowland LJ, Tanino K (2003) Induction and release of bud dormancy in woody perennials: a science comes of age. HortSci 38:911–921

    Google Scholar 

  • Bastow R, Mylne JS, Lister C, Lippman Z, Martienssen RA, Dean C (2004) Vernalization requires epigenetic silencing of FLC by histone methylation. Nature 427:164–167

    Article  CAS  PubMed  Google Scholar 

  • Bemer M, Wolters-Arts M, Grossniklaus U, Angenent GC (2008) The MADS domain protein DIANA acts together with AGAMOUS-LIKE80 to specify the central cell in Arabidopsis ovules. Plant Cell 20:2088–2101

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Berger N, Dubreucq B, Roudier F, Dubos C, Lepiniec L (2011) Transcriptional regulation of Arabidopsis LEAFY COTYLEDON2 involves RLE, a cis-element that regulates trimethylation of histone H3 at lysine-27. Plant Cell 23:4065–4078

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Bielenberg DG, Wang Y, Fan S, Reighard GL, Scorza R, Abbott AG (2004) A deletion affecting several gene candidates is present in the evergrowing peach mutant. J Hered 95:436–444

    Article  CAS  PubMed  Google Scholar 

  • Bielenberg DG, Wang Y, Li Z, Zhebentyayeva T, Fan S, Reighard GL, Scorza R, Abbott AG (2008) Sequencing and annotation of the evergrowing locus in peach (Prunus persica [L.] Batsch) reveals a cluster of six MADS-box transcription factors as candidate genes for regulation of terminal bud formation. Tree Genet Genomes 4:495–507

    Article  Google Scholar 

  • Bowman J, Alvarez J, Weigel D, Meyerowitz EM, Smyth DRM (1993) Control of flower development in Arabidopsis thaliana by APETALA1 and interacting genes. Development 119:721–743

    CAS  Google Scholar 

  • Chen X (2004) A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303:2022–2025

    Article  CAS  PubMed  Google Scholar 

  • Chen L, Cheng JC, Castle L, Sung ZR (1997) EMF genes regulate Arabidopsis inflorescence development. Plant Cell 9:2011–2024

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Chuine I (2010) Why does phenology drive species distribution? Philos Trans R Soc Lond B Biol Sci 365:3149–3160

    Article  PubMed Central  PubMed  Google Scholar 

  • Conde D, González-Melendi P, Allona I (2013) Poplar stems show opposite epigenetic patterns during winter dormancy and vegetative growth. Trees 27:311–320

    Article  Google Scholar 

  • Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676

    Article  CAS  PubMed  Google Scholar 

  • Cooke JEK, Eriksson ME, Junttila O (2012) The dynamic nature of bud dormancy in trees: environmental control and molecular mechanisms. Plant Cell Environ 35:1707–1728

    Article  CAS  PubMed  Google Scholar 

  • Couvillon GA, Erez A (1985) Influence of prolonged exposure to chilling temperatures on bud break and heat requirement for bloom of several fruit species. J Am Soc Hortic Sci 110:47–50

    Google Scholar 

  • Deng W, Liu C, Pei Y, Deng X, Niu L, Cao X (2007) Involvement of the histone acetyltransferase AtHAC1 in the regulation of flowering time via repression of FLOWERING LOCUS C in Arabidopsis. Plant Physiol 143:1660–1668

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Deng W, Buzas DM, Ying H, Robertson M, Taylor J, Peacock WJ, Dennis ES, Helliwell C (2013) Arabidopsis polycomb repressive complex 2 binding sites contain putative GAGA factor binding motifs within coding regions of genes. BMC Genomics 14:593

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Doyle MR, Amasino RM (2009) A single amino acid change in the enhancer of zeste ortholog CURLY LEAF results in vernalization-independent, rapid flowering in Arabidopsis. Plant Physiol 151:1688–1697

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Feng J, Liu T, Qin B, Zhang Y, Liu XS (2012) Identifying ChIP-seq enrichment using MACS. Nat Protoc 7:1728–1740

    Article  CAS  PubMed  Google Scholar 

  • Ferrándiz C, Gu Q, Martienssen R, Yanofsky MF (2000) Redundant regulation of meristem identity and plant architecture by FRUITFULL, APETALA1 and CAULIFLOWER. Development 127:725–734

