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Compensatory signals associated with the activation of human GC 5′ splice sites

By Jana Kralovicova, Gyulin Hwang, A. Charlotta Asplund, Alexander Churbanov, C. I. Edvard Smith and Igor Vorechovsky

Abstract

GC 5′ splice sites (5′ss) are present in ∼1% of human introns, but factors promoting their efficient selection are poorly understood. Here, we describe a case of X-linked agammaglobulinemia resulting from a GC 5′ss activated by a mutation in BTK intron 3. This GC 5′ss was intrinsically weak, yet it was selected in >90% primary transcripts in the presence of a strong and intact natural GT counterpart. We show that efficient selection of this GC 5′ss required a high density of GAA/CAA-containing splicing enhancers in the exonized segment and was promoted by SR proteins 9G8, Tra2β and SC35. The GC 5′ss was efficiently inhibited by splice-switching oligonucleotides targeting either the GC 5′ss itself or the enhancer. Comprehensive analysis of natural GC-AG introns and previously reported pathogenic GC 5′ss showed that their efficient activation was facilitated by higher densities of splicing enhancers and lower densities of silencers than their GT 5′ss equivalents. Removal of the GC-AG introns was promoted to a minor extent by the splice-site strength of adjacent exons and inhibited by flanking Alu repeats, with the first downstream Alus located on average at a longer distance from the GC 5′ss than other transposable elements. These results provide new insights into the splicing code that governs selection of noncanonical splice sites

Topics: Genomics
Publisher: Oxford University Press
OAI identifier: oai:pubmedcentral.nih.gov:3167603
Provided by: PubMed Central

