Genome-wide analysis of hepatic gene silencing in mammalian cell hybrids

Genomics

Volumn 96, Issue 6, 2010, Pages 323-332

  Bulla, Gary A ^a   Luong, Quang ^a   Shrestha, Sushma ^a   Reeb, Sarah ^a   Hickman, Sharon ^a  

^a EASTERN ILLINOIS UNIVERSITY   (United States)

Author keywords

Cell hybrids; Extinction; Hepatic; Hepatoma; Microarray

Indexed keywords

TRANSCRIPTION FACTOR;

ANIMAL CELL; ARTICLE; CANCER CELL CULTURE; CONTROLLED STUDY; FIBROBLAST; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; GENE REPRESSION; GENE SILENCING; GENOME ANALYSIS; HEPATOMA CELL; HYBRID CELL; MAMMAL CELL; MICROARRAY ANALYSIS; NONHUMAN; NUCLEAR REPROGRAMMING; PRIORITY JOURNAL; RAT; SIGNAL TRANSDUCTION; TISSUE SPECIFICITY;

ANIMALS; CELL LINE, TUMOR; EPIGENOMICS; FIBROBLASTS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE SILENCING; HYBRID CELLS; LIVER; NUCLEAR REPROGRAMMING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEINS; RATS; REPRODUCIBILITY OF RESULTS; SIGNAL TRANSDUCTION; TRANSCRIPTION FACTORS;

MAMMALIA;

EID: 78449240893     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2010.08.006     Document Type: Article

References (61)