    PubMed  Google Scholar 

  • Ferres-Maso M, Sacilotto N, Lopez-Rodas G, Dagorn JC, Iovanna JL, Closa D, Folch-Puy E (2009) PAP1 signaling involves MAPK signal transduction. Cell Mol Life Sci 66:2195–2204

    Article  CAS  PubMed  Google Scholar 

  • Fowler S, Lee K, Onouchi H, Samach A, Richardson K, Morris B, Coupland G, Putterill J (1999) GIGANTEA: a circadian clock-controlled gene that regulates photoperiodic flowering in Arabidopsis and encodes a protein with several possible membrane-spanning domains. EMBO J 18:4679–4688

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Gao Z, Luo X, Shi T, Cai B, Zhang Z, Cheng Z, Zhuang W (2012) Identification and validation of potential conserved microRNAs and their targets in peach (Prunus persica). Mol Cells 34:239–249

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Gu Q, Ferrándiz C, Yanofsky MF, Martienssen R (1998) The FRUITFULL MADS-box gene mediates cell differentiation during Arabidopsis fruit development. Development 125:1509–1517

    CAS  PubMed  Google Scholar 

  • Gupta S, Stamatoyannopoulos JA, Bailey TL, Noble WS (2007) Quantifying similarity between motifs. Genome Biol 8:R24

    Article  PubMed Central  PubMed  Google Scholar 

  • Hemming MN, Trevaskis B (2011) Make hay when the sun shines: the role of MADS-box genes in temperature-dependent seasonal flowering responses. Plant Sci 180:447–453

    Article  CAS  PubMed  Google Scholar 

  • Horvath D (2009) Common mechanisms regulate flowering and dormancy. Plant Sci 177:523–531

    Article  CAS  Google Scholar 

  • Horvath DP, Anderson JV, Chao WS, Foley ME (2003) Knowing when to grow: signals regulating bud dormancy. Trends Plant Sci 8:534–540

    Article  CAS  PubMed  Google Scholar 

  • Horvath DP, Sung S, Kim D, Chao W, Anderson J (2010) Characterization, expression and function of DORMANCY ASSOCIATED MADS-BOX genes from leafy spurge. Plant Mol Biol 73:169–179

    Article  CAS  PubMed  Google Scholar 

  • Hsu C-Y, Adams JP, Kim H, No K, Ma C, Strauss SH, Drnevich J, Vandervelde L, Ellis JD, Rice BM et al (2011) FLOWERING LOCUS T duplication coordinates reproductive and vegetative growth in perennial poplar. Proc Natl Acad Sci U S A 108:10756–10761

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Hu JY, Zhou Y, He F, Dong X, Liu LY, Coupland G, Turck F, de Meaux J (2014) miR824-regulated AGAMOUS-LIKE16 contributes to flowering time repression in Arabidopsis. Plant Cell 26:2024–2037

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Jiménez S, Reighard GL, Bielenberg DG (2010) Gene expression of DAM5 and DAM6 is suppressed by chilling temperatures and inversely correlated with bud break rate. Plant Mol Biol 73:157–167

    Article  PubMed  Google Scholar 

  • Julian C, Rodrigo J, Herrero M (2011) Stamen development and winter dormancy in apricot (Prunus armeniaca). Ann Bot 108:617–625

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Kang IH, Steffen JG, Portereiko MF, Lloyd A, Drews GN (2008) The AGL62 MADS domain protein regulates cellularization during endosperm development in Arabidopsis. Plant Cell 20:635–647

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Kania T, Russenberger D, Peng S, Apel K, Melzer S (1997) FPF1 promotes flowering in Arabidopsis. Plant Cell 9:1327–1338

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Kim SY, He Y, Jacob Y, Noh YS, Michaels S, Amasino R (2005) Establishment of the vernalization-responsive, winter-annual habit in Arabidopsis requires a putative histone H3 methyl transferase. Plant Cell 17:3301–3310

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Kumimoto RW, Adam L, Hymus GJ, Repetti PP, Reuber TL, Marion CM, Hempel FD, Ratcliffe OJ (2008) The Nuclear Factor Y subunits NF-YB2 and NF-YB3 play additive roles in the promotion of flowering by inductive long-day photoperiods in Arabidopsis. Planta 228:709–723

