Advertisement

Molecular Biology Reports

, Volume 41, Issue 4, pp 2353–2362 | Cite as

Porcine ubiquitin-like 5 (UBL5) gene: genomic organization, polymorphisms, mRNA cloning, splicing variants and association study

  • Martin Masopust
  • Filip Weisz
  • Heinz Bartenschlager
  • Aleš Knoll
  • Zuzana Vykoukalová
  • Hermann Geldermann
  • Stanislav ČepicaEmail author
Article
  • 221 Downloads

Abstract

Ubiquitin-like 5 (UBL5), which is supposed to be involved in regulation of feed intake, energy metabolism, obesity and type 2 diabetes, is located at position 62.1 cM on the pig chromosome 2 region harbouring quantitative trait loci for carcass and meat quality. The 4,354 bp genomic sequence (FR798948) of the porcine gene encompassing the promoter and entire gene was cloned by polymerase chain reaction. Comparative sequencing revealed 13 polymorphisms in noncoding regions. Synthesis of full-length cDNA sequences using rapid amplification of 5′ and 3′ ends showed three splice variants. Variants 1 and 2 differ in transcription length for the untranslated part of exon 1 with deduced protein of 73 amino acid (aa) residues and 100 % identities between human, mouse and other species. Variant 3, with 4 bp deletion at the 3′ end of exon 2, encodes a truncated protein with 28 aa residues. In a Wild boar×Meishan F2 population (n = 334) with 47 recorded traits, loci FR798948:g.2788G>A and FR798948:g.2141T>C were associated at nominal P < 0.05 with fat deposition, growth and fattening and muscling but after adjustment for multiple testing (Benjamini and Hochberg, J R Stat Soc B 57:289–300, 1995) only eight fat deposition traits showed suggestive association with FR798948:g.2788G>A at adjusted P < 0.10. In a Meishan×Large White (MLW) cross (n = 562) with six trait records available, FR798948:g.2141T>C showed suggestive association with growth (adjusted P = 0.0690). As association mapping conducted in the outbred MLW population is more precise than in the three generation F2 population the UBL5 gene tends to be associated with growth rather than with fat accretion.

Keywords

Pig UBL5 PCR cloning 5′ and 3′ RACE Splice variants Association analysis 

Notes

Acknowledgments

The authors thank Petra Šejnohová for technical assistance. DNA samples and trait records of the MLW cross were kindly provided by Genus plc, De Forest, Wisconsin, USA. This work was supported by the Czech Science Foundation (Grant No. P502/10/1216), Institute of Animal Physiology and Genetics AS CR, v.v.i. (RVO: 67985904), CEITEC project CZ.1.05/1.1.00/02.0068.

Supplementary material

11033_2014_3089_MOESM1_ESM.docx (44 kb)
Supplementary material 1 (DOCX 43 kb)

