VIMONT, Noémie; QUAH, Fu Xiang; SCHÖPFER, David Guillaume; ROUDIER, François; DIRLEWANGER, Elisabeth; WIGGE, Philip A.; WENDEN, Bénédicte; CORTIJO, Sandra

doi:10.1007/s11295-019-1395-9

Métadonnées

Afficher la notice complète

Licence d’utilisation du document

VIMONT, Noémie
The Sainsbury Laboratory [Norwich] [TSL]
Biologie du fruit et pathologie [BFP]

QUAH, Fu Xiang
The Sainsbury Laboratory [Norwich] [TSL]

SCHÖPFER, David Guillaume
The Sainsbury Laboratory [Norwich] [TSL]

Langue

Article de revue

Ce document a été publié dans

Tree Genetics and Genomes. 2020, vol. 16, n° 1, p. 9

Springer Verlag

Résumé en anglais

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.< Réduire

Mots clés en anglais

Tree buds

ChIP-seq/Chromatin immunoprecipitation-sequencing

RNA-seq/RNA-sequencing

Prunus avium L.

Prunus persica L Batch

Malus x domestica Borkh

Métadonnées

Licence d’utilisation du document

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

Langue

Ce document a été publié dans

Résumé en anglais

Mots clés en anglais

DOI

Origine

Unités de recherche