An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers

Smith, P. J., Zhang, C., Wang, J., Chew, S. L., Zhang, M. Q., Krainer, A. R. (August 2006) An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers. Hum Mol Genet, 15 (16). pp. 2490-508. ISSN 0964-6906 (Print)

URL: http://www.ncbi.nlm.nih.gov/pubmed/16825284
DOI: 10.1093/hmg/ddl171

Abstract

Numerous disease-associated point mutations exert their effects by disrupting the activity of exonic splicing enhancers (ESEs). We previously derived position weight matrices to predict putative ESEs specific for four human SR proteins. The score matrices are part of ESEfinder, an online resource to identify ESEs in query sequences. We have now carried out a refined functional SELEX screen for motifs that can act as ESEs in response to the human SR protein SF2/ASF. The test BRCA1 exon under selection was internal, rather than the 3'-terminal IGHM exon used in our earlier studies. A naturally occurring heptameric ESE in BRCA1 exon 18 was replaced with two libraries of random sequences, one seven nucleotides in length, the other 14. Following three rounds of selection for in vitro splicing via internal exon inclusion, new consensus motifs and score matrices were derived. Many winner sequences were demonstrated to be functional ESEs in S100-extract-complementation assays with recombinant SF2/ASF. Motif-score threshold values were derived from both experimental and statistical analyses. Motif scores were shown to correlate with levels of exon inclusion, both in vitro and in vivo. Our results confirm and extend our earlier data, as many of the same motifs are recognized as ESEs by both the original and our new score matrix, despite the different context used for selection. Finally, we have derived an increased specificity score matrix that incorporates information from both of our SF2/ASF-specific matrices and that accurately predicts the exon-skipping phenotypes of deleterious point mutations.

Item Type: Paper
Uncontrolled Keywords: Alternative Splicing genetics Amino Acid Motifs Base Sequence Forecasting methods Genes BRCA1 Hela Cells Humans Models Biological Models Theoretical Nuclear Proteins genetics Open Reading Frames RNA Precursors metabolism Regulatory Elements Transcriptional Research Design Sequence Homology Nucleic Acid
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > SR proteins
bioinformatics > genomics and proteomics > databases > databases
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > exons > exon splicing
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 > mutations
CSHL Authors:
Communities: CSHL labs > Krainer lab
CSHL labs > Zhang lab
Depositing User: CSHL Librarian
Date: 15 August 2006
Date Deposited: 09 Dec 2011 16:40
Last Modified: 09 Apr 2014 15:02
Related URLs:
URI: http://repository.cshl.edu/id/eprint/22902

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