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URT1-mediated uridylation prevents the production of spurious siRNAs targeting mRNAs in Arabidopsis thaliana

ABSTRACT: URT1-mediated uridylation prevents the production of spurious siRNAs targeting mRNAs in Arabidopsis thaliana

PROVIDER: PRJNA624174 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11521524.fastq.gz	Fastqsanger.gz
	SRR11521525.fastq.gz	Fastqsanger.gz
	SRR11521526.fastq.gz	Fastqsanger.gz
	SRR11521527.fastq.gz	Fastqsanger.gz
	SRR11521528.fastq.gz	Fastqsanger.gz

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URT1-mediated uridylation prevents the production of spurious siRNAs targeting mRNAs in Arabidopsis thaliana

Project description:To determine whether the developmental defects of urt1-1 xrn4-3 are linked to the biogenesis of spurious siRNAs, we analyzed small RNA libraries and indeed detected the accumulation of 21 nt siRNAs originating from mRNA loci in urt1-1 xrn4-3.

2020-05-28 | GSE148427 | GEO

The TUTase URT1 connects decapping activators and prevents the accumulation of excessively deadenylated mRNAs to avoid siRNA biogenesis

Project description:Uridylation is a widespread modification destabilizing eukaryotic mRNAs. Yet, molecular mechanisms underlying TUTase-mediated mRNA degradation remain mostly unresolved. Here, we report that the Arabidopsis TUTase URT1 participates in a molecular network connecting several translational repressors/decapping activators. URT1 directly interacts with DECAPPING 5 (DCP5), the Arabidopsis ortholog of human LSM14 and yeast Scd6, and this interaction connects URT1 to additional decay factors like DDX6/Dhh1-like RNA helicases. Nanopore direct RNA sequencing reveals a global role of URT1 in shaping poly(A) tail length, notably by preventing the accumulation of excessively deadenylated mRNAs. Based on in vitro and in planta data, we propose a model that explains how URT1 could reduce the accumulation of oligo(A)-tailed mRNAs both by favoring their degradation and because 3’ terminal uridines intrinsically hinder deadenylation. Importantly, preventing the accumulation of excessively deadenylated mRNAs avoids the biogenesis of illegitimate siRNAs that silence endogenous mRNAs and perturb Arabidopsis growth and development.

2020-12-01 | PXD022676 | Pride

Impact of URT1-mediated uridylation on small RNA tailing in Arabidopsis

Project description:To analyse the impact of URT1-mediated uridylation on miRNA and siRNA tailing, we deep-sequenced small RNA libraries for WT and urt1 duplicate samples at the same developmental stage that was analyzed by TAIL-seq, i.e., two-week-old seedlings. Examination of miRNA and siRNA tailing in WT and urt1 samples.

2016-03-11 | E-GEOD-72456 | biostudies-arrayexpress

Impact of URT1-mediated uridylation on small RNA tailing in Arabidopsis

2016-03-11 | GSE72456 | GEO

URT1-mediated uridylation shapes poly(A) tails in Arabidopsis

Project description:Using 3' RACE-seq method, we show that the Arabidopsis TUTase URT1 shapes poly(A) tail profiles by reducing the accumulation of short-tailed mRNAs in planta. We took advantage of the depth of this method to precisely compare polyadenylation and uridylation profiles for 22 mRNAs analyzed in two biological replicates of wild-type and urt1 plants in Arabidopsis

2020-05-28 | GSE148406 | GEO

Molecular connection between the TUTase URT1 and decapping activators

Project description:Uridylation is a widespread modification destabilizing eukaryotic mRNAs. Yet, molecular mechanisms underlying TUTase-mediated mRNA degradation remain mostly unresolved. Here, we report that the Arabidopsis TUTase URT1 participates in a molecular network connecting several translational repressors/decapping activators including DECAPPING 5 (DCP5), the Arabidopsis ortholog of human LSM14 and yeast Scd6. A conserved Helical Leucine-rich Motif (HLM) within an intrinsically disordered region of URT1 binds to the LSm domain of DCP5. This interaction connects URT1 to additional decay factors like DDX6/Dhh1-like RNA helicases. The combination of in planta and in vitro analyses supports a model that explains how URT1 reduces the accumulation of oligo(A)-tailed mRNAs: first, by connecting decapping factors and second, because 3’ terminal uridines can intrinsically hinder deadenylation. Importantly, preventing the accumulation of excessively deadenylated mRNAs in Arabidopsis avoids the biogenesis of illegitimate siRNAs that silence endogenous mRNAs and perturb plant growth and development.

2020-05-29 | PXD018672 | Pride

URT1-mediated uridylation shapes poly(A) tails in Arabidopsis

Project description:URT1-mediated uridylation shapes poly(A) tails in Arabidopsis

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Global view of mRNA uridylation in Arabidopsis

Project description:To obtain a global view of mRNA uridylation in Arabidopsis, we generated TAIL-seq libraries from WT plants, urt1 and xrn4 single mutants, and urt1 xrn4 double mutant. The TAIL-seq protocol was recently developed to deep-sequence the 3' ends of RNAs (Chang et al., 2014). We generated TAIL-seq libraries from WT plants, urt1 and xrn4 single mutants, and urt1 xrn4 double mutant.

2016-03-11 | E-GEOD-72457 | biostudies-arrayexpress

Distinct and cooperative activities of HESO1 and URT1 nucleotidyl transferases in microRNA turnover in Arabidopsis

Project description:3’ uridylation is increasingly recognized as a conserved RNA modification process associated with RNA turnover in eukaryotes. 2’-O-methylation on the 3’ terminal ribose protects micro(mi)RNAs from 3’ truncation and 3’ uridylation in Arabidopsis. Previously, we identified HESO1 as the nucleotidyl transferase that uridylates most unmethylated miRNAs in vivo, but substantial 3’ tailing of miRNAs still remains in heso1 loss-of-function mutants. In this study, we found that among nine HESO1 paralogs, UTP:RNA URIDYLYLTRANSFERASE 1 (URT1) is the single most predominant nucleotidyl transferase that tails miRNAs. URT1 and HESO1 prefer substrates with different 3’ end nucleotides in vitro and act cooperatively to tail different forms of the same miRNAs in vivo. Moreover, both HESO1 and URT1 exhibit nucleotidyl transferase activity on AGO1-bound miRNAs. Although these enzymes are able to add long tails to AGO1-bound miRNAs, the tailed miRNAs remain associated with AGO1. In fact, we show that a tailed miRNA acquires the ability to trigger the production of secondary siRNAs. Therefore, 3’ uridylation could endow new properties to miRNAs in addition to its known effects in miRNA degradation.

2015-08-19 | GSE61362 | GEO

Global view of mRNA uridylation in Arabidopsis

2016-03-11 | GSE72457 | GEO