Extensive in silico analysis of NF1 splicing defects uncovers determinants for splicing outcome upon 5 ' splice-site disruption

Wimmer, K., Roca, X., Beiglbock, H., Callens, T., Etzler, J., Rao, A. R., Krainer, A. R., Fonatsch, C., Messiaen, L. (June 2007) Extensive in silico analysis of NF1 splicing defects uncovers determinants for splicing outcome upon 5 ' splice-site disruption. Human Mutation, 28 (6). pp. 599-612. ISSN 1059-7794

URL: http://www.ncbi.nlm.nih.gov/pubmed/17311297
DOI: 10.1002/humu.20493

Abstract

We describe 94 pathogenic NF1 gene alterations in a cohort of 97 Austrian neurofibromatosis type I patients meeting the NIH criteria. All mutations were fully characterized at the genomic and mRNA levels. Over half of the patients carried novel mutations, and only a quarter carried recurrent minor-lesion mutations at 16 mutational warm spots. The remaining patients carried NF1 microdeletions (7%) and rare recurring mutations. Thirty-six of the mutations (38%) altered pre-mRNA splicing, and fall into five groups: exon skipping resulting from mutations at authentic splice sites (type I), cryptic exon inclusion caused by deep intronic mutations (type II), creation of de novo splice sites causing loss of exonic sequences (type III), activation of cryptic splice sites upon authentic splice-site disruption (type IV), and exonic sequence alterations causing exon skipping (type V). Extensive in silico analyses of 37 NF1 exons and surrounding intronic sequences suggested that the availability of a cryptic splice site combined with a strong natural upstream 3' splice site (3'ss)is the main determinant of cryptic splice-site activation upon 5' splice-site disruption. Furthermore, the exonic sequences downstream of exonic cryptic 5' splice sites (5'ss) resemble intronic more than exonic sequences with respect to exonic splicing enhancer and silencer density, helping to distinguish between exonic cryptic and pseudo 5'ss. This study provides valuable predictors for the splicing pathway used upon 5'ss mutation, and underscores the importance of using RNA-based techniques, together with methods to identify microdeletions and intragenic copy-number changes, for effective and reliable NF1 mutation detection.

Item Type: Paper
Uncontrolled Keywords: neurofibromatosis type 1 NF1 splicing cryptic splice site pseudo splice site splicing enhancer splicing silencer NEUROFIBROMATOSIS TYPE-1 NF1 PRE-MESSENGER-RNA BASE-PAIR SUBSTITUTIONS SPINAL NEUROFIBROMATOSIS HUMAN GENES GENOMIC ORGANIZATION RECURRENT MUTATIONS TUMOR-SUPPRESSOR SEQUENCE MOTIFS EARLY-ONSET
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > RNA expression
organism description > animal > mammal > primates > hominids > human
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > mutations
CSHL Authors:
Communities: CSHL labs > Krainer lab
Depositing User: CSHL Librarian
Date: June 2007
Date Deposited: 30 Aug 2011 23:35
Last Modified: 09 Apr 2014 14:22
Related URLs:
URI: http://repository.cshl.edu/id/eprint/15276

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