ArticleNucleic acids research2003
A novel approach to describe a U1 snRNA binding site.
Article in Nucleic acids research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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60 citing papers in PubMed, 97 citations in OpenAlex.
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- Fully haplotyped genome assemblies of healthy individuals reveal variability in 5'ss strength and support by splicing regulatory proteins.NAR genomics and bioinformatics · 2025Article
- Functional analysis of CYP4B1 enzymes from apes and humans uncovers evolutionary hot spots for adaptations of the catalytical function.PLoS genetics · 2025Article
- Difference Analysis Among Six Kinds of Acceptor Splicing Sequences by the Dispersion Features of 6-mer Subsets in Human Genes.Biology · 2025Article
- Splicing accuracy varies across human introns, tissues, age and disease.Nature communications · 2025Article
- Expanding the genetic and phenotypic spectrum of congenital myasthenic syndrome: new homozygous VAMP1 splicing variants in 2 novel individuals.Journal of human genetics · 2024Article
- Srsf1 and Elavl1 act antagonistically on neuronal fate choice in the developing neocortex by controlling TrkC receptor isoform expression.Nucleic acids research · 2023Article
- Alu RNA fold links splicing with signal recognition particle proteins.Nucleic acids research · 2023Article
- The plant epitranscriptome: revisiting pseudouridine and 2'-O-methyl RNA modifications.Plant biotechnology journal · 2022Review
- Principles and correction of 5'-splice site selection.RNA biology · 2022Review
- Splice site proximity influences alternative exon definition.RNA biology · 2022Article
- Altered HIV-1 mRNA Splicing Due to Drug-Resistance-Associated Mutations in Exon 2/2b.International journal of molecular sciences · 2021Article
- Article
- Functional analyses of human LUC7-like proteins involved in splicing regulation and myeloid neoplasms.Cell reports · 2021Article
- Modifying splice site usage withComputational and structural biotechnology journal · 2021Article
- Spliceosomal snRNA Epitranscriptomics.Frontiers in genetics · 2021Review
- Regulation and Function of RNA Pseudouridylation in Human Cells.Annual review of genetics · 2020Review
- VarCon: An R Package for Retrieving Neighboring Nucleotides of an SNV.Cancer informatics · 2020Article
- A scale-free analysis of the HIV-1 genome demonstrates multiple conserved regions of structural and functional importance.PLoS computational biology · 2019Article
Corrections and comments
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13 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA duplex formation between U1 snRNA and a splice donor (SD) site can protect pre-mRNA from degradation prior to splicing and initiates formation of the spliceosome. This process was monitored, using sub-genomic HIV-1 expression vectors, by expression analysis of the glycoprotein env, whose formation critically depends on functional SD4. We systematically derived a hydrogen bond model for the complementarity between the free 5' end of U1 snRNA and 5' splice sites and numerous mutations following transient transfection of HeLa-T4+ cells with 5' splice site mutated vectors. The resulting model takes into account number, interdependence and neighborhood relationships of predicted hydrogen bond formation in a region spanning the three most 3' base pairs of the exon (-3 to -1) and the eight most 5' base pairs of the intron (+1 to +8). The model is represented by an algorithm classifying U1 snRNA binding sites which can or cannot functionally substitute SD4 with respect to Rev-mediated env expression. In a data set of 5' splice site mutations of the human ATM gene we found a significant correlation between the algorithmic classification and exon skipping (P = 0.018, chi2-test), showing that the applicability of the proposed model reaches far beyond HIV-1 splicing. However, the algorithmic classification must not be taken as an absolute measure of SD usage as it may be modified by upstream sequence elements. Upstream to SD4 we identified a fragment supporting ASF/SF2 binding. Mutating GAR nucleotide repeats within this site decreased the SD4-dependent Rev-mediated env expression, which could be balanced simply by artificially increasing the complementarity of SD4.
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