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Lariats-derive siRNA by PTGS pathway mediate endogenous gene silencing and translational repression

ABSTRACT: Intron-derived lariat RNAs are generated by the spliceosome from pre-mRNAs. Typically, lariat RNAs undergo rapid elimination through DBR1-mediated debranching. There exists much stable lariats in Arabidopsis, indicating that a relatively high level of lariat RNAs would escape from the degradation by DBR1 under the physiological condition in plants. However, the mechanism underlying the biogenesis and function of those stable lariat RNAs remains elusive. Surprisingly, apart from a significant increase of lariat RNAs in a weak viable dbr1 mutant (dbr1-2), large amounts of double-stranded 21,22-nt sRNAs accumulated in the intronic regions where producing lariat RNAs, indicating that lariat RNAs may be further processed into sRNAs. Moreover, the increased 21,22-nt siRNAs in dbr1 mutant were demonstrated to be produced from lariat RNAs with the assistance of the RNA-dependent RNA polymerase 6 (RDR6) and Dicer-like proteins, implying the connection between lariat RNAs and the endogenous small RNA silencing pathway in plants. And we report the identification and characterization of a group of endogenous 22-siRNAs from lariats which could induce coding gene derived 22-nt siRNA that are generated by the DICER-LIKE 2 (DCL2) protein. When DBR1-mediated lariat RNA decay and DCL4 are deficient, the resulting massive accumulation of 22-nucleotide siRNAs from lariats which could induce coding gene derived 22-nt siRNA that are generated by the DICER-LIKE 2 (DCL2) protein restrains translation and inhibits plant growth. Thus, our research uncovers an unprecedented lariats-derived siRNA pathway which plays roles in plant development.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE284626 | GEO | 2026/07/06

REPOSITORIES: GEO

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Lariats-derived siRNA by PTGS pathway mediate endogenous gene silencing and translational repression

Project description:Intron-derived lariat RNAs are generated by the spliceosome from pre-mRNAs. Typically, lariat RNAs undergo rapid elimination through DBR1-mediated debranching. There exists much stable lariats in Arabidopsis, indicating that a relatively high level of lariat RNAs would escape from the degradation by DBR1 under the physiological condition in plants. However, the mechanism underlying the biogenesis and function of those stable lariat RNAs remains elusive. Surprisingly, apart from a significant increase of lariat RNAs in a weak viable dbr1 mutant (dbr1-2), large amounts of double-stranded 21,22-nt sRNAs accumulated in the intronic regions where producing lariat RNAs, indicating that lariat RNAs may be further processed into sRNAs. Moreover, the increased 21,22-nt siRNAs in dbr1 mutant were demonstrated to be produced from lariat RNAs with the assistance of the RNA-dependent RNA polymerase 6 (RDR6) and Dicer-like proteins, implying the connection between lariat RNAs and the endogenous small RNA silencing pathway in plants. And we report the identification and characterization of a group of endogenous 22-siRNAs from lariats which could induce coding gene derived 22-nt siRNA that are generated by the DICER-LIKE 2 (DCL2) protein. When DBR1-mediated lariat RNA decay and DCL4 are deficient, the resulting massive accumulation of 22-nucleotide siRNAs from lariats which could induce coding gene derived 22-nt siRNA that are generated by the DICER-LIKE 2 (DCL2) protein restrains translation and inhibits plant growth. Thus, our research uncovers an unprecedented lariats-derived siRNA pathway which plays roles in plant development.

2026-07-06 | GSE298301 | GEO

Plant 22-nt siRNAs mediate translational repression and stress adaptation

Project description:Small interfering RNAs (siRNAs) are critical for proper development and immunity in eukaryotes1. Plants produce siRNAs with lengths of 21-, 22-, or 24- nucleotides (nt), wherein the 21- and 24-nt siRNAs mediate mRNA cleavage and DNA methylation2,3, respectively. However, the biological functions of 22-nt siRNAs remain elusive. Here we report the identification and characterization of a group of endogenous 22-nt siRNAs generated from the action of DICER-LIKE 2 (DCL2). When cytoplasmic RNA decay and DCL4 are deficient, the massive accumulation of 22-nt siRNAs causes pleiotropic growth disorders, including severe dwarfism, meristem defect, and pigmentation. Notably, two genes that encode nitrate reductases, NIA1 and NIA2, produce nearly half of the total of 22-nt siRNAs. Production of 22-nt siRNA triggers explosive self-amplification that leads to a small RNA storm, and induces dramatic translational repression both gene-specifically and globally. 22-nt siRNAs are also found to preferentially accumulate upon nitrogen deficiency, which acts to restrain plant growth and promote stress responses. Thus, our research uncovers the unique properties of 22-nt siRNAs, a previously unexplored class of plant siRNAs, and highlights the length of small RNA as a major functional determinant.

