GEO DataSets

(Submitter supplied) Using 3' RACE-seq method, we analyzed global 3’ terminal RNA uridylation profiles for representatives of the main families of positive single-stranded RNA phytoviruses.

Organism:

Nicotiana benthamiana; Nicotiana obtusifolia; Chenopodium quinoa; Spinacia oleracea; Arabidopsis thaliana; Vitis vinifera

Type:

Expression profiling by high throughput sequencing

9 related Platforms

27 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Nicotiana benthamiana; Nicotiana obtusifolia; Chenopodium quinoa; Spinacia oleracea; Arabidopsis thaliana; Vitis vinifera

Type:

Expression profiling by high throughput sequencing

12 related Platforms

140 Samples

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(Submitter supplied) Small silencing RNAs are key regulators of gene expression in both plants and animals. HEN1-mediated 3’ terminal 2’-O-methylation plays a crucial role in small RNA stability control. In the absence of HEN1, small RNAs are frequently uridylated (untemplated uridine addition) and trimmed, a phenomenon that is conserved across species. However, the underlying molecular mechanism is largely unknown. In this study, we have discovered UTP: RNA uridylyltransferase (URT1) acts redundantly with HESO1 in the uridylation of miRNAs, in addition to its role in oligo-adenylated mRNA uridylation. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13222

12 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL13222 GPL17639

8 Samples

Download data: TXT

(Submitter supplied) 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).

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17639

4 Samples

Download data: TXT

(Submitter supplied) 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.

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13222

4 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13222

12 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Nicotiana benthamiana; Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL22072 GPL17970 GPL17639

67 Samples

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(Submitter supplied) 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.

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17639

8 Samples

Download data: TXT

(Submitter supplied) To estimate mRNA uridylation levels at a transcriptome-wide level, TAIL-seq libraries were generated for three biological replicates of Col-0 plants.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17970

3 Samples

Download data: TXT

(Submitter supplied) 3’RACE-seq experiments were conducted to determine the impact of URT1 ectopic expression on the poly(A) tail length profile of both a GFP reporter mRNA co-expressed in Nicotiana benthamiana leaves and an endogenous mRNA encoding PATHOGENESIS-RELATED PROTEIN 2 (PR2)

Organism:

Nicotiana benthamiana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22072

36 Samples

Download data: TXT

(Submitter supplied) 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

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17970

20 Samples

Download data: TXT

(Submitter supplied) 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.

Organism:

Arabidopsis thaliana

Type:

Other

Platform:

GPL17970

22 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL15520 GPL16791

30 Samples

Download data: TXT

(Submitter supplied) Uridylation occurs pervasively on mRNAs in mammals, yet its mechanism and significance remain unknown. Here we identify TUT4 and TUT7 (also known as ZCCHC11 and ZCCHC6, respectively) as the enzymes that uridylate mRNAs. Uridylation readily occurs on deadenylated mRNAs that are not associated with poly(A) binding protein (PABPC1) in cells. Consistently, purified TUT4 and TUT7 (TUT4/7) selectively uridylate RNAs with short A tails (< ~25 nt) while PABPC1 antagonizes uridylation of polyadenylated mRNAs in vitro. more...

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL16791 GPL15520

39 Samples

Download data: TXT

(Submitter supplied) Uridylation occurs pervasively on mRNAs in mammals, yet its mechanism and significance remain unknown. Here we identify TUT4 and TUT7 (also known as ZCCHC11 and ZCCHC6, respectively) as the enzymes that uridylate mRNAs. Uridylation readily occurs on deadenylated mRNAs that are not associated with poly(A) binding protein (PABPC1) in cells. Consistently, purified TUT4 and TUT7 (TUT4/7) selectively uridylate RNAs with short A tails (< ~25 nt) while PABPC1 antagonizes uridylation of polyadenylated mRNAs in vitro. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

16 Samples

Download data: CSV

(Submitter supplied) 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. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21179

63 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17639

16 Samples

Download data: TXT

(Submitter supplied) Using high-throughput sequencing of histone mRNAs and degradation intermediates, we find that knockdown of TUT7 reduces both the uridylation at the 3’ end as well as uridylation pattern at the 3’ end, and only had a small effect on the uridylation in the stemloop uridylation of the major during histone mRNA degradation. Knockdown of 3’ hEXO also altered the uridylation of histone mRNAs, revealing a dynamic equilibrium between 3’ hEXO digestion and TUT7 uridylation, suggesting that TUT7 and 3’ hExo function together in trimming and uridylating histone mRNAs.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15520

34 Samples

Download data: TXT

(Submitter supplied) AGO protein immunoprecipitation was combined with high-throughput sequencing of associated small RNAs. AGO2, AGO10, and to a lesser extent AGO1 were shown to associate with siRNAs derived from silencing suppressor (HC-Pro)-deficient TuMV-AS9, but not with siRNAs derived from wild-type TuMV. Co-immunoprecipitation and small RNA sequencing revealed that viral siRNAs broadly associated with wild-type HC-Pro during TuMV infection. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13222

104 Samples

Download data: GFF3