Temporal and functional profile of the transcriptional regulatory network in the early regenerative response to partial hepatectomy in the rat

BMC Genomics

Volumn 9, Issue , 2008, Pages

  Juskeviciute, Egle ^a   Vadigepalli, Rajanikanth ^a   Hoek, Jan B ^a  

^a THOMAS JEFFERSON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVATING TRANSCRIPTION FACTOR; CCAAT ENHANCER BINDING PROTEIN; CCAAT ENHANCER BINDING PROTEIN ALPHA; CCAAT ENHANCER BINDING PROTEIN BETA; CYCLIC AMP RESPONSIVE ELEMENT BINDING PROTEIN; HEPATOCYTE NUCLEAR FACTOR 1; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; LYMPHOID ENHANCER FACTOR 1; TRANSCRIPTION FACTOR AP 2; TRANSCRIPTION FACTOR GATA; TRANSCRIPTION FACTOR PAX6; TRANSCRIPTION FACTOR;

ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; BINDING SITE; CONTROLLED STUDY; DNA MICROARRAY; DOWN REGULATION; GENE CLUSTER; GENE EXPRESSION PROFILING; GENE FUNCTION; GENETIC ANALYSIS; LIVER REGENERATION; MALE; NONHUMAN; NUCLEOTIDE SEQUENCE; PARTIAL HEPATECTOMY; PROMOTER REGION; RAT; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION; UPREGULATION; ANIMAL; CELL CYCLE; CLUSTER ANALYSIS; CYTOLOGY; GENE REGULATORY NETWORK; GENETICS; LIVER; LIVER CELL; LIVER RESECTION; METABOLISM; PHYSIOLOGY; TIME;

ANIMALIA; RATTUS;

ANIMALS; CELL CYCLE; CLUSTER ANALYSIS; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; HEPATECTOMY; HEPATOCYTES; LIVER; LIVER REGENERATION; RATS; TIME FACTORS; TRANSCRIPTION FACTORS;

EID: 58149328652     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-9-527     Document Type: Article

References (59)

