The embryonic genes Dkk3, Hoxd8, Hoxd9 and Tbx1 identify muscle types in a diet-independent and fiber-type unrelated way

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  de Wilde, Janneke ^a,b   Hulshof, Martijn F M ^a,b   Boekschoten, Mark V ^a,c   de Groot, Philip ^a,c   Smit, Egbert ^a,b   Mariman, Edwin C M ^a,b  

^a TOP INSTITUTE FOOD AND NUTRITION   (Netherlands)

^b MAASTRICHT UNIVERSITY   (Netherlands)

^c WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; DEVELOPMENTAL GENE; DKK2 GENE; DKK3 GENE; EMBRYO DEVELOPMENT; GASTROCNEMIUS MUSCLE; GENE EXPRESSION REGULATION; HOXA10 GENE; HOXA5 GENE; HOXC10 GENE; HOXC6 GENE; HOXC9 GENE; HOXD8 GENE; HOXD9 GENE; LIPID DIET; LOW FAT DIET; MALE; MICROARRAY ANALYSIS; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; QUADRICEPS FEMORIS MUSCLE; QUANTITATIVE ANALYSIS; SIGNAL TRANSDUCTION; SOLEUS MUSCLE; TBX1 GENE; TBX15 GENE; ANIMAL; C57BL MOUSE; DIET; DNA MICROARRAY; FAT INTAKE; GENE EXPRESSION PROFILING; GENETICS; METABOLISM; SKELETAL MUSCLE;

MUS;

DKK3 PROTEIN, MOUSE; DNA BINDING PROTEIN; HOMEODOMAIN PROTEIN; HOXD8 PROTEIN, MOUSE; HOXD9 PROTEIN, MOUSE; SIGNAL PEPTIDE; T BOX TRANSCRIPTION FACTOR; TBX1 PROTEIN, MOUSE; TRANSCRIPTION FACTOR; TUMOR PROTEIN;

ANIMALS; DIET; DIETARY FATS; DNA-BINDING PROTEINS; GENE EXPRESSION PROFILING; HOMEODOMAIN PROTEINS; INTERCELLULAR SIGNALING PEPTIDES AND PROTEINS; MALE; MICE; MICE, INBRED C57BL; MUSCLE FIBERS, SKELETAL; MUSCLE, SKELETAL; NEOPLASM PROTEINS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; T-BOX DOMAIN PROTEINS; TRANSCRIPTION FACTORS;

EID: 77949478323     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-176     Document Type: Article

References (44)