1. Odom D.T., Zizlsperger N., Gordon D.B., Bell G.W., Rinaldi N.J., Murray H.L., Volkert T.L., Schreiber J., Rolfe P.A., Gifford D.K., Fraenkel E., Bell G.I., Young R.A. Control of pancreas and liver gene expression by HNF transcription factors. Science 2004, 303:1378-1381.
2. Cereghini S. Liver-enriched transcription factors and hepatocyte differentiation. FASEB J. 1996, 10:267-282.
3. Costa R.H., Kalinichenko V.V., Holterman A.X., Wang X. Transcription factors in liver development, differentiation and regeneration. Hepatology 2003, 38:1331-1347.
4. Duncan S.A., Navas M.A., Dufort D., Rossant J., Stoffel M. Regulation of a transcription factor network required for differentiation and metabolism. Science 1998, 281:692-695.
5. Lee C.S., Friedman J.R., Fulmer J.T., Kaestner K.H. The initiation of liver development is dependent on Foxa transcription factors. Nature 2005, 435:944-947.
6. Odom D.T., Dowell R.D., Jacobsen E.S., Nekludova L., Rolfe P.A., Danford T.W., Gifford D.K., Fraenkel E., Bell G.I., Young R.A. Core transcriptional regulatory circuitry in human hepatocytes. Mol. Syst. Biol. 2006, 2. 2006.0017. Electronic publication 2006 May 2.
7. Kuo C.J., Conley P.B., Chen L., Sladek F.M., Darnell J.E., Crabtree G.R. A transcriptional hierarchy involved in mammalian cell-type specification. Nature 1992, 355:457-461.
8. Bulla G.A. Hepatocyte nuclear factor-4 prevents silencing of hepatocyte nuclear factor-1 expression in hepatoma x fibroblast cell hybrids. Nucleic Acids Res. 1997, 25:2501-2508.
9. Friedman J.R., Larris B., Le P.P., Peiris T.H., Arsenlis A., Schug J., Tobias J.W., Kaestner K.H., Greenbaum L.E. Orthogonal analysis of C/EBPbeta targets in vivo during liver proliferation. Proc. Natl Acad. Sci. USA 2004, 101:12986-12991. Electronic publication 2004 Aug 18.
10. Deschatrette J., Weiss M.C. Extinction of liver-specific functions in hybrids between differentiated and dedifferentiated rat hepatoma cells. Somat. Cell Mol. Genet. 1975, 1:279-292.
11. Weiss M.C., Sparkes R.S., Bertolotti R. Expression of differentiated functions in hepatoma cell hybrids: IX extinction and reexpression of liver-specific enzymes in rat hepatoma-Chinese hamster fibroblast hybrids. Somat. Cell Genet. 1975, 1:27-40.
12. Chin A.C., Fournier R.E. A genetic analysis of extinction: trans-regulation of 16 liver-specific genes in hepatoma-fibroblast hybrid cells. Proc. Natl Acad. Sci. USA 1987, 84:1614-1618.
13. Chin A.C., Fournier R.E. Tse-2: a trans-dominant extinguisher of albumin gene expression in hepatoma hybrid cells. Mol. Cell. Biol. 1989, 9:3736-3743.
14. Ip Y.T., Fournier R.E., Chalkley R. Extinction of phosphoenolpyruvate carboxykinase gene expression is associated with loss of a specific chromatin-binding protein from a far upstream domain. Mol. Cell. Biol. 1990, 10:3782-3787.
15. Gourdeau H., Peterson T.C., Fournier R.E. Differential activity of a tissue-specific extinguisher locus in hepatic and nonhepatic cells. Mol. Cell. Biol. 1989, 9:1813-1822.
16. Junker S., Pedersen S., Schreiber E., Matthias P. Extinction of an immunoglobulin kappa promoter in cell hybrids is mediated by the octamer motif and correlates with suppression of Oct-2 expression. Cell 1990, 61:467-474.
17. Gourdeau H., Fournier R.E. Genetic analysis of mammalian cell differentiation. Annu. Rev. Cell Biol. 1990, 6:69-94.
18. Massa S., Junker S., Matthias P. Molecular mechanisms of extinction: old findings and new ideas. Int. J. Biochem. Cell Biol. 2000, 32:23-40.
19. Ben-Shushan E., Pikarsky E., Klar A., Bergman Y. Extinction of Oct-3/4 gene expression in embryonal carcinoma x fibroblast somatic cell hybrids is accompanied by changes in the methylation status, chromatin structure, and transcriptional activity of the Oct-3/4 upstream region. Mol. Cell. Biol. 1993, 13:891-901.
20. Weiss M.C. Molecular biology. Extinction by indirect means [news]. Nature 1992, 355:22-23.
21. Boshart M., Nitsch D., Schutz G. Extinction of gene expression in somatic cell hybrids-a reflection of important regulatory mechanisms?. Trends Genet. 1993, 9:240-245.
