{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,5]],"date-time":"2026-02-05T08:52:57Z","timestamp":1770281577478,"version":"3.49.0"},"reference-count":69,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1576,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Chimeric RNA transcripts are generated by different mechanisms including pre-mRNA trans-splicing, chromosomal translocations and\/or gene fusions. It was shown recently that at least some of chimeric transcripts can be translated into functional chimeric proteins.<\/jats:p><jats:p>Results: To gain a better understanding of the design principles underlying chimeric proteins, we have analyzed 7,424 chimeric RNAs from humans. We focused on the specific domains present in these proteins, comparing their permutations with those of known human proteins. Our method uses genomic alignments of the chimeras, identification of the gene\u2013gene junction sites and prediction of the protein domains. We found that chimeras contain complete protein domains significantly more often than in random data sets. Specifically, we show that eight different types of domains are over-represented among all chimeras as well as in those chimeras confirmed by RNA-seq experiments. Moreover, we discovered that some chimeras potentially encode proteins with novel and unique domain combinations. Given the observed prevalence of entire protein domains in chimeras, we predict that certain putative chimeras that lack activation domains may actively compete with their parental proteins, thereby exerting dominant negative effects. More generally, the production of chimeric transcripts enables a combinatorial increase in the number of protein products available, which may disturb the function of parental genes and influence their protein\u2013protein interaction network.<\/jats:p><jats:p>Availability: our scripts are available upon request.<\/jats:p><jats:p>Contact: \u00a0avalencia@cnio.es<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts216","type":"journal-article","created":{"date-parts":[[2012,6,11]],"date-time":"2012-06-11T14:09:18Z","timestamp":1339423758000},"page":"i67-i74","source":"Crossref","is-referenced-by-count":38,"title":["Novel domain combinations in proteins encoded by chimeric transcripts"],"prefix":"10.1093","volume":"28","author":[{"given":"Milana","family":"Frenkel-Morgenstern","sequence":"first","affiliation":[{"name":"Structural Biology and BioComputing Program, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain"}]},{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[{"name":"Structural Biology and BioComputing Program, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain"}]}],"member":"286","published-online":{"date-parts":[[2012,6,9]]},"reference":[{"key":"2023012512391699900_B1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2023012512391699900_B2","doi-asserted-by":"crossref","first-page":"610","DOI":"10.1016\/j.ymthe.2005.06.094","article-title":"Custom zinc-finger nucleases for use in human cells","volume":"12","author":"Alwin","year":"2005","journal-title":"Mol. 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