1. Liang H, Ward WF. PGC-1alpha: a key regulator of energy metabolism. Advances in physiology education 2006, 30(4):145-151. 10.1152/advan.00052.2006, 17108241.
2. Scott W, Stevens J, Binder-Macleod SA. Human skeletal muscle fiber type classifications. Physical therapy 2001, 81(11):1810-1816.
3. Berchtold MW, Brinkmeier H, Muntener M. Calcium ion in skeletal muscle: its crucial role for muscle function, plasticity, and disease. Physiological reviews 2000, 80(3):1215-1265.
4. Booth FW, Thomason DB. Molecular and cellular adaptation of muscle in response to exercise: perspectives of various models. Physiological reviews 1991, 71(2):541-585.
5. Chanseaume E, Malpuech-Brugere C, Patrac V, Bielicki G, Rousset P, Couturier K, Salles J, Renou JP, Boirie Y, Morio B. Diets high in sugar, fat, and energy induce muscle type-specific adaptations in mitochondrial functions in rats. The Journal of nutrition 2006, 136(8):2194-2200.
6. Wang YX, Zhang CL, Yu RT, Cho HK, Nelson MC, Bayuga-Ocampo CR, Ham J, Kang H, Evans RM. Regulation of muscle fiber type and running endurance by PPARdelta. PLoS biology 2004, 2(10):e294. 10.1371/journal.pbio.0020294, 509410, 15328533.
7. Kho AT, Kang PB, Kohane IS, Kunkel LM. Transcriptome-scale similarities between mouse and human skeletal muscles with normal and myopathic phenotypes. BMC musculoskeletal disorders 2006, 7:23. 10.1186/1471-2474-7-23, 1525166, 16522209.
8. Naya FJ, Mercer B, Shelton J, Richardson JA, Williams RS, Olson EN. Stimulation of slow skeletal muscle fiber gene expression by calcineurin in vivo. The Journal of biological chemistry 2000, 275(7):4545-4548. 10.1074/jbc.275.7.4545, 10671477.
9. Talmadge RJ, Otis JS, Rittler MR, Garcia ND, Spencer SR, Lees SJ, Naya FJ. Calcineurin activation influences muscle phenotype in a muscle-specific fashion. BMC cell biology 2004, 5:28. 10.1186/1471-2121-5-28, 509416, 15282035.
10. Lin J, Wu H, Tarr PT, Zhang CY, Wu Z, Boss O, Michael LF, Puigserver P, Isotani E, Olson EN, et al. Transcriptional co-activator PGC-1 alpha drives the formation of slow-twitch muscle fibres. Nature 2002, 418(6899):797-801. 10.1038/nature00904, 12181572.
11. Mortensen OH, Frandsen L, Schjerling P, Nishimura E, Grunnet N. PGC-1alpha and PGC-1beta have both similar and distinct effects on myofiber switching toward an oxidative phenotype. Am J Physiol Endocrinol Metab 2006, 291(4):E807-816. 10.1152/ajpendo.00591.2005, 16720625.
12. Luquet S, Lopez-Soriano J, Holst D, Fredenrich A, Melki J, Rassoulzadegan M, Grimaldi PA. Peroxisome proliferator-activated receptor delta controls muscle development and oxidative capability. Faseb J 2003, 17(15):2299-2301.
13. Hakimi P, Yang J, Casadesus G, Massillon D, Tolentino-Silva F, Nye CK, Cabrera ME, Hagen DR, Utter CB, Baghdy Y, et al. Overexpression of the Cytosolic Form of Phosphoenolpyruvate Carboxykinase (GTP) in Skeletal Muscle Repatterns Energy Metabolism in the Mouse. Journal of Biological Chemistry 2007, 282(45):32844-32855. 10.1074/jbc.M706127200, 17716967.
14. de Wilde J, Mohren R, Berg S, Boekschoten M, Dijk KW, de Groot P, Muller M, Mariman E, Smit E. Short-term high fat-feeding results in morphological and metabolic adaptations in the skeletal muscle of C57BL/6J mice. Physiol Genomics 2008, 32(3):360-369.
15. Pette D, Staron RS. Myosin isoforms, muscle fiber types, and transitions. Microscopy research and technique 2000, 50(6):500-509. 10.1002/1097-0029(20000915)50:6<500::AID-JEMT7>3.0.CO;2-7, 10998639.
16. Pette D, Staron RS. Transitions of muscle fiber phenotypic profiles. Histochemistry and cell biology 2001, 115(5):359-372.
17. Otto A, Collins-Hooper H, Patel K. The origin, molecular regulation and therapeutic potential of myogenic stem cell populations. Journal of anatomy 2009, 215(5):477-497. 10.1111/j.1469-7580.2009.01138.x, 19702867.
18. Figeac N, Daczewska M, Marcelle C, Jagla K. Muscle stem cells and model systems for their investigation. Development dynamics 2007, 236(12):3332-3342.
19. Monaghan AP, Kioschis P, Wu W, Zuniga A, Bock D, Poustka A, Delius H, Niehrs C. Dickkopf genes are co-ordinately expressed in mesodermal lineages. Mech Dev 1999, 87(1-2):45-56. 10.1016/S0925-4773(99)00138-0, 10495270.
20. Stennard FA, Harvey RP. T-box transcription factors and their roles in regulatory hierarchies in the developing heart. Development (Cambridge, England) 2005, 132(22):4897-4910.
21. Niehrs C. Function and biological roles of the Dickkopf family of Wnt modulators. Oncogene 2006, 25(57):7469-7481. 10.1038/sj.onc.1210054, 17143291.
