Development of a new set of reference genes for normalization of real-time RT-PCR data of porcine backfat and longissimus dorsi muscle, and evaluation with PPARGC1A

BMC Biotechnology

Volumn 6, Issue , 2006, Pages

  Erkens, Tim ^a   Van Poucke, Mario ^a   Vandesompele, Jo ^b   Goossens, Karen ^a   Van Zeveren, Alex ^a   Peelman, Luc J ^a  

^a GHENT UNIVERSITY   (Belgium)

^b GHENT UNIVERSITY HOSPITAL   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

FAT METABOLISM; MEAT QUALITY;

BIOMEDICAL ENGINEERING; DNA; GENES; METABOLISM; MUSCLE;

BIOTECHNOLOGY;

BETA 2 MICROGLOBULIN; BETA ACTIN; DNA TOPOISOMERASE (ATP HYDROLYSING) B; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE; MESSENGER RNA; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA COACTIVATOR 1ALPHA; PORPHOBILINOGEN DEAMINASE; RIBOSOME PROTEIN; RIBOSOME PROTEIN L13A; SUCCINATE DEHYDROGENASE; TATA BINDING PROTEIN; TYROSINE 3 MONOOXYGENASE; UNCLASSIFIED DRUG;

ANIMAL TISSUE; ARTICLE; BACK MUSCLE; CARCASS; CONTROLLED STUDY; FUNCTIONAL GENOMICS; GENE EXPRESSION; GENE SEQUENCE; LIPID METABOLISM; MEAT INDUSTRY; MUSCLE CELL; NONHUMAN; NUCLEOTIDE SEQUENCE; QUALITY CONTROL; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SAMPLE; STATISTICAL SIGNIFICANCE; SWINE; TISSUE TYPES;

ADIPOSE TISSUE; ANIMALS; GENE EXPRESSION; MEAT; MUSCLE, SKELETAL; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER; SWINE; TRANSCRIPTION FACTORS;

SUIDAE; SUS SCROFA;

EID: 33750277449     PISSN: 14726750     EISSN: 14726750     Source Type: Journal    
DOI: 10.1186/1472-6750-6-41     Document Type: Article

References (45)

