Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Deletions of singular U1 snRNA gene significantly interfere with transcription and 3'-end mRNA formation rather than pre-mRNA splicing

ABSTRACT: To investigate the functions of each singular copy of snRNA genes in Drosophila melanogaster, we focused on the U1 snRNA and systematically investigated all the five Drosophila U1 genes. We constructed two series of U1-gene strains, one is transgenic strains of U1 promoter-driven gfp that allows for detection of each U1-gene’s expression in various developmental stages and tissues, the other is the CRISPR/Cas9-mediated precise U1-gene deletion strains that allows for investigation of phenotypes and effects on multiple RNA processing steps, including transcription, splicing and 3'-end formation. Further in vitro pulldown assay reveal the Drosophila U1 variants have different activity in binding with Sm proteins.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE225604 | GEO | 2023/02/19

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Identification of U1 snRNA associated proteins

Project description:In this project, we isolate U1 snRNA associated proteins in Arabidopsis thaliana. We used an antisense oligonucleotide specific for the U1 snRNA and analyzed associated proteins by mass spectrometry. As a control, the same experiments were performed with U2 snRNA- and lacZ-specifc antisense oligonucleotides.

2023-12-04 | PXD045484 | Pride

Transcriptome analysis of U1 snRNA overexpression in human neurons

Project description:U1 snRNA is the small nuclear RNA that services as the backbone of U1 snRNP. Removing intron from pre-mRNA to produce mature mRNA is the core function of the U1 snRNA. As one of the most abundant small noncoding RNA in human cells – estimated to be in the region of 1x10^6 copies per human cell (Hela) – U1 snRNA level is much more abundant than the other snRNAs. However, the potential role of the different amounts of the snRNAs is still unknown. To study the function of U1 snRNA in human neurons, we used lentivirus vector to overexpression U1 snRNA. We analyzed the gene expression change and identified target genes of U1 snRNA overexpression. We uncovered a novel role of U1 snRNA in regulating gene expression in human neurons.

2020-01-01 | GSE124951 | GEO

Novel RNA-binding Proteins Bind U1 snRNA to Promote Splicing of Weak 5' Splice Sites

Project description:Removal of introns during pre-mRNA splicing, which is central to gene expression, initiates by base pairing of U1 snRNA with a 5' splice site (5'SS). In mammals, many introns contain weak 5'SSs that are not efficiently recognized by the canonical U1 snRNP, suggesting alternative mechanisms exist. Here, we develop a cross-linking immunoprecipitation coupled to a high-throughput sequencing method, BCLIP-seq, to identify NRDE2 (Nuclear RNAi defective-2) and CCDC174 (Coiled-Coil Domain-Containing 174) as novel RNA-binding proteins in mouse ES cells that associate with U1 snRNA and unspliced 5'SSs. Both proteins bind directly to U1 snRNA independently of canonical U1 snRNP specific proteins, and they are required for the selection and effective processing of weak 5'SSs. Our results reveal that mammalian cells use non-canonical splicing factors bound directly to U1 snRNA to effectively select suboptimal 5'SS sequences in hundreds of genes, promoting proper splice site choice and accurate pre-mRNA splicing.

2023-09-07 | PXD029392 | Pride

Platform comparison of U1 Adaptors - a new gene silencing technology vs. siRNA

Project description:The goal of the microarray experiment was to do a head-to-head comparison of the U1 Adaptor technology with siRNA in terms of specificity at the genome-wide level. U1 Adaptors represent a novel gene silencing method that employs a mechanism of action distinct from antisense and RNA interference (RNAi). The U1 Adaptor is a bifunctional oligonucleotide having a âTarget Domainâ that is complementary to a site in the target gene's terminal exon and a âU1 Domainâ that binds to the U1 small nuclear RNA (snRNA) component of the U1 small nuclear ribonucleoprotein (U1 snRNP) splicing factor. Tethering of U1 snRNP to the target pre-mRNA inhibits 3' end processing (i.e., polyA tail addition) leading to degradation of that RNA species within the nucleus thereby reducing mRNA levels. We demonstrate that U1 Adaptors can specifically inhibit both reporter and endogenous genes. Further, targeting the same gene either with multiple U1 Adaptors or with U1 Adaptors and small interfering RNAs (siRNAs), strongly enhances gene silencing, the latter as predicted from their distinct mechanisms of action. Such combinatorial targeting requires lower amounts of oligonucleotides to achieve potent silencing. Experiment Overall Design: For each sample total RNA was prepared from 3 independent transfections and then were pooled and analyzed by QPCR and also by microarray.

