Exonic splicing enhancer motif recognized by human SC35 under splicing conditions

Liu, H. X., Chew, S. L., Cartegni, L., Zhang, M. Q., Krainer, A. R. (February 2000) Exonic splicing enhancer motif recognized by human SC35 under splicing conditions. Molecular and Cellular Biology, 20 (3). pp. 1063-1071. ISSN 0270-7306

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URL: http://www.ncbi.nlm.nih.gov/pubmed/10629063
DOI: 10.1128/mcb.20.3.1063-1071.2000

Abstract

Exonic Splicing enhancers (ESEs) are important cis elements required for exon inclusion. Using an in vitro functional selection and amplification procedure, we have identified a novel ESE motif recognized by the human SR protein SC35 under splicing conditions. The selected sequences are functional and specific: they promote splicing in nuclear extract or in S100 extract complemented by SC35 but not by SF2/ASF. They can also function in a different exonic context from the one used for the selection procedure. The selected sequences share one or two close matches to a short and highly degenerate octamer consensus, GRYYcSYR. A score matrix was generated from the selected sequences according to the nucleotide frequency at each position of their best match to the consensus motif. The SC35 score matrix, along with our previously reported SF2/ASF score matrix, was used to search the sequences of two well-characterized splicing substrates derived from the mouse immunoglobulin M (IgM) and human immunodeficiency virus tat genes. Multiple SC35 high-score motifs, but only two widely separated SF2/ASF motifs, were found in the IgM C4 exon, which can be spliced in S100 extract complemented by SC35. In contrast, multiple high-score motifs for both SF2/ASF and SC35 were found in a variant of the Tat T3 exon (lacking an SC35-specific silencer) whose splicing can be complemented by either SF2/ASF or SC35. The motif score matrix can help locate SC35-specific enhancers in natural exon sequences.

Item Type: Paper
Uncontrolled Keywords: pre-messenger-rna protein-protein interactions t alternative exon sr-proteins premessenger rna factor sf2 in-vivo binding identification selection
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
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 > pre-mRNA
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > RNA splicing
CSHL Authors:
Communities: CSHL labs > Krainer lab
CSHL labs > Zhang lab
Depositing User: Matt Covey
Date: February 2000
Date Deposited: 11 Dec 2013 20:16
Last Modified: 11 Dec 2013 20:16
PMCID: PMC85223
Related URLs:
URI: http://repository.cshl.edu/id/eprint/28917

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