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

• Verfasst von: Suyama, Mikita [VerfasserIn]
• Verfasst von: Harrington, Eoghan D. [VerfasserIn]
• Verfasst von: Vinokourova, Svetlana [VerfasserIn]
• Verfasst von: Knebel Doeberitz, Magnus von [VerfasserIn]
• Verfasst von: Ohara, Osamu [VerfasserIn]
• Verfasst von: Bork, Peer [VerfasserIn]
• Titel: A network of conserved co-occurring motifs for the regulation of alternative splicing
• Verf.angabe: Mikita Suyama, Eoghan D. Harrington, Svetlana Vinokourova, Magnus von Knebel Doeberitz, Osamu Ohara, and Peer Bork
• E-Jahr: 2010
• Jahr: 10 August 2010
• Umfang: 11 S.
• Fussnoten: Gesehen am 06.09.2023
• Titel Quelle: Enthalten in: Nucleic acids research
• Ort Quelle: Oxford : Oxford Univ. Press, 1974
• Jahr Quelle: 2010
• Band/Heft Quelle: 38(2010), 22, Seite 7916-7926
• ISSN Quelle: 1362-4962
• DOI: doi:10.1093/nar/gkq705
• Datenträger: Online-Ressource
• Sprache: eng
• K10plus-PPN: 1858904196

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.