References

  1. 1.
    Hochstrasser M (2009) Origin and function of ubiquitin-like proteins. Nature 458:422–429PubMedCentralPubMedCrossRefGoogle Scholar
  2. 2.
    Friedman JS, Koop BF, Raymond V, Walter MA (2001) Isolation of a ubiquitin-like (UBL5) gene from a screen identifying highly expressed and conserved iris genes. Genomics 71:252–255PubMedCrossRefGoogle Scholar
  3. 3.
    Wilkinson CRM, Dittmar GAG, Ohi MD, Uetz P, Jones N, Finley D (2004) Ubiquitin-like protein Hub1 is required for pre-mRNA splicing factor in fission yeast. Curr Biol 14:2283–2288PubMedCrossRefGoogle Scholar
  4. 4.
    Makarova OV, Makarov EM, Urlaub H, Will CL, Gentzel H, Wilm M, Lührmann R (2004) A subset of human 35S U5 proteins, including Prp19, function prior to catalytic step 1 of splicing. EMBO J 23:2381–2391PubMedCentralPubMedCrossRefGoogle Scholar
  5. 5.
    Mishra SK, Ammon T, Popowicz GM, Krajewski M, Nagel RJ, Ares M Jr, Holak TA, Jentsch S (2011) Role of the ubiquitin-like protein Hub1 in splice-site usage and alternative splicing. Nature 474:173–178PubMedCentralPubMedCrossRefGoogle Scholar
  6. 6.
    Collier GR, McMillan JS, Windmill K, Walder K, Tenne-Brown J, de Silva A, Trevaskis J, Jones S, Morton GJ, Lee S, Augert G, Civitarese A, Zimmet PZ (2000) Beacon: a novel gene involved in the regulation of energy balance. Diabetes 49:1766–1771PubMedCrossRefGoogle Scholar
  7. 7.
    Walder K, Ziv E, Kalman R, Whitecross K, Shafrir E, Zimmet P, Collier GR (2002) Elevated hypothalamic beacon gene expression in Psammomys obesus prone to develop obesity and type 2 diabetes. Int J Obes 26:605–609CrossRefGoogle Scholar
  8. 8.
    Brailoiu GC, Dun SL, Chi M, Ohsawa M, Chang JK, Yang J, Dun NJ (2003) Beacon/ubiquitin-like 5-immunoreactivity in the hypothalamus and pituitary of the mouse. Brain Res 984:215–223PubMedCrossRefGoogle Scholar
  9. 9.
    Bernstein HG, Lendeckel U, Dobrowolny H, Stauch R, Steiner J, Grecksch G, Becker A, Jirikowski GF, Bogerts B (2008) Beacon-like/ubiquitin-5-like immunoreactivity is highly expressed in human hypothalamus and increased in haloperidol-treated schizophrenics and a rat model of schizophrenia. Psychoneuroendocrino 33:340–351CrossRefGoogle Scholar
  10. 10.
    Jowett JB, Elliott KS, Curran JE, Hunt N, Walder KR, Collier GR, Zimmet PZ, Blangero J (2004) Genetic variation in BEACON influences quantitative variation in metabolic syndrome-related phenotypes. Diabetes 53:2467–2472PubMedCrossRefGoogle Scholar
  11. 11.
    Bozaoglu K, Curran JE, Elliott KS, Walder KR, Dyer TD, Rainwater DL, VandeBerg JL, Comuzzie AG, Collier GR, Zimmet P, MacCluer JW, Jowett JB, Blangero J (2006) Association of genetic variation within UBL5 with phenotypes of metabolic syndrome. Hum Biol 78:147–159PubMedCrossRefGoogle Scholar
  12. 12.
    Sentinelli F, Romeo S, Cambuli VM, Cossu E, Cavallo MG, Zavarella S, Spoletini M, Buzzetti R, Baroni MG (2008) Identification of sequence variants in the UBL5 (ubiquitin-like 5 or BEACON) gene in obese children by PCR-SSCP: no evidence for association with obesity. J Pediatr Endocrinol Metab 21:1139–1145PubMedCrossRefGoogle Scholar
  13. 13.
    Čepica S, Ovilo C, Masopust M, Knoll A, Fernandez A, Lopez A, Rohrer GA, Nonneman D (2012) Four genes located on a SSC2 meat quality QTL region are associated with different meat quality traits in Landrace×Chinese–European crossbred population. Anim Genet 43:333–336PubMedCrossRefGoogle Scholar
  14. 14.
