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

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

PROVIDER: PRJNA744888 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15070630.fastq.gz	Fastqsanger.gz
	SRR15070631.fastq.gz	Fastqsanger.gz
	SRR15070632.fastq.gz	Fastqsanger.gz
	SRR15070633.fastq.gz	Fastqsanger.gz
	SRR15070635.fastq.gz	Fastqsanger.gz

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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

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

2023-05-04 | GSE179744 | 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

Prp4 Kinase Grants the License to Splice: Control of Weak Splice Sites during Spliceosome Activation

Project description:The genome of the fission yeast Schizosaccharomyces pombe encodes 17 kinases that are essential for cell growth. These include the cell-cycle regulator Cdc2, as well as several kinases that coordinate cell growth, polarity, and morphogenesis during the cell cycle. In this study, we further characterized another of these essential kinases, Prp4, and showed that the splicing of many introns is dependent on Prp4 kinase activity. For detailed characterization, we chose the genes res1 and ppk8, each of which contains one intron of typical size and position. Splicing of the res1 intron was dependent on Prp4 kinase activity, whereas splicing of the ppk8 intron was not. Extensive mutational analyses of the 5’ splice site of both genes revealed that proper transient interaction with the 5’ end of snRNA U1 governs the dependence of splicing on Prp4 kinase activity. Proper transient interaction between the branch sequence and snRNA U2 was also important. Therefore, the Prp4 kinase is required for recognition and efficient splicing of introns displaying weak exon1/5’ splice sites and weak branch sequences.

2015-12-01 | GSE75517 | GEO

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.

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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.

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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.

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Human PRPF39 is an alternative splicing factor recruiting U1 snRNP to weak 5' splice sites

Project description:Human PRPF39 is an alternative splicing factor recruiting U1 snRNP to weak 5' splice sites

| PRJNA866129 | ENA

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

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

Project description: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.

2023-02-19 | GSE225604 | GEO

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