Bldg. 38A, B2 conference room (library)
June 7 (Monday), 11 AM


Alissa M. Resch
UCLA-DOE Institute for Genomics and Proteomics
Department of Chemistry and Biochemistry
University of California, Los Angeles
aresch@mbi.ucla.edu

Alternative splicing has emerged as an increasingly important contributor to
genomic complexity and gene function. Unlike prokaryotic genomes, which do
not undergo alternative splicing, eukaryotic genomes utilize this mechanism
as a tool for increasing the number of unique transcripts encoded by a
single gene.  In the human genome more than 30,000 alternative splice
relationships have been identified from expressed sequence tags (ESTs) and
mRNA sequences mapped on genomic sequence, approximately doubling the number
of transcript forms expected from the estimated 32,000 genes.  Confronted
with so many new splice forms from high-throughput EST sequencing, it is
natural to ask whether these splice forms are functional and if so how they
contribute to the regulation of gene function.  

It is often difficult for biologists to go from a particular alternative
splice identified in genomics data, to a reliable protein isoform sequence
and its functional domain impact (only a small fraction of alternative
splices detected in the human genome is available in proteomics databases).
To make this connection, we have constructed a database of 13,384 protein
isoforms generated by alternative splicing.  We identified fifty protein
domain types that were selectively removed by alternative splicing at much
higher frequencies than average.  Our bioinformatics analysis indicates that
a major impact of alternative splicing is removal of protein-protein
interaction domains that mediate key linkages in protein interaction
networks.

We measured the functional selection pressure on alternatively spliced
single-exonskips, by calculating the fraction that are an exact multiple of
3 nucleotides in length and therefore preserve protein reading frame in both
the exon-inclusion and exonskip splice forms.  We compared the alternative
splicing patterns between five animal genomes (human, mouse, rat, zebrafish
and Drosophila) to investigate the role of alternative splicing in the
evolution of higher-order eukaryotes.   We observed an association between
conserved, orthologous alternative splicing events and increased selection
pressure for frame-preservation.  This effect became stronger as a function
of decreasing exon inclusion level: for alternatively spliced exons that
were included in a majority of the gene's transcripts, the
frame-preservation bias was no higher than that of constitutive exons,
whereas for alternatively spliced exons that were included in only a
minority of the gene's transcripts, the frame-preservation bias increased
nearly 20-fold.  These data indicate that a subpopulation of modern
alternative splicing events was present in the common ancestors of these
genomes, and was under functional selection pressure to preserve the protein
reading frame.  



Eugene V. Koonin, PhD, Senior Investigator
National Center for Biotechnology Information
National Library of Medicine
National Institutes of Health
Bldg. 38A, Rm 5N503
Telephone 301-435-5913
Fax 301-435-5913