GEO DataSets

(Submitter supplied) Total RNAs were cloned from wt, Dis3L2 and Tailor mutant testis tissues to study the role of Tailor and Dis3L2 TUTase/nuclease complex

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17275

8 Samples

Download data: XLS

(Submitter supplied) Mutations in the 3’-5’ exonuclease DIS3L2 are associated with Perlman syndrome and hypersusceptibility to Wilms’ tumorigenesis. Previously, we found that Dis3l2 specifically recognizes and degrades uridylated pre-let-7 microRNA. However, the widespread relevance of Dis3l2-mediated decay of uridylated substrates remains unknown. Here we applied an unbiased RNA immunoprecipitation strategy to identify Dis3l2 targets in mouse embryonic stem cells. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL13112

4 Samples

Download data: TXT

(Submitter supplied) Small RNAs were cloned from wt and tailor mutant cells or ovary tissues to study the role of Tailor in miRNA uridylation

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13304

4 Samples

Download data: TXT

(Submitter supplied) Uridylation of various cellular RNA species at the 3' end has been generally linked to RNA degradation. In mammals, uridylated pre-let-7 miRNAs and mRNAs are targeted by the 3' to 5' exoribonuclease DIS3L2. Mutations in DIS3L2 have been associated with Perlman syndrome and with Wilms tumor susceptibility. Using in vivo cross-linking and immunoprecipitation (CLIP) method, we discovered the DIS3L2-dependent cytoplasmic uridylome of human cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL11154

9 Samples

Download data

(Submitter supplied) Uridylation of various cellular RNA species at the 3’ end has been generally linked to RNA degradation. Uridylated pre-miRNAs in mammals and uridylated mRNAs in fission yeast are targeted by the 3′ to 5′ exoribonuclease DIS3L2. In humans, DIS3L2 mutations have been associated with Perlman syndrome development and Wilms tumor susceptibility. In this work, we employ crosslinking in vivo and immunoprecipitation (CLIP) method to assess the RNA binding capacity of human DIS3L2 on a genome-wide scale. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL11154

3 Samples

Download data: CSV

(Submitter supplied) Uridylation of various cellular RNA species at the 3’ end has been generally linked to RNA degradation. Uridylated pre-miRNAs in mammals and uridylated mRNAs in fission yeast are targeted by the 3′ to 5′ exoribonuclease DIS3L2. In humans, DIS3L2 mutations have been associated with Perlman syndrome development and Wilms tumor susceptibility. In this work, we employ crosslinking in vivo and immunoprecipitation (CLIP) method to assess the RNA binding capacity of human DIS3L2 on a genome-wide scale. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

6 Samples

Download data: CSV

(Submitter supplied) The exosome-independent exoribonuclease DIS3L2 is mutated in Perlman syndrome. Here we used extensive global transcriptomic and targeted biochemical analyses to identify novel DIS3L2 substrates in human cells. We show that DIS3L2 regulates pol II transcripts, comprising selected canonical and histone-coding mRNAs, and a novel FTL_short RNA from the ferritin mRNA 5' UTR. Importantly, DIS3L2 contributes to surveillance of pre-snRNAs during their cytoplasmic maturation. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL11154

12 Samples

Download data: BW, TXT

(Submitter supplied) The post-transcriptional addition of nucleotides to the 3´ end of RNA regulates the maturation, function, and stability of RNA species in all domains of life. Here, we show that, in flies, 3´ terminal RNA uridylation triggers the processive, 3´-to-5´ exoribonucleolytic decay via the RNase II/R enzyme CG16940, a homolog of the human Perlman syndrome exoribonuclease Dis3l2. Together with the TUTase Tailor, dmDis3l2 forms the cytoplasmic, uridylation-triggered RNA processing (TRUMP) complex, that functionally cooperates in the degradation of structured RNA. more...

Organism:

synthetic construct; Drosophila melanogaster

Type:

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

Platforms:

GPL19604 GPL17275

15 Samples

Download data: TXT, XLSX

(Submitter supplied) Uridylation of diverse RNA species represents an emerging theme in post-transcriptional gene regulation. In the microRNA pathway, such modifications regulate small RNA biogenesis and stability in plants, worms and mammals. Here, we report the first uridylyltransferase that acts on small RNAs in Drosophila, which we refer to as Tailor. Tailor is the source for the majority of 3´ end-modifications in microRNAs and predominantly targets precursor-hairpins. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17275

6 Samples

Download data: TXT

(Submitter supplied) Uridylation of diverse RNA species represents an emerging theme in post-transcriptional gene regulation. In the microRNA pathway, such modifications regulate small RNA biogenesis and stability in plants, worms and mammals. Here, we report the first uridylyltransferase that acts on small RNAs in Drosophila, which we refer to as Tailor. Tailor is the source for the majority of 3´ terminal uridine-modifications in small RNAs and predominantly targets precursor-miRNAs. more...

