Jeremie, B. | Search bioRxiv

bioRxiv2020

An Arabidopsis long noncoding RNA modulates the transcriptome through interactions with a network of splicing factors

Alternative splicing (AS) is a major source of transcriptome and proteome diversity in higher organisms. Long noncoding RNAs (lncRNAs) have emerged as regulators of AS through a range of molecular mechanisms. In Arabidopsis thaliana, the AS regulators NSRa and b, which affect auxin-driven lateral root formation, can interact with the ALTERNATIVE SPLICING COMPETITOR (ASCO) lncRNA. Here, we analyzed the effect of the knockdown and overexpression of ASCO at genome-wide level and found a high number of deregulated and differentially spliced genes, related to flagellin responses and biotic stress. In agreement, roots from ASCO-knocked down plants are more sensitive to flagellin. Surprisingly, only a minor subset of genes overlapped with the AS defects of the nsra/b double mutant. Using biotin-labelled oligonucleotides for RNA-mediated ribonucleoprotein purification, we found that ASCO binds to the highly conserved core spliceosome component PRP8a. ASCO deregulation impairs the recognition of specific flagellin-related transcripts by PRP8a and SmD1b, another spliceosome component, suggesting that ASCO function regulates AS through the interaction with multiple splicing factors. Hence, lncRNAs may interact in a dynamic network with many splicing factors to modulate transcriptome reprogramming in eukaryotes.

molecular biology↗

bioRxiv2019

Role of MPK4 in pathogen-associated molecular pattern-triggered alternative splicing in Arabidopsis

Alternative splicing (AS) of pre-mRNAs in plants is an important mechanism of gene regulation in environmental stress tolerance but plant signals involved are essentially unknown. Pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) is mediated by mitogen-activated protein kinases and the majority of PTI defense genes are regulated by MPK3, MPK4 and MPK6. These responses have been mainly analyzed at the transcriptional level, however many splicing factors are direct targets of MAPKs. Here, we studied alternative splicing induced by the PAMP flagellin in Arabidopsis. We identified 506 PAMP-induced differentially alternatively spliced (DAS) genes. Although many DAS genes are targets of nonsense-mediated degradation (NMD), only 19% are potential NMD targets. Importantly, of the 506 PAMP-induced DAS genes, only 89 overlap with the set of 1849 PAMP-induced differentially expressed genes (DEG), indicating that transcriptome analysis does not identify most DASevents. Global DAS analysis of mpk3, mpk4, and mpk6 mutants revealed that MPK4 is a key regulator of PAMP-induced differential splicing, regulating AS of a number of splicing factors and immunity-related protein kinases, such as the calcium-dependent protein kinase CPK28, the cysteine-rich receptor like kinases CRK13 and CRK29 or the FLS2 co-receptor SERK4/BKK1. These data suggest that MAP kinase regulation of splicing factors is a key mechanism in PAMP-induced AS regulation of PTI.\n\nSignificance statementAlternative pre-mRNA splicing (AS) affects plant responses to environmental stresses. So far, however, the regulation of AS is little understood. Here, we studied AS induced by the pathogen-associated molecular pattern (PAMP) flagellin in Arabidopsis. We identified 506 differentially alternatively spliced (DAS) genes, 89 of which overlap with the 1849 DEG, indicating that the majority of DAS events go undetected by common transcriptome analysis. PAMP-triggered immunity is mediated by mitogen-activated protein kinases. Global DAS analysis of MAPK mutants revealed that MPK4 is a key regulator of AS by affecting splicing factors and a number of important protein kinases involved in immunity. Since PAMP-triggered phosphorylation of several splicing factors is directly mediated by MAPKs, we discovered a key mechanism of AS regulation.

plant biology↗