    Hu ZL, Reecy JM (2007) AnimalQTLdb: beyond a repository—a public platform for QTL comparisons and integration with diverse types of structural genomic information. Mamm Genome 18:1–4PubMedCrossRefGoogle Scholar
  15. 15.
    Ochman H, Gerber AS, Hartl DL (1988) Genetic applications of an inverse polymerase chain reaction. Genetics 120:621–623PubMedCentralPubMedGoogle Scholar
  16. 16.
    Gaunt TR, Rodríguez S, Day IN (2007) Cubic exact solutions for the estimation of pairwise haplotype frequencies: implications for linkage disequilibrium analyses and web tool „Cubex“. BMC Bioinformatics 8:428PubMedCentralPubMedCrossRefGoogle Scholar
  17. 17.
    Geldermann H, Müller E, Moser G, Reiner G, Bartenschlager H, Čepica S, Stratil A, Kuryl J, Moran C, Davoli R, Brunsch C (2003) Genome-wide linkage and QTL mapping in porcine F2 families generated from Pietrain, Meishan and Wild Boar crosses. J Anim Breed Genet 120:363–393CrossRefGoogle Scholar
  18. 18.
    Müller E, Moser G, Bartenschlager H, Geldermann H (2000) Trait values of growth, carcass and meat quality in Wild Boar, Meishan and Pietrain pigs as well as their crossbred generations. J Anim Breed Genet 117:189–202CrossRefGoogle Scholar
  19. 19.
    Goldstein DB, Weale ME (2001) Population genomics: linkage disequilibrium holds the key. Curr Biol 11:R576–R579PubMedCrossRefGoogle Scholar
  20. 20.
    Georges M (2007) Mapping, fine mapping, and molecular dissection of quantitative trait loci in domestic animals. Annu Rev Genomics Hum Genet 8:131–162PubMedCrossRefGoogle Scholar
  21. 21.
    Benjamini Y, Hochberg Y (1995) Control ling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B 57:289–300Google Scholar
  22. 22.
    Kornblihtt AR (2005) Promoter usage and alternative splicing. Curr Opin Cell Biol 17:262–268PubMedCrossRefGoogle Scholar
  23. 23.
    Lewin B (2004) Genes VIII. Pearson Education Inc., Upper Saddle River, pp 609–610Google Scholar
  24. 24.
    Green MR (1986) PRE-mRNA splicing. Annu Rev Genet 20:671–708PubMedCrossRefGoogle Scholar
  25. 25.
    Kalsotra A, Cooper T (2011) Functional consequences of developmentally regulated alternative splicing. Nat Rev Genet 12:715–729PubMedCentralPubMedCrossRefGoogle Scholar
  26. 26.
    Wise H (2012) The roles played by highly truncated splice variants of G protein-coupled receptors. J Mol Signal 7:13PubMedCentralPubMedCrossRefGoogle Scholar
  27. 27.
    Yeo CV, Van Nostrand E, Holsze D, Poggio T, Burge CB (2005) Identification and analysis of alternative splicing events conserved in human and mouse. PNAS 102:2850–2855PubMedCentralPubMedCrossRefGoogle Scholar
  28. 28.
    Licatalosi DD, Darnell RB (2010) RNA processing and its regulation: global insights into biological networks. Nat Rev Genet 11:75–87PubMedCentralPubMedCrossRefGoogle Scholar
  29. 29.
    Nielsen TW, Graveley BR (2010) Expansion of the eukaryotic proteome by alternative splicing. Nature 463:457–463CrossRefGoogle Scholar
  30. 30.
    Du FX, Clutter AC, Lohuis MM (2007) Characterization of linkage disequilibrium in pig populations. Int J Biol Sci 3:166–178PubMedCentralPubMedCrossRefGoogle Scholar
  31. 31.
    de Koning DJ, Janss LL, Rattink AP, van Oers PA, de Vries BJ, Groenen MA, van der Poel JJ, de Groot PN, Brascamp EW, van Arendonk JA (1999) Detection of quantitative trait loci for backfat thickness and intramuscular fat content in pigs (Sus scrofa). Genetics 152:1679–1690PubMedCentralPubMedGoogle Scholar
  32. 32.
    Lee SS, Chen Y, Moran C, Čepica S, Reiner G, Bartenschlager H, Moser G, Geldermann H (2003) Linkage mapping and QTL-analysis for Sus scrofa chromosome 2. J Anim Breed Genet 120(Suppl. 1):11–19CrossRefGoogle Scholar
