Degradation of unmethylated miRNA/miRNA*s by a DEDDy-type 3’ to 5’ exoribonuclease ATRIMMER2 in Arabidopsis
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ABSTRACT:
PROVIDER: PRJNA418962 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6305000.fastq.gz | Fastqsanger.gz | |||
| SRR6305010.fastq.gz | Fastqsanger.gz | |||
| SRR6305001.fastq.gz | Fastqsanger.gz | |||
| SRR6305011.fastq.gz | Fastqsanger.gz | |||
| SRR6305002.fastq.gz | Fastqsanger.gz |
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Project description:3’ end methylation catalyzed by HUA ENHANCER1 (HEN1) is a crucial step of small RNA stabilization in plants, yet how unmethylated small RNAs undergo degradation remains largely unknown. Using a reverse genetic approach, we here show that ATRIMMER2 (ATRM2), a DEDDy-type 3’ to 5’ exoribonuclease, acts in the degradation of unmethylated miRNAs and miRNA*s in Arabidopsis. A loss-of-function mutations in ATRM2 partially suppress the morphological defects caused by HEN1 malfunction, with restored levels of a subset of miRNAs and receded expression of corresponding miRNA targets. Loss of ATRM2 has negligible effect on miRNA trimming, and further increase the fertility of hen1 heso1 urt1, a mutant with an almost complete abolishment of miRNA uridylation, indicating that ATRM2 may neither be involved in 3’ to 5’ trimming nor be the enzyme that specifically degrades uridylated miRNAs. Notably, the fold changes of miRNAs and their corresponding miRNA*s were significantly co-regulated in hen1 atrm2 as compared with those in hen1. Unexpectedly, we also observed a markedly increase of 3’ to 5’ trimming of several miRNA*s but not miRNAs in ATRM2 compromised backgrounds. These data suggest an action of ATRM2 on miRNA/miRNA* duplexes, and the existence of an unknown exoribonuclease for specific trimming of miRNA*. This asymmetric effect on miRNA/miRNA* is likely related to ARGONAUTE (AGO) proteins, which can distinguish miRNAs from miRNA*s. Finally, we show that ATRM2 colocalizes and physically interacts with ARGONAUTE1 (AGO1). Taken together, our results suggest that ATRM2 may be involved in the surveillance of unmethylated miRNA/miRNA* duplexes during the initiation step of RISC assembly.
2018-12-01 | GSE107070 | GEO
Project description:The 3' end methylation catalyzed by HUA Enhancer 1 (HEN1) is a crucial step of small RNA stabilization in plants, yet how unmethylated small RNAs undergo degradation remains largely unknown. Using a reverse genetic approach, we here show that Atrimmer 2 (ATRM2), a DEDDy-type 3' to 5' exoribonuclease, acts in the degradation of unmethylated miRNAs and miRNA*s in Arabidopsis Loss-of-function mutations in ATRM2 partially suppress the morphological defects caused by HEN1 malfunction, with restored levels of a subset of miRNAs and receded expression of corresponding miRNA targets. Dysfunction of ATRM2 has negligible effect on miRNA trimming, and further increase the fertility of hen1 heso1 urt1, a mutant with an almost complete abolishment of miRNA uridylation, indicating that ATRM2 may neither be involved in 3' to 5' trimming nor be the enzyme that specifically degrades uridylated miRNAs. Notably, the fold changes of miRNAs and their corresponding miRNA*s were significantly correlated in hen1 atrm2 versus hen1 Unexpectedly, we observed a marked increase of 3' to 5' trimming of several miRNA*s but not miRNAs in ATRM2 compromised backgrounds. These data suggest an action of ATRM2 on miRNA/miRNA* duplexes, and the existence of an unknown exoribonuclease for specific trimming of miRNA*. This asymmetric effect on miRNA/miRNA* is likely related to Argonaute (AGO) proteins, which can distinguish miRNAs from miRNA*s. Finally, we show that ATRM2 colocalizes and physically interacts with Argonaute 1 (AGO1). Taken together, our results suggest that ATRM2 may be involved in the surveillance of unmethylated miRNA/miRNA* duplexes during the initiation step of RNA-induced silencing complex assembly.
| S-EPMC6048527 | biostudies-literature
Project description:MiRNA degradation by NS3 of JEV [miRNA]
| PRJNA622917 | ENA
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.
