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
Idioma
en
Article de revue
Este ítem está publicado en
The Plant Journal. 2018, vol. 93, n° 2, p. 387--398
Wiley
Resumen en inglés
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 ...Leer más >
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.< Leer menos
Palabras clave en inglés
Plant
DNA
Data interpretation
CYTO
Cell Nucleus
PF
Technical Advance
Sorted nuclei
Solanum lycopersicum
Sequence Analysis
RNA
RNA-Seq profiling
Tomato
Ploidies
Lycopersicon esculentum
Gene Expression Profiling
Fruit development
Endoreduplication
Fruit
Orígen
Importado de HalCentros de investigación