    Article  CAS  PubMed  Google Scholar 

  • Kunieda T, Mitsuda N, Ohme-Takagi M, Takeda S, Aida M, Tasaka M, Kondo M, Nishimura M, Hara-Nishimura I (2008) NAC family proteins NARS1/NAC2 and NARS2/NAM in the outer integument regulate embryogenesis in Arabidopsis. Plant Cell 20:2631–2642

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Lafos M, Kroll P, Hohenstatt ML, Thorpe FL, Clarenz O, Schubert D (2011) Dynamic regulation of H3K27 trimethylation during Arabidopsis differentiation. PLoS Genet 7:e1002040

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Langmead B, Salzberg S (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Laufs P, Coen E, Kronenberger J, Traas J, Doonan J (2003) Separable roles of UFO during floral development revealed by conditional restoration of gene function. Development 130:785–796

    Article  CAS  PubMed  Google Scholar 

  • Lee DK, Geisler M, Springer PS (2009) LATERAL ORGAN FUSION1 and LATERAL ORGAN FUSION2 function in lateral organ separation and axillary meristem formation in Arabidopsis. Development 136:2423–2432

    Article  CAS  PubMed  Google Scholar 

  • Leida C, Terol J, Martí G, Agustí M, Llácer G, Badenes ML, Ríos G (2010) Identification of genes associated with bud dormancy release in Prunus persica by suppression subtractive hybridization. Tree Physiol 30:655–666

    Article  CAS  PubMed  Google Scholar 

  • Leida C, Romeu JF, García-Brunton J, Ríos G, Badenes ML (2012a) Gene expression analysis of chilling requirements for flower bud break in peach. Plant Breed 131:329–334

    Article  CAS  Google Scholar 

  • Leida C, Conesa A, Llácer G, Badenes ML, Ríos G (2012b) Histone modifications and expression of DAM6 gene in peach are modulated during bud dormancy release in a cultivar-dependent manner. New Phytol 193:67–80

    Article  CAS  PubMed  Google Scholar 

  • Leida C, Conejero A, Arbona V, Gómez-Cadenas A, Llácer G, Badenes ML, Ríos G (2012c) Chilling-dependent release of seed and bud dormancy in peach associates to common changes in gene expression. PLoS One 7:e35777

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Levin JZ, Meyerowitz EM (1995) UFO: an Arabidopsis gene involved in both floral meristem and floral organ development. Plant Cell 7:529–548

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Li C, Xie H, Zhang L, Xu Y, Li Y-F, Ma R-C (2012) Molecular characterization of the PpMADS1 gene from peach. Tree Genet Genomes 8:831–840

    Article  CAS  Google Scholar 

  • Liang Y, Tan ZM, Zhu L, Niu QK, Zhou JJ, Li M, Chen LQ, Zhang XQ, Ye D (2013) MYB97, MYB101 and MYB120 function as male factors that control pollen tube-synergid interaction in Arabidopsis thaliana fertilization. PLoS Genet 9:e1003933

    Article  PubMed Central  PubMed  Google Scholar 

  • Lindroth AM, Shultis D, Jasencakova Z, Fuchs J, Johnson L, Schubert D, Patnaik D, Pradhan S, Goodrich J, Schubert I et al (2004) Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3. EMBO J 23:4286–4296

    Article  CAS  PubMed  Google Scholar 

  • Machanick P, Bailey TL (2011) MEME-ChIP: motif analysis of large DNA datasets. Bioinformatics 27:1696–1697

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Makarevitch I, Eichten SR, Briskine R, Waters AJ, Danilevskaya ON, Meeley RB, Myers CL, Vaughn MW, Springer NM (2013) Genomic distribution of maize facultative heterochromatin marked by trimethylation of H3K27. Plant Cell 25:780–793

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Malone BM, Tan F, Bridges SM, Peng Z (2011) Comparison of four ChIP-Seq analytical algorithms using rice endosperm H3K27 trimethylation profiling data. PLoS One 6:e25260

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Mandaokar A, Browse J (2009) MYB108 acts together with MYB24 to regulate jasmonate-mediated stamen maturation in Arabidopsis. Plant Physiol 149:851–862

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Mandel MA, Gustafson-Brown C, Savidge B, Yanofsky MF (1992) Molecular characterization of the Arabidopsis floral homeotic gene APETALA1. Nature 360:273–277

