Functional significance of deep intronic mutation in the ATM gene and evidence for an alternative Exon 28a

Coutinho, G., Xie, J. Y., Du, L. T., Brusco, A., Krainer, A. R., Gatti, R. A. (2005) Functional significance of deep intronic mutation in the ATM gene and evidence for an alternative Exon 28a. Human Mutation, 25 (2). pp. 118-124. ISSN 1059-7794

URL: http://www.ncbi.nlm.nih.gov/pubmed/15643608
DOI: 10.1002/humu.20170

Abstract

Screening for ATM mutations is usually performed using genomic DNA as a template for PCR amplification across exonic regions, with the consequence that deep intronic sequences are not analyzed. Here we report a novel pseudoexon-retaining deep intronic mutation (IVS28-159A > G; g.75117A > G based on GenBank U82828.1) in a patient with ataxia-telangiectasia (A-T), as well as the identification of a previously unrecognized alternative exon in the ATM gene (exon 28a) expressed in lymphoblastoid cell lines (LCL) derived from normal individuals. cDNA analysis using the A-T patient's LCL showed the retention of two aberrant intronic segments of 112 and 190 nt between exons 28 and 29. Minigenes were constructed to determine the functional significance of two genomic changes in the region of aberrant splicing: IVS28-193C > T (g.75083C > T) and IVS28-159A > G, revealing that: 1) the first is a polymorphism; 2) IVS28-159A > G weakens the 5' splice site of the alternative exon 28a and activates a cryptic 5' splice site (ss) 83 nt downstream; and 3) wild-type constructs also retain a 29-nt segment (exon 28a) as part of both the 112- and 190-nt segments. Maximum entropy estimates of ss strengths corroborate the cDNA and minigene findings. Such mutations may prove relevant in planning therapy that targets specific splicing aberrations. (C) 2005 Wiley-Liss, Inc.

Item Type: Paper
Uncontrolled Keywords: ataxia-telangiectasia AT ATM deep intronic mutation alternative splicing ATAXIA-TELANGIECTASIA GENE ataxia telangiectasia gene SEQUENCE sequence PRODUCT product region REGION DNA IVS28-159A
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > cDNA
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > exons
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > splice site
CSHL Authors:
Communities: CSHL labs > Krainer lab
Depositing User: CSHL Librarian
Date: 2005
Date Deposited: 13 Jan 2012 20:25
Last Modified: 09 Apr 2014 16:23
Related URLs:
URI: http://repository.cshl.edu/id/eprint/22550

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