SnRNA 3' end sequencing
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1005226 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25634100.fastq.gz | Fastqsanger.gz | |||
| SRR25634100_1.fastq.gz | Fastqsanger.gz | |||
| SRR25634100_2.fastq.gz | Fastqsanger.gz | |||
| SRR25634101.fastq.gz | Fastqsanger.gz | |||
| SRR25634101_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 298 |
Similar Datasets
Project description:In order to identify factors involved in transcription of human snRNA genes and 3’ end processing of the transcripts, we have carried out CRISPR affinity purification in situ of regulatory elements (CAPTURE), which is deadCas9-mediated pull-down, of the tandemly-repeated U2 snRNA genes in human cells. Pull-down proteins were identified by mass spectrometry-based proteomics analysis.
2022-06-09 | PXD033580 | Pride
Project description:Competition between 3’ end maturation and degradation drives snRNA quality control
| PRJNA594409 | ENA
Project description:The post-transcriptional maturation of U6 snRNA 3′-end is important for spliceosomal assembly and RNA splicing, and is catalyzed by sequential enzymatic activities of TUT1 and USB1, that is, an oligo(U) tail is first added by TUT1 to the freshly transcribed U6 snRNA, and then trimmed by USB1 to generate mature U6 snRNA. However, biallelic inactivation of TUT1 or USB1 is linked to distinct human developmental disorders, and their physiological functions remain unknown. Here, using multiple genetically engineered mouse models, we show that Tut1, but unexpectedly not Usb1, is essential for the maintenance of the epiblast and neural stem cells in vivo. Loss of Tut1 weakens the interactions between essential splicing factors and U6 snRNA, causes defective RNA splicing, and triggers massive DNA damage and subsequent cell death. Importantly, cell death can be prevented by recombinant U6 snRNA containing an oligo(U) tail. These results challenge the current model of U6 snRNA 3′-end maturation and function. We propose that TUT1 is an essential U6 snRNA 3′-end maturation or repair factor, and discuss the implications of these results for understanding the etiologies of TUT1- and USB1-related human disorders.
2026-06-03 | GSE305663 | GEO
Project description:The post-transcriptional maturation of U6 snRNA 3′-end is important for spliceosomal assembly and RNA splicing, and is catalyzed by sequential enzymatic activities of TUT1 and USB1, that is, an oligo(U) tail is first added by TUT1 to the freshly transcribed U6 snRNA, and then trimmed by USB1 to generate mature U6 snRNA. However, biallelic inactivation of TUT1 or USB1 is linked to distinct human developmental disorders, and their physiological functions remain unknown. Here, using multiple genetically engineered mouse models, we show that Tut1, but unexpectedly not Usb1, is essential for the maintenance of the epiblast and neural stem cells in vivo. Loss of Tut1 weakens the interactions between essential splicing factors and U6 snRNA, causes defective RNA splicing, and triggers massive DNA damage and subsequent cell death. Importantly, cell death can be prevented by recombinant U6 snRNA containing an oligo(U) tail. These results challenge the current model of U6 snRNA 3′-end maturation and function. We propose that TUT1 is an essential U6 snRNA 3′-end maturation or repair factor, and discuss the implications of these results for understanding the etiologies of TUT1- and USB1-related human disorders.
