Paired box transcription factors play important role in development and tissue morphogenesis. The number of Pax homologs varies among species studied so far, due to genome and gene duplications that have affected PAX family to a great extent. Based on sequence similarity and functional domains, four Pax classes have been identified in chordates, namely Pax1/9, Pax2/5/8, Pax3/7, and Pax4/6. Numerous splicing events have been reported mainly for Pax2/5/8 and Pax6 genes. Of significant interest are those events that lead to Pax proteins with presumed novel properties, such as altered DNA-binding or transcriptional activity. In the current study, a thorough analysis of Pax2/5/8 splicing events from cephalochordates and vertebrates was performed. We focused more on Pax2/5/8 and Pax6 splicing events in which the paired domain is involved. Three new splicing events were identified in Oryzias latipes, one of which seems to be conserved in Acanthomorphata. Using representatives from deuterostome and protostome phyla, a comparative analysis of the Pax6 exon-intron structure of the paired domain was performed, during an attempt to estimate the time of appearance of the Pax6(5a) mRNA isoform. As shown in our analysis, this splicing event is characteristic of Gnathostomata and is absent in the other chordate subphyla. Moreover, expression pattern of alternative spliced variants was compared between cephalochordates and fish species. In summary, our data indicate expansion of alternative mRNA variants in paired box region of Pax2/5/8 and Pax6 genes during the course of vertebrate evolution.

Department of Transcriptional Regulation Institute of Molecular Genetics Prague Czech Republic

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Arseneau J. R., Laflamme M., Lewis S. M., Maïcas E., Ouellette R. J. (2009). Multiple isoforms of PubMed DOI

Azuma N., Tadokoro K., Asaka A., Yamada M., Yamaguchi Y., Handa H., et al. (2005). The PubMed DOI

Bassham S., Canestro C., Postlethwait J. (2008). Evolution of developmental roles of PubMed DOI PMC

Benson D. A., Cavanaugh M., Clark K., Karsch-Mizrachi I., Lipman D. J., Ostell J., et al. (2013). GenBank. Nucleic Acids Res. 41, D36–D42. 10.1093/nar/gks1195 PubMed DOI PMC

Bergthorsson U., Andersson D. I., Roth J. R. (2007). Ohno's dilemma: evolution of new genes under continuous selection. Proc. Natl. Acad. Sci. U.S.A. 104, 17004–17009. 10.1073/pnas.0707158104 PubMed DOI PMC

Bhatia S., Monahan J., Ravi V., Gautier P., Murdoch E., Brenner S., et al. (2014). A survey of ancient conserved non-coding elements in the PubMed DOI

Blake J. A., Ziman M. R. (2014). PubMed DOI

Bopp D., Jamet E., Baumgartner S., Burri M., Noll M. (1989). Isolation of two tissue-specific PubMed PMC

Borson N. D., Lacy M. Q., Wettstein P. J. (2002). Altered mRNA expression of Pax5 and Blimp-1 in B cells in multiple myeloma. Blood 100, 4629–4639. 10.1182/blood.V100.13.4629 PubMed DOI

Breitling R., Gerber J. K. (2000). Origin of the paired domain. Dev. Genes Evol. 210, 644–650. 10.1007/s004270000106 PubMed DOI

Burge C., Karlin S. (1997). Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268, 78–94. 10.1006/jmbi.1997.0951 PubMed DOI

Busse A., Rietz A., Schwartz S., Thiel E., Keilholz U. (2009). An intron 9 containing splice variant of PAX2. J. Transl. Med. 7:36. 10.1186/1479-5876-7-36 PubMed DOI PMC

Cameron R. A., Samanta M., Yuan A., He D., Davidson E. (2009). SpBase: the sea urchin genome database and web site. Nucleic Acids Res. 37, D750–D754. 10.1093/nar/gkn887 PubMed DOI PMC

Canestro C., Bassham S., Postlethwait J. (2005). Development of the central nervous system in the larvacean PubMed DOI

Chen L., Tovar-Corona J. M., Urrutia A. O. (2012). Alternative splicing: a potential source of functional innovation in the eukaryotic genome. Int. J. Evol. Biol. 2012:596274. 10.1155/2012/596274 PubMed DOI PMC