    Article  CAS  PubMed  Google Scholar 

  • Mathelier A, Zhao X, Zhang AW, Parcy F, Worsley-Hunt R, Arenillas DJ, Buchman S, Chen CY, Chou A, Ienasescu H et al (2014) JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res 42:D142–D147

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Mathieu J, Yant LJ, Murdter F, Kuttner F, Schmid M (2009) Repression of flowering by the miR172 target SMZ. PLoS Biol 7:e1000148

    Article  PubMed Central  PubMed  Google Scholar 

  • Matsumoto N, Okada K (2001) A homeobox gene, PRESSED FLOWER, regulates lateral axis-dependent development of Arabidopsis flowers. Genes Dev 15:3355–3364

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • McAbee JM, Hill TA, Skinner DJ, Izhaki A, Hauser BA, Meister RJ, Venugopala Reddy G, Meyerowitz EM, Bowman JL, Gasser CS (2006) ABERRANT TESTA SHAPE encodes a KANADI family member, linking polarity determination to separation and growth of Arabidopsis ovule integuments. Plant J 46:522–531

    Article  CAS  PubMed  Google Scholar 

  • Mishra RK, Mihaly J, Barges S, Spierer A, Karch F, Hagstrom K, Schweinsberg SE, Schedl P (2001) The iab-7 polycomb response element maps to a nucleosome-free region of chromatin and requires both GAGA and pleiohomeotic for silencing activity. Mol Cell Biol 21:1311–1318

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Mitsuda N, Seki M, Shinozaki K, Ohme-Takagi M (2005) The NAC transcription factors NST1 and NST2 of Arabidopsis regulate secondary wall thickenings and are required for anther dehiscence. Plant Cell 17:2993–3006

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Murmu J, Bush MJ, DeLong C, Li S, Xu M, Khan M, Malcolmson C, Fobert PR, Zachgo S, Hepworth SR (2010) Arabidopsis basic leucine-zipper transcription factors TGA9 and TGA10 interact with floral glutaredoxins ROXY1 and ROXY2 and are redundantly required for anther development. Plant Physiol 154:1492–1504

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Nallamilli BRR, Zhang J, Mujahid H, Malone BM, Bridges SM, Peng Z (2013) Polycomb group gene OsFIE2 regulates rice (Oryza sativa) seed development and grain filling via a mechanism distinct from Arabidopsis. PLoS Genet 9:e1003322

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Pelaz S, Ditta GS, Baumann E, Wisman E, Yanofsky MF (2000) B and C floral organ identity functions require SEPALLATA MADS-box genes. Nature 405:200–203

    Article  CAS  PubMed  Google Scholar 

  • Phan HA, Iacuone S, Li SF, Parish RW (2011) The MYB80 transcription factor is required for pollen development and the regulation of tapetal programmed cell death in Arabidopsis thaliana. Plant Cell 23:2209–2224

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Portereiko MF, Lloyd A, Steffen JG, Punwani JA, Otsuga D, Drews GN (2006) AGL80 is required for central cell and endosperm development in Arabidopsis. Plant Cell 18:1862–1872

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Ragni L, Belles-Boix E, Günl M, Pautot V (2008) Interaction of KNAT6 and KNAT2 with BREVIPEDICELLUS and PENNYWISE in Arabidopsis inflorescences. Plant Cell 20:888–900

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Rinne PL, Welling A, Vahala J, Ripel L, Ruonala R, Kangasjärvi J, van der Schoot C (2011) Chilling of dormant buds hyperinduces FLOWERING LOCUS T and recruits GA-inducible 1,3-beta-glucanases to reopen signal conduits and release dormancy in Populus. Plant Cell 23:130–146

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Ríos G, Tadeo FR, Leida C, Badenes ML (2013) Prediction of components of the sporopollenin synthesis pathway in peach by genomic and expression analyses. BMC Genomics 14:40

    Article  PubMed Central  PubMed  Google Scholar 

  • Ríos G, Leida C, Conejero A, Badenes ML (2014) Epigenetic regulation of bud dormancy events in perennial plants. Front Plant Sci 5:247

    PubMed Central  PubMed  Google Scholar 

  • Robinson MD, Oshlack A (2010) A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol 11:R25

    Article  PubMed Central  PubMed  Google Scholar 

  • Rohde A, Bhalerao RP (2007) Plant dormancy in the perennial context. Trends Plant Sci 12:217–223

