Chromatin Immunoprecipitation of Histone Modifications in Rosa chinensis

Petal were collected from R. chinensis ‘Old Blush’ and fixed in 1% (v/v) formaldehyde. ChIP assays were performed using anti-H3K9ac (Millipore, ref. 07-352) or anti-H3K27me3 (Millipore, ref. 07-449) antibodies according to a procedure adapted from Veluchamy et al61 (link). Library quality was assessed with Agilent 2100 Bioanalyzer (Agilent) and the libraries were subjected to high-throughput sequencing on Illumina NextSeq 500. After trimming, reads were aligned onto R. chinensis genome with bowtie262 (link) and a maximum mismatch of 1 bp and unique mapping reported. To determine the target regions of H3K9ac ChIP-seq, the Model-based Analysis of ChIP-seq (MACS2)63 (link) was used. Detection of H3K27me3 modification regions was performed using SICER64 (link). HOMER65 (link) was used to annotate H3K9ac peaks with nearby genes if peaks were located into -2k to +1kb window around the gene TSS. For H3K27me3 peaks, bedtools intersect 56 (link) was used and only genes that are overlapped with this specific modification were kept. Clustering of H3K9ac and H3K27me3 peaks was performed using SeqMINER66 (link). Rstudio, Circos67 (link) and NGSplot68 (link) were used for graphic representation of histone modifications.

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Raymond O., Gouzy J., Just J., Badouin H., Verdenaud M., Lemainque A., Vergne P., Moja S., Choisne N., Pont C., Carrère S., Caissard J.C., Couloux A., Cottret L., Aury J.M., Szecsi J., Latrasse D., Madoui M.A., François L., Fu X., Yang S.H., Dubois A., Piola F., Larrieu A., Perez M., Labadie K., Perrier L., Govetto B., Labrousse Y., Villand P., Bardoux C., Boltz V., Lopez-Roques C., Heitzler P., Vernoux T., Vandenbussche M., Quesneville H., Boualem A., Bendahmane A., Liu C., Le Bris M., Salse J., Baudino S., Benhamed M., Wincker P, & Bendahmane M. (2018). The Rosa genome provides new insights into the domestication of modern roses. Nature genetics, 50(6), 772-777.

Publication 2018

anti-H3K9ac anti-H3K27me3 Agilent 2100 Bioanalyzer NextSeq 500

Antibodies Blush Chip assays Chip seq Formaldehyde Genes Genome Histone modifications Library

Corresponding Organization :

Other organizations : Université Claude Bernard Lyon 1, École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Laboratoire de Reproduction et Développement des Plantes, Université de Toulouse, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Genoscope, Université Paris-Saclay, Génétique, Diversité, Écophysiologie des Céréales, Institut des Sciences des Plantes de Paris Saclay, Sorbonne Paris Cité, Université Paris Cité, Huazhong Agricultural University, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, École Nationale des Travaux Publics de l'État, Aix-Marseille Université, Institut de Recherche pour le Développement, Institut de Biologie Moléculaire des Plantes, University of Tübingen, Université d'Évry Val-d'Essonne

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Variable analysis

independent variables

Antibody used for ChIP assays: anti-H3K9ac (Millipore, ref. 07-352) or anti-H3K27me3 (Millipore, ref. 07-449)

dependent variables

Target regions of H3K9ac ChIP-seq detected using MACS2
H3K27me3 modification regions detected using SICER
Genes annotated near H3K9ac peaks using HOMER
Genes overlapped with H3K27me3 peaks using bedtools intersect

control variables

Petal samples collected from R. chinensis 'Old Blush'
Petal samples fixed in 1% (v/v) formaldehyde
ChIP assay procedure adapted from Veluchamy et al.
Reads aligned onto R. chinensis genome using bowtie2 with maximum 1 bp mismatch and unique mapping
Library quality assessed with Agilent 2100 Bioanalyzer
High-throughput sequencing performed on Illumina NextSeq 500

Annotations

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