Network based transcription factor analysis of regenerating axolotl limbs

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Jhamb, Deepali ^a   Rao, Nandini ^a,d   Milner, Derek J ^b   Song, Fengyu ^a,c   Cameron, Jo Ann ^a,b   Stocum, David L ^a   Palakal, Mathew J ^a  

^a INDIANA UNIVERSITY   (United States)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^c INDIANA UNIVERSITY SCHOOL OF DENTISTRY   (United States)

^d AMERICAN UNIVERSITY OF ANTIGUA   (Antigua and Barbuda)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL PROCESS; CONNECTED FACTOR; EXPERIMENTAL METHODS; MOLECULAR ENTITIES; MOLECULAR EVENTS; PROTEIN INTERACTION; RESEARCH TEAMS; SYSTEMS BIOLOGY;

ACTIVATION ANALYSIS; GENES; MOLECULAR BIOLOGY; STEM CELLS; TRANSCRIPTION FACTORS;

COMPLEX NETWORKS;

AMBYSTOMA; AMBYSTOMA MEXICANUM; AMPHIBIA;

COMPLEMENTARY DNA; TRANSCRIPTION FACTOR; TRANSFORMING GROWTH FACTOR BETA1;

AMBYSTOMA MEXICANUM; ANIMAL; ARTICLE; GENE EXPRESSION REGULATION; GENETICS; HUMAN; LIMB; PHYSIOLOGY; PROTEOMICS; REGENERATION;

AMBYSTOMA MEXICANUM; ANIMALS; DNA, COMPLEMENTARY; EXTREMITIES; GENE EXPRESSION REGULATION, DEVELOPMENTAL; HUMANS; PROTEOMICS; REGENERATION; TRANSCRIPTION FACTORS; TRANSFORMING GROWTH FACTOR BETA1;

EID: 79952694348     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-80     Document Type: Article

References (63)

