ArticleNucleic acids research2015
Identification of U2AF(35)-dependent exons by RNA-Seq reveals a link between 3' splice-site organization and activity of U2AF-related proteins.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 40 citations in OpenAlex.
- Homogentisate 1,2-dioxygenase (HGD) gene variants, their analysis and genotype-phenotype correlations in the largest cohort of patients with AKU.European journal of human genetics : EJHG · 2019Trial
- U2AF1 modulates alternative exon selection and guards zygotic splicing activation in mouse preimplantation embryogenesis.Cellular and molecular life sciences : CMLS · 2026Article
- U2AF2 controls alternative splicing in speckle-proximal regions in an RS domain-dependent manner.Nucleic acids research · 2026Article
- The splicing auxiliary factor OsU2AF35a enhances thermotolerance via protein separation and promoting proper splicing of OsHSA32 pre-mRNA in rice.Plant biotechnology journal · 2025Article
- Differences in alternative splicing and their potential underlying factors between animals and plants.Journal of advanced research · 2024Review
- The cap-binding complex modulates ABA-responsive transcript splicing during germination in barley (Hordeum vulgare).Scientific reports · 2024Article
- Critical Differential Expression Assessment for Individual Bulk RNA-Seq Projects.bioRxiv : the preprint server for biology · 2024Article
- Exonic splicing code and coordination of divalent metals in proteins.Nucleic acids research · 2024Article
- PUF60 promotes cell cycle and lung cancer progression by regulating alternative splicing of CDC25C.Cell reports · 2023Article
- Alu RNA fold links splicing with signal recognition particle proteins.Nucleic acids research · 2023Article
- mRNA alternative polyadenylation (APA) in regulation of gene expression and diseases.Genes & diseases · 2023Review
- Recruitment of a splicing factor to the nuclear lamina for its inactivation.Communications biology · 2022Article
- Article
- Aberrant Alternative Splicing in U2af1/Tet2 Double Mutant Mice Contributes to Major Hematological Phenotypes.International journal of molecular sciences · 2021Article
- Restriction of an intron size en route to endothermy.Nucleic acids research · 2021Article
- Splicing Enhancers at Intron-Exon Borders Participate in Acceptor Splice Sites Recognition.International journal of molecular sciences · 2020Article
- Article
- A splice site-sensing conformational switch in U2AF2 is modulated by U2AF1 and its recurrent myelodysplasia-associated mutation.Nucleic acids research · 2020Article
- Characterizing the interplay between gene nucleotide composition bias and splicing.Genome biology · 2019Article
- mTOR-regulated U2af1 tandem exon splicing specifies transcriptome features for translational control.Nucleic acids research · 2019Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
The auxiliary factor of U2 small nuclear RNA (U2AF) is a heterodimer consisting of 65- and 35-kD proteins that bind the polypyrimidine tract (PPT) and AG dinucleotides at the 3' splice site (3'ss). The gene encoding U2AF35 (U2AF1) is alternatively spliced, giving rise to two isoforms U2AF35a and U2AF35b. Here, we knocked down U2AF35 and each isoform and characterized transcriptomes of HEK293 cells with varying U2AF35/U2AF65 and U2AF35a/b ratios. Depletion of both isoforms preferentially modified alternative RNA processing events without widespread failure to recognize 3'ss or constitutive exons. Over a third of differentially used exons were terminal, resulting largely from the use of known alternative polyadenylation (APA) sites. Intronic APA sites activated in depleted cultures were mostly proximal whereas tandem 3'UTR APA was biased toward distal sites. Exons upregulated in depleted cells were preceded by longer AG exclusion zones and PPTs than downregulated or control exons and were largely activated by PUF60 and repressed by CAPERα. The U2AF(35) repression and activation was associated with a significant interchange in the average probabilities to form single-stranded RNA in the optimal PPT and branch site locations and sequences further upstream. Although most differentially used exons were responsive to both U2AF subunits and their inclusion correlated with U2AF levels, a small number of transcripts exhibited distinct responses to U2AF35a and U2AF35b, supporting the existence of isoform-specific interactions. These results provide new insights into function of U2AF and U2AF35 in alternative RNA processing.
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