GEO DataSets

(Submitter supplied) Single-strand selective uracil DNA-glycosylase (SMUG1) associates with the DKC1-H/ACA ribonucleoprotein complex, which is essential for telomerase biogenesis. We show herein, that SMUG1 interacts with the telomerase RNA component, hTERC, and is required for co-transcriptional processing of the nascent transcript towards mature hTERC. We demonstrate that SMUG1 regulates the presence of base modifications between the CR4/CR5 region and the H-box situated towards the 3´-end of hTERC. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL15520

10 Samples

Download data: TXT

(Submitter supplied) We aimed to investigate whether treatment with a small molecule drug RG7834 significantly affected the transcriptome of human embryonic stem cells carrying a pathogenic mutation in the gene DKC1.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

6 Samples

Download data: CSV

(Submitter supplied) Human telomerase RNA (hTR) is transcribed as a precursor that is then posttranscriptionally modified and processed. A fraction of the transcripts is oligoadenylated by TRAMP and either processed into the mature hTR or degraded by the exosome. Here, we characterize the processing of 3’ extended forms of varying length by PARN and RRP6. We show that tertiary RNA interactions unique to the longer precursor forms favor RNA degradation, whereas H/ACA RNP assembly stimulates productive processing. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

6 Samples

Download data: TSV

(Submitter supplied) The paired-end next-generation sequencing of all hTR versions of less than 200 nucleotides in length was used to analyze the 3’ end distribution of hTR associated to Flag-tagged versions of PABPN1, hTERT and Dyskerin. In total, we obtained 2,716,342, 3,152,013, and 3,077,395 hTR-specific reads for the PABPN1, hTERT, and Dyskerin purifications, respectively. We found that the majority of polyadenylated telomerase RNA recovered in the PABPN1, hTERT, and Dyskerin purifications had poly(A) tails starting immediately after the annotated hTR 3’ end. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL15520

3 Samples

Download data: XLS

(Submitter supplied) The telomerase RNA component (TERC) is a critical determinant of cellular self renewal. Poly(A)-specific ribonuclease (PARN) is required for post-transcriptional maturation of TERC. PARN mutations lead to incomplete 3′ end processing and increased destruction of nascent TERC RNA transcripts, resulting in telomerase deficiency and telomere diseases. Here, we determined that overexpression of TERC increased telomere length in PARN-deficient cells and hypothesized that decreasing post-transcriptional 3′ oligo-adenylation of TERC would counteract the deleterious effects of PARN mutations. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

8 Samples

Download data: CSV

(Submitter supplied) Here, we develop nascent RNAend-Seq, in which we isolate nascent RNA and sequence the 3' ends of RNA precursors. Using a pulse-chase experimental design, we follow extended precursors of the telomerase RNA component (hTR) and show that the mature telomerase RNA derives from these species with slow kinetics compared to other small non-coding RNAs. The human disease causing gene PARN further delays maturation of the hTR precursor in PARN- mutant cancer cell lines. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL15520

56 Samples

Download data: XLSX

(Submitter supplied) The Microprocessor complex (DGCR8/Drosha) is required for microRNA (miRNA) biogenesis but also binds and regulates the stability of several types of cellular RNAs. Of particular interest, DGCR8 controls the stability of mature small nucleolar RNA (snoRNA) transcripts independently of Drosha, suggesting the existence of alternative DGCR8 complex/es with other nucleases to process a variety of cellular RNAs. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL11154 GPL16791

11 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) We tested whether Dis3 and Exosc10 depletion impact erythropoiesis by interfering with RNA processing and generating an aberrant transcriptome.

Organism:

Mus musculus domesticus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29744

12 Samples

Download data: TXT

(Submitter supplied) Primary telomerase RNA transcripts are processed into shorter mature forms that assemble into a complex with the catalytic subunit and provide the template for telomerase activity. In diverse fungi telomerase RNA 3’ end processing involves a single cleavage reaction by the spliceosome akin to the first step of splicing. Longer forms of human telomerase RNA (hTR) have been reported, but how the mature form of precisely 451 nucleotides is generated is still unknown. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

16 Samples

Download data: XLSX

(Submitter supplied) RNA sequencing of HeLa cells treated with siRNA against the RNA exosome components hRRP40, hRRP6, hDIS3, and hRRP6/hDIS3 or the splicing inhibitors Isoginkgetin and spliceostatin A, respectively.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

33 Samples

Download data: TXT

(Submitter supplied) Reduced oxygen availability (hypoxia) triggers adaptive cellular responses via hypoxia-inducible factor (HIF)-dependent transcriptional activation. Adaptation to hypoxia also involves transcription-independent processes like post-translational modifications, however these mechanisms are poorly characterized. Investigating the involvement of protein SUMOylation in response to hypoxia, we discovered that hypoxia strongly decreases the SUMOylation of Exosome subunit 10 (EXOSC10), the catalytic subunit of the RNA exosome, in a HIF-independent manner. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

10 Samples

Download data: BW

(Submitter supplied) Ribonucleoprotein enzymes require specific and dynamic conformations of their RNA constituents for regulated catalysis. Telomerase RNA components (TRs) rely on two conserved domains, a pseudoknot/template sequence and a three-way junction (CR4/5), each of which binds the telomerase reverse transcriptase protein (TERT). Vertebrate TRs evolved a third element, the H/ACA domain, involved in assembly and trafficking of telomerase through binding telomerase cofactors, dyskerin and TCAB1, respectively. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

36 Samples

Download data: TXT

(Submitter supplied) Growing mammalian oocytes accumulate substantial amounts of RNA, most of which are degraded during the subsequent maturation stage. The growth-to-maturation transition begins with germinal vesicle breakdown (GVBD, envisioned as nuclear envelope breakdown) and is critical for oocyte quality. However, the concomitant changes in the transcriptome during GVBD as well as the underlying machinery remained unclear. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

108 Samples

Download data: TXT

(Submitter supplied) We identified a germline heterozygous loss-of-function mutation in ZCCHC8, an RNA exosome targeting component, in a family with autosomal dominant pulmonary fibrosis and telomerase RNA insufficiency. To understand the in vivo consequences of Zcchc8 loss, we targeted the gene locus. Zccchc8+/- showed no significant phenotypes but Zcchc8-/- mice showed severe neurodevelopmental defects and died early in adulthood by 60 days. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

14 Samples

Download data: TXT

(Submitter supplied) In our RIP-seq experiment, RNAs were purified from the E12.5 WT mouse cortex. By sequencing of the Exosc10-bound RNAs, binding enrichment of Exosc10 on 3159 transcripts was identified (adjusted p-value < 0.05). GO analysis revealed that the Exosc10-bound transcripts participate in various processes of brain development.

Organism:

Mus musculus

Type:

Other

Platform:

GPL21103

8 Samples

Download data: TXT