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Alternative RNA Splicing

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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

Alternative splicing enhances transcriptome complexity in desiccating seeds.

Arunkumar Srinivasan^1,2, José M Jiménez-Gómez^1,3, Fabio Fornara⁴

¹Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany.

Journal of Integrative Plant Biology

|April 29, 2016

Summary

Seed maturation involves dehydration, establishing desiccation tolerance through gene regulation. This study reveals alternative splicing (AS) significantly impacts gene expression during seed development and desiccation in Arabidopsis thaliana.

Keywords:

Alternative splicing Arabidopsis thaliana seed desiccation

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Using the E1A Minigene Tool to Study mRNA Splicing Changes

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Area of Science:

Plant Biology
Molecular Biology
Genetics

Background:

Seed maturation is crucial for plant survival, involving dehydration and desiccation tolerance.
Alternative splicing (AS) is known to regulate some key seed maturation genes.
A comprehensive analysis of AS during seed maturation was previously lacking.

Purpose of the Study:

To investigate gene expression and AS globally during Arabidopsis thaliana seed development.
To analyze AS patterns before and after seed desiccation.
To identify the role of AS in establishing seed desiccation tolerance.

Main Methods:

Global gene expression and AS analysis during Arabidopsis thaliana seed development.
Bioinformatics tool development for identifying differentially spliced regions.
Comparison of AS patterns before and after seed desiccation.

Main Results:

Alternative splicing (AS) was identified in 34% of genes expressed before and after desiccation.
Most identified AS transcript variants were novel and specific to seed tissues.
AS was found to regulate 6% of transcripts without transcriptional changes during desiccation, including seed master regulators.

Conclusions:

Alternative splicing plays a significant and unique role during seed desiccation and maturation.
AS contributes to establishing desiccation tolerance by modifying gene expression.
Routine consideration of AS in transcriptomic analysis is recommended to uncover regulatory mechanisms.