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

  • Lorena de la Fuente
  • Ana Conesa
  • Alba Lloret
  • María Luisa Badenes
  • Gabino Ríos
Original Paper
Part of the following topical collections:
  1. Epigenetics

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.

Keywords

Bud dormancy Chromatin immunoprecipitation sequencing (ChIP-seq) DAM gene Flowering Histone H3 lysine 27 trimethylation Prunus persica (peach) 

Notes

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.

Supplementary material

11295_2015_869_MOESM1_ESM.pdf (75 kb)
Online Resource Table S1 Primers used in this study. (PDF 75 kb)
11295_2015_869_MOESM2_ESM.pdf (56 kb)
Online Resource Table S2 Reciprocal Blast analysis of unmapped sequences. (PDF 55 kb)
11295_2015_869_MOESM3_ESM.pdf (66 kb)
Online Resource Table S3 H3K27me3 regions identified after analysis with and without input subtraction. (PDF 65 kb)
11295_2015_869_MOESM4_ESM.xls (228 kb)
Online Resource Table S4 List of differential H3K27me3 regions and genes. (XLS 228 kb)
11295_2015_869_MOESM5_ESM.pdf (56 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)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Lorena de la Fuente
    • 1
  • Ana Conesa
    • 1
    • 3
  • Alba Lloret
    • 2
  • María Luisa Badenes
    • 2
  • Gabino Ríos
    • 2
  1. 1.Genomics of Gene ExpressionCentro de Investigaciones Príncipe Felipe (CIPF)ValenciaSpain
  2. 2.Instituto Valenciano de Investigaciones Agrarias (IVIA)MoncadaSpain
  3. 3.Microbiology and Cell Science Department, Institute of Food and Agricultural SciencesUniversity of FloridaGainesvilleUSA

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