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Arabidopsis thaliana

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

PROVIDER: PRJNA260855 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1573890.fastq.gz	Fastqsanger.gz
	SRR1573891.fastq.gz	Fastqsanger.gz
	SRR1573892.fastq.gz	Fastqsanger.gz
	SRR1573893.fastq.gz	Fastqsanger.gz
	SRR1573894.fastq.gz	Fastqsanger.gz

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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.

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NTP4 modulates miRNA accumulation via asymmetric modification of miRNA-3p/5p duplex

Project description:Arabidopsis uridylyltransferase on unmethylated sRNAs and directed their degradation. Here, the small RNA deep sequencing of the uridylyltransferase mutants of Arabidopsis were performed, which include Col-0, heso1-1, urt1-1, ntp4-1.

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Project description:Using 3' RACE-seq method, we analyzed the impact of URT1 and/or HESO1 inactivation on the uridylation of GFLV, TuMV and TCV RNAs in Arabidopsis.

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Project description:This SuperSeries is composed of the following subset Series: GSE26802: Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity (hESC) GSE26803: Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity (KD) GSE26916: Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity (Validation 1) GSE26919: Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity (Validation 2) GSE29904: Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity (normal prostate and prostate cells) Refer to individual Series

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Prevalent cytidylation and uridylation of precursor miRNAs in Arabidopsis

Project description:A key step in microRNA (miRNA) biogenesis is the processing of a primary precursor RNA by the microprocessor into a precursor miRNA (pre-miRNA) intermediate. In plants, little is known about the processes that act on pre-miRNAs to influence miRNA biogenesis. Here, we performed 3’ RACE-seq to profile pre-miRNA 3’ ends in Arabidopsis. 3’ end heterogeneity was prevalent and the three microprocessor components promoted 3’ end precision. Extensive cytidylation and uridylation of precise and imprecise pre-miRNA 3’ ends were uncovered. The nucleotidyl transferase HESO1 uridylated pre-miRNAs in vitro and was responsible for most pre-miRNA uridylation in vivo. HESO1, NTP6 and NTP7 contribute to pre-miRNA cytidylation. Tailing of pre-miRNAs tended to restore trimmed pre-miRNAs to intact lengths to promote further processing. In addition, HESO1-mediated uridylation led to the degradation of some imprecisely processed pre-miRNAs. Thus, we uncovered widespread cytidylation and uridylation of pre-miRNAs and demonstrated diverse functions of pre-miRNA tailing in plants.

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Project description:Using 3' RACEseq method, we compared the tailing and nibbling patterns of RISC-cleaved MYB33 and SPL13 transcripts between wild-type plants and mutant plants depleted for the terminal uridylyltransferases (TUTases) HESO1 and URT1. Our data reveal a major and minor role for HESO and URT1, respectively, in the uridylation of RISC-cleaved transcripts.

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Synergistic and independent actions of multiple terminal nucleotidyl transferases in 3’ tailing of small RNAs in Arabidopsis

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ARGONAUTE10 promotes the degradation of miR165/6 through the SDN1 and SDN2 exonucleases in Arabidopsis [AGO10SDN]

Project description:The degradation of small RNAs in plants and animals is associated with small RNA 3’ truncation and 3’ uridylation and thus relies on exonucleases and nucleotidyl transferases. Argonaute proteins associate with small RNAs in vivo and are essential for not only the activities but also the stability of small RNAs. Arabidopsis ARGONAUTE10 (AGO10) maintains stem cell homeostasis in meristems by sequestration of miR165/6, a conserved miRNA acting through AGO1. Here, we report that AGO10 reduces miR165/6 accumulation by enhancing its degradation. This is contrary to the stabilizing effect of all known argonaute proteins on their associated small RNAs. We show that SMALL RNA DEGRADING NUCLEASES (SDNs) are responsible for miRNA 3’ truncation in general and AGO10 promotes the degradation of miR165/6 by SDNs. Our work identifies the exonucleases responsible for miRNA 3’ truncation in vivo and uncovers a mechanism of specificity determination in miRNA turnover. This work, together with previous studies on AGO10, demonstrates that spatially regulated miRNA degradation underlies stem cell maintenance in plants.

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