A comprehensive search for HNF-3α-regulated genes in mouse hepatoma cells by 60K cDNA microarray and chromatin immunoprecipitation/PCR analysis

Biochemical and Biophysical Research Communications

Volumn 310, Issue 2, 2003, Pages 667-674

  Tomaru, Yasuhiro ^a,b   Kondo, Shinji ^a   Suzuki, Masanori ^a,c   Hayashizaki, Yoshihide ^a,b,c,d  

^a RIKEN YOKOHAMA INSTITUTE   (Japan)

^b UNIVERSITY OF TSUKUBA   (Japan)

^c YOKOHAMA CITY UNIVERSITY   (Japan)

^d Japan Science and Technology Agency   (Japan)

Author keywords

cDNA microarray; Chromatin immunoprecipitation; Cross linking; Gene expression perturbation; Hepatocyte nuclear factor 3 ; Transcription regulatory factor

Indexed keywords

ALBUMIN; ALPHA FETOPROTEIN; COMPLEMENTARY DNA; CYTIDINE DIPHOSPHATE DIACYLGLYCEROL INOSITOL 3 PHOSPHATIDYLTRANSFERASE; HEPATOCYTE NUCLEAR FACTOR 3; HEPATOCYTE NUCLEAR FACTOR 3ALPHA; PHOSPHATIDYLSERINE DECARBOXYLASE; PHOSPHOLIPASE A2; UNCLASSIFIED DRUG;

ANALYTIC METHOD; ANIMAL CELL; ARTICLE; BINDING AFFINITY; CHROMATIN; CLASSIFICATION; COMPARATIVE STUDY; CONSENSUS SEQUENCE; CONTROLLED STUDY; CROSS LINKING; DNA FLANKING REGION; DNA MICROARRAY; GENE CONTROL; GENE FUNCTION; GENE IDENTIFICATION; GENE LOCATION; GENE MAPPING; GENE OVEREXPRESSION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC CODE; GENETIC TRANSCRIPTION; GENOME ANALYSIS; GENOMICS; HEPATOMA CELL; IMMUNOPRECIPITATION; IN VIVO STUDY; LIPID METABOLISM; LIVER METABOLISM; MOLECULAR CLONING; MOUSE; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; REGULATORY MECHANISM; SEQUENCE ANALYSIS; TUMOR CELL LINE;

EID: 0141681892     PISSN: 0006291X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbrc.2003.08.148     Document Type: Article

References (34)