22. Ambrosi D.J., Rasmussen T.P. Reprogramming mediated by stem cell fusion. J. Cell. Mol. Med. 2005, 9:320-330.
23. McCormick A., Wu D., Castrillo J.-L., Dana S., Strobl J., Thompson E.B., Karin M. Extinction of growth hormone expression in somatic cell hybrids involves repression of the specific trans-activator GHF-1. Cell 1988, 55:379-389.
24. Junker S., Nielsen V., Matthias P., Picard D. Both immunoglobulin promoter and enhancer sequences are targets for suppression in myeloma-fibroblast hybrid cells. EMBO J. 1988, 7:3093-3098.
25. Bulla G.A., DeSimone V., Cortese R., Fournier R.E. Extinction of alpha 1-antitrypsin gene expression in somatic cell hybrids: evidence for multiple controls. Genes Dev. 1992, 6:316-327.
26. Zaller D.M., Yu H., Eckhardt L.A. Genes activated in the presence of an immunoglobulin enhancer or promoter are negatively regulated by a T-lymphoma cell line. Mol. Cell. Biol. 1988, 8:1932-1939.
27. Leshkowitz D., Walker M.D. Extinction of insulin gene expression in hybrids between β cells and fibroblasts is accompanied by loss of the putative β-cell-specific transcription factor IEF1. Mol. Cell. Biol. 1991, 11:1547-1552.
28. Boshart M., Weih F., Schmidt A., Fournier R.E., Schutz G. A cyclic AMP response element mediates repression of tyrosine aminotransferase gene transcription by the tissue-specific extinguisher locus Tse-1. Cell 1990, 61:905-916.
29. Yu H., Porton B., Shen L.Y., Eckhardt L.A. Role of the octamer motif in hybrid cell extinction of immunoglobulin gene expression: extinction is dominant in a two enhancer system. Cell 1989, 58:441-448.
30. Radomska H.S., Shen C.P., Kadesch T., Eckhardt L.A. Constitutively expressed Oct-2 prevents immunoglobulin gene silencing in myeloma x T cell hybrids. Immunity 1994, 1:623-634.
31. Kuo C.J., Conley P.B., Chen L., Sladek F.M., Darnell J.E., Crabtree G.R. A transcriptional hierarchy in mammalian cell-type specification. Nature 1992, 355:457-461.
32. Bulla G.A. Extinction of a1-antitrypsin expression in cell hybrids is independent of HNF1a and HNF4 and involves both promoter and internal DNA sequences. Nucleic Acids Res. 1999, 27:1190-1197.
33. Rollini P., Fournier R.E.K. The HNF4/HNF1a transactivation cascade regulates gene activity and chromatin structure of the human serine protease inhibitor cluster at 14q32.1. Proc. Natl Acad. Sci. USA 1999, 96:10308-10313.
34. Li Y., Shen R.F., Tsai S.Y., Woo S.L. Multiple hepatic trans-acting factors are required for in vitro transcription of the human alpha-1-antitrypsin gene. Mol. Cell. Biol. 1988, 8:4362-4369.
35. De Simone V., Ciliberto G., Hardon E., Paonessa G., Palla F., Lundberg L., Cortese R. Cis- and trans-acting elements responsible for the cell-specific expression of the human alpha 1-antitrypsin gene. EMBO J. 1987, 6:2759-2766.
36. Monaci P., Nicosia A., Cortese R. Two different liver-specific factors stimulate in vitro transcription from the human alpha 1-antitrypsin promoter. EMBO J. 1988, 7:2075-2087.
37. Shapero M.H., Langston A.A., Fournier R.E. Tissue-specific extinguisher loci in the human genome: a screening study based on random marking and transfer of human chromosomes. Somat. Cell Mol. Genet. 1994, 20:215-231.
38. Schafer A.J., Fournier R.E. Multiple elements regulate phosphoenolpyruvate carboxykinase gene expression in hepatoma hybrid cells. Somat. Cell Mol. Genet. 1992, 18:571-581.
39. Cerosaletti K., Fournier R.E.K. Extinction of albumin gene expression in a panel of human chromosome 2 microcell hybrids. Genomics 1996, 31:348-358.
40. Phuc Le P., Friedman J.R., Schug J., Brestelli J.E., Parker J.B., Bochkis I.M., Kaestner K.H. Glucocorticoid receptor-dependent gene regulatory networks. PLoS Genet. 2005, 1:e16. Electronic publication 2005 Aug 5.
41. Zhang X., Odom D.T., Koo S.H., Conkright M.D., Canettieri G., Best J., Chen H., Jenner R., Herbolsheimer E., Jacobsen E., Kadam S., Ecker J.R., Emerson B., Hogenesch J.B., Unterman T., Young R.A., Montminy M. Genome-wide analysis of cAMP-response element binding protein occupancy, phosphorylation, and target gene activation in human tissues. Proc. Natl Acad. Sci. USA 2005, 102:4459-4464. Electronic publication 2005 Mar 7.