2020-02-14 | GSE135962 | GEO

Plant 22-nt siRNAs mediate translational repression and stress adaptation

2020-02-14 | GSE135961 | GEO

Plant 22-nt siRNAs mediate translational repression and stress adaptation

2020-02-14 | GSE135959 | GEO

Plant 22-nt siRNAs mediate translational repression and stress adaptation

2020-02-14 | GSE135957 | GEO

22-nucleotide siRNAs mediate translational repression and trigger a silencing storm

2020-04-13 | GSE148513 | GEO

22-nucleotide siRNAs mediate translational repression and trigger a silencing storm [es]

2020-04-13 | GSE148512 | GEO

Debranching enzyme DBR1-mediated lariat RNA turnover requires ALBA proteins in Arabidopsis

Project description:Lariat RNAs, generated as by-products of RNA splicing from excised introns, must be removed. RNA debranching enzyme (DBR1) is the core factor responsible for lariat RNA removal. However, the mechanism by which DBR1 debranches lariat RNAs remains unclear. Here, we demonstrate that six ALBA (Acetylation Lowers Binding Affinity) proteins interact with DBR1 to enhance its debranching activity and facilitate DBR1's accessibility to lariat RNAs, thereby promoting lariat RNA turnover. Similar to dbr1, alba mutants exhibit pleiotropic developmental defects and accumulate lariat RNAs. ALBAs bind to lariat RNAs via their C-terminal RGG/RG-rich repeats and assist DBR1 in binding to these RNAs. The N-terminal ALBA domain mediates the interaction with DBR1 and enhances its enzymatic activity. Cold stress induces lariat RNA accumulation by attenuating the ALBA–DBR1 interaction, which in turn reduces the induction of cold-responsive genes by impairing their transcription. Together, these findings uncover that lariat RNA turnover requires ALBA proteins.

2025-11-20 | GSE284756 | GEO

The Debranching Enzyme Dbr1 Regulates Lariat Turnover and Intron Splicing

Project description:The majority of genic transcription is intronic. Introns are removed by splicing as branched lariat RNAs which require rapid recycling. The branch site is recognized during splicing catalysis and later debranched by Dbr1 in the rate-limiting step of lariat turnover. Through generation of the first viable DBR1 knockout cell line, we find the predominantly nuclear Dbr1 enzyme to encode the sole debranching activity in human cells. Dbr1 preferentially debranches substrates that contain canonical U2 binding motifs, suggesting that branchsites discovered through sequencing do not necessarily represent those favored by the spliceosome. We find that Dbr1 also exhibits specificity for particular 5' splice site sequences. We identify Dbr1 interactors through co-immunoprecipitation mass spectroscopy. We present a mechanistic model for Dbr1 recruitment to the branchpoint through the intron-binding protein AQR. In addition to a 20-fold increase in lariats, Dbr1 depletion increases exon skipping. Using ADAR fusions to timestamp lariats, we demonstrate a defect in spliceosome recycling. In the absence of Dbr1, spliceosomal components remain associated with the lariat for a longer period of time. As splicing is co-transcriptional, slower recycling increases the likelihood that downstream exons will be available for exon skipping.

2023-06-26 | MSV000092263 | MassIVE

Lariat mapping of wild type and DBR1 KO cells after knockdown of AQR

Project description:Using wild type HEK293T cells and our DBR1 CRISPR knockout cell line (C22), we investigated the effect of AQR knockdown on cellular lariat levels. Samples were taken after transfection with either one of two AQR-targeting siRNAs or a non-targeting control siRNA. After sequencing the samples, lariat mapping of the reads revealed that AQR knockdown increased the lariat recovery rate by ~50% relative to the level observed in the negative control samples.

2022-01-31 | GSE195668 | GEO

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