The Nuclear Ribonucleoprotein SmD1 Interplays with Splicing, RNA Quality Control, and Posttranscriptional Gene Silencing in Arabidopsis

Elvira-Matelot, Emilie; Bardou, Florian; Ariel, Federico; Jauvion, Vincent; Bouteiller, Nathalie; Masson, Ivan Le; Cao, Jun; Crespi, Martín; Vaucheret, Hervé

doi:10.1105/tpc.15.01045

Cited by 42 publications

(64 citation statements)

References 39 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Sm proteins can also have functions in RNA metabolism beyond splicing of primary transcripts (Lu et al 2014;Xiong et al 2015). In Arabidopsis, SmD1 participates in pre-mRNA splicing, RNA quality control, and post-transcriptional gene silencing (Elvira-Matelot et al 2016).…”

Section: Smfamentioning

confidence: 99%

A genetic screen implicates a CWC16/Yju2/CCDC130 protein and SMU1 in alternative splicing in Arabidopsis thaliana

Kanno

Lin

et al. 2017

RNA

View full text Add to dashboard Cite

To identify regulators of pre-mRNA splicing in plants, we developed a forward genetic screen based on an alternatively spliced GFP reporter gene in Arabidopsis thaliana. In wild-type plants, three major splice variants issue from the GFP gene but only one represents a translatable GFP mRNA. Compared to wild-type seedlings, which exhibit an intermediate level of GFP expression, mutants identified in the screen feature either a "GFP-weak" or "Hyper-GFP" phenotype depending on the ratio of the three splice variants. GFP-weak mutants, including previously identified prp8 and rtf2, contain a higher proportion of unspliced transcript or canonically spliced transcript, neither of which is translatable into GFP protein. In contrast, the coilindeficient hyper-gfp1 (hgf1) mutant displays a higher proportion of translatable GFP mRNA, which arises from enhanced splicing of a U2-type intron with noncanonical AT-AC splice sites. Here we report three new hgf mutants that are defective, respectively, in spliceosome-associated proteins SMU1, SmF, and CWC16, an Yju2/CCDC130-related protein that has not yet been described in plants. The smu1 and cwc16 mutants have substantially increased levels of translatable GFP transcript owing to preferential splicing of the U2-type AT-AC intron, suggesting that SMU1 and CWC16 influence splice site selection in GFP pre-mRNA. Genome-wide analyses of splicing in smu1 and cwc16 mutants revealed a number of introns that were variably spliced from endogenous pre-mRNAs. These results indicate that SMU1 and CWC16, which are predicted to act directly prior to and during the first catalytic step of splicing, respectively, function more generally to modulate splicing patterns in plants.

show abstract

Section: Smfamentioning

confidence: 99%

A genetic screen implicates a CWC16/Yju2/CCDC130 protein and SMU1 in alternative splicing in Arabidopsis thaliana

Kanno

Lin

et al. 2017

RNA

View full text Add to dashboard Cite

show abstract

“…To date, however, only two putative Arabidopsis Sms, SMD3 and SMD1, have been characterized. The analysis of smd3b and smd1b null mutants revealed that SMD3 and SMD1 are involved in plant development as well as in the processing of the few pre-mRNAs whose splicing patterns were examined (Swaraz et al, 2011;Elvira-Matelot et al, 2016). Nonetheless, whether they are functional Sm proteins that ensure precise levels of U snRNAs and what their relevance is in modulating pre-mRNA splicing at the genomic level is unknown.…”

Section: Introductionmentioning

confidence: 99%

Arabidopsis SME1 Regulates Plant Development and Response to Abiotic Stress by Determining Spliceosome Activity Specificity

et al. 2019

View full text Add to dashboard Cite

J.A.J.); 0000-0003-2020-0950 (J.S.)The control of precursor-messenger RNA (pre-mRNA) splicing is emerging as an important layer of regulation in plant responses to endogenous and external cues. In eukaryotes, pre-mRNA splicing is governed by the activity of a large ribonucleoprotein machinery, the spliceosome, whose protein core is composed of the Sm ring and the related Sm-like 2-8 complex. Recently, the Arabidopsis (Arabidopsis thaliana) Sm-like 2-8 complex has been characterized. However, the role of plant Sm proteins in pre-mRNA splicing remains largely unknown. Here, we present the functional characterization of Sm protein E1 (SME1), an Arabidopsis homolog of the SME subunit of the eukaryotic Sm ring. Our results demonstrate that SME1 regulates the spliceosome activity and that this regulation is controlled by the environmental conditions. Indeed, depending on the conditions, SME1 ensures the efficiency of constitutive and alternative splicing of selected pre-mRNAs. Moreover, missplicing of most targeted pre-mRNAs leads to the generation of nonsense-mediated decay signatures, indicating that SME1 also guarantees adequate levels of the corresponding functional transcripts. In addition, we show that the selective function of SME1 in ensuring appropriate gene expression patterns through the regulation of specific pre-mRNA splicing is essential for adequate plant development and adaptation to freezing temperatures. These findings reveal that SME1 plays a critical role in plant development and interaction with the environment by providing spliceosome activity specificity.

show abstract

“…Remarkably, similar AS defects were shown between the prp8a mutant and RNAi-ASCO lines for pathogenrelated genes (Figs 6BC and EV10), indicating that the flg22 differential phenotype of RNAi-ASCO plants may be related to the interaction with the spliceosome components. Recently, we identified another core component of the spliceosome, SmD1b, linked to both AS and the recognition of aberrant ncRNAs to trigger gene silencing (Elvira-Matelot et al, 2016). Interestingly, ASCO expression levels are also increased in the smd1b mutant ( Fig 6D), exhibiting the same transcript accumulation as in prp8a and nsra/b mutants.…”

Section: Asco Interacts With the Spliceosome Core Components Prp8a Anmentioning

confidence: 85%

AnArabidopsislong noncoding RNA modulates the transcriptome through interactions with a network of splicing factors

Rigo

Bazin

Romero-Barrios

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

and FA (fariel@santafeconicet.gov.ar)Running title: LncRNA shapes alternative splicing ABSTRACT 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 biotinlabelled 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.Keywords: core splicing factors/flagellin/long noncoding RNA/PRP8a/SmD1b

show abstract

The Nuclear Ribonucleoprotein SmD1 Interplays with Splicing, RNA Quality Control, and Posttranscriptional Gene Silencing in Arabidopsis

Cited by 42 publications

References 39 publications

A genetic screen implicates a CWC16/Yju2/CCDC130 protein and SMU1 in alternative splicing in Arabidopsis thaliana

A genetic screen implicates a CWC16/Yju2/CCDC130 protein and SMU1 in alternative splicing in Arabidopsis thaliana

Arabidopsis SME1 Regulates Plant Development and Response to Abiotic Stress by Determining Spliceosome Activity Specificity

AnArabidopsislong noncoding RNA modulates the transcriptome through interactions with a network of splicing factors

Contact Info

Product

Resources

About