Prediction of gene network models in limb muscle precursors

Gene

Volumn 509, Issue 1, 2012, Pages 16-23

  Campbell, Adam L ^a   Eng, Diana ^a   Gross, Michael K ^a   Kioussi, Chrissa ^a  

^a OREGON STATE UNIVERSITY   (United States)

Author keywords

Bioinformatics; Development; Gene Expression Analysis; Homeobox; Myoblast; Pitx2

Indexed keywords

HOMEODOMAIN PROTEIN; HOMEODOMAIN PROTEIN PITX2; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR LBX1; UNCLASSIFIED DRUG;

ANIMAL CELL; ARTICLE; BINDING SITE; CELL LINEAGE; CELL MIGRATION; CYTOSKELETON; EMBRYO; FORELIMB; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENE LOSS; GENE SEQUENCE; GENE TARGETING; GENETIC CONSERVATION; INTRON; MOUSE; MUSCLE DEVELOPMENT; MYOBLAST; MYOTOME; NONHUMAN; PRIORITY JOURNAL; SKELETAL MUSCLE;

ANIMALS; BINDING SITES; FORELIMB; GENE REGULATORY NETWORKS; HOMEODOMAIN PROTEINS; MICE; MICE, INBRED ICR; MICE, TRANSGENIC; MODELS, GENETIC; MUSCLE DEVELOPMENT; MUSCLE, SKELETAL; MYOBLASTS, SKELETAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; TRANSCRIPTION FACTORS;

EID: 84866158652     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2012.08.016     Document Type: Article

References (54)

