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Related Experiment Video

Updated: Feb 15, 2026

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

Published on: April 30, 2011

High-resolution spatiotemporal transcriptome mapping of tomato fruit development and ripening.

Yoshihito Shinozaki¹, Philippe Nicolas², Noe Fernandez-Pozo²

¹Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.

Nature Communications

|January 27, 2018

Summary

This summary is machine-generated.

This study maps gene expression during tomato fruit development and ripening, revealing spatial and temporal patterns. It uncovers regulatory networks influencing fruit quality traits like texture, color, and aroma.

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Area of Science:

Plant Biology
Molecular Biology
Genomics

Background:

Tomato (Solanum lycopersicum) is a key model for fruit biology research.
Previous studies often used homogenized pericarp, neglecting internal tissue-specific gene expression during fruit growth and ripening.

Purpose of the Study:

To perform a spatiotemporally resolved transcriptome analysis of tomato fruit ontogeny.
To define regulatory and structural gene networks across different tissues and developmental stages.
To investigate spatial variations in epigenetic control during fruit ripening.

Main Methods:

Laser microdissection (LM) or hand dissection coupled with RNA-Seq analysis.
Spatiotemporal transcriptome profiling of tomato fruit development.
Bioinformatic analysis of gene regulatory networks and epigenetic patterns.

Main Results:

Identified gradients of gene expression during ripening, originating internally and radiating outwards.
Revealed basipetal gene expression changes along a latitudinal axis.
Defined regulatory networks including transcription factors and hormone pathways.
Discovered spatial epigenetic variations superimposed on ripening gradients.
Elucidated previously masked regulatory phenomena impacting fruit quality traits (texture, color, aroma, metabolites).

Conclusions:

Ripening is a complex process with distinct spatial and temporal gene expression patterns.
Epigenetic modifications play a role in regulating tomato fruit development and quality.
This high-resolution transcriptomic data provides new insights into fruit biology and breeding.