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ChIP-seq and RNA-seq for complex and low-abundance tree buds reveal chromatin and expression co-dynamics during sweet cherry bud dormancy

hal.structure.identifierBiologie du fruit et pathologie [BFP]
hal.structure.identifierThe Sainsbury Laboratory [Norwich] [TSL]
dc.contributor.authorVIMONT, Noémie
hal.structure.identifierThe Sainsbury Laboratory [Norwich] [TSL]
dc.contributor.authorQUAH, Fu Xiang
hal.structure.identifierThe Sainsbury Laboratory [Norwich] [TSL]
dc.contributor.authorSCHÖPFER, David Guillaume
hal.structure.identifierReproduction et développement des plantes [RDP]
dc.contributor.authorROUDIER, François
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorDIRLEWANGER, Elisabeth
hal.structure.identifierThe Sainsbury Laboratory [Norwich] [TSL]
dc.contributor.authorWIGGE, Philip A.
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorWENDEN, Bénédicte
hal.structure.identifierThe Sainsbury Laboratory [Norwich] [TSL]
dc.contributor.authorCORTIJO, Sandra
dc.date.issued2020
dc.identifier.issn1614-2942
dc.description.abstractEnChromatin 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.language.isoen
dc.publisherSpringer Verlag
dc.subject.enTree buds
dc.subject.enChIP-seq/Chromatin immunoprecipitation-sequencing
dc.subject.enRNA-seq/RNA-sequencing
dc.subject.enPrunus avium L.
dc.subject.enPrunus persica L Batch
dc.subject.enMalus x domestica Borkh
dc.title.enChIP-seq and RNA-seq for complex and low-abundance tree buds reveal chromatin and expression co-dynamics during sweet cherry bud dormancy
dc.typeArticle de revue
dc.identifier.doi10.1007/s11295-019-1395-9
dc.subject.halSciences du Vivant [q-bio]/Biologie végétale
bordeaux.journalTree Genetics and Genomes
bordeaux.page9
bordeaux.volume16
bordeaux.issue1
bordeaux.peerReviewedoui
hal.identifierhal-02623341
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-02623341v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Tree%20Genetics%20and%20Genomes&rft.date=2020&rft.volume=16&rft.issue=1&rft.spage=9&rft.epage=9&rft.eissn=1614-2942&rft.issn=1614-2942&rft.au=VIMONT,%20No%C3%A9mie&QUAH,%20Fu%20Xiang&SCH%C3%96PFER,%20David%20Guillaume&ROUDIER,%20Fran%C3%A7ois&DIRLEWANGER,%20Elisabeth&rft.genre=article


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