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The pseudouridine synthase DKC1 binds to cytoplasmic transcripts containing H/ACA-box SnoRNA sequences affecting nuclear hormone receptor dependence [RNA-seq]

ABSTRACT: Total and polysomal RNA profiling of control and DKC1-silenced MCF7 cells

ORGANISM(S): Homo sapiens

PROVIDER: GSE161480 | GEO | 2022/08/04

REPOSITORIES: GEO

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The pseudouridine synthase DKC1 binds to cytoplasmic transcripts containing H/ACA-box SnoRNA sequences affecting nuclear hormone receptor dependence [RIP-seq]

Project description:RIP-seq of DKC1 in MCF7 cells

2022-08-04 | GSE161479 | GEO

The pseudouridine synthase DKC1 binds to cytoplasmic transcripts containing H/ACA-box SnoRNA sequences affecting nuclear hormone receptor dependence

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-08-04 | GSE161481 | GEO

The pseudouridine synthase DKC1 binds to cytoplasmic transcripts containing H/ACA-box SnoRNA sequences affecting nuclear hormone receptor dependence

Project description:The pseudouridine synthase DKC1 binds to cytoplasmic transcripts containing H/ACA-box SnoRNA sequences affecting nuclear hormone receptor dependence

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The pseudouridine synthase DKC1 binds to cytoplasmic transcripts containing H/ACA-box SnoRNA sequences affecting nuclear hormone receptor dependence [RNA-seq]

Project description:The pseudouridine synthase DKC1 binds to cytoplasmic transcripts containing H/ACA-box SnoRNA sequences affecting nuclear hormone receptor dependence [RNA-seq]

| PRJNA678373 | ENA

The pseudouridine synthase DKC1 binds to cytoplasmic transcripts containing H/ACA-box SnoRNA sequences affecting nuclear hormone receptor dependence [RIP-seq]

Project description:The pseudouridine synthase DKC1 binds to cytoplasmic transcripts containing H/ACA-box SnoRNA sequences affecting nuclear hormone receptor dependence [RIP-seq]

| PRJNA678371 | ENA

Genome-wide RNAi Screening Identifies pseudouridine synthase DKC1 promotes CRC proliferation through regulating ribosomal proteins expression

Project description:Colorectal cancer (CRC) with high rate of mortality is one of the most commonly diagnosed cancers in worldwide. Advanced colorectal cancer is often accompanied by malignant proliferation of tumor cells. Further researches on colorectal cancer proliferation to find new targets and develop new therapeutic regimen are an important direction for colorectal cancer treatment. In this study, genome-wide RNAi screening was used to discover the essential genes associated with colorectal cancer cell proliferation. We found DKC1 (dyskerin pseudouridine synthase 1) promoted CRC proliferation through binding and modifying ribosomal proteins (RPL10A, RPL22L1, RPL34, RPS3) mRNA to increase the mRNAs stability and eventually increasing their expression. Besides, DKC1 is highly expressed in colorectal cancer and its aberrantly high expression is associated with poor prognosis of colorectal cancer patients. These results suggest that DKC1 could be a new therapeutic target for colorectal cancer.

2021-04-30 | GSE147348 | GEO

Genome-wide RNAi Screening Identifies pseudouridine synthase DKC1 promotes CRC proliferation through regulating ribosomal proteins expression

2021-02-08 | PXD018103 | Pride

Reconstitution and structural analysis of the yeast box H/ACA RNA-guided pseudouridine synthase.

