A network of conserved co-occurring motifs for the regulation of alternative splicing

Mikita Suyama, Eoghan D. Harrington, Svetlana Vinokourova, Magnus Von Knebel Doeberitz, Osamu Ohara, Peer Bork

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

Cis-acting short sequence motifs play important roles in alternative splicing. It is now possible to identify such sequence motifs as conserved sequence patterns in genome sequence alignments. Here, we report the systematic search for motifs in the neighboring introns of alternatively spliced exons by using comparative analysis of mammalian genome alignments. We identified 11 conserved sequence motifs that might be involved in the regulation of alternative splicing. These motifs are not only significantly overrepresented near alternatively spliced exons, but they also co-occur with each other, thus, forming a network of cis-elements, likely to be the basis for context-dependent regulation. Based on this finding, we applied the motif co-occurrence to predict alternatively skipped exons. We verified exon skipping in 29 cases out of 118 predictions (25) by EST and mRNA sequences in the databases. For the predictions not verified by the database sequences, we confirmed exon skipping in 10 additional cases by using both RT-PCR experiments and the publicly available RNA-Seq data. These results indicate that even more alternative splicing events will be found with the progress of large-scale and high-throughput analyses for various tissue samples and developmental stages.

Original languageEnglish
Pages (from-to)7916-7926
Number of pages11
JournalNucleic acids research
Volume38
Issue number22
DOIs
Publication statusPublished - Dec 1 2010

Fingerprint

Alternative Splicing
Exons
Conserved Sequence
Genome
Databases
Sequence Alignment
Expressed Sequence Tags
Introns
RNA
Polymerase Chain Reaction
Messenger RNA

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

Suyama, M., Harrington, E. D., Vinokourova, S., Von Knebel Doeberitz, M., Ohara, O., & Bork, P. (2010). A network of conserved co-occurring motifs for the regulation of alternative splicing. Nucleic acids research, 38(22), 7916-7926. https://doi.org/10.1093/nar/gkq705

A network of conserved co-occurring motifs for the regulation of alternative splicing. / Suyama, Mikita; Harrington, Eoghan D.; Vinokourova, Svetlana; Von Knebel Doeberitz, Magnus; Ohara, Osamu; Bork, Peer.

In: Nucleic acids research, Vol. 38, No. 22, 01.12.2010, p. 7916-7926.

Research output: Contribution to journalArticle

Suyama, M, Harrington, ED, Vinokourova, S, Von Knebel Doeberitz, M, Ohara, O & Bork, P 2010, 'A network of conserved co-occurring motifs for the regulation of alternative splicing', Nucleic acids research, vol. 38, no. 22, pp. 7916-7926. https://doi.org/10.1093/nar/gkq705
Suyama M, Harrington ED, Vinokourova S, Von Knebel Doeberitz M, Ohara O, Bork P. A network of conserved co-occurring motifs for the regulation of alternative splicing. Nucleic acids research. 2010 Dec 1;38(22):7916-7926. https://doi.org/10.1093/nar/gkq705
Suyama, Mikita ; Harrington, Eoghan D. ; Vinokourova, Svetlana ; Von Knebel Doeberitz, Magnus ; Ohara, Osamu ; Bork, Peer. / A network of conserved co-occurring motifs for the regulation of alternative splicing. In: Nucleic acids research. 2010 ; Vol. 38, No. 22. pp. 7916-7926.
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