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Analysis of transcriptome changes in HeLa cells after knock-down of variant U1.8 snRNA

ABSTRACT: U1 small nuclear (sn)RNA, required for splicing of pre-mRNA, is encoded by genes on chromosome 1p36. Imperfect copies of these ‘true’ (t)U1 snRNA genes, located on chromosome 1q12-21, were thought to be pseudogenes. However, many of these ‘variant’ (v)U1 snRNA genes produce fully-processed transcripts that are packaged into potentially functional particles. Using antisense oligonucleotides, we have achieved functional knockdown of a specific vU1 snRNA in HeLa cells and identified over 400 transcriptome changes following interrogation of the Affymetrix Human Exon ST 1.0 array. Total RNA from 4 biological repeats of vU1.8 snRNA and control knock-down were analysed using Affymetrix Human Exon ST 1.0 Array.

ORGANISM(S): Homo sapiens

SUBMITTER: Martin Dienstbier

PROVIDER: E-GEOD-37623 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Analysis of transcriptome changes in HeLa cells after knock-down of variant U1.8 snRNA

Project description:U1 small nuclear (sn)RNA, required for splicing of pre-mRNA, is encoded by genes on chromosome 1p36. Imperfect copies of these ‘true’ (t)U1 snRNA genes, located on chromosome 1q12-21, were thought to be pseudogenes. However, many of these ‘variant’ (v)U1 snRNA genes produce fully-processed transcripts that are packaged into potentially functional particles. Using antisense oligonucleotides, we have achieved functional knockdown of a specific vU1 snRNA in HeLa cells and identified over 400 transcriptome changes following interrogation of the Affymetrix Human Exon ST 1.0 array.

2012-10-01 | GSE37623 | GEO

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

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

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

Arabidopsis SME interactome reveals spliceosome components

Project description:Alternative splicing (AS) can produce multiple transcripts with different exon-intron structures from a single pre-mRNA. Pre-mRNA splicing is catalyzed by a dynamic macromolecular ribonucleoprotein (RNP) complex termed the spliceosome. The spliceosome consists of several small nuclear ribonucleoproteins (snRNPs) that bind uridine-rich small nuclear RNA (snRNA). In U1, U2, U4 and U5 snRNPs, snRNA interacts with the conserved Smith antigen (Sm) proteins via a bipartite Sm sequence motif. In eukaryotes, seven Sm proteins (B, D1/2/3, E, F and G) form a heptameric ring-shaped complex surrounding the snRNA. Here, we performed a tandem affinity purification using SMEB as a bait in Arabidopsis cell suspension cultures. At least 45 known/hypothesized and potential novel spliceosome components were identified in Arabidopsis.

2023-03-03 | PXD016607 | Pride

ALS-causative mutations in FUS/TLS confer gain- and loss-of-function by altered association with SMN and U1-snRNP

Project description:The RNA-binding protein FUS/TLS, mutation in which is causative of the fatal motor neuron disease ALS, is demonstrated to directly bind to the U1-snRNP and SMN complexes. ALS-causative mutations in FUS/TLS are shown to abnormally enhance their interaction with SMN and reduce interaction with U1-snRNP. Correspondingly, global RNA analysis reveals a mutant-dependent loss of splicing activity, with ALS-linked mutants failing to reverse changes caused by loss of wild-type FUS/TLS. Furthermore, a common FUS/TLS mutant-associated RNA splicing signature is identified in ALS patient fibroblasts. Taken together, our studies establish potentially converging disease mechanisms in ALS and spinal muscular atrophy, with ALS-causative mutants acquiring properties representing both gain (dysregulation of SMN) and loss (reduced RNA processing mediated by U1-snRNP) of function. RNA-mediated oligonucleotide Annealing, Selection, and Ligation with Next-Generation sequencing (RASL-seq) method was used for analyzing alternative splicing changes. Oligonucleotide probes are designed to anneal to the exon-exon junctions. The probe library was assembled to assess 5530 unique alternative splicing events, most of which were exon inclusion or skipping, with a minority for alternative 5’- or 3’- splice sites. The splicing changes were compared among groups of reducing FUS/TLS or SMN levels, or expressing various FUS mutations to determine the loss versus gain of FUS/TLS function on splicing regulation.

2015-02-10 | E-GEOD-64078 | biostudies-arrayexpress

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

Identification of the altered transcripts in the NMF291–/– cerebellum by exon array.

Project description:The U2 snRNA is a basal component of the major spliceosome, which is responsible for >90% human pre-mRNA splicing. A 5-nucleotide deletion in one of the mouse U2 snRNA genes (Rnu2-8) causes cerebellar granule cell degeneration in the NMF291 mouse mutant strain. To identify the altered transcripts in the NMF291–/– cerebellum, we interograted Affy. mouse 1.0 ST Exon arrays with total RNAs from three postnatal-30-day (P30) wild type and three NMF291–/– cerebella. Affy. mouse 1.0 ST Exon arrays were hybridized with total RNAs derived from three P30 female wild type and NMF291–/– mice (biological replicates).

2011-10-19 | E-GEOD-33069 | biostudies-arrayexpress

U1 RAP-RNA-Seq analysis of A2Lox mouse embryonic stem cells treated with a control or Srrt-specific siRNA

Project description:The experiment was carried out to examine the effect of Srrt knockdown on the U1 snRNP/pre-mRNA interaction pattern. A2Lox mouse embryonic stem cells were transfected with either an Srrt-specific or a non-targeting siRNA. 48 hours post transfection the cells were cross-linked using 2% formaldehyde and lysed. RNA was partially fragmented by sonication, hybridized with U1 snRNA-specific biotinilated probes and pulled down. U1-associated RNA sequences were then purified and RNA-seq libraries were generated using a NEBNext® rRNA Depletion Kit and NEBNext® Ultra8482 II Directional RNA Library Preparation kit. Paired-end sequencing was performed using a HiSeq4000 75bp platform.

2019-11-27 | E-MTAB-7635 | biostudies-arrayexpress

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

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