Genome-wide changes in histone H3 lysine 27 trimethylation associated with bud dormancy release in peach
- 435 Downloads
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.
KeywordsBud dormancy Chromatin immunoprecipitation sequencing (ChIP-seq) DAM gene Flowering Histone H3 lysine 27 trimethylation Prunus persica (peach)
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.
- Arora R, Rowland LJ, Tanino K (2003) Induction and release of bud dormancy in woody perennials: a science comes of age. HortSci 38:911–921Google 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 4:495–507CrossRefGoogle 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 119:721–743Google 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 110:47–50Google 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 18:4679–4688PubMedCentralPubMedCrossRefGoogle 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–D147PubMedCentralPubMedCrossRefGoogle 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 46:522–531PubMedCrossRefGoogle 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 21:1311–1318PubMedCentralPubMedCrossRefGoogle 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 154:1492–1504PubMedCentralPubMedCrossRefGoogle 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 23:130–146PubMedCentralPubMedCrossRefGoogle 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 27:649–659Google Scholar