Molecular Biology Reports

, Volume 38, Issue 5, pp 2975–2986 | Cite as

Annotation of novel transcripts putatively relevant for bovine fat metabolism

  • Annett Eberlein
  • Claudia Kalbe
  • Tom Goldammer
  • Ronald M. Brunner
  • Christa Kuehn
  • Rosemarie WeikardEmail author


Two bovine transcripts encoded by the interleukin-1 receptor-associated kinase 1 (IRAK1) gene and the locus LOC618944 predicted as similar to human chromosome 6 open reading frame 52 (C6orf52) gene had indicated divergent expression in bovine skeletal muscle containing different amount of intramuscular fat in a pilot screening experiment. However, for both loci any role in the regulation of energy or fat metabolism is not yet described. In this study, we validated and refined gene structure, screened for mRNA splice variants and analyzed the tissue-specific gene expression patterns of both loci as a prerequisite to elucidate their potential physiological function. Based on comparative sequence analysis, a new full-length gene model for the bovine IRAK1 gene was developed and confirmed experimentally. Expression of IRAK1 mRNA was found in a variety of tissues, and a splice variant was identified in skeletal muscle caused by an in-frame deleted segment of 210 bp affecting regions of intrinsic disorder in the respective protein. For the locus LOC618944, our data contributed to a revised gene model and its assignment to BTA23 (bovine chromosome 23) on the current bovine genome assembly supported by comparative similarity analysis between the bovine and human genomes and experimental data. Furthermore, we identified several splice variants in mammary gland, fat and skeletal muscle tissue and detected a highly similar processed pseudogene on BTA26. All transcript variants of LOC618944 detected in the analyzed tissues represent noncoding RNAs. For both loci, our results suggest yet undetected physiological functions in tissues relevant for fat or energy metabolism in cattle.


Cattle mRNA expression Splice variant IRAK1 C6orf52 Noncoding RNA 



We thank the German Federal Ministry of Education and Research (BMBF) for the financial support of this work within the scope of the FUGATO QUALIPID project (FKZ 0313391C). Also, we thank our colleagues at the FBN Dummerstorf involved in the generation and care of the SEGFAM F2 resource population for their continuous support of our work. Skillful technical assistance of Astrid Kühl, Marlies Fuchs, Hilke Brandt, and Simone Wöhl is thankfully acknowledged.