2026-06-03 | GSE305664 | GEO
Project description:Spliceosomal snRNA are key components of small nuclear ribonucleoprotein particles (snRNPs), the building blocks of the spliceosome. The biogenesis of snRNPs is a complex process involving multiple cellular and subcellular compartments, the details of which are yet to be described. In short, the snRNA is exported to the cytoplasm as 3‘-end extended precursor (pre-snRNA), where it acquires a heptameric Sm ring. The SMN complex which catalyses this step, recruits Sm proteins and assembles them around the pre-snRNA at the single stranded Sm site. After additional modification, the complex is re-imported into the nucleus where the final maturation step occurs. Our modeling suggests that during the cytoplasmic stage of maturation pre-snRNA assumes a compact secondary structure containing Near Sm site Stem (NSS) which is not compattible with the formation of the Sm ring. To validate our in silico predictions we employed selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) on U2 snRNA in vivo, ex vivo and in vitro, and U4 pre-snRNA in vitro. For the in vivo experiment HeLa cells were incubated for 10 min at 37°C with NAI or DMSO to final concentration 200 mM. RNA was isolated using Trizol (Sigma) and 200 µl chloroform and precipitated with ethanol at -20°C overnight. For the ex vivo experiment, RNA was isolated from HeLa cells after Protease K treatment at room temperature for 45 min. After incubation, RNA was isolated using equilibrated phenol/chloroform/isoamyl alcohol buffered by folding buffer (110 mM HEPES pH 8.0, 110 mM KCl, 11 mM MgCl2) and cleaned on a PD-10 column according to the manufacturer’s instructions. Isolated RNA was treated with 100mM NAI or DMSO for 10 min at 37°C. For the in vitro experiment, U2WT and U4 pre-snRNA were transcribed by T7 polymerase followed by DNase I (30 min at 37 °C) and Proteinase K (30 min at 37°C) treatments. U2 snRNA was purified on 30 kDa Amicon columns, folded for 30 min at 37°C in 57 mM MgCl2 and incubated with 100 mM NAI at 37°C for 10 min. DMSO was used as a negative control. U4 pre-snRNA was purified on Superdex 200 Increase 10/300GL, folded for 30 min at 37°C in 60 mM MgCl2 and incubated with 100 mM NAI at 37°C for 10 min. DMSO was used as a negative control. All prepared RNA samples (in vitro, ex vivo, in vivo) were used for reverse transcription with the gene-specific primer 5’-CGTTCCTGGAGGTACTGCAA for U2 snRNA and 5’- AAAAATTCAGTCTCCG for U4 pre-snRNA. We used SHAPE MaP buffer (50 mM Tris-HCl pH 8.0, 75 mM KCl, 10 mM DTT, 0.5 mM dNTP, 6 mM MnCl2) and SuperScript II (Invitrogen). Amplicons for snRNAs were generated using gene-specific forward and reverse primers. Importantly, the primers include Nextera adaptors required for downstream library construction. PCR reaction products were cleaned using Monarch PCR&DNA Clean-up Kits. Remaining Illumina adaptor sequences were added using the PCR MasterMix and index primers provided in the NexteraXT DNA Library Preparation Kit (Illumina) according to the manufacturer’s protocol. Libraries were quantified using Qubit (Invitrogen) and BioAnalyzer (Agilent). Amplicons were sequenced on a NextSeq 500/550 platform using a 150 cycle mid-output kit. All sequencing data was analyzed using the ShapeMapper 2 analysis pipeline1. The ‘—amplicon’ and ‘—primers’ flags were used, along with sequences of gene-specific handles PCR primers, to ensure primer binding sites are excluded from reactivity calculations. Default read-depth thresholds of 5000x were used. Analysis of statistically significant reactivity differences between ex vivo and in vivo-determined SHAPE reactivities was performed using the DeltaSHAPE automated analysis tool and default settings2. 1. Busan, S. & Weeks, K.M. Accurate detection of chemical modifications in RNA by mutational profiling (MaP) with ShapeMapper 2. RNA 24, 143-148 (2018). 2. Smola, M.J., Rice, G.M., Busan, S., Siegfried, N.A. & Weeks, K.M. Selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis. Nat Protoc 10, 1643-69 (2015).
2023-09-08 | E-MTAB-13248 | biostudies-arrayexpress
Project description:Polymerases and exonucleases act on 3’ ends of nascent RNAs to promote their maturation or degradation but how the balance between these activities is controlled to dictate the fates of cellular RNAs remains poorly understood. Here, we identify a central role for the human DEDD deadenylase TOE1 in distingushing the fates of small nuclear (sn)RNAs of the spliceosome from genome-encoded snRNA variants. We find that TOE1 promotes maturation of all regular RNA polymerase II-transcribed snRNAs of the major and minor spliceosomes by removing post-transcriptional oligo(A)-tails, trimming 3’ ends, and preventing nuclear exosome targeting. By contrast, TOE1 promotes little to no maturation of tested U1 variant snRNAs, which are instead targeted by the nuclear exosome. These observations suggest that TOE1 is positioned at the center of a 3’ end quality control pathway that selectively promotes maturation and stability of regular snRNAs while leaving snRNA variants unprocessed and exposed to degradation in what could be a widespread mechanism of RNA quality control given the large number of non-coding RNAs processed by DEDD deadenylases.
