Nuclear Speckle RNA Binding Proteins Remodel Alternative Splicing and the Non-coding Arabidopsis Transcriptome to Regulate a Cross-Talk Between Auxin and Immune Responses

Jérémie Bazin,Martin Crespi,Natali Romero,Richard Rigo,Thomas Blein,Federico Ariel,Celine Charon

doi:10.3389/fpls.2018.01209

Abstract

Nuclear speckle RNA binding proteins (NSRs) act as regulators of alternative splicing (AS) and auxin-regulated developmental processes such as lateral root formation in Arabidopsis thaliana. These proteins were shown to interact with specific alternatively spliced mRNA targets and at least with one structured lncRNA, named Alternative Splicing Competitor RNA. Here, we used genome-wide analysis of RNAseq to monitor the NSR global role on multiple tiers of gene expression, including RNA processing and AS. NSRs affect AS of 100s of genes as well as the abundance of lncRNAs particularly in response to auxin. Among them, the FPA floral regulator displayed alternative polyadenylation and differential expression of antisense COOLAIR lncRNAs in nsra/b mutants. This may explains the early flowering phenotype observed in nsra and nsra/b mutants. GO enrichment analysis of affected lines revealed a novel link of NSRs with the immune response pathway. A RIP-seq approach on an NSRa fusion protein in mutant background identified that lncRNAs are privileged direct targets of NSRs in addition to specific AS mRNAs. The interplay of lncRNAs and AS mRNAs in NSR-containing complexes may control the crosstalk between auxin and the immune response pathway.

Highlights

RNA binding proteins (RBPs) have been shown to affect all steps of post-transcriptional gene expression control, including alternative splicing (AS), silencing, RNA decay, and translational control (Bailey-Serres et al, 2009)
To characterize the role of Nuclear speckle RNA binding proteins (NSRs) in the control of auxin regulated gene expression, we performed paired-end strand specific RNA sequencing on the nsra/nsrb double mutant and wild type (Col-0) seedlings treated for 24 h with the synthetic auxin NAA (100 nM) or a mock solution (Bardou et al, 2014; Tran et al, 2016) (Figure 1A)
Multifactor analysis of differential gene expression further showed that nsra/b mutation has a major effect on auxin-regulated gene expression

Summary

Introduction

RNA binding proteins (RBPs) have been shown to affect all steps of post-transcriptional gene expression control, including alternative splicing (AS), silencing, RNA decay, and translational control (Bailey-Serres et al, 2009). The Arabidopsis thaliana genome encodes for more than 200 proteins predicted to bind RNAs. The picture becomes even more complex since over 500 proteins were found to bind polyA+ RNA in a recent study attempting to define the RNA interactome using affinity capture and proteomics (Marondedze et al, 2016). Only a small subset of RBPs has been functionally assigned in plants. The versatility of RBPs on gene expression regulation has been recently highlighted by the identification of several among them acting at multiple steps of post-transcriptional gene regulation (Lee and Kang, 2016; Oliveira et al, 2017).

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