  1. 1.
    Andersson L, Georges M (2004) Domestic-animal genomics: deciphering the genetics of complex traits. Nat Rev Genet 5:202–212PubMedCrossRefGoogle Scholar
  2. 2.
    De Smet S, Raes K, Demeyer D (2004) Meat fatty acid composition as affected by fatness and genetic factors: a review. Anim Res 53:81–92CrossRefGoogle Scholar
  3. 3.
    Abe T, Saburi J, Hasebe H, Nakagawa T, Kawamura T, Saito K, Nade T, Misumi S, Okumura T, Kuchida K, Hayashi T, Nakane S, Mitsuhasi T, Nirasawa K, Sugimoto Y, Kobayashi E (2008) Bovine quantitative trait loci analysis for growth, carcass, and meat quality traits in an F-2 population from a cross between Japanese Black and Limousin. J Anim Sci 86:2821–2832PubMedCrossRefGoogle Scholar
  4. 4.
    Thaller G, Kuhn C, Winter A, Ewald G, Bellmann O, Wegner J, Zuhlke H, Fries R (2003) DGAT1, a new positional and functional candidate gene for intramuscular fat deposition in cattle. Anim Genet 34:354–357PubMedCrossRefGoogle Scholar
  5. 5.
    Barendse W, Bunch RJ, Kijas JW, Thomas MB (2007) The effect of genetic variation of the retinoic acid receptor-related orphan receptor C gene on fatness in cattle. Genetics 175:843–853PubMedCrossRefGoogle Scholar
  6. 6.
    Barendse W, Bunch RJ, Thomas MB, Harrison BE (2009) A splice site single nucleotide polymorphism of the fatty acid binding protein 4 gene appears to be associated with intramuscular fat deposition in longissimus muscle in Australian cattle. Anim Genet 40:770–773PubMedCrossRefGoogle Scholar
  7. 7.
    Fortes MRS, Curi RA, Chardulo LAL, Silveira AC, Assumpcao MEOD, Visintin JA, de Oliveira HN (2009) Bovine gene polymorphisms related to fat deposition and meat tenderness. Genet Mol Biol 32:75–82Google Scholar
  8. 8.
    Kuehn C, Bellmann O, Voigt J, Wegner J, Guiard V, Ender K (2002) An experimental approach for studying the genetic and physiological background of nutrient transformation in cattle with respect to nutrient secretion and accretion type. Arch Anim Breed 45:317–330Google Scholar
  9. 9.
    Connor EE, Cates EA, Williams JL, Bannerman DD (2006) Cloning and radiation hybrid mapping of bovine toll-like receptor-4 (TLR-4) signaling molecules. Vet Immunol Immunopathol 112:302–308PubMedCrossRefGoogle Scholar
  10. 10.
    Gottipati S, Rao NL, Fung-Leung WP (2008) IRAK1: a critical signaling mediator of innate immunity. Cell Signal 20:269–276PubMedCrossRefGoogle Scholar
  11. 11.
    Elsik CG, Tellam RL, Worley KC, Bovine Genome Sequencing Anal Cons (2009) The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 324:522–528PubMedCrossRefGoogle Scholar
  12. 12.
    Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402PubMedCrossRefGoogle Scholar
  13. 13.
    Zhang Z, Schwartz S, Wagner L, Miller W (2000) A greedy algorithm for aligning DNA sequences. J Comput Biol 7:203–214PubMedCrossRefGoogle Scholar
  14. 14.
    Cao ZD, Henzel WJ, Gao XO (1996) IRAK: a kinase associated with the interleukin-1 receptor. Science 271:1128–1131PubMedCrossRefGoogle Scholar
  15. 15.
    Jensen LE, Whitehead AS (2001) IRAK1b, a novel alternative splice variant of interleukin-1 receptor-associated kinase (IRAK), mediates interleukin-1 signaling and has prolonged stability. J Biol Chem 276:29037–29044PubMedCrossRefGoogle Scholar
  16. 16.
    Rao N, Nguyen S, Ngo K, Fung-Leung WP (2005) A novel splice variant of interleukin-1 receptor (IL-1R)-associated kinase 1 plays a negative regulatory role in toll/IL-1R-induced inflammatory signaling. Mol Cell Biol 25:6521–6532PubMedCrossRefGoogle Scholar
  17. 17.
    Tellam RL, Lemay DG, Van Tassell CP, Lewin HA, Worley KC, Elsik CG (2009) Unlocking the bovine genome. BMC Genomics 10:193PubMedCrossRefGoogle Scholar
  18. 18.