Chi N., Epstein J. A. (2002). Getting your pax straight: pax proteins in development and disease. Trends Genet. 18, 41–47. 10.1016/S0168-9525(01)02594-X PubMed DOI

Chisholm A. D., Horvitz H. R. (1995). Patterning of the PubMed DOI

Cinar H. N., Chisholm A. D. (2004). Genetic Analysis of the PubMed DOI PMC

Cunningham F., Amode M. R., Barrell D., Beal K., Billis K., Brent S., et al. (2015). Ensembl 2015. Nucleic Acids Res. 43, D662–D669. 10.1093/nar/gku1010 PubMed DOI PMC

Czerny T., Schaffner G., Busslinger M. (1993). DNA sequence recognition by pax proteins: bipartite structure of the paired domain and its binding site. Genes Dev. 7, 2048–2061. 10.1101/gad.7.10.2048 PubMed DOI

De Castro E., Sigrist C. J. A., Gattiker A., Bulliard V., Langendijk-Genevaux P. S., Gasteiger E., et al. (2006). ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Res. 34, W362–W365. 10.1093/nar/gkl124 PubMed DOI PMC

Dressler G. R., Deutsch U., Chowdhury K., Nornes H. O., Gruss P. (1990). PubMed

Eberhard D., Jimenez G., Heavey B., Busslinger M. (2000). Transcriptional repression by Pax5 (BSAP) through interaction with corepressors of the Groucho family. EMBO J. 19, 2292–2303. 10.1093/emboj/19.10.2292 PubMed DOI PMC

Edgar R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797. 10.1093/nar/gkh340 PubMed DOI PMC

Epstein D. J., Vekemans M., Gros P. (1991). PubMed DOI

Epstein J. A., Glaser T., Cai J., Jepeal L., Walton D. S., Maas R. L. (1994). Two independent and interactive DNA-binding subdomains of the Pax6 paired domain are regulated by alternative splicing. Genes Dev. 8, 2022–2034. 10.1101/gad.8.17.2022 PubMed DOI

Escriva H., Manzon L., Youson J., Laudet V. (2002). Analysis of lamprey and hagfish genes reveals a complex history of gene duplications during early vertebrate evolution. Mol. Biol. Evol. 19, 1440–1450. 10.1093/oxfordjournals.molbev.a004207 PubMed DOI

Fletcher J., Hu M., Berman Y., Collins F., Grigg J., Mciver M., et al. (2005). Multicystic Dysplastic kidney and variable phenotype in a family with a novel deletion mutation of PubMed DOI

Friedrich M., Caravas J. (2011). New insights from hemichordate genomes: prebilaterian origin and parallel modifications in the paired domain of the pax gene eyegone. J. Exp. Zool. B Mol. Dev. Evol. 316, 387–392. 10.1002/jez.b.21412 PubMed DOI

Fu W., Noll M. (1997). The Pax2 homolog sparkling is required for development of cone and pigment cells in the PubMed DOI PMC

Fuentes M., Benito E., Bertrand S., Paris M., Mignardot A., Godoy L., et al. (2007). Insights into spawning behavior and development of the European amphioxus ( PubMed DOI

Gehring W. J. (1996). The master control gene for morphogenesis and evolution of the eye. Genes Cells 1, 11–15. 10.1046/j.1365-2443.1996.11011.x PubMed DOI

Gehring W. J. (2002). The genetic control of eye development and its implications for the evolution of the various eye-types. Int. J. Dev. Biol. 46, 65–73. PubMed

Gehring W. J. (2012). The evolution of vision. Wiley Interdiscip. Rev. Dev. Biol. 3, 1–40. 10.1002/wdev.96 PubMed DOI

Glardon S., Holland L. Z., Gehring W. J., Holland N. D. (1998). Isolation and developmental expression of the amphioxus PubMed

Glaser T., Walton D. S., Maas R. L. (1992). Genomic structure, evolutionary conservation and aniridia mutations in the human PubMed DOI