42. Bulla G.A. Selective loss of the hepatic phenotype due to the absence of a transcriptional activation pathway. Somat. Cell Mol. Genet. 1997, 23:185-201.
43. Schafer A.J., Bulla G.A., Fournier R.E. Tissue-specific extinguisher loci in the murine genome: a screening study based on a rat/mouse microcell hybrid panel. Somat. Cell Mol. Genet. 1994, 20:195-213.
44. Pajukanta P., Lilja H.E., Sinsheimer J.S., Cantor R.M., Lusis A.J., Gentile M., Duan X.J., Soro-Paavonen A., Naukkarinen J., Saarela J., Laakso M., Ehnholm C., Taskinen M.R., Peltonen L. Familial combined hyperlipidemia is associated with upstream transcription factor 1 (USF1). Nat. Genet. 2004, 36:371-376.
45. Jones K.W., Shapero M.H., Chevrette M., Fournier R.E. Subtractive hybridization cloning of a tissue-specific extinguisher: TSE1 encodes a regulatory subunit of protein kinase A. Cell 1991, 66:861-872.
46. Killary A.M., Fournier R.E. A genetic analysis of extinction: trans-dominant loci regulate expression of liver-specific traits in hepatoma hybrid cells. Cell 1984, 38:523-534.
47. Thayer M.J., Fournier R.E. Hormonal regulation of TSE1-repressed genes: evidence for multiple genetic controls in extinction. Mol. Cell. Biol. 1989, 9:2837-2846.
48. Cereghini S., Yaniv M., Cortese R. Hepatocyte dedifferentiation and extinction is accompanied by a block in the synthesis of mRNA coding for the transcription factor HNF1/LFB1. EMBO J. 1990, 9:2257-2263.
49. Komiya Y., Habas R. Wnt signal transduction pathways. Organogenesis 2008, 4:68-75.
50. Thompson M.D., Monga S.P. WNT/beta-catenin signaling in liver health and disease. Hepatology 2007, 45:1298-1305.
51. Nejak-Bowen K., Monga S.P. Wnt/beta-catenin signaling in hepatic organogenesis. Organogenesis 2008, 4:92-99.
52. Ober E.A., Verkade H., Field H.A., Stainier D.Y. Mesodermal Wnt2b signalling positively regulates liver specification. Nature 2006, 442:688-691.
53. Thomas P.Q., Brown A., Beddington R.S. Hex: a homeobox gene revealing peri-implantation asymmetry in the mouse embryo and an early transient marker of endothelial cell precursors. Development 1998, 125:85-94.
54. Hallaq H., Pinter E., Enciso J., McGrath J., Zeiss C., Brueckner M., Madri J., Jacobs H.C., Wilson C.M., Vasavada H., Jiang X., Bogue C.W. A null mutation of Hhex results in abnormal cardiac development, defective vasculogenesis and elevated Vegfa levels. Development 2004, 131:5197-5209.
55. Martinez Barbera J.P., Clements M., Thomas P., Rodriguez T., Meloy D., Kioussis D., Beddington R.S. The homeobox gene Hex is required in definitive endodermal tissues for normal forebrain, liver and thyroid formation. Development 2000, 127:2433-2445.
56. Marfil V., Moya M., Pierreux C.E., Castell J.V., Lemaigre F.P., Real F.X., Bort R. Interaction between HHEX and SOX13 modulates WNT/TCF activity. J. Biol. Chem. 2009.
57. Hsieh J.C., Kodjabachian L., Rebbert M.L., Rattner A., Smallwood P.M., Samos C.H., Nusse R., Dawid I.B., Nathans J. A new secreted protein that binds to Wnt proteins and inhibits their activities. Nature 1999, 398:431-436.
58. Wissmann C., Wild P.J., Kaiser S., Roepcke S., Stoehr R., Woenckhaus M., Kristiansen G., Hsieh J.C., Hofstaedter F., Hartmann A., Knuechel R., Rosenthal A., Pilarsky C. WIF1, a component of the Wnt pathway, is down-regulated in prostate, breast, lung, and bladder cancer. J. Pathol. 2003, 201:204-212.
59. Hwa V., Oh Y., Rosenfeld R.G. The insulin-like growth factor-binding protein (IGFBP) superfamily. Endocr. Rev. 1999, 20:761-787.
60. Lahuna O., Rastegar M., Maiter D., Thissen J.P., Lemaigre F.P., Rousseau G.G. Involvement of STAT5 (signal transducer and activator of transcription 5) and HNF-4 (hepatocyte nuclear factor 4) in the transcriptional control of the hnf6 gene by growth hormone. Mol. Endocrinol. 2000, 14:285-294.
61. Terranova R., Pereira C.F., Du Roure C., Merkenschlager M., Fisher A.G. Acquisition and extinction of gene expression programs are separable events in heterokaryon reprogramming. J. Cell Sci. 2006, 119:2065-2072.