1. Stocum DL, Zupanc GK. Stretching the limits: stem cells in regeneration science. Dev Dyn 2008, 237(12):3648-3671. 10.1002/dvdy.21774, 18985720.
2. Stocum DL. Regenerative Biology and Medicine. 2006, Elsevier Inc..
3. Spallanzani L. Concepts of generation and regeneration. A History of Regeneration Research 1991, Dinsmore CE.
4. Bryant SV, Endo T, Gardiner DM. Vertebrate limb regeneration and the origin of limb stem cells. Int J Dev Biol 2002, 46(7):887-896.
5. Nye HL, Cameron JA, Chernoff EA, Stocum DL. Regeneration of the urodele limb: a review. Dev Dyn 2003, 226(2):280-294. 10.1002/dvdy.10236, 12557206.
6. Morrison JI, Loof S, He P, Simon A. Salamander limb regeneration involves the activation of a multipotent skeletal muscle satellite cell population. J Cell Biol 2006, 172(3):433-440. 10.1083/jcb.200509011, 2063652, 16449193.
7. Carlson BM. Principles of Regenerative Biology. 2007, Academic Press.
8. Sauer U, Heinemann M, Zamboni N. Genetics. Getting closer to the whole picture. Science 2007, 316(5824):550-551. 10.1126/science.1142502, 17463274.
9. Putta S, Smith JJ, Walker JA, Rondet M, Weisrock DW, Monaghan J, Samuels AK, Kump K, King DC, Maness NJ, et al. From biomedicine to natural history research: EST resources for ambystomatid salamanders. BMC Genomics 2004, 5(1):54. 10.1186/1471-2164-5-54, 509418, 15310388.
10. Monaghan JR, Epp LG, Putta S, Page RB, Walker JA, Beachy CK, Zhu W, Pao GM, Verma IM, Hunter T, et al. Microarray and cDNA sequence analysis of transcription during nerve-dependent limb regeneration. BMC Biol 2009, 7:1. 10.1186/1741-7007-7-1, 2630914, 19144100.
11. Stocum DL, Rao N. Mechanisms of Blastema Formation in Regenerating Amphibian Limbs. Principles of Regenerative Medicine Elsevier/Academic Press San Diego, Lanza R, Thompson J, Nerem R, .
12. King MW, Nguyen T, Calley J, Harty MW, Muzinich MC, Mescher AL, Chalfant C, N'Cho M, McLeaster K, McEntire J, et al. Identification of genes expressed during Xenopus laevis limb regeneration by using subtractive hybridization. Dev Dyn 2003, 226(2):398-409. 10.1002/dvdy.10250, 12557218.
13. Grow M, Neff AW, Mescher AL, King MW. Global analysis of gene expression in Xenopus hindlimbs during stage-dependent complete and incomplete regeneration. Dev Dyn 2006, 235(10):2667-2685. 10.1002/dvdy.20897, 16871633.
14. King MW, Neff AW, Mescher AL. Proteomics analysis of regenerating amphibian limbs: changes during the onset of regeneration. Int J Dev Biol 2009, 53(7):955-969. 10.1387/ijdb.082719mk, 19598114.
15. Rao N, Jhamb D, Milner DJ, Li B, Song F, Wang M, Voss SR, Palakal M, King MW, Saranjami B, et al. Proteomic analysis of blastema formation in regenerating axolotl limbs. BMC Biol 2009, 7:83. 10.1186/1741-7007-7-83, 2794268, 19948009.
16. Takahashi K, Yamanaka S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 2006, 126(4):663-676. 10.1016/j.cell.2006.07.024, 16904174.
17. Yu J, Vodyanik MA, Smuga-Otto K, Antosiewicz-Bourget J, Frane JL, Tian S, Nie J, Jonsdottir GA, Ruotti V, Stewart R, et al. Induced pluripotent stem cell lines derived from human somatic cells. Science 2007, 318(5858):1917-1920. 10.1126/science.1151526, 18029452.
18. Maki N, Suetsugu-Maki R, Tarui H, Agata K, Del Rio-Tsonis K, Tsonis PA. Expression of stem cell pluripotency factors during regeneration in newts. Dev Dyn 2009, 238(6):1613-1616. 10.1002/dvdy.21959, 2749736, 19384853.
19. BLAST. , http://blast.ncbi.nlm.nih.gov/Blast.cgi
20. UniProt. , http://www.uniprot.org/
21. Dennis G, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 2003, 4(5):P3. 10.1186/gb-2003-4-5-p3, 12734009.
22. Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009, 4(1):44-57. 10.1038/nprot.2008.211, 19131956.
23. Ekins S, Nikolsky Y, Bugrim A, Kirillov E, Nikolskaya T. Pathway mapping tools for analysis of high content data. Methods Mol Biol 2007, 356:319-350.
24. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13(11):2498-2504. 10.1101/gr.1239303, 403769, 14597658.
25. Killcoyne S, Carter GW, Smith J, Boyle J. Cytoscape: a community-based framework for network modeling. Methods Mol Biol 2009, 563:219-239. full_text, 19597788.
