Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases
| Autor: | Forrest, Alistair RR, Taylor, Darrin F, Crowe, Mark L, Chalk, Alistair M, Waddell, Nic J, Kolle, Gabriel, Faulkner, Geoffrey J, Kodzius, Rimantas, Katayama, Shintaro, Wells, Christine, Kai, Chikatoshi, Kawai, Jun, Carninci, Piero, Hayashizaki, Yoshihide, Grimmond, Sean M |
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| Jazyk: | angličtina |
| Rok vydání: | 2006 |
| Předmět: | |
| Zdroj: | Genome Biology |
| ISSN: | 1465-6914 1465-6906 |
| Popis: | A systematic study of the transcript variants of all protein kinase- and phosphatase-like loci in mouse shows that at least 75% of them generate alternative transcripts, many of which encode different domain structures. Background Alternative transcripts of protein kinases and protein phosphatases are known to encode peptides with altered substrate affinities, subcellular localizations, and activities. We undertook a systematic study to catalog the variant transcripts of every protein kinase-like and phosphatase-like locus of mouse . Results By reviewing all available transcript evidence, we found that at least 75% of kinase and phosphatase loci in mouse generate alternative splice forms, and that 44% of these loci have well supported alternative 5' exons. In a further analysis of full-length cDNAs, we identified 69% of loci as generating more than one peptide isoform. The 1,469 peptide isoforms generated from these loci correspond to 1,080 unique Interpro domain combinations, many of which lack catalytic or interaction domains. We also report on the existence of likely dominant negative forms for many of the receptor kinases and phosphatases, including some 26 secreted decoys (seven known and 19 novel: Alk, Csf1r, Egfr, Epha1, 3, 5,7 and 10, Ephb1, Flt1, Flt3, Insr, Insrr, Kdr, Met, Ptk7, Ptprc, Ptprd, Ptprg, Ptprl, Ptprn, Ptprn2, Ptpro, Ptprr, Ptprs, and Ptprz1) and 13 transmembrane forms (four known and nine novel: Axl, Bmpr1a, Csf1r, Epha4, 5, 6 and 7, Ntrk2, Ntrk3, Pdgfra, Ptprk, Ptprm, Ptpru). Finally, by mining public gene expression data (MPSS and microarrays), we confirmed tissue-specific expression of ten of the novel isoforms. Conclusion These findings suggest that alternative transcripts of protein kinases and phosphatases are produced that encode different domain structures, and that these variants are likely to play important roles in phosphorylation-dependent signaling pathways. |
| Databáze: | OpenAIRE |
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