Transcriptome profiling of sorted endoreduplicated nuclei from tomato fruits: how the global shift in expression ascribed to DNA ploidy influences RNA-Seq data normalization and interpretation
| hal.structure.identifier | Biologie du fruit et pathologie [BFP] | |
| hal.structure.identifier | Génomique et Biotechnologie des Fruits [GBF] | |
| dc.contributor.author | PIRRELLO, Julien | |
| hal.structure.identifier | Biologie du fruit et pathologie [BFP] | |
| dc.contributor.author | DELUCHE, Cynthia | |
| hal.structure.identifier | Biologie du fruit et pathologie [BFP] | |
| dc.contributor.author | FRANGNE, Nathalie | |
| hal.structure.identifier | Biologie du fruit et pathologie [BFP] | |
| dc.contributor.author | GEVAUDANT, Frederic | |
| hal.structure.identifier | Génomique et Biotechnologie des Fruits [GBF] | |
| dc.contributor.author | MAZA, Elie | |
| hal.structure.identifier | Génomique et Biotechnologie des Fruits [GBF] | |
| dc.contributor.author | DJARI, Anis | |
| hal.structure.identifier | Institut de Biologie Intégrative de la Cellule [I2BC] | |
| dc.contributor.author | BOURGE, Mickael | |
| hal.structure.identifier | Biologie du fruit et pathologie [BFP] | |
| dc.contributor.author | RENAUDIN, Jean-Pierre | |
| hal.structure.identifier | Institut de Biologie Intégrative de la Cellule [I2BC] | |
| dc.contributor.author | BROWN, Spencer | |
| hal.structure.identifier | Institut de biologie de l'ENS Paris [IBENS] | |
| dc.contributor.author | BOWLER, Chris | |
| hal.structure.identifier | Génomique et Biotechnologie des Fruits [GBF] | |
| dc.contributor.author | ZOUINE, Mohamed | |
| hal.structure.identifier | Biologie du fruit et pathologie [BFP] | |
| dc.contributor.author | CHEVALIER, Christian | |
| hal.structure.identifier | Biologie du fruit et pathologie [BFP] | |
| dc.contributor.author | GONZALEZ, Nathalie | |
| dc.date.issued | 2018 | |
| dc.identifier.issn | 0960-7412 | |
| dc.description.abstractEn | As part of normal development most eukaryotic organisms, ranging from insects and mammals to plants, display variations in nuclear ploidy levels resulting from somatic endopolyploidy. Endoreduplication is the major source of endopolyploidy in higher plants. Endoreduplication is a remarkable characteristic of the fleshy pericarp tissue of developing tomato fruits, where it establishes a highly integrated cellular system that acts as a morphogenetic factor supporting cell growth. However, the functional significance of endoreduplication is not fully understood. Although endoreduplication is thought to increase metabolic activity due to a global increase in transcription, the issue of gene-specific ploidy-regulated transcription remains open. To investigate the influence of endoreduplication on transcription in tomato fruit, we tested the feasibility of a RNA sequencing (RNA-Seq) approach using total nuclear RNA extracted from purified populations of flow cytometry-sorted nuclei based on their DNA content. Here we show that cell-based approaches to the study of RNA-Seq profiles need to take into account the putative global shift in expression between samples for correct analysis and interpretation of the data. From ploidy-specific expression profiles we found that the activity of cells inside the pericarp is related both to the ploidy level and their tissue location. | |
| dc.language.iso | en | |
| dc.publisher | Wiley | |
| dc.rights.uri | http://creativecommons.org/licenses/by/ | |
| dc.subject.en | Fruit | |
| dc.subject.en | Endoreduplication | |
| dc.subject.en | Fruit development | |
| dc.subject.en | Gene Expression Profiling | |
| dc.subject.en | Lycopersicon esculentum | |
| dc.subject.en | Ploidies | |
| dc.subject.en | Tomato | |
| dc.subject.en | RNA-Seq profiling | |
| dc.subject.en | RNA | |
| dc.subject.en | Sequence Analysis | |
| dc.subject.en | Solanum lycopersicum | |
| dc.subject.en | Sorted nuclei | |
| dc.subject.en | Technical Advance | |
| dc.subject.en | PF | |
| dc.subject.en | Cell Nucleus | |
| dc.subject.en | CYTO | |
| dc.subject.en | Data interpretation | |
| dc.subject.en | DNA | |
| dc.subject.en | Plant | |
| dc.title.en | Transcriptome profiling of sorted endoreduplicated nuclei from tomato fruits: how the global shift in expression ascribed to DNA ploidy influences RNA-Seq data normalization and interpretation | |
| dc.type | Article de revue | |
| dc.identifier.doi | 10.1111/tpj.13783 | |
| dc.subject.hal | Sciences du Vivant [q-bio] | |
| bordeaux.journal | Plant Journal | |
| bordeaux.page | 387--398 | |
| bordeaux.volume | 93 | |
| bordeaux.issue | 2 | |
| bordeaux.peerReviewed | oui | |
| hal.identifier | hal-02183254 | |
| hal.version | 1 | |
| hal.popular | non | |
| hal.audience | Internationale | |
| hal.origin.link | https://hal.archives-ouvertes.fr//hal-02183254v1 | |
| bordeaux.COinS | ctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Plant%20Journal&rft.date=2018&rft.volume=93&rft.issue=2&rft.spage=387--398&rft.epage=387--398&rft.eissn=0960-7412&rft.issn=0960-7412&rft.au=PIRRELLO,%20Julien&DELUCHE,%20Cynthia&FRANGNE,%20Nathalie&GEVAUDANT,%20Frederic&MAZA,%20Elie&rft.genre=article |
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