Green R. E., Lewis B. P., Hillman R. T., Blanchette M., Lareau L. F., Garnett A. T., et al. (2003). Widespread predicted nonsense-mediated mRNA decay of alternatively-spliced transcripts of human normal and disease genes. Bioinformatics 19(Suppl. 1), i118–i121. 10.1093/bioinformatics/btg1015 PubMed DOI

Grigoriev I. V., Nordberg H., Shabalov I., Aerts A., Cantor M., Goodstein D., et al. (2012). The genome portal of the department of energy joint Genome Institute. Nucleic Acids Res. 40, D26–D32. 10.1093/nar/gkr947 PubMed DOI PMC

Hartung F., Blattner F. R., Puchta H. (2002). Intron gain and loss in the evolution of the conserved eukaryotic recombination machinery. Nucleic Acids Res. 30, 5175–5181. 10.1093/nar/gkf649 PubMed DOI PMC

Heller N., Brandli A. W. (1997). PubMed DOI

Heller N., Brandli A. W. (1999). PubMed DOI

Hill A., Boll W., Ries C., Warner L., Osswalt M., Hill M., et al. (2010). Origin of Pax and Six gene families in sponges: single PubMed DOI

Holland L. Z., Short S. (2010). Alternative splicing in development and function of chordate endocrine systems: a focus on PubMed DOI

Holland L. Z., Yu J. K. (2004). Cephalochordate (amphioxus) embryos: procurement, culture, and basic methods. Methods Cell. Biol. 74, 195–215. 10.1016/S0091-679X(04)74009-1 PubMed DOI

Hoshiyama D., Iwabe N., Miyata T. (2007). Evolution of the gene families forming the PubMed DOI

Howard-Ashby M., Materna S. C., Brown C. T., Chen L., Cameron R. A., Davidson E. H. (2006). Identification and characterization of homeobox transcription factor genes in PubMed DOI

Irvine S. Q., Fonseca V. C., Zompa M. A., Antony R. (2008). PubMed DOI PMC

Iwamatsu T. (2004). Stages of normal development in the medaka PubMed DOI

Jaillon O., Aury J. M., Brunet F., Petit J. L., Stange-Thomann N., Mauceli E., et al. (2004). Genome duplication in the teleost fish PubMed DOI

Jeffares D. C., Mourier T., Penny D. (2006). The biology of intron gain and loss. Trends Genet. 22, 16–22. 10.1016/j.tig.2005.10.006 PubMed DOI

Karolchik D., Barber G. P., Casper J., Clawson H., Cline M. S., Diekhans M., et al. (2014). The UCSC Genome Browser database: 2014 update. Nucleic Acids Res. 42, D764–D770. 10.1093/nar/gkt1168 PubMed DOI PMC

Kelemen O., Convertini P., Zhang Z., Wen Y., Shen M., Falaleeva M., et al. (2013). Function of alternative splicing. Gene 514, 1–30. 10.1016/j.gene.2012.07.083 PubMed DOI PMC

Kimmel C. B., Ballard W. W., Kimmel S. R., Ullmann B., Schilling T. F. (1995). Stages of embryonic development of the zebrafish. Dev. Dyn. 203, 253–310. 10.1002/aja.1002030302 PubMed DOI

Kleinjan D. A., Bancewicz R. M., Gautier P., Dahm R., Schonthaler H. B., Damante G., et al. (2008). Subfunctionalization of duplicated zebrafish PubMed DOI PMC

Klimova L., Kozmik Z. (2014). Stage-dependent requirement of neuroretinal Pax6 for lens and retina development. Development 141, 1292–1302. 10.1242/dev.098822 PubMed DOI

Koralewski T. E., Krutovsky K. V. (2011). Evolution of exon-intron structure and alternative splicing. PLoS ONE 6:e18055. 10.1371/journal.pone.0018055 PubMed DOI PMC

Kozmik Z., Czerny T., Busslinger M. (1997). Alternatively spliced insertions in the paired domain restrict the DNA sequence specificity of Pax6 and Pax8. EMBO J. 16, 6793–6803. 10.1093/emboj/16.22.6793 PubMed DOI PMC

