Conjoined gene

A conjoined gene (CG) is defined as a gene, which gives rise to transcripts by combining at least part of one exon from each of two or more distinct known (parent) genes which lie on the same chromosome, are in the same orientation, and often (95%) translate independently into different proteins. In some cases, the transcripts formed by CGs are translated to form chimeric or completely novel proteins.

Figure 1: Cartoonic representation of the formation of conjoined gene A-B from parent genes A and B.

Several alternative names are used to address conjoined genes, including combined gene and complex gene (both from Roginski et al, "The human GRINL1A gene defines a complex transcription unit, an unusual form of gene organization in eukaryotes" Genomics 84: 265-276, 2004. pmid=15233991), fusion gene, fusion protein, read-through transcript, co-transcribed genes, bridged genes, spanning genes, hybrid genes, locus-spanning transcripts, etc.

At present, 800 CGs have been identified in the entire human genome by different research groups across the world including Prakash et al.,^[1] Akiva et al.,^[2] Parra et al.,^[3] Kim et al.,^[4] and in the 1% of the human genome in the ENCODE pilot project.^[5] 36% of all these CGs could be validated experimentally using RT-PCR and sequencing techniques. However, only a very limited number of these CGs are found in the public human genome resources such as the Entrez Gene database, the UCSC Genome Browser and the Vertebrate Genome Annotation (Vega) database. More than 70% of the human conjoined genes are found to be conserved across other vertebrate genomes with higher order vertebrates showing more conservation, including the closest human ancestor, chimpanzee. Formation of CGs is not only limited to the human genome but some CGs have also been identified in other eukaryotic genomes, including mouse and drosophila. There are a few web resources which include information about some CGs in addition to the other fusion genes, for example, ChimerDB and HYBRIDdb. Another database, ConjoinG, is a comprehensive resource dedicated only to the 800 Conjoined Genes identified in the entire human genome.

See also

• Gene expression

References

1. ^ Prakash T, Sharma VK, Adati N, Ozawa R, Kumar N, et al. (October 2010). Michalak, Pawel. ed. "Expression of Conjoined Genes: Another Mechanism for Gene Regulation in Eukaryotes.". PLoS ONE 5 (10): e13284. doi:10.1371/journal.pone.0013284. PMC 2953495. PMID 20967262. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2953495. 
2. ^ Akiva P, Toporik A, Edelheit S, et al. (January 2006). "Transcription-mediated gene fusion in the human genome". Genome Research 16 (1): 30–6. doi:10.1101/gr.4137606. PMC 1356126. PMID 16344562. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1356126. 
3. ^ Parra G, Reymond A, Dabbouseh N, et al. (January 2006). "Tandem chimerism as a means to increase protein complexity in the human genome". Genome Research 16 (1): 37–44. doi:10.1101/gr.4145906. PMC 1356127. PMID 16344564. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1356127. 
4. ^ Kim P, Yoon S, Kim N, et al. (November 2009). "ChimerDB 2.0--a knowledgebase for fusion genes updated". Nucleic Acids Research 38 (Database issue): D81–D85. doi:10.1093/nar/gkp982. PMC 2808913. PMID 19906715. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2808913. 
5. ^ Denoeud F, Kapranov P, Ucla C, et al. (June 2007). "Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions". Genome Research 17 (6): 746–59. doi:10.1101/gr.5660607. PMC 1891335. PMID 17567994. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1891335.