1. Futcher B. Microarrays and cell cycle transcription in yeast. Curr. Opin. Cell Biol. 12:2000;710-715.
2. Young R.A. Biomedical discovery with DNA arrays. Cell. 102:2000;9-15.
3. Devaux F., Marc P., Jacq C. Transcriptomes, transcription activators and microarrays. FEBS Lett. 498:2001;140-144.
4. Solomon M.J., Varshavsky A. Formaldehyde-mediated DNA-protein crosslinking: a probe for in vivo chromatin structures. Proc. Natl. Acad. Sci. USA. 82:1985;6470-6474.
5. Shang Y., Hu X., DiRenzo J., Lazar M.A., Brown M. Cofactor dynamics and sufficiency in estrogen receptor-regulated transcription. Cell. 103:2000;843-852.
6. Sharma D., Fondell J.D. Ordered recruitment of histone acetyltransferases and the TRAP/Mediator complex to thyroid hormone-responsive promoters in vivo. Proc. Natl. Acad. Sci. USA. 99:2002;7934-7939.
7. Hecht A., Grunstein M. Mapping DNA interaction sites of chromosomal proteins using immunoprecipitation and polymerase chain reaction. Methods Enzymol. 304:1999;399-414.
8. Orlando V. Mapping chromosomal proteins in vivo by formaldehyde-crosslinked-chromatin immunoprecipitation. Trends Biochem. Sci. 25:2000;99-104.
9. Lai E., Prezioso V.R., Smith E., Litvin O., Costa R.H., Darnell J.E. Jr. HNF-3A, a hepatocyte-enriched transcription factor of novel structure is regulated transcriptionally. Genes Dev. 4:1990;1427-1436.
10. Costa R.H., Grayson D.R., Darnell J.E. Jr. Multiple hepatocyte-enriched nuclear factors function in the regulation of transthyretin and alpha 1-antitrypsin genes. Mol. Cell. Biol. 9:1989;1415-1425.
11. Costa R.H., Grayson D.R. Site-directed mutagenesis of hepatocyte nuclear factor (HNF) binding sites in the mouse transthyretin (TTR) promoter reveal synergistic interactions with its enhancer region. Nucleic Acids Res. 19:1991;4139-4145.
12. Paulweber B., Sandhofer F., Levy-Wilson B. The mechanism by which the human apolipoprotein B gene reducer operates involves blocking of transcriptional activation by hepatocyte nuclear factor 3. Mol. Cell. Biol. 13:1993;1534-1546.
13. O'Brien R.M., Noisin E.L., Suwanichkul A., Yamasaki T., Lucas P.C., Wang J.C., Powell D.R., Granner D.K. Hepatic nuclear factor 3- and hormone-regulated expression of the phosphoenolpyruvate carboxykinase and insulin-like growth factor-binding protein 1 genes. Mol. Cell. Biol. 15:1995;1747-1758.
14. Hsiang C.H., Marten N.W., Straus D.S. Upstream region of rat serum albumin gene promoter contributes to promoter activity: presence of functional binding site for hepatocyte nuclear factor-3. Biochem. J. 338(Part 2):1999;241-249.
15. Ogden S.K., Lee K.C., Wernke-Dollries K., Stratton S.A., Aronow B., Barton M.C. p53 targets chromatin structure alteration to repress alpha-fetoprotein gene expression. J. Biol. Chem. 276:2001;42057-42062.
16. Terenzi H., Petropoulos I., Ellouze C., Takahashi M., Zakin M.M. Interaction of DNA binding domain of HNF-3 alpha with its transferrin enhancer DNA specific target site. FEBS Lett. 369:1995;277-282.
17. Yabuki T., Ejiri S., Tsutsumi K. Ubiquitous factors that interact simultaneously with two distinct cis-elements on the rat aldolase B gene promoter. Biochim. Biophys. Acta. 1216:1993;15-19.
18. Weinmann A.S., Yan P.S., Oberley M.J., Huang T.H., Farnham P.J. Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. Genes Dev. 16:2002;235-244.
19. Phillips J., Eberwine J.H. Antisense RNA amplification: a linear amplification method for analyzing the mRNA population from single living cells. Methods. 10:1996;283-288.
20. Bono H., Yagi K., Kasukawa T., Nikaido I., Tominaga N., Miki R., Mizuno Y., Tomaru Y., Goto H., Nitanda H., Shimizu D., Makino H., Morita T., Fujiyama J., Sakai T., Shimoji T., Hume D.A., Hayashizaki Y., Okazaki Y. Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays. Genome Res. 13:2003;1318-1323.
21. Miki R., Kadota K., Bono H., Mizuno Y., Tomaru Y., Carninci P., Itoh M., Shibata K., Kawai J., Konno H., Watanabe S., Sato K., Tokusumi Y., Kikuchi N., Ishii Y., Hamaguchi Y., Nishizuka I., Goto H., Nitanda H., Satomi S., Yoshiki A., Kusakabe M., DeRisi J.L., Eisen M.B., Iyer V.R., Brown P.O., Muramatsu M., Shimada H., Okazaki Y., Hayashizaki Y. Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays. Proc. Natl. Acad. Sci. USA. 98:2001;2199-2204.
22. Mizuno Y., Sotomaru Y., Katsuzawa Y., Kono T., Meguro M., Oshimura M., Kawai J., Tomaru Y., Kiyosawa H., Nikaido I., Amanuma H., Hayashizaki Y., Okazaki Y. Asb4, Ata3, and Dcn are novel imprinted genes identified by high-throughput screening using RIKEN cDNA microarray. Biochem. Biophys. Res. Commun. 290:2002;1499-1505.
23. Kadota K., Miki R., Bono H., Shimizu K., Okazaki Y., Hayashizaki Y. Preprocessing implementation for microarray (PRIM): an efficient method for processing cDNA microarray data. Physiol. Genomics. 4:2001;183-188.
24. Christova R., Oelgeschlager T. Association of human TFIID-promoter complexes with silenced mitotic chromatin in vivo. Nat. Cell Biol. 4:2002;79-82.
25. Ichikawa J.K., Norris A., Bangera M.G., Geiss G.K., 't Wout A.B., Bumgarner R.E., Lory S. Interaction of Pseudomonas aeruginosa with epithelial cells: identification of differentially regulated genes by expression microarray analysis of human cDNAs. Proc. Natl. Acad. Sci. USA. 97:2000;9659-9664.
26. FANTOM Consortium, Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs, Nature 420 (2002) 563-573.
27. RIKEN Genome Exploration Research Group Phase II Team and the FANTOM Consortium, Functional annotation of a full-length mouse cDNA collection, Nature 409 (2001) 685-690.
28. Hughes T.R., Marton M.J., Jones A.R., Roberts C.J., Stoughton R., Armour C.D., Bennett H.A., Coffey E., Dai H., He Y.D., Kidd M.J., King A.M., Meyer M.R., Slade D., Lum P.Y., Stepaniants S.B., Shoemaker D.D., Gachotte D., Chakraburtty K., Simon J., Bard M., Friend S.H. Functional discovery via a compendium of expression profiles. Cell. 102:2000;109-126.
29. Smoot L.M., Smoot J.C., Graham M.R., Somerville G.A., Sturdevant D.E., Migliaccio C.A., Sylva G.L., Musser J.M. Global differential gene expression in response to growth temperature alteration in group A Streptococcus. Proc. Natl. Acad. Sci. USA. 98:2001;10416-10421.
30. Thorburn A.W., Gumbiner B., Bulacan F., Brechtel G., Henry R.R. Multiple defects in muscle glycogen synthase activity contribute to reduced glycogen synthesis in non-insulin dependent diabetes mellitus. J. Clin. Invest. 87:1991;489-495.
31. Mamane Y., Heylbroeck C., Genin P., Algarte M., Servant M.J., LePage C., DeLuca C., Kwon H., Lin R., Hiscott J. Interferon regulatory factors: the next generation. Gene. 237:1999;1-14.
32. Magdaleno S.M., Wang G., Jackson K.J., Ray M.K., Welty S., Costa R.H., DeMayo F.J. Interferon-gamma regulation of Clara cell gene expression: in vivo and in vitro. Am. J. Physiol. 272:1997;L1142-L1151.
33. Duncan S.A., Navas M.A., Dufort D., Rossant J., Stoffel M. Regulation of a transcription factor network required for differentiation and metabolism. Science. 281:1998;692-695.
34. Shih D.Q., Bussen M., Sehayek E., Ananthanarayanan M., Shneider B.L., Suchy F.J., Shefer S., Bollileni J.S., Gonzalez F.J., Breslow J.L., Stoffel M. Hepatocyte nuclear factor-1alpha is an essential regulator of bile acid and plasma cholesterol metabolism. Nat. Genet. 27:2001;375-382.