scholarly journals In plants, decapping prevents RDR6-dependent production of small interfering RNAs from endogenous mRNAs

2015 ◽  
Author(s):  
Angel Emilio Martínez de Alba ◽  
Ana Moreno ◽  
Marc Gabriel ◽  
Allison C Mallory ◽  
Aurélie Christ ◽  
...  
Keyword(s):  
Quality Control ◽  
Rna Polymerase ◽  
Gene Silencing ◽  
Transcriptional Gene Silencing ◽  
Small Interfering Rnas ◽  
Rna Dependent Rna Polymerase ◽  
P Bodies ◽  
New Class ◽  
Post Transcriptional Gene Silencing ◽  
Rna Quality Control

Cytoplasmic degradation of endogenous RNAs is an integral part of RNA quality control (RQC) and often relies on the removal of the 5’ cap structure and their subsequent 5’ to 3’ degradation in cytoplasmic processing (P-)bodies. In parallel, many eukaryotes degrade exogenous and selected endogenous RNAs through post-transcriptional gene silencing (PTGS). In plants, PTGS depends on small interfering (si)RNAs produced after the conversion of single-stranded RNAs to doublestranded RNAs by the cellular RNA DEPENDENT RNA POLYMERASE 6 (RDR6) in cytoplasmic siRNA-bodies. PTGS and RQC compete for transgene-derived RNAs, but it is unknown whether this competition also occurs for endogenous transcripts. We show that the lethality of decapping mutants is suppressed by impairing RDR6 activity. We establish that upon decapping impairment hundreds of endogenous mRNAs give rise to a new class of rqc-siRNAs, that over-accumulate when RQC processes are impaired, a subset of which depending on RDR6 for their production. We observe that P- and siRNA-bodies often are dynamically juxtaposed, potentially allowing for crosstalk of the two machineries. Our results suggest that the decapping of endogenous RNA limits their entry into the PTGS pathway. We anticipate that the rqc-siRNAs identified in decapping mutants represent a subset of a larger ensemble of endogenous siRNAs.

scholarly journals An atypical class of non-coding small RNAs produced in rice leaves upon bacterial infection

2021 ◽  
Author(s):  
Ganna Reshetnyak ◽  
Jonathan M. Jacobs ◽  
Florence Auguy ◽  
Coline Sciallano ◽  
Lisa Claude ◽  
...  
Keyword(s):  
Gene Silencing ◽  
Stress Responses ◽  
Small Rnas ◽  
Early Stage ◽  
Kinase Domain ◽  
Transcriptional Gene Silencing ◽  
Small Interfering Rnas ◽  
Post Transcriptional Gene Silencing ◽  
Virulent Strains ◽  
Microbe Interactions

ABSTRACTNon-coding small RNAs (sRNA) act as mediators of gene silencing and regulate plant growth, development and stress responses. Early insights into plant sRNAs established a role in antiviral defense and they are now extensively studied across plant-microbe interactions. Here, sRNA sequencing discovered a class of sRNA in rice (Oryza sativa) specifically associated with foliar diseases caused by Xanthomonas oryzae bacteria. Xanthomonas-induced small RNAs (xisRNAs) loci were distinctively upregulated in response to diverse virulent strains at an early stage of infection producing a single duplex of 20-22nt sRNAs. xisRNAs production was dependent on the Type III secretion system, a major bacterial virulence factor for host colonization. xisRNA loci overlap with annotated transcripts sequences often encoding protein kinase domain proteins. A number of the corresponding rice cis-genes have documented functions in immune signaling and some xisRNA loci coincide with the coding sequence of a conserved kinase motif. xisRNAs exhibit features of small interfering RNAs and their biosynthesis depend on canonical components OsDCL1 and OsHEN1. xisRNA induction possibly mediates post-transcriptional gene silencing but they do not broadly suppress cis-genes expression on the basis of mRNA-seq data. Overall, our results identify a group of unusual sRNAs with a potential role in plant-microbe interactions.

The long hand of the small RNAs reaches into several levels of gene regulation

2004 ◽  
Vol 82 (4) ◽  
pp. 472-481 ◽  
Author(s):  
Tony Nolan ◽  
Carlo Cogoni
Keyword(s):  
Gene Silencing ◽  
Small Rnas ◽  
Developmental Regulation ◽  
Transcriptional Gene Silencing ◽  
Rna Molecules ◽  
New Class ◽  
Post Transcriptional Gene Silencing ◽  
Wide Range ◽  
Cellular Defence ◽  
Genomic Organisation

