Searching for regulatory elements of alternative splicing events using phylogenetic footprinting

Daichi Shigemizu, Osamu Maruyama

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1 Citation (Scopus)

Abstract

We consider the problem of finding candidates for regulatory elements of alternative splicing events from orthologous genes, using phylogenetic footprinting. The problem is formulated as follows: We are given orthologous sequences P1, . . . , Pa and N1, . . . , N b from a + b different species, and a phylogenetic tree relating these species. Assume that for i = 1, . . . , a, Pi is known to have some alternative splicing events, although Nj does not have any alternative splicing events. Our objective is to find all sets of substrings s1, . . . , sa of P1, . . . , Pa such that s1, . . . ,sa are similar to each other to some extent, and such that any substrings of N1, . . . , Nb are not similar to s1, . . . , sa. To this aim, we have modified the phylogenetic footprinting algorithm given by Blanchette et al. to solve our problem. We report the results of our preliminary computational experiments on several sets of orthologous genes of the five species, H.sapiens, M.musculus, D.melanogaster, C.elegans, and A.thaliana. It is interesting that many of the substrings selected by our algorithm from the coding sequences of H.sapiens are substrings in the intronic sequences flanking the alternatively spliced exons of the coding sequence. This result implies that regulatory elements of alternative splicing events would be located in intronic sequences flanking the alternatively spliced exons.

Original languageEnglish
Pages (from-to)147-158
Number of pages12
JournalLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume3240
Publication statusPublished - Dec 1 2004

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Alternative Splicing
Phylogenetics
Genes
Coding
Gene
Phylogenetic Tree
Pi
Computational Experiments
Experiments
Imply

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

Cite this

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abstract = "We consider the problem of finding candidates for regulatory elements of alternative splicing events from orthologous genes, using phylogenetic footprinting. The problem is formulated as follows: We are given orthologous sequences P1, . . . , Pa and N1, . . . , N b from a + b different species, and a phylogenetic tree relating these species. Assume that for i = 1, . . . , a, Pi is known to have some alternative splicing events, although Nj does not have any alternative splicing events. Our objective is to find all sets of substrings s1, . . . , sa of P1, . . . , Pa such that s1, . . . ,sa are similar to each other to some extent, and such that any substrings of N1, . . . , Nb are not similar to s1, . . . , sa. To this aim, we have modified the phylogenetic footprinting algorithm given by Blanchette et al. to solve our problem. We report the results of our preliminary computational experiments on several sets of orthologous genes of the five species, H.sapiens, M.musculus, D.melanogaster, C.elegans, and A.thaliana. It is interesting that many of the substrings selected by our algorithm from the coding sequences of H.sapiens are substrings in the intronic sequences flanking the alternatively spliced exons of the coding sequence. This result implies that regulatory elements of alternative splicing events would be located in intronic sequences flanking the alternatively spliced exons.",
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