1. Abmayr S.M., Balagopalan L., Galletta B.J., Hong S.J. Cell and molecular biology of myoblast fusion. Int. Rev. Cytol. 2003, 225:33-89.
2. Agarwala K.L., Ganesh S., Tsutsumi Y., Suzuki T., Amano K., Yamakawa K. Cloning and functional characterization of DSCAML1, a novel DSCAM-like cell adhesion molecule that mediates homophilic intercellular adhesion. Biochem. Biophys. Res. Commun. 2001, 285:760-772.
3. An C.I., Dong Y., Hagiwara N. Genome-wide mapping of Sox6 binding sites in skeletal muscle reveals both direct and indirect regulation of muscle terminal differentiation by Sox6. BMC Dev. Biol. 2011, 11:59.
4. Berry F.B., et al. Positive and negative regulation of myogenic differentiation of C2C12 cells by isoforms of the multiple homeodomain zinc finger transcription factor ATBF1. J. Biol. Chem. 2001, 276:25057-25065.
5. Bladt F., Riethmacher D., Isenmann S., Aguzzi A., Birchmeier C. Essential role for the c-met receptor in the migration of myogenic precursor cells into the limb bud. Nature 1995, 376:768-771.
6. Bober E., Franz T., Arnold H.H., Gruss P., Tremblay P. Pax-3 is required for the development of limb muscles: a possible role for the migration of dermomyotomal muscle progenitor cells. Development 1994, 120:603-612.
7. Campbell A.L., Shih H.-P., Xu J., Gross M.K., Kioussi C. Regulation of Motility of Myogenic Cells in Filling Limb Muscle Anlagen by Pitx2. PLoS One 2012, 7:e35822.
8. Cantor A.B., Orkin S.H. Coregulation of GATA factors by the Friend of GATA (FOG) family of multitype zinc finger proteins. Semin. Cell Dev. Biol. 2005, 16:117-128.
9. Capdevila J., Tsukui T., Rodriquez Esteban C., Zappavigna V., Izpisua Belmonte J.C. Control of vertebrate limb outgrowth by the proximal factor Meis2 and distal antagonism of BMPs by Gremlin. Mol. Cell 1999, 4:839-849.
10. Christ B., Brand-Saberi B. Limb muscle development. Int. J. Dev. Biol. 2002, 46:905-914.
11. Cunha S.R., et al. Defects in ankyrin-based membrane protein targeting pathways underlie atrial fibrillation. Circulation 2011, 124:1212-1222.
12. Dennis G., et al. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol. 2003, 4:P3.
13. Dietrich S., et al. The role of SF/HGF and c-Met in the development of skeletal muscle. Development 1999, 126:1621-1629.
14. Edgar R., Domrachev M., Lash A.E. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2002, 30:207-210.
15. Eng D., Campbell A., Hilton T., Leid M., Gross M.K., Kioussi C. Prediction of regulatory networks in mouse abdominal wall. Gene 2010, 469:1-8.
16. Fantauzzo K.A., Christiano A.M. Trps1 activates a network of secreted Wnt inhibitors and transcription factors crucial to vibrissa follicle morphogenesis. Development 2012, 139:203-214.
17. Fuerst P.G., et al. DSCAM and DSCAML1 function in self-avoidance in multiple cell types in the developing mouse retina. Neuron 2009, 64:484-497.
18. Gage P.J., Suh H., Camper S.A. Dosage requirement of Pitx2 for development of multiple organs. Development 1999, 126:4643-4651.
19. Gai Z., Gui T., Muragaki Y. The function of TRPS1 in the development and differentiation of bone, kidney, and hair follicles. Histol. Histopathol. 2011, 26:915-921.
20. Goulding M., Lumsden A., Paquette A.J. Regulation of Pax-3 expression in the dermomyotome and its role in muscle development. Development 1994, 120:957-971.
21. Gross M.K., Moran-Rivard L., Velasquez T., Nakatsu M.N., Jagla K., Goulding M. Lbx1 is required for muscle precursor migration along a lateral pathway into the limb. Development 2000, 127:413-424.
22. Hayashi K., Ozawa E. Myogenic cell migration from somites is induced by tissue contact with medial region of the presumptive limb mesoderm in chick embryos. Development 1995, 121:661-669.
23. Hilton T., Gross M.K., Kioussi C. Pitx2-dependent occupancy by histone deacetylases is associated with T-box gene regulation in mammalian abdominal tissue. J Biol Chem 2010, 285:11129-11142.
24. Hofmann F., Bernhard D., Lukowski R., Weinmeister P. cGMP regulated protein kinases (cGK). Handb. Exp. Pharmacol. 2009, 137-162.
25. Huang da W., Sherman B.T., Lempicki R.A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 2009, 4:44-57.
26. Jin L., Yoshida T., Ho R., Owens G.K., Somlyo A.V. The actin-associated protein Palladin is required for development of normal contractile properties of smooth muscle cells derived from embryoid bodies. J. Biol. Chem. 2009, 284:2121-2130.