1. Fausto N Campbell JS Riehle KJ Liver regeneration Hepatology 2006, 43(2 Suppl 1):S45-53. 16447274
2. Taub R Liver regeneration: From myth to mechanism Nat Rev Mol Cell Biol 2004, 5:836-847. 15459664
3. Michalopoulos GK DeFrances MC Liver regeneration Science 1997, 276:60-66. 9082986
4. Michalopoulos GK Liver regeneration J Cell Physiol 2007, 213:286-300. 17559071
5. Crumm S Cofan M Juskeviciute E Hoek JB Adenine nucleotide changes changes in the remnant liver: An early signal for regeneration after partial hepatectomy Hepatology 2008, 48:898-908. 18697206
6. Fausto N Liver regeneration J Hepatol 2000, 32(1 Suppl):19-31. 10728791
7. Cressman DE Greenbaum LE DeAngelis RA Ciliberto G Furth EE Poli V Taub R Liver failure and defective hepatocyte regeneration in interleukin-6-deficient mice Science 1996, 274:1379-1383. 8910279
8. Yamada Y Kirillova I Peschon JJ Fausto N Initiation of liver growth by tumor necrosis factor: Deficient liver regeneration in mice lacking type I tumor necrosis factor receptor Proc Natl Acad Sci USA 1997, 94:1441-1446. 19810 9037072
9. Cressman DE Diamond RH Taub R Rapid activation of the Stat3 transcription complex in liver regeneration Hepatology 1995, 21:1443-1449. 7737651
10. FitzGerald MJ Webber EM Donovan JR Fausto N Rapid DNA binding by nuclear factor kappa B in hepatocytes at the start of liver regeneration Cell Growth Differ 1995, 6:417-427. 7794809
11. Greenbaum LE Li W Cressman DE Peng Y Ciliberto G Poli V Taub R CCAAT enhancer-binding protein beta is required for normal hepatocyte proliferation in mice after partial hepatectomy J Clin Invest 1998, 102:996-1007. 508965 9727068
12. Heim MH Gamboni G Beglinger C Gyr K Specific activation of AP-1 but not Stat3 in regenerating liver in mice Eur J Clin Invest 1997, 27:948-955. 9395792
13. Morello D Fitzgerald MJ Babinet C Fausto N c-myc, c-fos, and c-jun regulation in the regenerating livers of normal and H-2K/c-myc transgenic mice Mol Cell Biol 1990, 10:3185-3193. 360683 2111449
14. Thompson NL Mead JE Braun L Goyette M Shank PR Fausto N Sequential protooncogene expression during rat liver regeneration Cancer Res 1986, 46:3111-3117. 3516391
15. Haber BA Mohn KL Diamond RH Taub R Induction patterns of 70 genes during nine days after hepatectomy define the temporal course of liver regeneration J Clin Invest 1993, 91:1319-1326. 288102 8473485
16. Taub R Liver regeneration 4: Transcriptional control of liver regeneration FASEB J 1996, 10:413-427. 8647340
17. Arai M Yokosuka O Chiba T Imazeki F Kato M Hashida J Ueda Y Sugano S Hashimoto K Saisho H Takiguchi M Seki N Gene expression profiling reveals the mechanism and pathophysiology of mouse liver regeneration J Biol Chem 2003, 278:29813-29818. 12782638
18. Otu HH Naxerova K Ho K Can H Nesbitt N Libermann TA Karp SJ Restoration of liver mass after injury requires proliferative and not embryonic transcriptional patterns J Biol Chem 2007, 282:11197-11204. 17227769
19. Su AI Guidotti LG Pezacki JP Chisari FV Schultz PG Gene expression during the priming phase of liver regeneration after partial hepatectomy in mice Proc Natl Acad Sci USA 2002, 99:11181-11186. 123230 12177410
20. White P Brestelli JE Kaestner KH Greenbaum LE Identification of transcriptional networks during liver regeneration J Biol Chem 2005, 280:3715-3722. 15546871
21. Vadigepalli R Chakravarthula P Zak DE Schwaber JS Gonye GE PAINT: A promoter analysis and interaction network generation tool for gene regulatory network identification OMICS 2003, 7:235-252. 14583114
22. Gonye GE Chakravarthula P Schwaber JS Vadigepalli R From Promoter Analysis to Transcriptional Regulatory Network Prediction Using PAINT Methods in Molecular Biology, v408: Gene Function Analysis Totowa, NJ: Totowa: Humana Ochs M 2007:49-68.
23. Aubert J Bar-Hen A Daudin JJ Robin S Determination of the differentially expressed genes in microarray experiments using local FDR BMC Bioinformatics 2004, 5:125. 520755 15350197
24. Morey JS Ryan JC Van Dolah FM Microarray validation: Factors influencing correlation between oligonucleotide microarrays and real-time PCR Biol Proced Online 2006, 8:175-193. 1779618 17242735
25. Wurmbach E Yuen T Sealfon SC Focused microarray analysis Methods 2003, 31:306-316. 14597315
26. Ashburner M Ball CA Blake JA Botstein D Butler H Cherry JM Davis AP Dolinski K Dwight SS Eppig JT Harris MA Hill DP Issel-Tarver L Kasarskis A Lewis S Matese JC Richardson JE Ringwald M Rubin GM Sherlock G Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium Nat Genet 2000, 25:25-29. 10802651
27. Hosoya-Ohmura S Mochizuki N Suzuki M Ohneda O Ohneda K Yamamoto M GATA-4 incompletely substitutes for GATA-1 in promoting both primitive and definitive erythropoiesis in vivo J Biol Chem 2006, 281:32820-32830. 16945928
28. Leu JI Crissey MA Leu JP Ciliberto G Taub R Interleukin-6-induced STAT3 and AP-1 amplify hepatocyte nuclear factor 1-mediated transactivation of hepatic genes, an adaptive response to liver injury Mol Cell Biol 2001, 21:414-424. 86585 11134330
29. Plumpe J Malek NP Bock CT Rakemann T Manns MP Trautwein C NF-kappaB determines between apoptosis and proliferation in hepatocytes during liver regeneration Am J Physiol Gastrointest Liver Physiol 2000, 278:G173-83. 10644576
30. Servillo G Della Fazia MA Sassone-Corsi P Coupling cAMP signaling to transcription in the liver: Pivotal role of CREB and CREM Exp Cell Res 2002, 275:143-154. 11969286
31. Rodger J King CE Lukehurst S Chen PB Dunlop SA Beazley LD Ziman MR Changing Pax6 expression correlates with axon outgrowth and restoration of topography during optic nerve regeneration Neuroscience 2006, 142:1043-1054. 16973301
