Genome-wide identification of snoRNA-guided 2’-O-methylation sites [Ribometh-seq]
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE77024 | GEO | 2016/05/01
SECONDARY ACCESSION(S): PRJNA309292
REPOSITORIES: GEO
Similar Datasets
Project description:We combine two experimental high-throughput sequencing methods to identify new 2'-O-methylation sites in human and assign snoRNA guides to sites with previously unknown guides.
2016-05-01 | GSE77027 | GEO
Project description:Genome-wide identification of snoRNA-guided 2?-O-methylation sites with CLIP and Ribometh-seq
| PRJNA309294 | ENA
Project description:This SuperSeries is composed of the SubSeries listed below.
2016-05-01 | GSE77028 | GEO
Project description:RNA can be extensively modified post-transcriptionally with >170 covalent modifications, expanding its functional and structural repertoire. Pseudouridine (Ψ), the most abundant modified nucleoside in rRNA and tRNA, has recently been found within mRNA molecules. Due to technical challenges, it remained unclear whether pseudouridylation of mRNA can be snoRNA-guided, which has important implications for understanding the physiological target spectrum of snoRNAs and for their potential therapeutic exploitation in genetic diseases. Here, using a massively parallel reporter based strategy we simultaneously interrogate Ψ levels across hundreds of synthetic constructs with predesigned complementarity against endogenous snoRNAs. Our results demonstrate that snoRNA-mediated pseudouridylation can occur on mRNA targets. However, this is typically achieved at low efficiencies, and is constrained by the localization of mRNA, by the expression levels of snoRNAs and by the length of the snoRNA:mRNA complementarity stretches. We exploited these insights for the design of snoRNAs targeting pseudouridylation at premature termination codons, which was previously suggested to suppress translational termination. However, in contrast to previous studies, in this and follow-up experiments we observe no evidence for readthrough of pseudouridylated stop codons. Our study enhances our understanding of the scope, ‘design rules’ and constraints of snoRNA-mediated pseudouridylation, and challenges a key functional outcome associated with this modification.
2024-06-02 | GSE159749 | GEO
Project description:Box C/D small nucleolar RNAs (snoRNAs) are a conserved class of RNA known for their role in guiding ribosomal RNA 2’-O-ribose methylation through base pairing with targeted sequences. Recently, C/D snoRNAs were also implicated in regulating the expression of non-ribosomal genes through different modes of binding. Large scale RNA-RNA interaction datasets detect many snoRNAs binding messenger RNA. However, these studies provide a narrow portrait of snoRNA targets forming under specific experimental conditions. To enable a more comprehensive study of C/D snoRNA interactions, we created snoGloBe, a human C/D snoRNA machine learning interaction predictor based on a gradient boosting classifier. SnoGloBe considers the target type, and position and sequence of the interactions, enabling it to outperform existing predictors. Interestingly, for specific snoRNAs, snoGloBe identifies strong enrichment of interactions near gene expression regulatory elements including splice sites. Abundance and splicing of predicted targets were altered upon the knockdown of their associated snoRNA. Strikingly, the predicted snoRNA interactions often overlap with the binding sites of functionally related RNA binding proteins, reinforcing their role in gene expression regulation. The interactions of snoRNAs are not randomly distributed but often accumulate in functionally related transcripts sharing common regulatory elements suggesting coordinated regulatory function. The wide scope of snoGloBe makes it an excellent tool for discovering viral RNA targets, which is evident from its capacity to identify snoRNAs targeting SARS-CoV-2 RNA, known to be heavily methylated. Overall, snoGloBe is capable of identifying experimentally validated binding sites and predicting novel sites with shared regulatory function.
2022-05-18 | GSE184173 | GEO
Project description:High-throughput sequencing has greatly facilitated the discovery of long and short non-coding RNAs (ncRNAs), which frequently guide ribonucleoprotein complexes to RNA targets, to modulate their metabolism and expression. However, for many ncRNAs, the targets remain to be discovered. In this study, we developed computational methods to map C/D box snoRNA target sites using data from core small nucleolar ribonucleoprotein crosslinking and immunoprecipitation and from transcriptome-wide mapping of 2΄-O-ribose methylation sites. We thereby assigned the snoRNA guide to a known methylation site in the 18S rRNA, we uncovered a novel partially methylated site in the 28S ribosomal RNA, and we captured a site in the 28S rRNA in interaction with multiple snoRNAs. Although we also captured mRNAs in interaction with snoRNAs, we did not detect 2΄-O-methylation of these targets. Our study provides an integrated approach to the comprehensive characterization of 2΄-O-methylation targets of snoRNAs in species beyond those in which these interactions have been traditionally studied and contributes to the rapidly developing field of 'epitranscriptomics'.
| S-EPMC5389715 | biostudies-literature
Project description:The majority of Saccharomyces cerevisiae snoRNA promoters contain an aRCCCTaa sequence motif located at the upstream border of a TATA-containing nucleosome-free region. Genome-wide ChIP-seq analysis showed that these motifs are bound in vivo by Tbf1, a telomere-binding protein known to recognize mammalian-like T2AG3 repeats at sub-telomeric regions. Tbf1 has over 100 additional promoter targets, including the TBF1 gene itself. Tbf1 is required for full snoRNA expression, yet it does not influence nucleosome positioning at snoRNA promoters. Analysis of Tbf1-binding sites in Saccharomyces cerevisiae by ChIP-seq of a Myc-tagged strain and a control untagged strain. 1 sample per strain, 1 lane per sample.