Project description:Box H/ACA ribonucleoprotein particles (RNPs) mediate pseudouridine synthesis, ribosome formation, and telomere maintenance. The structure of eukaryotic H/ACA RNPs remains poorly understood. We reconstituted functional Saccharomyces cerevisiae H/ACA RNPs with recombinant proteins Cbf5, Nop10, Gar1, and Nhp2 and a two-hairpin H/ACA RNA; determined the crystal structure of a Cbf5, Nop10, and Gar1 ternary complex at 1.9 Å resolution; and analyzed the structure-function relationship of the yeast complex. Although eukaryotic H/ACA RNAs have a conserved two-hairpin structure, isolated single-hairpin RNAs are also active in guiding pseudouridylation. Nhp2, unlike its archaeal counterpart, is largely dispensable for the activity, reflecting a functional adaptation of eukaryotic H/ACA RNPs to the variable RNA structure that Nhp2 binds. The N-terminal extension of Cbf5, a hot spot for dyskeratosis congenita mutation, forms an extra structural layer on the PUA domain. Gar1 is distinguished from the assembly factor Naf1 by containing a C-terminal extension that controls substrate turnover and the Gar1-Naf1 exchange during H/ACA RNP maturation. Our results reveal significant novel features of eukaryotic H/ACA RNPs.

| S-EPMC3222906 | biostudies-literature

Human miRNA precursors with box H/ACA snoRNA features.

Project description:MicroRNAs (miRNAs) and small nucleolar RNAs (snoRNAs) are two classes of small non-coding regulatory RNAs, which have been much investigated in recent years. While their respective functions in the cell are distinct, they share interesting genomic similarities, and recent sequencing projects have identified processed forms of snoRNAs that resemble miRNAs. Here, we investigate a possible evolutionary relationship between miRNAs and box H/ACA snoRNAs. A comparison of the genomic locations of reported miRNAs and snoRNAs reveals an overlap of specific members of these classes. To test the hypothesis that some miRNAs might have evolved from snoRNA encoding genomic regions, reported miRNA-encoding regions were scanned for the presence of box H/ACA snoRNA features. Twenty miRNA precursors show significant similarity to H/ACA snoRNAs as predicted by snoGPS. These include molecules predicted to target known ribosomal RNA pseudouridylation sites in vivo for which no guide snoRNA has yet been reported. The predicted folded structures of these twenty H/ACA snoRNA-like miRNA precursors reveal molecules which resemble the structures of known box H/ACA snoRNAs. The genomic regions surrounding these predicted snoRNA-like miRNAs are often similar to regions around snoRNA retroposons, including the presence of transposable elements, target site duplications and poly (A) tails. We further show that the precursors of five H/ACA snoRNA-like miRNAs (miR-151, miR-605, mir-664, miR-215 and miR-140) bind to dyskerin, a specific protein component of functional box H/ACA small nucleolar ribonucleoprotein complexes suggesting that these molecules have retained some H/ACA snoRNA functionality. The detection of small RNA molecules that share features of miRNAs and snoRNAs suggest that these classes of RNA may have an evolutionary relationship.

| S-EPMC2730528 | biostudies-literature

Trypanosoma brucei spliced leader RNA maturation by the cap 1 2'-O-ribose methyltransferase and SLA1 H/ACA snoRNA pseudouridine synthase complex.

Project description:Kinetoplastid flagellates attach a 39-nucleotide spliced leader (SL) upstream of protein-coding regions in polycistronic RNA precursors through trans splicing. SL modifications include cap 2'-O-ribose methylation of the first four nucleotides and pseudouridine (psi) formation at uracil 28. In Trypanosoma brucei, TbMTr1 performs 2'-O-ribose methylation of the first transcribed nucleotide, or cap 1. We report the characterization of an SL RNA processing complex with TbMTr1 and the SLA1 H/ACA small nucleolar ribonucleoprotein (snoRNP) particle that guides SL psi(28) formation. TbMTr1 is in a high-molecular-weight complex containing the four conserved core proteins of H/ACA snoRNPs, a kinetoplastid-specific protein designated methyltransferase-associated protein (TbMTAP), and the SLA1 snoRNA. TbMTAP-null lines are viable but have decreased SL RNA processing efficiency in cap methylation, 3'-end maturation, and psi(28) formation. TbMTAP is required for association between TbMTr1 and the SLA1 snoRNP but does not affect U1 small nuclear RNA methylation. A complex methylation profile in the mRNA population of TbMTAP-null lines indicates an additional effect on cap 4 methylations. The TbMTr1 complex specializes the SLA1 H/ACA snoRNP for efficient processing of multiple modifications on the SL RNA substrate.

| S-EPMC2643836 | biostudies-literature

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