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. 1990 Jul;10(7):3334–3342. doi: 10.1128/mcb.10.7.3334

Chromatin structures of the rat tyrosine aminotransferase gene relate to the function of its cis-acting elements.

D Nitsch 1, A F Stewart 1, M Boshart 1, R Mestril 1, F Weih 1, G Schütz 1
PMCID: PMC360754  PMID: 1972541

Abstract

The relationship between DNase I-hypersensitive sites (HSs) and transcriptional enhancers of the rat tyrosine aminotransferase (TAT) gene was examined by comparing HSs in and around the TAT gene with the activity of the corresponding DNA sequences in transient transfection assays. In this manner, we identified two HSs as liver-specific enhancers. Of three hepatoma cell lines examined, only one sustained TAT mRNA levels comparable to those of liver. In this cell line, both enhancers were strongly active, and strong hypersensitivity in chromatin over the enhancers was evident. The other two hepatoma cell lines had reduced levels of TAT mRNA and no or altered hypersensitivity over either the enhancers or the promoter. One of these lines carried a negative regulator of the TAT gene, the tissue specific extinguisher Tse-1. This cell line exhibited all HSs characteristic of the strongly active gene except at the promoter; however, one enhancer was inactive even though hypersensitive in chromatin. In a TAT-nonexpressing cell line, inactivity of both enhancers correlated with absence of the respective HSs. We conclude that although hypersensitivity in chromatin necessarily accompanies cell-type-specific enhancer activity, the occurrence of cell-type-specific HSs does not imply that the underlying sequences harbor enhancers active in transient transfection assays.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Becker P. B., Ruppert S., Schütz G. Genomic footprinting reveals cell type-specific DNA binding of ubiquitous factors. Cell. 1987 Nov 6;51(3):435–443. doi: 10.1016/0092-8674(87)90639-8. [DOI] [PubMed] [Google Scholar]
  2. Becker P., Renkawitz R., Schütz G. Tissue-specific DNaseI hypersensitive sites in the 5'-flanking sequences of the tryptophan oxygenase and the tyrosine aminotransferase genes. EMBO J. 1984 Sep;3(9):2015–2020. doi: 10.1002/j.1460-2075.1984.tb02084.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Blom van Assendelft G., Hanscombe O., Grosveld F., Greaves D. R. The beta-globin dominant control region activates homologous and heterologous promoters in a tissue-specific manner. Cell. 1989 Mar 24;56(6):969–977. doi: 10.1016/0092-8674(89)90630-2. [DOI] [PubMed] [Google Scholar]
  4. Bradford M. M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem. 1976 May 7;72:248–254. doi: 10.1016/0003-2697(76)90527-3. [DOI] [PubMed] [Google Scholar]
  5. Cathala G., Savouret J. F., Mendez B., West B. L., Karin M., Martial J. A., Baxter J. D. A method for isolation of intact, translationally active ribonucleic acid. DNA. 1983;2(4):329–335. doi: 10.1089/dna.1983.2.329. [DOI] [PubMed] [Google Scholar]
  6. Costa R. H., Lai E., Darnell J. E., Jr Transcriptional control of the mouse prealbumin (transthyretin) gene: both promoter sequences and a distinct enhancer are cell specific. Mol Cell Biol. 1986 Dec;6(12):4697–4708. doi: 10.1128/mcb.6.12.4697. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Crabb D. W., Dixon J. E. A method for increasing the sensitivity of chloramphenicol acetyltransferase assays in extracts of transfected cultured cells. Anal Biochem. 1987 May 15;163(1):88–92. doi: 10.1016/0003-2697(87)90096-0. [DOI] [PubMed] [Google Scholar]
  8. 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 Sep;6(9):2759–2766. doi: 10.1002/j.1460-2075.1987.tb02570.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Dobner P. R., Kawasaki E. S., Yu L. Y., Bancroft F. C. Thyroid or glucocorticoid hormone induces pre-growth-hormone mRNA and its probable nuclear precursor in rat pituitary cells. Proc Natl Acad Sci U S A. 1981 Apr;78(4):2230–2234. doi: 10.1073/pnas.78.4.2230. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Elgin S. C. The formation and function of DNase I hypersensitive sites in the process of gene activation. J Biol Chem. 1988 Dec 25;263(36):19259–19262. [PubMed] [Google Scholar]