22. Dastjerdi A, Robson L, Walker R, Hadley J, Zhang Z, Rodriguez-Niedenfuhr M, Ataliotis P, Baldini A, Scambler P, Francis-West P. Tbx1 regulation of myogenic differentiation in the limb and cranial mesoderm. Dev Dyn 2007, 236(2):353-363. 10.1002/dvdy.21010, 17117436.
23. Grifone R, Jarry T, Dandonneau M, Grenier J, Duprez D, Kelly RG. Properties of branchiomeric and somite-derived muscle development in Tbx1 mutant embryos. Dev Dyn 2008, 237(10):3071-3078. 10.1002/dvdy.21718, 18816853.
24. Chieffo C, Garvey N, Gong W, Roe B, Zhang G, Silver L, Emanuel BS, Budarf ML. Isolation and characterization of a gene from the DiGeorge chromosomal region homologous to the mouse Tbx1 gene. Genomics 1997, 43(3):267-277. 10.1006/geno.1997.4829, 9268629.
25. Svingen T, Tonissen KF. Hox transcription factors and their elusive mammalian gene targets. Heredity 2006, 97(2):88-96. 10.1038/sj.hdy.6800847, 16721389.
26. Calvo R, West J, Franklin W, Erickson P, Bemis L, Li E, Helfrich B, Bunn P, Roche J, Brambilla E, et al. Altered HOX and WNT7A expression in human lung cancer. Proceedings of the National Academy of Sciences of the United States of America 2000, 97(23):12776-12781. 10.1073/pnas.97.23.12776, 18840, 11070089.
27. Cantile M, Pettinato G, Procino A, Feliciello I, Cindolo L, Cillo C. In vivo expression of the whole HOX gene network in human breast cancer. Eur J Cancer 2003, 39(2):257-264. 10.1016/S0959-8049(02)00599-3, 12509959.
28. Cillo C. HOX genes in human cancers. Invasion & metastasis 1994, 14(1-6):38-49.
29. Cillo C, Cantile M, Faiella A, Boncinelli E. Homeobox genes in normal and malignant cells. Journal of cellular physiology 2001, 188(2):161-169. 10.1002/jcp.1115, 11424082.
30. Houghton L, Rosenthal N. Regulation of a muscle-specific transgene by persistent expression of Hox genes in postnatal murine limb muscle. Dev Dyn 1999, 216(4-5):385-397. 10.1002/(SICI)1097-0177(199912)216:4/5<385::AID-DVDY7>3.0.CO;2-G, 10633858.
31. de Wit NJ, Bosch-Vermeulen H, de Groot PJ, Hooiveld GJ, Bromhaar MM, Jansen J, Muller M, Meer R. The role of the small intestine in the development of dietary fat-induced obesity and insulin resistance in C57BL/6J mice. BMC medical genomics 2008, 1:14. 10.1186/1755-8794-1-14, 2396659, 18457598.
32. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome biology 2004, 5(10):R80. 10.1186/gb-2004-5-10-r80, 545600, 15461798.
33. Dai M, Wang P, Boyd AD, Kostov G, Athey B, Jones EG, Bunney WE, Myers RM, Speed TP, Akil H, et al. Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res 2005, 33(20):e175. 10.1093/nar/gni179, 1283542, 16284200.
34. Wu Z, Irizarry R, Gentleman R, Martinez-Murillo F, Spencer F. A model-based background adjustment for oligonucleotide expression arrays. Journal of the American Statistical Association 2004, 99(468):909-917.
35. Smyth GK. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 2004, 3. Article3.
36. Xinmin L, Kim J, Zhou J, Gu W, Quigg R. Use of signal thresholds to determine significant changes in microarray data analyses. Genetics and Molecular Biology 2005, 28:191-200.
37. Storey JD, Tibshirani R. Statistical significance for genomewide studies. Proceedings of the National Academy of Sciences of the United States of America 2003, 100(16):9440-9445. 10.1073/pnas.1530509100, 170937, 12883005.
38. Lee HK, Braynen W, Keshav K, Pavlidis P. ErmineJ: tool for functional analysis of gene expression data sets. BMC Bioinformatics 2005, 6:269. 10.1186/1471-2105-6-269, 1310606, 16280084.
39. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences of the United States of America 2005, 102(43):15545-15550. 10.1073/pnas.0506580102, 1239896,1239896, 16199517.
40. Dahlquist KD, Salomonis N, Vranizan K, Lawlor SC, Conklin BR. GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nat Genet 2002, 31(1):19-20. 10.1038/ng0502-19, 11984561.
41. Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28(1):27-30. 10.1093/nar/28.1.27, 102409, 10592173.
42. Wang X, Seed B. A PCR primer bank for quantitative gene expression analysis. 2003, 31:e154. 291882, 14654707.
43. Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome biology 2002, 3(7):RESEARCH0034. 10.1186/gb-2002-3-7-research0034, 126239, 12184808.
44. Hellemans J, Mortier G, De Paepe A, Speleman F, Vandesompele J. qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data. Genome biology 2007, 8(2):R19. 10.1186/gb-2007-8-2-r19, 1852402, 17291332.