Dataset Information

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

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.

SUBMITTER: Bazin J

PROVIDER: S-EPMC6111844 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Publications

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

Bazin Jérémie J Romero Natali N Rigo Richard R Charon Celine C Blein Thomas T Ariel Federico F Crespi Martin M

Frontiers in plant science 20180821

Nuclear speckle RNA binding proteins (NSRs) act as regulators of alternative splicing (AS) and auxin-regulated developmental processes such as lateral root formation in <i>Arabidopsis thaliana</i>. These proteins were shown to interact with specific alternatively spliced mRNA targets and at least with one structured lncRNA, named <i>Alternative Splicing Competitor</i> RNA. Here, we used genome-wide analysis of RNAseq to monitor the NSR global role on multiple tiers of gene expression, including ...[more]

PMID: 30186296

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Project description:BackgroundSeveral recent studies indicate that alternative splicing in Arabidopsis and other plants is a common mechanism for post-transcriptional modulation of gene expression. However, few analyses have been done so far to elucidate the functional relevance of alternative splicing in higher plants. Representing a frequent and universal subtle alternative splicing event among eukaryotes, alternative splicing at NAGNAG acceptors contributes to transcriptome diversity and therefore, proteome plasticity. Alternatively spliced NAGNAG acceptors are overrepresented in genes coding for proteins with RNA-recognition motifs (RRMs). As SR proteins, a family of RRM-containing important splicing factors, are known to be extensively alternatively spliced in Arabidopsis, we analyzed alternative splicing at NAGNAG acceptors in SR and SR-related genes.ResultsIn a comprehensive analysis of the Arabidopsis thaliana genome, we identified 6,772 introns that exhibit a NAGNAG acceptor motif. Alternative splicing at these acceptors was assessed using available EST data, complemented by a sequence-based prediction method. Of the 36 identified introns within 30 SR and SR-related protein-coding genes that have a NAGNAG acceptor, we selected 15 candidates for an experimental analysis of alternative splicing under several conditions. We provide experimental evidence for 8 of these candidates being alternatively spliced. Quantifying the ratio of NAGNAG-derived splice variants under several conditions, we found organ-specific splicing ratios in adult plants and changes in seedlings of different ages. Splicing ratio changes were observed in response to heat shock and most strikingly, cold shock. Interestingly, the patterns of differential splicing ratios are similar for all analyzed genes.ConclusionNAGNAG acceptors frequently occur in the Arabidopsis genome and are particularly prevalent in SR and SR-related protein-coding genes. A lack of extensive EST coverage can be compensated by using the proposed sequence-based method to predict alternative splicing at these acceptors. Our findings indicate that the differential effects on NAGNAG alternative splicing in SR and SR-related genes are organ- and condition-specific rather than gene-specific.

Dataset Information

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

Publications

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

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