2010-05-28 | E-GEOD-20870 | biostudies-arrayexpress
Project description:Comparison of mRNA transcriptome after differential expression of U17 snoRNA. We hypothesiaed that if U17 snoRNA regulates cholesterol homeostasis by modulating the expression of target mRNAs, genes that are differentially expressed by the loss-of-function or gain-of-function of U17 snoRNA would be candidate U17 targets. Results revealed negative regulation of target genes by U17 snoRNA, in which increasing dosage of U17 snoRNA from U17 knockdown to WT to U17 overexpression lead to decreases in target levels. Total RNA were isolated by TRIzol reagent (Invitrogen) from WT, U17 snoRNA KD (ShSnhg3 stable clone), and U17 snoRNA OE (pMDβglobinU17b stable clone) cells grown in LPDS media for 24 hours.
2015-04-04 | E-GEOD-67569 | biostudies-arrayexpress
Project description:Osteoarthritis (OA) is a chronic debilitating joint disease which is strongly associated with ageing. OA involves pathological cellular processes in all joint structures and affects articular cartilage integrity, leading to dysfunctional joint articulation. The biomolecular processes that catalyze the disturbances in the articular chondrocyte phenotype leading to OA are poorly understood, and it is expected that a comprehensive understanding of the avenues leading to catabolic changes and disruption of articular chondrocyte homeostasis will provide important cues for future treatments of the condition. Chondrocytes are specialized secretory cells with highly active protein translational machinery, enabling the synthesis and maintenance of the protein-rich cartilage extracellular matrix (ECM). Disturbances in chondrocyte protein translation in cartilage development and OA are connected to mTOR activity, ER stress, unfolded protein response (UPR)and CHOP-mediated apoptosis. These responses change the downstream translational activity of the biosynthesized ribosome. The assembled mammalian ribosome is built from ribosomal RNAs (rRNAs), together with more than 80 different protein subunits. At the heart of the ribosome, the 18S rRNA guides the decoding of the mRNA message, while an ancient ribozyme activity in the 28S rRNA forms the core of the peptidyltransferase center that polymerizes the amino acid sequence encoded by the mRNA into functional proteins. Post-transcriptional maturation of rRNAs is an integral part of the biosynthesis of ribosomes and ribonucleolytic processing of the major 47S rRNA precursor into mature 18S, 5.8S, and 28S rRNAs is rate limiting for ribosome biogenesis. The U3 small nucleolar RNA (snoRNA) is an evolutionarily highly conserved box C/D-class snoRNA which catalyzes the endoribonucleolytic processing of the 5’ external transcribed spacer (ETS) of the 47S pre-rRNA by base complementarity-guided pre-rRNA substrate recognition and plays a crucial role in the maturation of 18S rRNA. Although extensively studied in yeast, it was only recently demonstrated that U3 snoRNA is indispensable for rRNA maturation in human cells. Pathways controlling ribosome activity have previously been described in the regulation of chondrocyte homeostasis. We here now postulate that not only ribosome activity is involved in chondrocyte homeostasis, but that OA pathophysiological situations can also cause alterations in chondrocyte ribosome biogenesis with consequences for cellular protein translation. Since U3 snoRNA-driven rRNA production is rate-limiting in ribosome biogenesis, we hypothesized that the U3 snoRNA is critical for chondrocyte homeostasis. In this study we therefor aimed to determine whether OA pathophysiological conditions interact with chondrocyte U3 snoRNA levels, thereby influencing rRNA levels and chondrocyte translation capacity.
2020-08-21 | PXD017253 | Pride
Project description:Background: Small nucleolar RNAs (snoRNAs) are mid-size non-coding RNAs required for ribosomal RNA modification, implying a ubiquitous tissue distribution linked to ribosome synthesis. However, increasing numbers of studies identify extra-ribosomal roles of snoRNAs in modulating gene expression, suggesting more complex snoRNA abundance patterns. Therefore, there is a great need for mapping the snoRNome in different human tissues as the blueprint for snoRNA functions. Results: We used a low structure bias RNA-Seq approach to accurately quantify snoRNAs and compare them to the entire transcriptome in seven healthy human tissues (breast, ovary, prostate, testis, skeletal muscle, liver and brain). We identify 475 expressed snoRNAs categorized in two abundance classes that differ significantly in their function, conservation level and correlation with their host gene: 390 snoRNAs are uniformly expressed and 85 are enriched in the brain or reproductive tissues. Most tissue-enriched snoRNAs are embedded in lncRNAs and display strong correlation of abundance with them, whereas uniformly expressed snoRNAs are mostly embedded in protein-coding host genes and are mainly non- or anticorrelated with them. 59% of the non-correlated or anticorrelated protein-coding host gene/snoRNA pairs feature dual-initiation promoters, compared to only 16% of the correlated non-coding host gene/snoRNA pairs. Conclusions: Our results demonstrate that snoRNAs are not a single homogeneous group of housekeeping genes but include highly regulated tissue-enriched RNAs. Indeed, our work indicates that the architecture of snoRNA host genes varies to uncouple the host and snoRNA expressions in order to meet the different snoRNA abundance levels and functional needs of human tissues.
2021-05-13 | GSE157846 | GEO