    Smith TPL, Grosse WM, Freking BA, Roberts AJ, Stone RT, Casas E, Wray JE, White J, Cho J, Fahrenkrug SC, Bennett GL, Heaton MP, Laegreid WW, Rohrer GA, Chitko-McKown CG, Pertea G, Holt I, Karamycheva S, Liang F, Quackenbush J, Keele JW (2001) Sequence evaluation of four pooled-tissue normalized bovine cDNA libraries and construction of a gene index for cattle. Genome Res 11:626–630PubMedCrossRefGoogle Scholar
  19. 19.
    Whitworth K, Springer GK, Forrester LJ, Spollen WG, Ries J, Lamberson WR, Bivens N, Murphy CN, Mathialigan N, Green JA, Prather RS (2004) Developmental expression of 2489 gene clusters during pig embryogenesis: an expressed sequence tag project. Biol Reprod 71:1230–1243PubMedCrossRefGoogle Scholar
  20. 20.
    Vanin EF (1985) Processed pseudogenes—characteristics and evolution. Annu Rev Genet 19:253–272PubMedCrossRefGoogle Scholar
  21. 21.
    Torrents D, Suyama M, Zdobnov E, Bork P (2003) A genome-wide survey of human pseudogenes. Genome Res 13:2559–2567PubMedCrossRefGoogle Scholar
  22. 22.
    Gerstein M, Zheng DY (2006) The real life of pseudogenes. Sci Am 295:48–55PubMedCrossRefGoogle Scholar
  23. 23.
    Amaral PP, Mattick JS (2008) Noncoding RNA in development. Mamm Genome 19:454–492PubMedCrossRefGoogle Scholar
  24. 24.
    Mattick JS, Amaral PP, Dinger ME, Mercer TR, Mehler MF (2009) RNA regulation of epigenetic processes. Bioessays 31:51–59PubMedCrossRefGoogle Scholar
  25. 25.
    Mattick JS (2009) The genetic signatures of noncoding RNAs. PLoS Genet 5:e1000459PubMedCrossRefGoogle Scholar
  26. 26.
    Gerstein MB, Bruce C, Rozowsky JS, Zheng DY, Du J, Korbel JO, Emanuelsson O, Zhang ZDD, Weissman S, Snyder M (2007) What is a gene, post-ENCODE? History and updated definition. Genome Res 17:669–681PubMedCrossRefGoogle Scholar
  27. 27.
    Zheng DY, Frankish A, Baertsch R, Kapranov P, Reymond A, Choo SW, Lu YT, Denoeud F, Antonarakis SE, Snyder M, Ruan YJ, Wei CL, Gingeras TR, Guigo R, Harrow J, Gerstein MB (2007) Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res 17:839–851PubMedCrossRefGoogle Scholar
  28. 28.
    Cabral GA (2005) Lipids as bioeffectors in the immune system. Life Sci 77:1699–1710PubMedCrossRefGoogle Scholar
  29. 29.
    Yaqoob P (2004) Fatty acids and the immune system: from basic science to clinical applications. Proc Nutr Soc 63:89–104PubMedCrossRefGoogle Scholar
  30. 30.
    Moyes KM, Drackley JK, Morin DE, Bionaz M, Rodriguez-Zas SL, Everts RE, Lewin HA, Loor JJ (2009) Gene network and pathway analysis of bovine mammary tissue challenged with streptococcus uberis reveals induction of cell proliferation and inhibition of PPAR-gamma signaling as potential mechanism for the negative relationships between immune response and lipid metabolism. BMC Genomics 10:542PubMedCrossRefGoogle Scholar
  31. 31.
    Dunker AK, Brown CJ, Lawson JD, Iakoucheva LM, Obradovic Z (2002) Intrinsic disorder and protein function. Biochemistry 41:6573–6582PubMedCrossRefGoogle Scholar
  32. 32.
    Dunker AK, Obradovic Z (2001) The protein trinity—linking function and disorder. Nat Biotechnol 19:805–806PubMedCrossRefGoogle Scholar
  33. 33.
    Dyson HJ, Wright PE (2005) Intrinsically unstructured proteins and their functions. Nat Rev Mol Cell Biol 6:197–208PubMedCrossRefGoogle Scholar
  34. 34.
    Dunker AK, Oldfield CJ, Meng JW, Romero P, Yang JY, Chen JW, Vacic V, Obradovic Z, Uversky VN (2007) The unfoldomics decade: an update on intrinsically disordered proteins. BMC Genomics 9:S1CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Annett Eberlein
    • 1
  • Claudia Kalbe
    • 2
  • Tom Goldammer
    • 1
  • Ronald M. Brunner
    • 1
  • Christa Kuehn
    • 1
  • Rosemarie Weikard
    • 1
    Email author
  1. 1.Research Unit Molecular BiologyResearch Institute for the Biology of Farm Animals (FBN)DummerstorfGermany
  2. 2.Research Unit Muscle Biology and GrowthResearch Institute for the Biology of Farm Animals (FBN)DummerstorfGermany

Personalised recommendations