2020-05-23 | GSE151036 | GEO
Project description:MiRNA degradation by NS3 of JEV
| PRJNA622915 | ENA
Project description:It is largely unknown how microRNAs (miRNAs) are degraded in vivo or whether active miRNA turnover is critical to specific developmental processes. Arabidopsis ARGONAUTE10 (AGO10) maintains stem cell homeostasis in meristems by repression of miR165/6, a conserved miRNA acting through AGO1. Here, we report that AGO10, through its binding to miR165/6, reduces miR165/6 accumulation by enhancing its decay. We show that AGO10 promotes the 3’ truncation of miR165/6 by SMALL RNA DEGRADING NUCLEASES (SDNs) and that AGO10-bound miR165/6 is more susceptible to degradation by SDN1 than AGO1-bound miR165/6. Our work uncovers a mechanism that governs the stability of miRNAs, establishes the importance of spatially controlled miRNA decay in stem cell homeostasis, and sheds light on the diversification and specialization of Argonaute proteins. Both biogenesis and degradation contribute to the steady-state levels of microRNAs (miRNAs). miRNA degradation in both plants and animals is associated with 3’ truncation and 3’ uridylation, and in Arabidopsis, the nucleotidyl transferase HEN1 SUPPRESSOR1 is responsible for 3’ uridylation. The SMALL RNA DEGRADING NUCLEASE (SDN) family of 3’ to 5 exonucleases degrades short RNAs in vitro and limits the accumulation of miRNAs in vivo, but it is not known whether SDNs are responsible for the accumulation of 3’ truncated miRNA species in vivo. In addition, there has not been an example of active miRNA turnover being critical to specific developmental processes. 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, through binding to miR165/6, reduces miR165/6 accumulation by enhancing its degradation. We show that SDNs are responsible for the generation of 3’ truncated miRNAs in vivo and AGO10 promotes the 3’ truncation of miR165/6 by SDNs. Our work uncovers a novel mechanism of miRNA degradation mediated by an argonaute protein, which contrasts the known stabilizing effects of most AGO proteins on their associated miRNAs. This work, together with previous studies on AGO10, demonstrates that spatially regulated miRNA degradation underlies stem cell maintenance in plants.
2017-01-25 | GSE58138 | GEO
Project description:To determine the effect of RNA degradation on miRNA expression profiling.
2009-11-24 | GSE19104 | GEO
Project description:To determine the effect of RNA degradation on miRNA expression profiling. To mimic total RNA degradation in snap-frozen livers and duodenums from mice (wild type female, C57/Bl6) tissues were stored in a -80°C freezer and then transferred to dry ice. Each frozen tissue was sliced into five identical pieces which then were transferred into eppendorf tubes. At time point zero (T0), all samples were placed on ice and total RNA was extracted immediately from (T0) and at later time points [30 min (T30), 60 min (T60), 120 min (T120) and 240 min (T240)]. RNA integrities were assessed using the Agilent Bioanalyzer 2100 which calculates RIN values of assayed RNAs. We found that at T0, the RNA integrity for both liver and duodenum was above 7, indicating good quality total RNA. However, 30 min on ice was sufficient to reduce RNA integrity, indicated by the decrease in RINs. These findings indicate that RNA degradation can take place in defrosted tissue at low temperature (i.e. on ice). For comparison, we assessed the extent to which RNA integrity is preserved in freshly harvested tissues when tissue processing is delayed. Liver and duodenum samples were collected from mice and either processed immediately or maintained on ice, as described above. Bioanalyzer electropherograms of the liver samples did not indicate any significant total RNA degradation even when samples remained on ice for up to 4 hrs. By contrast, duodenal samples (which are rich in RNases) do show high susceptibility to degradation similar to the snap-frozen defrosted material. These findings suggest that tissues such as duodenum or pancreas should either be processed immediately or snap-frozen and processed individually. To assess to which extent total RNA degradation affects miRNA expression profiles, we hybridized to the miCHIP microarray total RNAs extracted from freshly harvested livers and duodenums liver and from snap frozen livers and duodenums. Hierarchical clustering (HCL), by Pearson correlation, was used to cluster samples based on their miRNA expression profiles. Our analysis shows that miRNAs extracted from freshly harvested liver is less degraded (matrix plot analyses). Consistent with high level of RNases present in duodenum, miRNAs from freshly harvested duodenum are extensively degraded. Based on these data, we conclude that samples with low RIN values (less than 7) do not merit analysis on miRNA arrays.
2010-05-19 | E-GEOD-19104 | biostudies-arrayexpress
Project description:MiRNA degradation by NS3 of JEV [mRNA]
| PRJNA622918 | ENA
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.
2017-01-25 | GSE87351 | GEO