Small RNA molecules such as siRNAs and miRNAs represent a new class of molecules that have been implicated in a wide range of diverse gene silencing phenomena. It is now becoming clear that these two similar molecules share several common features in both their biogenesis and their mechanism of action. Thus, the siRNA and miRNA pathways may have evolved from a common ancestral mechanism that has diverged to play important roles in developmental regulation, genomic organisation, and cellular defence against foreign nucleic acids.Key words: miRNA, siRNA, post-transcriptional gene silencing, RNAi, heterochromatin.

scholarly journals Comparison between the Repression Potency of siRNA Targeting the Coding Region and the 3′-Untranslated Region of mRNA

2013 ◽  
Vol 2013 ◽  
pp. 1-5 ◽  
Author(s):  
Ching-Fang Lai ◽  
Chih-Ying Chen ◽  
Lo-Chun Au
Keyword(s):  
Gene Silencing ◽  
Thermodynamic Stability ◽  
Untranslated Region ◽  
Stop Codon ◽  
Secondary Structures ◽  
Transcriptional Gene Silencing ◽  
Small Interfering Rnas ◽  
Coding Region ◽  
Post Transcriptional Gene Silencing ◽  
Flanking Sequences

Small interfering RNAs (siRNAs) are applied for post-transcriptional gene silencing by binding target mRNA. A target coding region is usually chosen, although the3′-untranslated region (3′-UTR) can also be a target. This study elucidates whether the coding region or3′-UTR elicits higher repression. pFLuc and pRLuc are two reporter plasmids. A segment ofFLucgene was PCR-amplified and inserted behind the stop codon of theRLucgene of the pRLuc. Similarly, a segment ofRLucgene was inserted behind the stop codon ofFLuc. Two siFLuc and two siRLuc were siRNAs designed to target the central portions of these segments. Therefore, the siRNA encountered the same targets and flanking sequences. Results showed that the two siFLuc elicited higher repression when theFLucsegment resided in the coding region. Conversely, the two siRLuc showed higher repression when theRLucsegment was in the3′-UTR. These results indicate that both the coding region and the3′-UTR can be more effective targets. The thermodynamic stability of the secondary structures was analyzed. The siRNA elicited higher repression in the coding region when the target configuration was stable, and needed to be solved by translation. A siRNA may otherwise favor the target at3′-UTR.

scholarly journals Cytoplasmic and nuclear quality control and turnover of single-stranded RNA modulate post-transcriptional gene silencing in plants

2013 ◽  
Vol 41 (8) ◽  
pp. 4699-4708 ◽  
Author(s):  
Ana Beatriz Moreno ◽  
Angel Emilio Martínez de Alba ◽  
Florian Bardou ◽  
Martin D. Crespi ◽  
Hervé Vaucheret ◽  
...  
Keyword(s):  
Quality Control ◽  
Gene Silencing ◽  
Transcriptional Gene Silencing ◽  
Post Transcriptional Gene Silencing

scholarly journals Small circular interfering RNAs (sciRNAs) as a potent therapeutic platform for gene-silencing

2021 ◽  
Vol 49 (18) ◽  
pp. 10250-10264
Author(s):  
Hartmut Jahns ◽  
Rohan Degaonkar ◽  
Peter Podbevsek ◽  
Swati Gupta ◽  
Anna Bisbe ◽  
...  
Keyword(s):  
Gene Silencing ◽  
Circular Rna ◽  
Antisense Strand ◽  
Rnai Pathway ◽  
Transcriptional Gene Silencing ◽  
Small Interfering Rnas ◽  
Post Transcriptional Gene Silencing ◽  
Sense Strand

Abstract In order to achieve efficient therapeutic post-transcriptional gene-silencing mediated by the RNA interference (RNAi) pathway, small interfering RNAs (siRNAs) must be chemically modified. Several supra-RNA structures, with the potential to stabilize siRNAs metabolically have been evaluated for their ability to induce gene silencing, but all have limitations or have not been explored in therapeutically relevant contexts. Covalently closed circular RNA transcripts are prevalent in eukaryotes and have potential as biomarkers and disease targets, and circular RNA mimics are being explored for use as therapies. Here we report the synthesis and evaluation of small circular interfering RNAs (sciRNAs). To synthesize sciRNAs, a sense strand functionalized with the trivalent N-acetylgalactosamine (GalNAc) ligand and cyclized using ‘click’ chemistry was annealed to an antisense strand. This strategy was used for synthesis of small circles, but could also be used for synthesis of larger circular RNA mimics. We evaluated various sciRNA designs in vitro and in vivo. We observed improved metabolic stability of the sense strand upon circularization and off-target effects were eliminated. The 5′-(E)-vinylphosphonate modification of the antisense strand resulted in GalNAc-sciRNAs that are potent in vivo at therapeutically relevant doses. Physicochemical studies and NMR-based structural analysis, together with molecular modeling studies, shed light on the interactions of this novel class of siRNAs, which have a partial duplex character, with the RNAi machinery.

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