32. Sasaki T Suzuki H Yagi K Furuhashi M Yao R Susa S Noda T Arai Y Miyazono K Kato M Lymphoid enhancer factor 1 makes cells resistant to transforming growth factor beta-induced repression of c-myc Cancer Res 2003, 63:801-806. 12591729
33. Zhang J Hagopian-Donaldson S Serbedzija G Elsemore J Plehn-Dujowich D McMahon AP Flavell RA Williams T Neural tube, skeletal and body wall defects in mice lacking transcription factor AP-2 Nature 1996, 381:238-241. 8622766
34. Leite AR Correa-Giannella ML Dagli ML Fortes MA Vegas VM Giannella-Neto D Fibronectin and laminin induce expression of islet cell markers in hepatic oval cells in culture Cell Tissue Res 2007, 327:529-537. 17149594
35. Busson M Carazo A Seyer P Grandemange S Casas F Pessemesse L Rouault JP Wrutniak-Cabello C Cabello G Coactivation of nuclear receptors and myogenic factors induces the major BTG1 influence on muscle differentiation Oncogene 2005, 24:1698-1710. 15674337
36. Diehl AM Roles of CCAAT/enhancer-binding proteins in regulation of liver regenerative growth J Biol Chem 1998, 273:30843-30846. 9812973
37. Flodby P Antonson P Barlow C Blanck A Porsch-Hallstrom I Xanthopoulos KG Differential patterns of expression of three C/EBP isoforms, HNF-1, and HNF-4 after partial hepatectomy in rats Exp Cell Res 1993, 208:248-256. 8359219
38. Friedman JR Larris B Le PP Peiris TH Arsenlis A Schug J Tobias JW Kaestner KH Greenbaum LE Orthogonal analysis of C/EBPbeta targets in vivo during liver proliferation Proc Natl Acad Sci USA 2004, 101:12986-12991. 516505 15317935
39. Jiang MS Tang QQ McLenithan J Geiman D Shillinglaw W Henzel WJ Lane MD Derepression of the C/EBPalpha gene during adipogenesis: Identification of AP-2alpha as a repressor Proc Natl Acad Sci USA 1998, 95:3467-3471. 19859 9520389
40. Diehl AM Yang SQ Regenerative changes in C/EBP alpha and C/EBP beta expression modulate binding to the C/EBP site in the c-fos promoter Hepatology 1994, 19:447-456. 8294101
41. Rana B Xie Y Mischoulon D Bucher NL Farmer SR The DNA binding activity of C/EBP transcription factor is regulated in the G1 phase of the hepatocyte cell cycle J Biol Chem 1995, 270:18123-18132. 7629124
42. Lekstrom-Himes J Xanthopoulos KG Biological role of the CCAAT/ enhancer-binding protein family of transcription factors J Biol Chem 1998, 273:28545-28548. 9786841
43. Luedde T Duderstadt M Streetz KL Tacke F Kubicka S Manns MP Trautwein C C/EBP beta isoforms LIP and LAP modulate progression of the cell cycle in the regenerating mouse liver Hepatology 2004, 40:356-365. 15368440
44. Rudnick DA Perlmutter DH Muglia LJ Prostaglandins are required for CREB activation and cellular proliferation during liver regeneration Proc Natl Acad Sci USA 2001, 98:8885-8890. 37530 11447268
45. Diaz-Guerra MJ Velasco M Martin-Sanz P Bosca L Nuclear factor kappaB is required for the transcriptional control of type II NO synthase in regenerating liver Biochem J 1997, 326(Pt 3):791-797. 1218734 9307029
46. Li W Liang X Kellendonk C Poli V Taub R STAT3 contributes to the mitogenic response of hepatocytes during liver regeneration J Biol Chem 2002, 277(32):28411-28417. 12032149
47. Li W Liang X Leu JI Kovalovich K Ciliberto G Taub R Global changes in interleukin-6-dependent gene expression patterns in mouse livers after partial hepatectomy Hepatology 2001, 33:1377-1386. 11391526
48. Locker J Tian J Carver R Concas D Cossu C Ledda-Columbano GM Columbano A A common set of immediate-early response genes in liver regeneration and hyperplasia Hepatology 2003, 38:314-325. 12883475
49. Fukuhara Y Hirasawa A Li XK Kawasaki M Fujino M Funeshima N Katsuma S Shiojima S Yamada M Okuyama T Suzuki S Tsujimoto G Gene expression profile in the regenerating rat liver after partial hepatectomy J Hepatol 2003, 38:784-792. 12763372
50. Higgins GM Anderson RM Experimental pathology of the liver. Restoration of the liver of the white rat following partial surgical removal Arch Pathol 1931, 12:186-202.
51. Khan RL Gonye GE Gao G Schwaber JS A universal reference sample derived from clone vector for improved detection of differential gene expression BMC Genomics 2006, 7:109. 1475850 16677381
52. Yang YH Dudoit S Luu P Lin DM Peng V Ngai J Speed TP Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation Nucleic Acids Res 2002, 30:e15. 100354 11842121
53. Pavlidis P Using ANOVA for gene selection from microarray studies of the nervous system Methods 2003, 31:282-289. 14597312
54. Scholtens D Miron A Merchant FM Miller A Miron PL Iglehart JD Gentleman R Analyzing factorial designed microarray experiments J Multivariate Anal 2004, 90:19-43.
55. Benjamini Y Hochberg Y Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing J Royal Stat Soc B 1995, 57:289-300.
56. Kaufman L Rousseeuw PJ Finding Groups in Data. An Introduction to Cluster Analysis Wiley Series in Probability and Mathematical Statistics Anonymous New York: John Wiley and Sons 1990:68-122.
57. Keller MA Addya S Vadigepalli R Banini B Delgrosso K Huang H Surrey S Transcriptional regulatory network analysis of developing human erythroid progenitors reveals patterns of coregulation and potential transcriptional regulators Physiol Genomics 2006, 28:114-128. 16940433
58. Pearson RK Zylkin T Schwaber JS Gonye GE Analytical Evaluation of Clustering Results Using Computational Negative Controls Proc 4th Soc Indust Appl Math Int Conf Data Mining 188-199 2004.
59. Matys V Fricke E Geffers R Gossling E Haubrock M Hehl R Hornischer K Karas D Kel AE Kel-Margoulis OV Kloos DU Land S Lewicki-Potapov B Michael H Munch R Reuter I Rotert S Saxel H Scheer M Thiele S Wingender E TRANSFAC: Transcriptional regulation, from patterns to profiles Nucleic Acids Res 2003, 31:374-378. 165555 12520026