1. Fiedler I, Nürnberg K, Hardge T, Nürnberg G, Ender K: Phenotypic variations of muscle fibre and intramuscular fat traits in Longissimus muscle of F2 population DurocxBerlin Miniature Pig and relationships to meat quality. Meat Sci 2003, 63:131-139.
2. Klont RE, Brocks L, Eikelenboom G: Muscle fibre type and meat quality. Meat Sci 1998, 49:S219-229.
3. Smith SB, Lunt DK, Zembayashi M: Intramuscular fat deposition: the physiological process and the potential for its manipulation. In Plains Nutrition Council Spring Conference (publ no AREC 00-22) Amarillo: Texas A&M Research and Extension Center; 2000:1-12.
4. Karlsson AH, Klont RE, Fernandez X: Skeletal muscle fibres as factors for pork quality. Livest Prod Sci 1999, 60:255-269.
5. Kolstad K, Jopson NB, Vangen O: Breed and sex differences in fat distribution and mobilization in growing pigs fed at maintenance. Livest Prod Sci 1996, 47:33-41.
6. Chang KC, Da Costa N, Blackley R, Southwood O, Evans G, Plastow G, Wood JD, Richardson RI: Relationships of myosin heavy chain fibre types to meat quality traits in traditional and modern pigs. Meat Sci 2003, 64:93-103.
7. Cameron ND: Genetic and phenotypic parameters for carcass traits, meat and eating quality traits in pigs. Livest Prod Sci 1990, 26:119-135.
8. Brocks L, Klont RE, Buist W, de Greef K, Tieman M, Engel B: The effects of selection of pigs on growth rate vs leanness on histochemical characteristics of different muscles. J Anim Sci 2000, 78:1247-1254.
9. Puigserver P, Wu Z, Park CW, Graves R, Wright M, Spiegelman BM: A cold-inducible coactivator of nuclear receptors linked to adaptive thermogenesis. Cell 1998, 92:829-839.
10. Wu Z, Puigserver P, Andersson U, Zhang C, Adelmant G, Mootha V, Troy A, Cinti S, Lowell B, Scarpulla RC, Spiegelman BM: Mechanisms controlling mitochondrial biogenesis and respiration through the thermogenic coactivator PGC-1. Cell 1999, 98:115-124.
11. Spiegelman BM, Puigserver P, Wu Z: Regulation of adipogenesis and energy balance by PPARγ and PGC-1. Int J Obes 2000, 24:S8-10.
12. Oberkofler H, Esterbauer H, Linnemayr V, Strosberg AD, Krempler F, Patsch W: Peroxisome proliferator-activated receptor (PPAR) γ coactivator-1 recruitment regulates PPAR subtype specificity. J Biol Chem 2002, 277:16750-16757.
13. Yoon JC, Puigserver P, Chen GX, Donovan J, Wu ZD, Rhee J, Adelmant G, Stafford J, Kahn CR, Granner DK, Newgard CB, Spiegelman BM: Control of hepatic gluconeogenesis through the transcriptional coactivator PGC-1. Nature 2001, 413:131-138.
14. Goto M, Terada S. Kato M, Katoh M, Yokozeki T, Tabata I, Shimokawa T: cDNA cloning and mRNA analysis of PGC-1 in epitrochlearis muscle in swimming-exercised rats. Biochem Biophys Res Commun 2000, 274:350-354.
15. Lin J, Wu H, Tarr PT, Zhang C-Y, Wu Z, Boss O, Michael LF, Puigserver P, Isotani E, Olson EN, Lowell BB, Bassel-Duby R, Spiegelman BM: Transcriptional co-activator PGC-1 α drives the formation of slow-twitch muscle fibres. Nature 2002, 418:797-801.
16. Zhao R-Q, Yang X-J, Xu Q-F, Wei X-H, Xia D, Chen J: Expression of GHR and PGC-1α in association with changes of MyHC isoform types in longissimus muscle of Erhualian and Large White pigs (Sus scrofa) during postnatal growth. Anim Sci 2004, 79:203-211.
17. Michael LF, Wu Z, Cheatham RB, Puigserver P, Adelmant G, Lehman JJ, Kelly DP, Spiegelman BM: Restoration of insulin-sensitive glucose transporter (GLUT4) gene expression in muscle cells by the transcriptional coactivator PGC-1. Proc Natl Acad Sci US4 2001, 98:3820-3825.
18. Jacobs K, Rohrer G, Van Poucke M, Piumi F, Yerle M, Barthenschlager H, Mattheeuws M, Van Zeveren A, Peelman LJ: Porcine PPARGC1A (peroxisome proliferative activated receptor gamma coactivator 1A): coding sequence, genomic organization, polymorphisms and mapping. Cytogenet Genome Res 2006, 112:106-113.
19. Ek J, Andersen G, Urhammer SA, Gæde PH, Drivshom T, Borch-Johnsen K, Hansen T, Pedersen O: Mutation analysis of peroxisome proliferator activated receptor-γ coactivator-1 (PGC-1) and relationships of identified amino acid polymorphisms to type II diabetes mellitus. Diabetologia 2001, 44:2220-2226.
20. Hammarstedt A, Jansson P-A, Wesslau C, Yang X, Smith U: Reduced expression of PGC-1 and insulin-signaling molecules in adipose tissue is associated with insulin resistance. Biochem Biophys Res Commun 2003, 301:578-582.