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Citations

  1. (1987). 50 cleavage site in eukaryotic pre-mRNA splicing is determined by the overall 50 splice region, not by the conserved 50 GU.
  2. (1986). A compensatory base change in U1 snRNA suppresses a 50 splice site mutation.
  3. (1996). A complex of nuclear proteins mediates SR protein binding to a purine-rich splicing enhancer.
  4. (2010). A method of predicting changes in human gene splicing induced by genetic variants in context of cis-acting elements.
  5. (2005). A mutation hotspot at the p14ARF splice site.
  6. (2003). A negative element in SMN2 exon 7 inhibits splicing in spinal muscular atrophy.
  7. (2002). A new type of mutation causes a splicing defect in ATM.
  8. (2001). A novel intronic mutation of the TAZ (G4.5) gene in a patient with Barth syndrome: creation of a 50 splice donor site with variant GC consensus and elongation of the upstream exon.
  9. (2005). A novel XPA gene mutation and its functional analysis in a Japanese patient with xeroderma pigmentosum group
  10. (2003). A protein interaction map of Drosophila melanogaster.
  11. (1991). A reappraisal of non-consensus mRNA splice sites.
  12. (2000). A story: unpaired adenosine bases in ribosomal RNAs.
  13. (1995). A subset of SR proteins activates splicing of the cardiac troponin T alternative exon by direct interactions with an exonic enhancer.
  14. (2001). A universal mode of helix packing in RNA.
  15. (2009). Ab initio prediction of cryptic splice-site activation and exon skipping.
  16. (2006). Aberrant 30 splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.
  17. (2007). Aberrant 50 splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.
  18. (2008). Accumulation of GC donor splice signals in mammals.
  19. (2001). Activation of a cryptic 50 splice site by U1 snRNA.
  20. (1994). Alu sequences in the coding regions of mRNA: a source of protein variability.
  21. (2006). An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers.
  22. (2000). Analysis of canonical and non-canonical splice sites in mammalian genomes.
  23. (1996). Assembly of specific SR protein complexes on distinct regulatory elements of the Drosophila doublesex splicing enhancer.
  24. (2004). Autoregulation of polypyrimidine tract 7090
  25. (2005). Biased exon/intron distribution of cryptic and de novo 30 splice sites.
  26. (2004). Branch sites haplotypes that control alternative splicing.
  27. (2004). Characterization of the splice sites in GT-AG and GC-AG introns in higher eukaryotes using full-length cDNAs.
  28. (2011). Comparative analysis of information contents relevant to recognition of introns in many species.
  29. (2006). Comparison of multiple vertebrate genomes reveals the birth and evolution of human exons.
  30. (2005). Comparison of splice sites in mammals and chicken.
  31. (2010). Competing upstream 50 splice sites enhance the rate of proximal splicing.
  32. (1994). Complementation by SR proteins of pre-mRNA splicing reactions depleted of U1 snRNP.
  33. (2006). Comprehensive splice-site analysis using comparative genomics.
  34. (2004). Computational definition of sequence motifs governing constitutive exon splicing.
  35. (2002). Congenital afibrinogenemia: first identification of splicing mutations in the fibrinogen Bbeta-chain gene causing activation of cryptic splice sites.
  36. (2007). Crossregulation and functional redundancy between the splicing regulator PTB and its paralogs nPTB and ROD1.
  37. (2005). Cryptic 50 splice site activation in SCN5A associated with Brugada syndrome.
  38. (2004). Cryptic splicing at a non-consensus splice-donor in a patient with a novel mutation in the plakophilin-1 gene.
  39. (2010). DARNED: a DAtabase of RNa EDiting in humans.
  40. (2011). DBASS3 and DBASS5: databases of aberrant 30 and 50 splice sites in human disease genes.
  41. (2005). Deficiency of Bruton0s tyrosine kinase in B cell precursor leukemia cells.
  42. (2005). Determinants of the inherent strength of human 50 splice sites.
  43. (2003). ESEfinder: a web resource to identify exonic splicing enhancers.
  44. (2004). Evidence that RNA editing modulates splice site selection in the 5-HT2C receptor gene.
  45. (2005). Exonization of AluYa5 in the human ACE gene requires mutations in both 30 and 50 splice sites and is facilitated by a conserved splicing enhancer.
  46. (2007). Extensive in silico analysis of NF1 splicing defects uncovers determinants for splicing outcome upon 50 splice-site disruption.
  47. (1997). G triplets located throughout a class of small vertebrate introns enforce intron borders and regulate splice site selection.
  48. (2010). Genetic variations regulate alternative splicing in the 50 untranslated regions of the mouse glioma-associated oncogene 1, Gli1.
  49. (2000). Genomic sequence, splicing, and gene annotation.
  50. (2006). Genomic splice-site analysis reveals frequent alternative splicing close to the dominant splice site.
  51. (2007). Global control of aberrant splice site activation by auxiliary splicing sequences: evidence for a gradient in exon and intron definition.
  52. (2003). HnRNP G and Tra2beta: opposite effects on splicing matched by antagonism in RNA binding.
  53. (2004). How did alternative splicing evolve?