Kozmik Z., Daube M., Frei E., Norman B., Kos L., Dishaw L. J., et al. (2003). Role of PubMed DOI

Kozmik Z., Holland N. D., Kalousova A., Paces J., Schubert M., Holland L. Z. (1999). Characterization of an amphioxus paired box gene, PubMed

Kozmik Z., Kurzbauer R., Dorfler P., Busslinger M. (1993). Alternative splicing of PubMed DOI PMC

Kozmik Z. (2008). The role of PubMed DOI

Krauss S., Johansen T., Korzh V., Fjose A. (1991). Expression of the zebrafish paired box gene PubMed

Kreslova J., Holland L. Z., Schubert M., Burgtorf C., Benes V., Kozmik Z. (2002). Functional equivalency of amphioxus and vertebrate Pax258 transcription factors suggests that the activation of mid-hindbrain specific genes in vertebrates occurs via the recruitment of Pax regulatory elements. Gene 282, 143–150. 10.1016/S0378-1119(01)00840-X PubMed DOI

Kwak S. J., Vemaraju S., Moorman S. J., Zeddies D., Popper A. N., Riley B. B. (2006). Zebrafish PubMed DOI

Lang D., Powell S. K., Plummer R. S., Young K. P., Ruggeri B. A. (2007). PubMed DOI

Lewis B. P., Green R. E., Brenner S. E. (2003). Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans. Proc. Natl. Acad. Sci. U.S.A 100, 189–192. 10.1073/pnas.0136770100 PubMed DOI PMC

Louis A., Muffato M., Roest Crollius H. (2013). Genomicus: five genome browsers for comparative genomics in eukaryota. Nucleic Acids Res. 41, D700–D705. 10.1093/nar/gks1156 PubMed DOI PMC

Lun K., Brand M. (1998). A series of PubMed

Maere S., Van De Peer Y. (2010). Duplicate retention after small- and large-scale duplications, in Evolution after Gene Duplication, eds Dittmar K., Liberles D. (Hoboken, NJ: John Wiley & Sons, Inc; ), 31–56.

Nilsen T. W., Graveley B. R. (2010). Expansion of the eukaryotic proteome by alternative splicing. Nature 463, 457–463. 10.1038/nature08909 PubMed DOI PMC

Noll M. (1993). Evolution and role of PubMed DOI

Nornes S., Mikkola I., Krauss S., Delghandi M., Perander M., Johansen T. (1996). Zebrafish PubMed DOI

Paixao-Cortes V. R., Salzano F. M., Bortolini M. C. (2013). Evolutionary history of chordate PubMed DOI PMC

Pfeffer P. L., Gerster T., Lun K., Brand M., Busslinger M. (1998). Characterization of three novel members of the zebrafish PubMed

Poleev A., Wendler F., Fickenscher H., Zannini M. S., Yaginuma K., Abbott C., et al. (1995). Distinct functional properties of three human paired-box-protein, PAX8, isoforms generated by alternative splicing in thyroid, kidney and Wilms' tumors. Eur. J. Biochem. 228, 899–911. 10.1111/j.1432-1033.1995.0899m.x PubMed DOI

Puschel A. W., Gruss P., Westerfield M. (1992). Sequence and expression pattern of PubMed

Putnam N. H., Butts T., Ferrier D. E., Furlong R. F., Hellsten U., Kawashima T., et al. (2008). The amphioxus genome and the evolution of the chordate karyotype. Nature 453, 1064–1071. 10.1038/nature06967 PubMed DOI

Ravi V., Bhatia S., Gautier P., Loosli F., Tay B. H., Tay A., et al. (2013). Sequencing of PubMed DOI PMC

Reese M. G., Eeckman F. H., Kulp D., Haussler D. (1997). Improved splice site detection in Genie. J. Comput. Biol. 4, 311–323. 10.1089/cmb.1997.4.311 PubMed DOI

Rice P., Longden I., Bleasby A. (2000). EMBOSS: the European molecular biology open software suite. Trends Genet. 16, 276–277. 10.1016/S0168-9525(00)02024-2 PubMed DOI

