Alternative Splicing Regulation During Light-Induced Germination of Arabidopsis thaliana Seeds.

Rocío Soledad Tognacca,Lucas Servi,Carlos Esteban Hernando,Javier Francisco Botto,Maite Saura-Sanchez,Marcelo Javier Yanovsky,Ezequiel Petrillo

doi:10.3389/fpls.2019.01076

Abstract

Seed dormancy and germination are relevant processes for a successful seedling establishment in the field. Light is one of the most important environmental factors involved in the relief of dormancy to promote seed germination. In Arabidopsis thaliana seeds, phytochrome photoreceptors tightly regulate gene expression at different levels. The contribution of alternative splicing (AS) regulation in the photocontrol of seed germination is still unknown. The aim of this work is to study gene expression modulated by light during germination of A. thaliana seeds, with focus on AS changes. Hence, we evaluated transcriptome-wide changes in stratified seeds irradiated with a pulse of red (Rp) or far-red (FRp) by RNA sequencing (RNA-seq). Our results show that the Rp changes the expression of ∼20% of the transcriptome and modifies the AS pattern of 226 genes associated with mRNA processing, RNA splicing, and mRNA metabolic processes. We further confirmed these effects for some of the affected AS events. Interestingly, the reverse transcriptase–polymerase chain reaction (RT–PCR) analyses show that the Rp modulates the AS of splicing-related factors (At-SR30, At-RS31a, At-RS31, and At-U2AF65A), a light-signaling component (At-PIF6), and a dormancy-related gene (At-DRM1). Furthermore, while the phytochrome B (phyB) is responsible for the AS pattern changes of At-U2AF65A and At-PIF6, the regulation of the other AS events is independent of this photoreceptor. We conclude that (i) Rp triggers AS changes in some splicing factors, light-signaling components, and dormancy/germination regulators; (ii) phyB modulates only some of these AS events; and (iii) AS events are regulated by R and FR light, but this regulation is not directly associated with the intensity of germination response. These data will help in boosting research in the splicing field and our understanding about the role of this mechanism during the photocontrol of seed germination.

Highlights

Seed dormancy is a developmental checkpoint that allows plants to regulate when and where they grow
We identified a total of 5,785 genes whose mRNA levels are significantly affected, either increased or decreased, more than 1.5-fold (FDR < 0.05) in response to the red pulse (Rp) (Figure 1C and Supplementary Table 1)
We evaluated the effects of R light on alternative splicing (AS) and identified a total of 226 genes with AS events that are regulated by the light pulse (Figure 1C and Supplementary Table 1)

Summary

Introduction

Seed dormancy is a developmental checkpoint that allows plants to regulate when and where they grow. Temperature, light, and nitrates are the most relevant environmental factors regulating the relief of seed dormancy to promote seed germination (BenechArnold et al, 2000). These cues can trigger molecular responses including hormone signaling, mainly those of abscisic acid (ABA) and gibberellin (GA). ABA promotes primary dormancy induction and later maintenance, whereas GA promotes seed germination. Environmental signals regulate this balance by modifying the expression of metabolic enzymes as well as those of positive and negative regulators of both hormones, many of which are feedback regulated (Finkelstein et al, 2008)

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