2009-02-21 | E-GEOD-14434 | biostudies-arrayexpress

Exogenous expression analysis of U1 snRNA mutation

Project description:To reveal the effect of U1 snRNA mutation, we performed exogenous expression analysis of U1 snRNA mutation. The pLKO.1-puro U6 sgRNA BfuAI stuffer lentiviral vector was modified by removing the internal U6 promoter. It was replaced by the U1 locus, including 393 bases of internal native U1 promoter, the U1 sequence, and 39 bases of 3’-flanking region. The r.3A>G mutation was introduced by site-directed mutagenesis. HEK-293T cells were transfected using Lipofectamine Plus with either pLKO.1-U1wt or pLKO.1-U1r.3a>g in duplicate. Messenger RNA library construction was performed based on oligo dT-based mRNA isolation using NEBNext® Poly(A) mRNA Magnetic Isolation Module. RNA Sequence was performed on NextSeq 550 using 100-bp paired-end mode.

2019-10-09 | GSE128005 | GEO

The Evolutionarily Conserved AU-Dinucleotide at the 5’ End of U1 snRNA is Critical for the Biogenesis and Functionality of U1 snRNP

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

Gene expression profiling reveals cytoplasmic U1 snRNA accumulation may cause cancers

Project description:In this study, we built a model of cytoplasmic aggregation of U1 snRNA in a rat cell line. By comparing the gene expression profiling of U1 snRNA accumulated cells with their controls, 916 (about 4% of 20,000) genes were identified significantly differentially expressed. These 595 over-expressed genes and 321 repressed genes were further analyzed by GO and KEGG pathway enrichment. As a result, three of 12 enriched pathways are well-known cancer pathways, while nine of them were associated to cancers in previous studies. These findings suggest that cytoplasmic U1 snRNA accumulation may cause cancers.

2016-07-13 | GSE84304 | GEO

U1 snRNP regulates alternative polyadenylation in DNA damage response

Project description:The DNA damage response (DDR) involves coordinated control of gene expression and DNA repair. Using deep sequencing we found widespread changes of alternative cleavage and polyadenylation (APA) site usage upon UV-treatment in mammalian cells. APA regulation in the 3’ untranslated region (3’UTR) is substantial, leading to both shortening and lengthening of 3’UTRs. Interestingly, a strong activation of intronic APA sites is detected, resulting in widespread expression of truncated transcripts. Intronic APA events are biased to the 5’ end of genes and affect gene groups with important functions in DDR. Moreover, intronic APA site activation during DDR correlates with a decrease in U1 snRNA levels, and this is reversed by U1 snRNA overexpression. Importantly, U1 snRNA overexpression decreases UV-induced apoptosis. Together, these studies describe a significant gene regulatory scheme in DDR where U1 snRNP impacts gene expression via APA.

2016-05-01 | GSE71801 | GEO

Targeted RNase H-mediated Extraction of crosslinked RBPs (TREX) for assessing U1 RNA interactome

Project description:We used Targeted RNase H-mediated Extraction of crosslinked RBPs (TREX)to assess the endogenous binding partners of U1 small nuclear RNA (U1 snRNA) in human HCT116 cells. Extracted proteins from U1 digested and control cells (5 replicate per condition) were compared, using label-free (LFQ) Quantitative proteomics.

2023-12-27 | PXD044643 | Pride

Novel RNA-binding Proteins Bind U1 snRNA to Promote Splicing of Weak 5' Splice Sites

2023-05-04 | GSE179744 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data