The Arabidopsis lncRNA ASCO modulates the transcriptome through interaction with splicing factors

Richard Rigo, Jérémie Bazin, Natali Romero-Barrios, Michaël Moison, Leandro Lucero, Aurélie Christ, Moussa Benhamed, Thomas Blein, Stéphanie Huguet, Céline Charon, Martin Crespi, Federico Ariel

Research output: Contribution to journalArticlepeer-review

54 Scopus citations

Abstract

Alternative splicing (AS) is a major source of transcriptome diversity. Long noncoding RNAs (lncRNAs) have emerged as regulators of AS through different molecular mechanisms. In Arabidopsis thaliana, the AS regulators NSRs interact with the ALTERNATIVE SPLICING COMPETITOR (ASCO) lncRNA. Here, we analyze the effect of the knock-down and overexpression of ASCO at the genome-wide level and find a large number of deregulated and differentially spliced genes related to flagellin responses and biotic stress. In agreement, ASCO-silenced plants are more sensitive to flagellin. However, only a minor subset of deregulated genes overlaps with the AS defects of the nsra/b double mutant, suggesting an alternative way of action for ASCO. Using biotin-labeled oligonucleotides for RNA-mediated ribonucleoprotein purification, we show that ASCO binds to the highly conserved spliceosome component PRP8a. ASCO overaccumulation impairs the recognition of specific flagellin-related transcripts by PRP8a. We further show that ASCO also binds to another spliceosome component, SmD1b, indicating that it interacts with multiple splicing factors. Hence, lncRNAs may integrate a dynamic network including spliceosome core proteins, to modulate transcriptome reprogramming in eukaryotes.
Original languageEnglish (US)
JournalEMBO Reports
Volume21
Issue number5
DOIs
StatePublished - Apr 14 2020
Externally publishedYes

Bibliographical note

KAUST Repository Item: Exported on 2022-06-14
Acknowledgements: Synthetic flg22 peptide was kindly provided by J. Colcombet (IPS2). Seeds from the prp8-7 and the smd1b mutants were kindly provided by H. Vaucheret. We thank Wil Prall for critical reading of the manuscript. This work was supported by grants from ANPCyT (PICT 2016-0289 and -0007, Argentina), CNRS (Laboratoire International Associé NOCOSYM), the “Laboratoire d'Excellence (LABEX)” Saclay Plant Sciences (SPS; ANR-10-LABX-40), the Ministère Français de l'Enseignement Supérieur et de la Recherche (RR), and the ANR grants (ANR-15-CE20-0002-01 EPISYM and ANR 16-CE20-0003-04 SPLISIL) as well as the EPIMMUNITY International project between IPS2, France and KAUST University, Saudi Arabia. The POPS platform benefits from the support of the LabEx Saclay Plant Sciences-SPS (ANR-10-LABX-0040-SPS).
This publication acknowledges KAUST support, but has no KAUST affiliated authors.

ASJC Scopus subject areas

  • Biochemistry
  • Genetics
  • Molecular Biology

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