27. Jin L., et al. The actin associated protein palladin is important for the early smooth muscle cell differentiation. PLoS One 2010, 5:e12823.
28. Kent W.J., et al. The human genome browser at UCSC. Genome Res. 2002, 12:996-1006.
29. Kioussi C., Gross M.K. How to build transcriptional network models of mammalian pattern formation. PLoS One 2008, 3:e2179.
30. Kioussi C., et al. Identification of a Wnt/Dvl/beta-Catenin->Pitx2 pathway mediating cell-type-specific proliferation during development. Cell 2002, 111:673-685.
31. Kitamura K., et al. Mouse Pitx2 deficiency leads to anomalies of the ventral body wall, heart, extra- and periocular mesoderm and right pulmonary isomerism. Development 1999, 126:5749-5758.
32. Kunath M., Ludecke H.J., Vortkamp A. Expression of Trps1 during mouse embryonic development. Gene Expr. Patterns 2002, 2:119-122.
33. Lin C.R., et al. Pitx2 regulates lung asymmetry, cardiac positioning and pituitary and tooth morphogenesis. Nature 1999, 401:279-282.
34. Lin P.T., Gleeson J.G., Corbo J.C., Flanagan L., Walsh C.A. DCAMKL1 encodes a protein kinase with homology to doublecortin that regulates microtubule polymerization. J. Neurosci. 2000, 20:9152-9161.
35. Liu E., Knutzen C.A., Krauss S., Schweiger S., Chiang G.G. Control of mTORC1 signaling by the Opitz syndrome protein MID1. Proc. Natl. Acad. Sci. U. S. A. 2011, 108:8680-8685.
36. Longabaugh W.J., Davidson E.H., Bolouri H. Computational representation of developmental genetic regulatory networks. Dev. Biol. 2005, 283:1-16.
37. Lu M.F., Pressman C., Dyer R., Johnson R.L., Martin J.F. Function of Rieger syndrome gene in left-right asymmetry and craniofacial development. Nature 1999, 401:276-278.
38. Mennerich D., Schafer K., Braun T. Pax-3 is necessary but not sufficient for lbx1 expression in myogenic precursor cells of the limb. Mech. Dev. 1998, 73:147-158.
39. Murai K., Vernon A.E., Philpott A., Jones P. Hes6 is required for MyoD induction during gastrulation. Dev. Biol. 2007, 312:61-76.
40. Salsi V., Vigano M.A., Cocchiarella F., Mantovani R., Zappavigna V. Hoxd13 binds in vivo and regulates the expression of genes acting in key pathways for early limb and skeletal patterning. Dev. Biol. 2008, 317:497-507.
41. Schafer K., Braun T. Early specification of limb muscle precursor cells by the homeobox gene Lbx1h. Nat. Genet. 1999, 23:213-216.
42. Shannon P., et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003, 13:2498-2504.
43. Shih H.P., Gross M.K., Kioussi C. Cranial muscle defects of Pitx2 mutants result from specification defects in the first branchial arch. Proc. Natl. Acad. Sci. U. S. A. 2007, 104:5907-5912.
44. Shih H.P., Gross M.K., Kioussi C. Expression pattern of the homeodomain transcription factor Pitx2 during muscle development. Gene Expr. Patterns 2007, 7:441-451.
45. Shih H.P., Gross M.K., Kioussi C. Muscle development: forming the head and trunk muscles. Acta Histochem. 2008, 110:97-108.
46. Shu W., Lu M.M., Zhang Y., Tucker P.W., Zhou D., Morrisey E.E. Foxp2 and Foxp1 cooperatively regulate lung and esophagus development. Development 2007, 134:1991-2000.
47. Sossey-Alaoui K., Srivastava A.K. DCAMKL1, a brain-specific transmembrane protein on 13q12.3 that is similar to doublecortin (DCX). Genomics 1999, 56:121-126.
48. Sureban S.M., et al. DCAMKL-1 regulates epithelial-mesenchymal transition in human pancreatic cells through a miR-200a-dependent mechanism. Cancer Res. 2011, 71:2328-2338.
49. Svensson E.C., et al. A syndrome of tricuspid atresia in mice with a targeted mutation of the gene encoding Fog-2. Nat. Genet. 2000, 25:353-356.
50. Tevosian S.G., et al. FOG-2, a cofactor for GATA transcription factors, is essential for heart morphogenesis and development of coronary vessels from epicardium. Cell 2000, 101:729-739.
51. Tremblay P., Dietrich S., Mericskay M., Schubert F.R., Li Z., Paulin D. A crucial role for Pax3 in the development of the hypaxial musculature and the long-range migration of muscle precursors. Dev. Biol. 1998, 203:49-61.
52. Tusher V.G., Tibshirani R., Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. U. S. A. 2001, 98:5116-5121.
53. Van Hateren N., Belsham A., Randall V., Borycki A.G. Expression of avian Groucho-related genes (Grgs) during embryonic development. Gene Expr. Patterns 2005, 5:817-823.
54. Waki H., et al. Global mapping of cell type-specific open chromatin by FAIRE-seq reveals the regulatory role of the NFI family in adipocyte differentiation. PLoS Genet. 2011, 7:e1002311.