Organism:

Drosophila melanogaster; synthetic construct

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL15228 GPL13304

22 Samples

Download data: TXT

(Submitter supplied) Nibbler (Nbr) is a 3′-to-5′exoribonuclease whose catalytic 3′-end trimming activity impacts miRNA and piRNA biogenesis. Here, we report on structural and functional studies to decipher the contributions of Nbr’s N-terminal (NTD) and exonucleolytic (EXO) domains in miRNA 3′-end trimming. We have solved the crystal structures of the NTD-core and EXO domains of Nbr, both in the apo-state. The NTD-core domain of Aedes aegypti Nbr adopts a HEAT-like repeat scaffold, with basic patches constituting an RNA-binding surface exhibiting a preference for binding dsRNA over ssRNA. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17275

4 Samples

Download data: TXT

(Submitter supplied) Rapid and widespread mRNA decay is a previously unappreciated feature of apoptosis. Previous work showed that apoptotic mRNA decay depends on mitochondrial outer membrane permeabilization (MOMP) and the RNA-processing enzymes, TUT4, TUT7, and DIS3L2. Which RNAs are decayed, however, was not known. Here we present RNA-seq data of TRAIL-induced apoptosis in HCT116 cells showing global decay of mRNAs as well as polyadenylated noncoding RNAs, beginning at the 3’-end.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

4 Samples

Download data: CSV

(Submitter supplied) microRNAs (miRNAs) associating with Argonaute proteins (AGOs) regulate gene expression in mammals. miRNA 3' ends are subject to frequent sequence modifications, which have been proposed to affect miRNA stability. However, the underlying mechanism is not well understood. Here, by genetic and biochemical studies as well as deep sequencing analyses, we find that AGO mutations disrupting miRNA 3' binding are sufficient to trigger extensive miRNA 3’ modifications in HEK293T cells and in cancer patients. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15520

25 Samples

Download data: TSV

(Submitter supplied) Many microRNAs (miRNAs) exist alongside abundant miRNA isoforms (isomiRs), most of which arise from post-maturation sequence modifications, such as 3’ uridylation. However, the ways in which these sequence modifications affect miRNA function remain poorly understood. Here, using human miR-27a in cell lines as a model, we have discovered that a nonfunctional target site unable to base pair extensively with the miRNA seed sequence can regain function when an upstream adenosine is able to base-pair with a post-transcriptionally added uridine in the miR-27a tail. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL15520 GPL11154

29 Samples

Download data: TAB, TSV

(Submitter supplied) This study uncovers a population of eRpL22 paralogue-specific specialized ribosomes in the fly testis. Wildtype testes were used to isolate eRpL22 paralogue-specific ribosomes complexed with RNA molecules. RNA-sequencing determined the distribution of RNAs (mRNA and ncRNA) on each type of eRpL22 paralogue-specific ribosome, revealing unique translatomes for both eRpL22- and eRpL22-like- ribosomes, as well as an overlapping translatome.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL21306

8 Samples

Download data: XLSX

(Submitter supplied) Input mRNAs and ribosome protected fragments (RPFs) from Heterozygout (Control) and Dis3l2 knockout (KO) mESCs cultures were analyzed by TruSeq Ribo Profile (Illumina) library preparation and high throughput sequencing

Organism:

Mus musculus

Type:

Other

Platform:

GPL19057

8 Samples

Download data: XLSX

(Submitter supplied) RNA sequencing was performed using shLacZ and shDis3l2 undifferentiated mESCs as well as EB differentiated cells

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

14 Samples

Download data: CSV, TXT

(Submitter supplied) During mammalian oocyte development, transcriptome undergoes accumulation in the oocyte growth phase and elimination in the oocyte maturation phase. At the transition point between growth and maturation, which is the germinal vesicle intact oocyte (GV), terminal uridylation labels RNA for degradation. In our study, we show that a small cohort of RNA are polyadenylated after tail uridylation (defined as uridylated-poly(A) RNA). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL29177 GPL21493

87 Samples

Download data: CSV, TXT

(Submitter supplied) The Drosophila polypyrimidine tract-binding protein (dmPTB or hephaestus) plays an important role during spermatogenesis. The heph2 mutation in this gene results in a specific defect in spermatogenesis, causing aberrant spermatid individualization and male sterility. However, the array of molecular defects in the mutant remains uncharacterized. This study provides the first comprehensive list of genes misregulated in vivo in the heph2 mutant in Drosophila and offers insight into the role of dmPTB during spermatogenesis.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13304

2 Samples

Download data: TXT

(Submitter supplied) Purpose: Loss of DIS3L2 in humans is associated with congenital overgrowth in Perlman syndrome, as well as with the development of Wilms tumors. DIS3L2 is an exoribonuclease with a demonstrated preference for 3’-uridylated RNA substrates. However, its targets relevant to human disease are poorly understood. Our goal was to address transcriptomic changes in DIS3L2 deficient mouse nephron progenitor cells, a cell type of the developing kidney with demonstrated relevance to Wilms tumorigenesis. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

5 Samples

Download data: TXT