Robichaud G. A., Nardini M., Laflamme M., Cuperlovic-Culf M., Ouellette R. J. (2004). Human Pax-5 C-terminal isoforms possess distinct transactivation properties and are differentially modulated in normal and malignant B cells. J. Biol. Chem. 279, 49956–49963. 10.1074/jbc.M407171200 PubMed DOI

Rogozin I. B., Wolf Y. I., Sorokin A. V., Mirkin B. G., Koonin E. V. (2003). Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution. Curr. Biol. 13, 1512–1517. 10.1016/S0960-9822(03)00558-X PubMed DOI

Schimmenti L. A., Cunliffe H. E., Mcnoe L. A., Ward T. A., French M. C., Shim H. H., et al. (1997). Further delineation of renal-coloboma syndrome in patients with extreme variability of phenotype and identical PubMed PMC

Schwartz S., Zhang Z., Frazer K. A., Smit A., Riemer C., Bouck J., et al. (2000). PipMaker–a web server for aligning two genomic DNA sequences. Genome Res. 10, 577–586. 10.1101/gr.10.4.577 PubMed DOI PMC

Short S., Holland L. Z. (2008). The evolution of alternative splicing in the PubMed DOI

Short S., Kozmik Z., Holland L. Z. (2012). The function and developmental expression of alternatively spliced isoforms of amphioxus and PubMed DOI

Stephens R. M., Schneider T. D. (1992). Features of spliceosome evolution and function inferred from an analysis of the information at human splice sites. J. Mol. Biol. 228, 1124–1136. 10.1016/0022-2836(92)90320-J PubMed DOI

Stuart E. T., Kioussi C., Gruss P. (1994). Mammalian PubMed DOI

Takatori N., Butts T., Candiani S., Pestarino M., Ferrier D. K., Saiga H., et al. (2008). Comprehensive survey and classification of homeobox genes in the genome of amphioxus, PubMed DOI

Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. (2011). MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28, 2731–2739. 10.1093/molbev/msr121 PubMed DOI PMC

Tavassoli K., Ruger W., Horst J. (1997). Alternative splicing in PAX2 generates a new reading frame and an extended conserved coding region at the carboxy terminus. Hum. Genet. 101, 371–375. 10.1007/s004390050644 PubMed DOI

Van De Peer Y. (2004). PubMed DOI PMC

Wada S., Tokuoka M., Shoguchi E., Kobayashi K., Di Gregorio A., Spagnuolo A., et al. (2003). A genomewide survey of developmentally relevant genes in PubMed DOI

Walther C., Gruss P. (1991). PubMed

Wang E. T., Sandberg R., Luo S., Khrebtukova I., Zhang L., Mayr C., et al. (2008a). Alternative isoform regulation in human tissue transcriptomes. Nature 456, 470–476. 10.1038/nature07509 PubMed DOI PMC

Wang Q., Fang W. H., Krupinski J., Kumar S., Slevin M., Kumar P. (2008b). PubMed DOI PMC

Ward T. A., Nebel A., Reeve A. E., Eccles M. R. (1994). Alternative messenger RNA forms and open reading frames within an additional conserved region of the human PubMed

Xu H. E., Rould M. A., Xu W., Epstein J. A., Maas R. L., Pabo C. O. (1999). Crystal structure of the human Pax6 paired domain–DNA complex reveals specific roles for the linker region and carboxy-terminal subdomain in DNA binding. Genes Dev 13, 1263–1275. 10.1101/gad.13.10.1263 PubMed DOI PMC

Xu W., Rould M. A., Jun S., Desplan C., Pabo C. O. (1995). Crystal structure of a paired domain-DNA complex at 2.5 A resolution reveals structural basis for Pax developmental mutations. Cell 80, 639–650. 10.1016/0092-8674(95)90518-9 PubMed DOI

Zwollo P., Arrieta H., Ede K., Molinder K., Desiderio S., Pollock R. (1997). The PubMed DOI

Genetic analysis of medaka fish illuminates conserved and divergent roles of Pax6 in vertebrate eye development

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