26. Feng X, Liu X, Luo Q, Liu BF. Mass spectrometry in systems biology: an overview. Mass Spectrom Rev 2008, 27(6):635-660. 10.1002/mas.20182, 18636545.
27. Prakash A, Mallick P, Whiteaker J, Zhang H, Paulovich A, Flory M, Lee H, Aebersold R, Schwikowski B. Signal maps for mass spectrometry-based comparative proteomics. Mol Cell Proteomics 2006, 5(3):423-432.
28. Yang EV, Gardiner DM, Carlson MR, Nugas CA, Bryant SV. Expression of Mmp-9 and related matrix metalloproteinase genes during axolotl limb regeneration. Dev Dyn 1999, 216(1):2-9. 10.1002/(SICI)1097-0177(199909)216:1<2::AID-DVDY2>3.0.CO;2-P, 10474160.
29. Park IS, Kim WS. Modulation of gelatinase activity correlates with the dedifferentiation profile of regenerating salamander limbs. Mol Cells 1999, 9(2):119-126.
30. Pardali K, Kurisaki A, Moren A, ten Dijke P, Kardassis D, Moustakas A. Role of Smad proteins and transcription factor Sp1 in p21(Waf1/Cip1) regulation by transforming growth factor-beta. J Biol Chem 2000, 275(38):29244-29256. 10.1074/jbc.M909467199, 10878024.
31. Bachman KE, Park BH. Duel nature of TGF-beta signaling: tumor suppressor vs. tumor promoter. Curr Opin Oncol 2005, 17(1):49-54. 10.1097/01.cco.0000143682.45316.ae, 15608513.
32. Shi Y, Massague J. Mechanisms of TGF-beta signaling from cell membrane to the nucleus. Cell 2003, 113(6):685-700. 10.1016/S0092-8674(03)00432-X, 12809600.
33. Knoepfler PS. Why myc? An unexpected ingredient in the stem cell cocktail. Cell Stem Cell 2008, 2(1):18-21. 10.1016/j.stem.2007.12.004, 18371417.
34. Eilers M, Eisenman RN. Myc's broad reach. Genes Dev 2008, 22(20):2755-2766. 10.1101/gad.1712408, 2751281, 18923074.
35. Hourdry J, Geraudie J, Singer M, Mechali M. Expression of the c-Myc proto-oncogene in the ofrelimb regenerate of the newt Notophthalmus Viridescens, visualized by in situ hybridization. M Singer Symposium 1988, 307-313.
36. Geraudie J, Hourdry J, Boehm K, Singer M, Mechali M. c-Myc proto-oncogene expression during newt limb regeneration. Recent Trends in Regeneration Research 1989, 172:27-36. New York: Plenum Press, Kiortsis V, Koussoulallos S, Wallace H.
37. Stojadinovic O, Brem H, Vouthounis C, Lee B, Fallon J, Stallcup M, Merchant A, Galiano RD, Tomic-Canic M. Molecular pathogenesis of chronic wounds: the role of beta-catenin and c-myc in the inhibition of epithelialization and wound healing. Am J Pathol 2005, 167(1):59-69. 10.1016/S0002-9440(10)62953-7, 1603435, 15972952.
38. Wierstra I. Sp1: emerging roles--beyond constitutive activation of TATA-less housekeeping genes. Biochem Biophys Res Commun 2008, 372(1):1-13. 10.1016/j.bbrc.2008.03.074, 18364237.
39. Tan NY, Khachigian LM. Sp1 phosphorylation and its regulation of gene transcription. Mol Cell Biol 2009, 29(10):2483-2488. 10.1128/MCB.01828-08, 2682032, 19273606.
40. Safe S, Abdelrahim M. Sp transcription factor family and its role in cancer. Eur J Cancer 2005, 41(16):2438-2448. 10.1016/j.ejca.2005.08.006, 16209919.
41. Simon HG, Tabin CJ. Analysis of Hox-4.5 and Hox-3.6 expression during newt limb regeneration: differential regulation of paralogous Hox genes suggest different roles for members of different Hox clusters. Development 1993, 117(4):1397-1407.
42. Savard P, Gates PB, Brockes JP. Position dependent expression of a homeobox gene transcript in relation to amphibian limb regeneration. EMBO J 1988, 7(13):4275-4282. 455141, 2907476.
43. Gardiner DM, Blumberg B, Komine Y, Bryant SV. Regulation of HoxA expression in developing and regenerating axolotl limbs. Development 1995, 121(6):1731-1741.
44. Brown R, Brockes JP. Identification and expression of a regeneration-specific homeobox gene in the newt limb blastema. Development 1991, 111(2):489-496.
45. Beauchemin M, Noiseux N, Tremblay M, Savard P. Expression of Hox A11 in the limb and the regeneration blastema of adult newt. Int J Dev Biol 1994, 38(4):641-649.