  33. 33.
    Rattink AP, De Koning DJ, Faivre M, Harlizius B, van Arendonk JA, Groenen MA (2000) Fine mapping and imprinting analysis for fatness trait QTLs in pigs. Mamm Genome 11:656–661PubMedCrossRefGoogle Scholar
  34. 34.
    Stearns TM, Beever JE, Southey BR, Ellis M, McKeith FK, Rodriguez-Zas SL (2005) Evaluation of approaches to detect quantitative trait loci for growth, carcass, and meat quality on swine chromosomes 2, 6, 13, and 18. I. Univariate outbred F2 and sib-pair analyses. J Anim Sci 83:1481–1493PubMedGoogle Scholar
  35. 35.
    Xu X, Xing S, Du ZQ, Rothschild MF, Yerle M, Liu B (2008) Porcine TEF1 and RTEF1: molecular characterization and association analyses with growth traits. Comp Biochem Physiol B 150:447–453PubMedCrossRefGoogle Scholar
  36. 36.
    Qiu H, Xu X, Fan B, Rothschild MF, Martin Y, Liu B (2010) Investigation of LDHA and COPB1 as candidate genes for muscle development in the MYOD1 region of pig chromosome 2. Mol Biol Rep 37:629–636PubMedCrossRefGoogle Scholar
  37. 37.
    Tortereau F, Gilbert H, Heuven HC, Bidanel JP, Groenen MA, Riquet J (2010) Combining two Meishan F2 crosses improves the detection of QTL on pig chromosomes 2, 4 and 6. Genet Sel Evol 42:42PubMedCentralPubMedCrossRefGoogle Scholar
  38. 38.
    Geldermann H, Čepica S, Stratil A, Bartenschlager H, Preuss S (2010) Genome-wide mapping of quantitative trait loci for fatness, fat cell characteristics and fat metabolism in three porcine F2 crosses. Genet Sel Evol 42:31PubMedCentralPubMedCrossRefGoogle Scholar
  39. 39.
    Tortereau F, Sanchez MP, Fève K, Gilbert H, Iannuccelli N, Billon Y, Milan D, Bidanel JP, Riquet J (2011) Progeny-testing of full-sibs IBD in a SSC2 QTL region highlights epistatic interactions for fatness traits in pigs. BMC Genet 12:92PubMedCentralPubMedCrossRefGoogle Scholar
  40. 40.
    Čepica S, Zambonelli P, Weisz F, Bigi M, Knoll A, Vykoukalová Z, Masopust M, Gallo M, Buttazzoni L, Davoli R (2013) Association mapping of quantitative trait loci for carcass and meat quality traits at the central part of chromosome 2 in Italian Large White pigs. Meat Sci 95:368–375Google Scholar
  41. 41.
    Schwartz MW, Woods SC, Porte D Jr, Seeley RJ, Baskin DG (2000) Central nervous system control of food intake. Nature 404:661–671PubMedGoogle Scholar
  42. 42.
    Brailoiu GC, Dun SL, Yang J, Chang JK, Castellino S, Dun NJ (2002) Beacon-like immunoreactivity in the hypothalamus of Sprague–Dawley rats. Neurosci Lett 317:166–168PubMedCrossRefGoogle Scholar
  43. 43.
    Ng YK, Brailoiu GC, Dun SL, Ling EA, Yang J, Chang JK, Dun NJ (2006) Beacon immunoreactivity in the rat hypothalamus. J Neurosci Res 83:1106–1117PubMedCrossRefGoogle Scholar
  44. 44.
    Esposito V, de Girolamo P, Gargiulo G, Dun NJ (2006) Beacon-like immunoreactivity in the hypothalamus of domestic chick. Anat Histol Embryol 35:361–364PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Martin Masopust
    • 1
  • Filip Weisz
    • 1
    • 2
  • Heinz Bartenschlager
    • 3
  • Aleš Knoll
    • 2
  • Zuzana Vykoukalová
    • 2
  • Hermann Geldermann
    • 3
  • Stanislav Čepica
    • 1
    Email author
  1. 1.Institute of Animal Physiology and GeneticsAcademy of Sciences of the Czech RepublicLiběchovCzech Republic
  2. 2.CEITEC MENDELUMendel University in BrnoBrnoCzech Republic
  3. 3.Department of Animal Breeding and BiotechnologyUniversity of HohenheimStuttgartGermany

Personalised recommendations