Subject: | Computational comparative analyses of alternative splicing regulation |
Presenter: | Mirela Andronescu |
Paper: | " Computational comparative analyses of alternative splicing regulation " |
  | by Hitomi Itoh, Takanori Washio and Masaru Tomita |
Abstract |
Computational comparative analyses of alternative splicing regulation
We previously reported a computational approach to infer alternative
splicing patterns from Mus musculus full-length cDNA clones and microarray
data. Although we predicted a large number of unreported splice variants,
the general mechanisms regulating alternative splicing were yet unknown.
In the present study, we compared alternative exons and constitutive exons
in terms of splice-site strength and frequency of potential regulatory
sequences. These regulatory features were further compared among five
different species: Homo sapiens, M. musculus, Arabidopsis thaliana, Oryza
sativa, and Drosophila melanogaster. Solid statistical validations of our
comparative analyses indicated that alternative exons have (1) weaker
splice sites and (2) more potential regulatory sequences than constitutive
exons. Based on our observations, we propose a combinatorial model of
alternative splicing mechanisms, which suggests that alternative exons
contain weak splice sites regulated alternatively by potential regulatory
sequences on the exons.
Reference:
HITOMI ITOH, TAKANORI WASHIO and MASARU TOMITA,
Computational comparative analyses of alternative splicing regulation
using full-length cDNA of various eukaryotes,
RNA (2004) 10:1005-1018
The paper is available at www.cs.ubc.ca/~andrones/temp/itoh.pdf
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