46. Mercader N, Tanaka EM, Torres M. Proximodistal identity during vertebrate limb regeneration is regulated by Meis homeodomain proteins. Development 2005, 132(18):4131-4142. 10.1242/dev.01976, 16107473.
47. Cadinouche MZ, Liversage RA, Muller W, Tsilfidis C. Molecular cloning of the Notophthalmus viridescens radical fringe cDNA and characterization of its expression during forelimb development and adult forelimb regeneration. Dev Dyn 1999, 214(3):259-268. 10.1002/(SICI)1097-0177(199903)214:3<259::AID-AJA9>3.0.CO;2-G, 10090152.
48. Crews L, Gates PB, Brown R, Joliot A, Foley C, Brockes JP, Gann AA. Expression and activity of the newt Msx-1 gene in relation to limb regeneration. Proc Biol Sci 1995, 259(1355):161-171. 10.1098/rspb.1995.0024, 7732036.
49. Shimizu-Nishikawa K, Tsuji S, Yoshizato K. Identification and characterization of newt rad (ras associated with diabetes), a gene specifically expressed in regenerating limb muscle. Dev Dyn 2001, 220(1):74-86. 10.1002/1097-0177(20010101)220:1<74::AID-DVDY1090>3.0.CO;2-Q, 11146509.
50. Koshiba K, Kuroiwa A, Yamamoto H, Tamura K, Ide H. Expression of Msx genes in regenerating and developing limbs of axolotl. J Exp Zool 1998, 282(6):703-714. 10.1002/(SICI)1097-010X(19981215)282:6<703::AID-JEZ6>3.0.CO;2-P, 9846382.
51. Schnapp E, Tanaka EM. Quantitative evaluation of morpholino-mediated protein knockdown of GFP, MSX1, and PAX7 during tail regeneration in Ambystoma mexicanum. Dev Dyn 2005, 232(1):162-170. 10.1002/dvdy.20203, 15580632.
52. Levesque M, Gatien S, Finnson K, Desmeules S, Villiard E, Pilote M, Philip A, Roy S. Transforming growth factor: beta signaling is essential for limb regeneration in axolotls. PLoS One 2007, 2(11):e1227. 10.1371/journal.pone.0001227, 2082079, 18043735.
53. Ho DM, Whitman M. TGF-beta signaling is required for multiple processes during Xenopus tail regeneration. Dev Biol 2008, 315(1):203-216. 10.1016/j.ydbio.2007.12.031, 2292344, 18234181.
54. Christensen RN, Tassava RA. Apical epithelial cap morphology and fibronectin gene expression in regenerating axolotl limbs. Dev Dyn 2000, 217(2):216-224. 10.1002/(SICI)1097-0177(200002)217:2<216::AID-DVDY8>3.0.CO;2-8, 10706145.
55. Nace JD, Tassava RA. Examination of fibronectin distribution and its sources in the regenerating newt limb by immunocytochemistry and in situ hybridization. Dev Dyn 1995, 202(2):153-164. 10.1002/aja.1002020207, 7734733.
56. Thornton CS. Influence of an eccentric epidermal cap on limb regeneration in Amblystoma larvae. Dev Biol 1960, 2:551-569. 10.1016/0012-1606(60)90054-3, 13776717.
57. Thornton CS, Thronton MT. The regeneration of accessory limb parts following epidermal cap transplantation in urodeles. Experientia 1965, 21(3):146-148. 10.1007/BF02141984, 5318741.
58. Cho HJ, Baek KE, Saika S, Jeong MJ, Yoo J. Snail is required for transforming growth factor-beta-induced epithelial-mesenchymal transition by activating PI3 kinase/Akt signal pathway. Biochem Biophys Res Commun 2007, 353(2):337-343. 10.1016/j.bbrc.2006.12.035, 17187756.
59. Zavadil J, Bottinger EP. TGF-beta and epithelial-to-mesenchymal transitions. Oncogene 2005, 24(37):5764-5774. 10.1038/sj.onc.1208927, 16123809.
60. Frederick JP, Liberati NT, Waddell DS, Shi Y, Wang XF. Transforming growth factor beta-mediated transcriptional repression of c-myc is dependent on direct binding of Smad3 to a novel repressive Smad binding element. Mol Cell Biol 2004, 24(6):2546-2559. 10.1128/MCB.24.6.2546-2559.2004, 355825, 14993291.
61. Kawakami Y, Rodriguez Esteban C, Raya M, Kawakami H, Marti M, Dubova I, Izpisua Belmonte JC. Wnt/beta-catenin signaling regulates vertebrate limb regeneration. Genes Dev 2006, 20(23):3232-3237. 10.1101/gad.1475106, 1686599, 17114576.
62. Ling L, Nurcombe V, Cool SM. Wnt signaling controls the fate of mesenchymal stem cells. Gene 2009, 433(1-2):1-7. 10.1016/j.gene.2008.12.008, 19135507.
63. Ng JK, Kawakami Y, Buscher D, Raya A, Itoh T, Koth CM, Rodriguez Esteban C, Rodriguez-Leon J, Garrity DM, Fishman MC, et al. The limb identity gene Tbx5 promotes limb initiation by interacting with Wnt2b and Fgf10. Development 2002, 129(22):5161-5170.