    Article  CAS  PubMed  Google Scholar 

  • Rohde A, Storme V, Jorge V, Gaudet M, Vitacolonna N, Fabbrini F, Ruttink T, Zaina G, Marron N, Dillen S et al (2011) Bud set in poplar-genetic dissection of a complex trait in natural and hybrid populations. New Phytol 189:106–121

    Article  CAS  PubMed  Google Scholar 

  • Romeu JF, Monforte AJ, Sánchez G, Granell A, García-Brunton J, Badenes ML, Ríos G (2014) Quantitative trait loci affecting reproductive phenology in peach. BMC Plant Biol 14:52

    Article  PubMed Central  PubMed  Google Scholar 

  • Sablowski RW, Meyerowitz EM (1998) A homolog of NO APICAL MERISTEM is an immediate target of the floral homeotic genes APETALA3/PISTILLATA. Cell 92:93–103

    Article  CAS  PubMed  Google Scholar 

  • Saleh A, Alvarez-Venegas R, Avramova Z (2008) An efficient chromatin immunoprecipitation (ChIP) protocol for studying histone modifications in Arabidopsis plants. Nat Protoc 3:1018–1025

    Article  CAS  PubMed  Google Scholar 

  • Sandoval J, Rodríguez JL, Tur G, Serviddio G, Pereda J, Boukaba A, Sastre J, Torres L, Franco L, López-Rodas G (2004) RNAPol-ChIP: a novel application of chromatin immunoprecipitation to the analysis of real-time gene transcription. Nucleic Acids Res 32:e88

    Article  PubMed Central  PubMed  Google Scholar 

  • Sani E, Herzyk P, Perrella G, Colot V, Amtmann A (2013) Hyperosmotic priming of Arabidopsis seedlings establishes a long-term somatic memory accompanied by specific changes of the epigenome. Genome Biol 14:R59

    Article  PubMed Central  PubMed  Google Scholar 

  • Santamaría ME, Hasbún R, Valera MJ, Meijón M, Valledor L, Rodríguez JL, Toorop PE, Cañal MJ, Rodríguez R (2009) Acetylated H4 histone and genomic DNA methylation patterns during bud set and bud burst in Castanea sativa. J Plant Physiol 166:1360–1369

    Article  PubMed  Google Scholar 

  • Sarkar AK, Luijten M, Miyashima S, Lenhard M, Hashimoto T, Nakajima K, Scheres B, Heidstra R, Laux T (2007) Conserved factors regulate signalling in Arabidopsis thaliana shoot and root stem cell organizers. Nature 446:811–814

    Article  CAS  PubMed  Google Scholar 

  • Sasaki R, Yamane H, Ooka T, Jotatsu H, Kitamura Y, Akagi T, Tao R (2011) Functional and expressional analyses of PmDAM genes associated with endodormancy in Japanese apricot. Plant Physiol 157:485–497

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Schwartz YB, Kahn TG, Nix DA, Li XY, Bourgon R, Biggin M, Pirrotta V (2006) Genome-wide analysis of polycomb targets in Drosophila melanogaster. Nat Genet 38:700–705

    Article  CAS  PubMed  Google Scholar 

  • Srinivasan C, Dardick C, Callahan A, Scorza R (2012) Plum (Prunus domestica) trees transformed with poplar FT1 result in altered architecture, dormancy requirement, and continuous flowering. PLoS One 7:e40715

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Tani E, Polidoros AN, Tsaftaris AS (2007) Characterization and expression ana lysis of FRUITFULL- and SHATTERPROOF-like genes from peach (Prunus persica) and their role in split-pit formation. Tree Physiol 27:649–659

  • Tarazona S, García-Alcalde F, Dopazo J, Ferrer A, Conesa A (2011) Differential expression in RNA-seq: a matter of depth. Genome Res 21:2213–2223

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Vroemen CW, Mordhorst AP, Albrecht C, Kwaaitaal MA, de Vries SC (2003) The CUP-SHAPED COTYLEDON3 gene is required for boundary and shoot meristem formation in Arabidopsis. Plant Cell 15:1563–1577

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Wang X, Elling AA, Li X, Li N, Peng Z, He G, Sun H, Qi Y, Liu XS, Deng XW (2009) Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize. Plant Cell 21:1053–1069

