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dc.contributor.authorVimont, Noémie
dc.contributor.authorQuah, Fu Xiang
dc.contributor.authorSchöepfer, David Guillaume
dc.contributor.authorRoudier, François
dc.contributor.authorDirlewanger, Elisabeth
dc.contributor.authorWigge, Philip A.
dc.contributor.authorWenden, Bénédicte
dc.contributor.authorCortijo, Sandra
dc.date.accessioned2020-12-22T18:53:10Z
dc.date.available2020-12-22T18:53:10Z
dc.date.issued2019-12-14
dc.date.submitted2019-07-02
dc.identifier.issn1614-2942
dc.identifier.others11295-019-1395-9
dc.identifier.other1395
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/315383
dc.descriptionFunder: CIFRE
dc.description.abstractAbstract: Chromatin immunoprecipitation-sequencing (ChIP-seq) is a robust technique to study interactions between proteins, such as histones or transcription factors and DNA. This technique in combination with RNA-sequencing (RNA-seq) is a powerful tool to better understand biological processes in eukaryotes. We developed a combined ChIP-seq and RNA-seq protocol for tree buds (Prunus avium L., Prunus persica L Batch, Malus x domestica Borkh.) that has also been successfully tested on Arabidopsis thaliana and Saccharomyces cerevisiae. Tree buds contain phenolic compounds that negatively interfere with ChIP and RNA extraction. In addition to solving this problem, our protocol is optimised to work on small amounts of material. Furthermore, one of the advantages of this protocol is that samples for ChIP-seq are cross-linked after flash freezing, making it possible to work on trees growing in the field and to perform ChIP-seq and RNA-seq on the same starting material. Focusing on dormant buds in sweet cherry, we explored the link between expression level and H3K4me3 enrichment for all genes, including a strong correlation between H3K4me3 enrichment at the DORMANCY-ASSOCIATED MADS-BOX 5 (PavDAM5) loci and its expression pattern. This protocol will allow analysis of chromatin and transcriptomic dynamics in tree buds, notably during its development and response to the environment.
dc.languageen
dc.publisherSpringer Berlin Heidelberg
dc.rightsAttribution 4.0 International (CC BY 4.0)en
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en
dc.subjectOriginal Article
dc.subjectEpigenetics
dc.subjectTree buds
dc.subjectChIP-seq/chromatin Immunoprecipitation-sequencing
dc.subjectRNA-seq/RNA-sequencing
dc.subjectPrunus avium L.
dc.subjectPrunus persica L batch
dc.subjectMalus x domestica Borkh
dc.titleChIP-seq and RNA-seq for complex and low-abundance tree buds reveal chromatin and expression co-dynamics during sweet cherry bud dormancy
dc.typeArticle
dc.date.updated2020-12-22T18:53:09Z
prism.issueIdentifier1
prism.publicationNameTree Genetics & Genomes
prism.volume16
dc.identifier.doi10.17863/CAM.62490
dcterms.dateAccepted2019-10-21
rioxxterms.versionofrecord10.1007/s11295-019-1395-9
rioxxterms.versionVoR
rioxxterms.licenseref.urihttp://creativecommons.org/licenses/by/4.0/
dc.contributor.orcidCortijo, Sandra [0000-0003-3291-6729]
dc.identifier.eissn1614-2950
pubs.funder-project-idEMBO (ALTF 290-2013)
pubs.funder-project-idGatsby Charitable Foundation (GAT3273/GLB)


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Attribution 4.0 International (CC BY 4.0)
Except where otherwise noted, this item's licence is described as Attribution 4.0 International (CC BY 4.0)