2020-07-13 | GSE141709 | GEO
Project description:snRNA-sequencing data for macaque LIP area. We isolated single nuclei from the LIP region. annotating the dataset with the canonical classification and integration with other datasets.
2026-05-31 | E-MTAB-13364 | biostudies-arrayexpress
Project description:Splicing is initiated by a productive interaction of pre-mRNA and the U1 snRNP, which dictates the formation a short RNA duplex between the 5’ splice site of a pre-mRNA and the 5’ end of the U1 snRNA. A long-standing puzzle has been why the AU dincucleotide at the 5’-end of the U1 snRNA shows strict conservation, despite the absence of an apparent role in duplex formation. To explore this conundrum, we varied this AU dinucleotide into to all possible permutations and analyzed the resulting molecular, biochemical, and physiological consequences. This led to the findings that the AU dinucleotide governs the precision of transcription start site, the methylation status of the U1 snRNA 5’-cap, appropriate maturation of a functional U1 snRNP, and its subsequent utilization in the splicing pathway. Our data also provide an insight as to why the identity of the AU dinucleotide is strongly favored during evolution.
2018-02-22 | GSE97015 | GEO
Project description:The 3’ end of most cellular U6 snRNA has a 2′,3′-cyclic phosphate group, a post-transcriptional modification thought to be essential for proper RNA splicing and cellular function. Recent studies have established that the biogenesis of 2′,3′-cyclic phosphate requires two enzymes: first TUT1 adds a poly(U) tail to the 3’ end of U6 snRNA, followed by USB1-catalyzed trimming of the poly(U) tail. Here, we use nine genetically engineered mouse models of Tut1 and Usb1 to show that, contrary to what was previously believed, Usb1 and thus 2′,3′-cyclic phosphate is dispensable for intra-embryonic cell lineages. We find that Tut1, but not Usb1, is essential for the maintenance of the epiblast and neural stem cells. Loss of Tut1 causes defective RNA splicing, triggering massive DNA damage and subsequent cell death. In contrast, loss of Usb1 primarily damages endothelial cells of the extra-embryonic vasculature in the yolk sac by both cell-intrinsic and -extrinsic mechanisms, leading to fetal growth restriction. These results demonstrate that TUT1-catalyzed U6 snRNA 3’ end oligouridylation, rather than 2′,3′-cyclic phosphate as previously thought, is required for proper RNA splicing. Further studies are warranted to elucidate how these different post-transcriptional modifications regulate the function of U6 snRNA in RNA splicing in development and disease.
2026-06-03 | GSE277838 | GEO
Project description:The 3’ end of most cellular U6 snRNA has a 2′,3′-cyclic phosphate group, a post-transcriptional modification thought to be essential for proper RNA splicing and cellular function. Recent studies have established that the biogenesis of 2′,3′-cyclic phosphate requires two enzymes: first TUT1 adds a poly(U) tail to the 3’ end of U6 snRNA, followed by USB1-catalyzed trimming of the poly(U) tail. Here, we use nine genetically engineered mouse models of Tut1 and Usb1 to show that, contrary to what was previously believed, Usb1 and thus 2′,3′-cyclic phosphate is dispensable for intra-embryonic cell lineages. We find that Tut1, but not Usb1, is essential for the maintenance of the epiblast and neural stem cells. Loss of Tut1 causes defective RNA splicing, triggering massive DNA damage and subsequent cell death. In contrast, loss of Usb1 primarily damages endothelial cells of the extra-embryonic vasculature in the yolk sac by both cell-intrinsic and -extrinsic mechanisms, leading to fetal growth restriction. These results demonstrate that TUT1-catalyzed U6 snRNA 3’ end oligouridylation, rather than 2′,3′-cyclic phosphate as previously thought, is required for proper RNA splicing. Further studies are warranted to elucidate how these different post-transcriptional modifications regulate the function of U6 snRNA in RNA splicing in development and disease.
2026-06-03 | GSE277839 | GEO