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Weinhofer I, Hehenberger E, Roszak P, Hennig L, Köhler C (2010) H3K27me3 profiling of the endosperm implies exclusion of polycomb group protein targeting by DNA methylation. PLoS Genet 6:e1001152

    Article  PubMed Central  PubMed  Google Scholar 

  • Wilkinson MD, Haughn GW (1995) UNUSUAL FLORAL ORGANS controls meristem identity and organ primordia fate in Arabidopsis. Plant Cell 7:1485–1499

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Xu Y, Zhang L, Ma RC (2008) Functional characterization and mapping of two MADS box genes from peach (Prunus persica). Chin Sci Bull 53:853–859

    Article  CAS  Google Scholar 

  • Yamane H, Ooka T, Jotatsu H, Hosaka Y, Sasaki R, Tao R (2011) Expressional regulation of PpDAM5 and PpDAM6, peach (Prunus persica) dormancy-associated MADS-box genes, by low temperature and dormancy-breaking reagent treatment. J Exp Bot 62:3481–3488

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Yang S, Johnston N, Talideh E, Mitchell S, Jeffree C, Goodrich J, Ingram G (2008) The endosperm-specific ZHOUPI gene of Arabidopsis thaliana regulates endosperm breakdown and embryonic epidermal development. Development 135:3501–3509

    Article  CAS  PubMed  Google Scholar 

  • Zhang X, Clarenz O, Cokus S, Bernatavichute YV, Pellegrini M, Goodrich J, Jacobsen SE (2007) Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol 5:e129

    Article  PubMed Central  PubMed  Google Scholar 

  • Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W et al (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol 9:R137

    Article  PubMed Central  PubMed  Google Scholar 

  • Zhebentyayeva TN, Fan S, Chandra A, Bielenberg DG, Reighard GL, Okie WR, Abbott AG (2014) Dissection of chilling requirement and bloom date QTLs in peach using a whole genome sequencing of sibling trees from an F2 mapping population. Tree Genet Genomes 10:35–51

    Article  Google Scholar 

Download references

Acknowledgments

This work was supported by the Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)-FEDER, the Ministry of Science and Innovation of Spain (grant number AGL2010-20595) and the Ministry of Education of Spain (grant number FPU13/02348).

Conflict of interest

The authors declare that they have no conflict of interest.

Data archiving statement

Raw sequence data have been submitted to the Short Read Archive (SRA) database with ID SRP055071.

Author information

Authors and Affiliations

  1. Genomics of Gene Expression, Centro de Investigaciones Príncipe Felipe (CIPF), Avda. Eduardo Primo Yúfera 3, 46012, Valencia, Spain

    Lorena de la Fuente & Ana Conesa

  2. Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera Moncada-Náquera km 4.5, 46113, Moncada, Valencia, Spain

    Alba Lloret, María Luisa Badenes & Gabino Ríos

  3. Microbiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, 32603, USA

    Ana Conesa

Authors
  1. Lorena de la Fuente
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ana Conesa
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Alba Lloret
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. María Luisa Badenes
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Gabino Ríos
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Gabino Ríos.

Additional information

Communicated by D. Chagné

This article is part of the Topical Collection on Epigenetics

Electronic supplementary material

Below is the link to the electronic supplementary material.

Online Resource Table S1

Primers used in this study. (PDF 75 kb)

Online Resource Table S2

Reciprocal Blast analysis of unmapped sequences. (PDF 55 kb)

Online Resource Table S3

H3K27me3 regions identified after analysis with and without input subtraction. (PDF 65 kb)

Online Resource Table S4

List of differential H3K27me3 regions and genes. (XLS 228 kb)

Online Resource Fig. S1

Relative H3K27me3 enrichment in DAM6, ppa012373m and ppa009007m by real-time RT-PCR. Primers used are shown in Online Resource Table S1. Gene-specific values are normalized with the input signal. Data are means from two biological samples with three technical replicates each. Error bars represent standard deviations. (PDF 56 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

de la Fuente, L., Conesa, A., Lloret, A. et al. Genome-wide changes in histone H3 lysine 27 trimethylation associated with bud dormancy release in peach. Tree Genetics & Genomes 11, 45 (2015). https://doi.org/10.1007/s11295-015-0869-7

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s11295-015-0869-7

Keywords

Search

Navigation