21. Yoon JC, Xu G, Deeney JT, Yang SN, Rhee J, Puigserver P, Levens AR, Yang R, Zhang CY, Lowell BB, Berggren PO, Newgard CB, Bonner-Weir S, Weir G, Spiegelman BM: Suppression of β cell energy metabolism and insulin release by PGC-1α. Dev Cell 2003, 5:73-83.
22. Roehe R, Plastow GS, Knap PW: Quantitative and molecular genetic determination of protein and fat deposition. Homo 2003, 54:119-131.
23. Wernersson R, Schierup MH, Jorgensen FG, Gorodkin J, Panitz F, Staerfeldt HH, Christensen OF, Mailund T, Hornshoj H, Klein A, Wang J, Liu B, Hu S, Dong W, Li W, Wong GK, Yu J, Wang J, Bendixen C, Fredholm M, Brunak S, Yang H, Bolund L: Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing. BMC Genomics 2005, 6:70.
24. Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F: Accurate normalization of real-time quantative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biology 2002, 3:34 [http://medgen.ugent.be/~jvdesomp/genorm].
25. Heid CA, Stevens J, Livak KJ, Williams PM: Real time quantitative PCR. Genome Res 1996, 6:986-994.
26. Thellin O, Zorzi W, Lakaye B, De Borman B, Coumans B, Hennen G, Grisar T, Igout A, Heinen E: Housekeeping genes as internal standards: use and limits. J Biotechnol 1999, 75:291-295.
27. Bustin SA: Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J Mol Endocrinol 2000, 25:169-193.
28. Schmittgen TD, Zakrajsek BA: Effect of experimental treatment on housekeeping gene expression: validation by real-time, quantitative RT-PCR. J Biochem Biophys Methods 2000, 46:69-81.
29. Kenmochi N, Kawaguchi T, Rozen S, Davis E, Goodman N, Hudson TJ, Tanaka T, Page DC: A map of 75 human ribosomal protein genes. Genome Res 1998, 8:509-523.
30. Higa S, Yoshihama M, Tanaka T, Kenmochi N: Gene organization and sequence of the region containing the ribosomal protein genes RPL13A and RPS11 in the human genome and conserved features in the mouse genome. Gene 1999, 240:371-377.
31. Dresios J, Panopoulos P, Synetos D: Eukaryotic ribosomal proteins lacking a eubacterial counterpart: important players in ribosomal function. Mol Microbiol 2006, 59:1651-1663.
32. Cuccurese M, Russo G, Russo A, Pietropaolo C: Alternative splicing and nonsense-mediated mRNA decay regulate mammalian ribosomal gene expression. Nucleic Acids Res 2005, 33:5965-5977.
33. Neverov AD, Artamonova II, Nurtdinov RN, Frishman D, Gelfand MS, Mironov AA: Alternative splicing and protein function. BMC Bioinformatics 2005, 6:266.
34. Brière JJ, Favier J, El Ghouzzi V, Djouadi F, Benit P, Gimenez AP, Rustin P: Succinate dehydrogenase deficiency in human. Cell Mol Life Sci 2005, 62:2317-2324.
35. Kunej T, Wu XL, Berlic TM, Michal JJ, Jiang Z, Dovc P: Frequency distribution of a Cys430Ser polymorphism in peroxisome proliferator-activated receptor-γ coactivator-1 (PPARGC1A) gene sequence in Chinese and Western pig breeds. J Anim Breed Genet 2005, 122:7-11.
36. Larrouy D, Vidal H, Andreelli F, Laville M, Langin D: Cloning and mRNA tissue distribution of human PPARγ coactivator-1. Int J Obes 1999, 23:1327-1332.
37. Omi T, Brenig B, Špilar Kramer Š, Iwamoto S, Stranzinger G, Neuenschwander S: Identification and characterization of novel peroxisome proliferator-activated receptor-gamma (PPAR-γ) transcriptional variants in pig and human. J Anim Breed Genet 2005, 122:45-53.
38. Terada S, Tabata I: Effects of acute bouts of running and swimming exercise on PGC-1α protein expression in rat epitrochlearis and soleus muscle. Am J Physiol-Endocrinol Metab 2004, 286:E208-216.
39. Gygi SP, Rochon Y, Franza BR, Aebersold R: Correlation between protein and mRNA abundance in yeast. Mol Cell Biol 1999, 19:1720-1730.
40. Van Poucke M, Yerle M, Tuggle C, Piumi F, Genet C, Van Zeveren A, Peelman LJ: Integration of porcine chromosome 13 maps. Cytogen Cell Genet 2001, 93:297-303.
41. National Center for Biotechnology Information [http://www.ncbi.nlm.nih.gov]
42. Ensembl Genome Browser [http://www.ensembl.org/index.html]
43. Rozen S, Skaletsky HJ: Primer3 on the WWW for general users and for biologist programmers. Bioinformatics Methods and Protocols: Methods in Molecular Biology 2000:365-386 [http://frodo.wi.mit.edu/cgi-bin/primer3/ primer3_www.cgi]. Totowa: Humana Press
44. Zuker M: Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 2003, 31:3406-3415 [http://www.bioinfo.rpi.edu/applications/mfold/dna/form1.cgi].
45. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215:403-410 [http://www.ncbi.nlm.nih.gov/blast].