  54. (2000). Htra2-beta 1 stimulates an exonic splicing enhancer and can restore full-length SMN expression to survival motor neuron 2 (SMN2).
  55. (2001). Human GC-AG alternative intron isoforms with weak donor sites show enhanced consensus at acceptor exon positions.
  56. (1998). Human Tra2 proteins are sequence-specific activators of pre-mRNA splicing.
  57. (2004). Human tra2-beta1 autoregulates its protein concentration by influencing alternative splicing of its pre-mRNA.
  58. (1997). Identification of a new class of exonic splicing enhancers by in vivo selection.
  59. (1992). Identification of cis-acting intron and exon regions in influenza virus NS1 mRNA that inhibit splicing and cause the formation of aberrantly sedimenting presplicing complexes.
  60. (2005). Identification of splicing silencers and enhancers in sense Alus: a role for pseudo-acceptors in splice site repression.
  61. (1996). Inhibition by SR proteins of splicing of a regulated adenovirus pre-mRNA.
  62. (2001). Initial sequencing and analysis of the human genome.
  63. (1995). Interactions between the terminal bases of mammalian introns are retained in inosine-containing pre-mRNAs.
  64. (2008). Intronic Alus influence alternative splicing.
  65. (2004). Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals.
  66. (2004). Minimal conditions for exonization of intronic sequences: 50 splice site formation in Alu exons.
  67. (2011). Molecular basis of purine-rich RNA recognition by the human SR-like protein Tra2-beta1.
  68. (2000). Mutations affecting mRNA splicing are the most common molecular defects in patients with neurofibromatosis type 1.
  69. (2008). Mutations in a novel, cryptic exon of the luteinizing hormone/chorionic gonadotropin receptor gene cause male pseudohermaphroditism.
  70. (2008). Nature and mRNA effect of 282 different NF1 point mutations: focus on splicing alterations.
  71. (1993). Occurrence of a 2-bp (AT) deletion allele and a nonsense (G-to-T) mutant allele at the E2 (DBT) locus of six patients with maple syrup urine disease: multiple-exon skipping as a secondary effect of the mutations.
  72. (1993). Pathways for selection of 50 splice sites by U1 snRNPs and SF2/ASF.
  73. (2009). Pre-mRNA processing reaches back to transcription and ahead to translation.
  74. (2007). Pre-mRNA secondary structures influence exon recognition.
  75. (2011). Prediction of single-nucleotide substitutions that result in exon skipping: identification of a splicing silencer in BRCA1 exon 5.
  76. (2002). Predictive identification of exonic splicing enhancers in human genes.
  77. (1999). Redefinition of exon 7 in the COL1A1 gene of type I collagen by an intron 8 splice-donor-site mutation in a form of osteogenesis imperfecta: influence of intron splice order on outcome of splice-site mutation.
  78. (1999). Regulation of alternative splicing by RNA editing.
  79. (2004). RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons.
  80. (2004). RNA folding affects the recruitment of SR proteins by mouse and human polypurinic enhancer elements in the fibronectin EDA exon.
  81. (2008). RNA landscape of evolution for optimal exon and intron discrimination.
  82. (2001). RNA tertiary interactions in the large ribosomal subunit: the A-minor motif.
  83. (2007). RNA-editing-mediated exon evolution.
  84. (2010). RNAstructure: software for RNA secondary structure prediction and analysis.
  85. (2010). Role of RNA structure in regulating pre-mRNA splicing.
  86. (1995). Seven novel mutations in the methylenetetrahydrofolate reductase gene and genotype/phenotype correlations in severe methylenetetrahydrofolate reductase deficiency.
  87. (2002). Silencing of Bruton0s tyrosine kinase (Btk) using short interfering RNA duplexes (siRNA).
  88. (1990). Spliced leader RNA sequences can substitute for the essential 50 end of U1 RNA during splicing in a mammalian in vitro system.
  89. (2001). SpliceDB: database of canonical and non-canonical mammalian splice sites.
  90. (2007). SR protein-mediated inhibition of CFTR exon 9 inclusion: molecular characterization of the intronic splicing silencer.
  91. (2009). SR proteins in vertical integration of gene expresion from transcription to RNA processing to translation.
  92. (2010). Structural basis for the dual RNA-recognition modes of human Tra2-{beta} RRM.
  93. (1999). Supravalvular aortic stenosis: a splice site mutation within the elastin gene results in reduced expression of two aberrantly spliced transcripts.
  94. (2004). Systematic identification and analysis of exonic splicing silencers.
  95. (2003). The birth of an alternatively spliced exon: 30 splice-site selection in Alu exons.
  96. (1990). The essential pre-mRNA splicing factor SF2 influences 50 splice site selection by activating proximal sites.
  97. (1993). The gene involved in X-linked agammaglobulinaemia is a member of the src family of protein-tyrosine kinases.
  98. (2009). The spliceosome: design principles of a dynamic RNP machine.
  99. (1992). Three novel mutations in the cystic fibrosis gene detected by chemical cleavage: analysis of variant splicing and a nonsense mutation.
  100. (2010). Transposable elements in disease-associated cryptic exons.
  101. (2008). Two wobble-splicing events affect ING4 protein subnuclear localization and degradation.