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TranscriptomicsRNA-Seq of monoclonal cell lines after CRISPR/Cas9-mediated editing of box C/D snoRNA genes (SNORDs)
In this study monoclonal cell lines carrying mutations in snoRNA genes (SNORD74, SNORD75, SNORD77, SNORD80) were obtained. Next, whole transcriptome analysis of obtained cell lines was performed on an Illumina NextSeq 500 platform. RNA-seq libraries was constructed on PolyA mRNA-enriched fraction. T...
ORGANISM(S): Homo sapiens 
2019-10-14 | E-MTAB-8269 | biostudies-arrayexpress
TranscriptomicsGene expression comparison between WT, U17 snoRNA knockdown and U17 overexpression NIH-3T3 cells to identify target mRNAs regulated by U17 snoRNA
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...
ORGANISM(S): Mus musculus 
2015-04-04 | E-GEOD-67569 | biostudies-arrayexpress
GenomicsThe telomere-binding protein Tbf1 demarcates snoRNA gene promoters in Saccharomyces cerevisiae
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 mam...
ORGANISM(S): Saccharomyces cerevisiae 
2010-05-28 | E-GEOD-20870 | biostudies-arrayexpress
ProteomicsIMPAIRED CHONDROCYTE U3 SNORNA EXPRESSION IN OSTEOARTHRITIS AND ITS IMPACT ON THE CHONDROCYTE’S PROTEIN TRANSLATION APARATUS
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 t...
ORGANISM(S): Homo sapiens (Human) 
2020-08-21 | PXD017253 | Pride
Osteoarthritis Snorna Translation 
TranscriptomicsHuman Nonsense-Mediated RNA Decay Initiates Widely by Endonucleolysis and Targets snoRNA Host Genes
Eukaryotic RNAs with premature termination codons (PTCs) are eliminated by nonsense-mediated decay (NMD). While human nonsense RNA degradation can be initiated either by an endonucleolytic cleavage event near the PTC or through decapping, the individual contribution of these activities on endogenous...
ORGANISM(S): Homo sapiens 
2014-11-18 | E-GEOD-57433 | biostudies-arrayexpress
ProteomicsAtypical U3 snoRNA Suppresses the Process of Pterygia through Modulating 18S Ribosomal RNA Synthesis
Ribosome biosynthesis plays a crucial role in regulating protein translation and is essential for cell growth and development in physiological progress. The progression and recurrence of Pterygia mainly occur due to the abnormal proliferation and migration of stromal Pterygia fibroblasts. Small nucl...
ORGANISM(S): Homo sapiens (Human) 
2022-05-20 | PXD030801 | Pride
Pterygium U3 snorna 47s rrna 18s rrna 5' ets Ribosome biosynthesis 
TranscriptomicsNext generation sequencing identifies discrete classes of box C/D snoRNAs featuring different ends and RNA binding protein dependency
The paired-end next-generation sequencing of all small RNAs of less than 200 nucleotides in length from four different human cell lines (SKOV3ip1, MCF-7, BJ-Tielf, INOF) allowed us to determine the exact sequence(s) and variations of human box C/D snoRNAs (small nucleolar RNAs), revealing processing...
ORGANISM(S): Homo sapiens 
2014-07-01 | E-GEOD-55946 | biostudies-arrayexpress
ProteomicsEnhanced snoMEN vectors facilitate establishment of GFP–HIF-1? protein replacement human cell lines
The snoMEN (snoRNA Modulator of gene ExpressioN) vector technology was developed from a human box C/D snoRNA, HBII-180C, which contains an internal sequence that can be manipulated to make it complementary to RNA targets, allowing knock-down of targeted genes. Here we have screened additional human ...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-31 | MSV000080828 | MassIVE
TranscriptomicsEffects of the Paf1 complex and histone modifications on snoRNA 3'-end formation reveal broad and locus-specific regulation.
High-density tiling arrays were used to compare transcriptional profiles between the paf1 deletion strain and a wild-type reference strain. This included assessment of signal within ORFs, as well as read-through transcription associated with each of the snoRNAs annotated in SGD. For the latter, hybr...
ORGANISM(S): Saccharomyces cerevisiae 
2012-10-26 | E-MTAB-1342 | biostudies-arrayexpress
TranscriptomicsHuman PA-1 cells treated with scrambled or specific ASOs
We describe the discovery of sno-lncRNAs, a class of nuclear-enriched intron-derived long noncoding RNAs (lncRNAs) that are processed on both ends by the snoRNA machinery. During exonucleolytic trimming, the sequences between the snoRNAs are not degraded, leading to the accumulation of lncRNAs flank...
ORGANISM(S): Homo sapiens 
2013-04-26 | E-GEOD-38541 | biostudies-arrayexpress
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