  11. Felgner P. L., Gadek T. R., Holm M., Roman R., Chan H. W., Wenz M., Northrop J. P., Ringold G. M., Danielsen M. Lipofection: a highly efficient, lipid-mediated DNA-transfection procedure. Proc Natl Acad Sci U S A. 1987 Nov;84(21):7413–7417. doi: 10.1073/pnas.84.21.7413. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Forrester W. C., Takegawa S., Papayannopoulou T., Stamatoyannopoulos G., Groudine M. Evidence for a locus activation region: the formation of developmentally stable hypersensitive sites in globin-expressing hybrids. Nucleic Acids Res. 1987 Dec 23;15(24):10159–10177. doi: 10.1093/nar/15.24.10159. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Fort P., Marty L., Piechaczyk M., el Sabrouty S., Dani C., Jeanteur P., Blanchard J. M. Various rat adult tissues express only one major mRNA species from the glyceraldehyde-3-phosphate-dehydrogenase multigenic family. Nucleic Acids Res. 1985 Mar 11;13(5):1431–1442. doi: 10.1093/nar/13.5.1431. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Fritton H. P., Igo-Kemenes T., Nowock J., Strech-Jurk U., Theisen M., Sippel A. E. DNase I-hypersensitive sites in the chromatin structure of the lysozyme gene in steroid hormone target and non-target cells. Biol Chem Hoppe Seyler. 1987 Feb;368(2):111–119. doi: 10.1515/bchm3.1987.368.1.111. [DOI] [PubMed] [Google Scholar]
  15. Godbout R., Ingram R. S., Tilghman S. M. Fine-structure mapping of the three mouse alpha-fetoprotein gene enhancers. Mol Cell Biol. 1988 Mar;8(3):1169–1178. doi: 10.1128/mcb.8.3.1169. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Godbout R., Ingram R., Tilghman S. M. Multiple regulatory elements in the intergenic region between the alpha-fetoprotein and albumin genes. Mol Cell Biol. 1986 Feb;6(2):477–487. doi: 10.1128/mcb.6.2.477. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Godbout R., Tilghman S. M. Configuration of the alpha-fetoprotein regulatory domain during development. Genes Dev. 1988 Aug;2(8):949–956. doi: 10.1101/gad.2.8.949. [DOI] [PubMed] [Google Scholar]
  18. Gorman C. M., Moffat L. F., Howard B. H. Recombinant genomes which express chloramphenicol acetyltransferase in mammalian cells. Mol Cell Biol. 1982 Sep;2(9):1044–1051. doi: 10.1128/mcb.2.9.1044. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Gorski K., Carneiro M., Schibler U. Tissue-specific in vitro transcription from the mouse albumin promoter. Cell. 1986 Dec 5;47(5):767–776. doi: 10.1016/0092-8674(86)90519-2. [DOI] [PubMed] [Google Scholar]
  20. Grange T., Roux J., Rigaud G., Pictet R. Two remote glucocorticoid responsive units interact cooperatively to promote glucocorticoid induction of rat tyrosine aminotransferase gene expression. Nucleic Acids Res. 1989 Nov 11;17(21):8695–8709. doi: 10.1093/nar/17.21.8695. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Granner D. K. Restoration of sensitivity of cultured hepatoma cells to cyclic nucleotides shows permissive effect of dexamethasone. Nature. 1976 Feb 19;259(5544):572–573. doi: 10.1038/259572a0. [DOI] [PubMed] [Google Scholar]
  22. Gross D. S., Garrard W. T. Nuclease hypersensitive sites in chromatin. Annu Rev Biochem. 1988;57:159–197. doi: 10.1146/annurev.bi.57.070188.001111. [DOI] [PubMed] [Google Scholar]
  23. Grosveld F., van Assendelft G. B., Greaves D. R., Kollias G. Position-independent, high-level expression of the human beta-globin gene in transgenic mice. Cell. 1987 Dec 24;51(6):975–985. doi: 10.1016/0092-8674(87)90584-8. [DOI] [PubMed] [Google Scholar]
  24. Hammer R. E., Krumlauf R., Camper S. A., Brinster R. L., Tilghman S. M. Diversity of alpha-fetoprotein gene expression in mice is generated by a combination of separate enhancer elements. Science. 1987 Jan 2;235(4784):53–58. doi: 10.1126/science.2432657. [DOI] [PubMed] [Google Scholar]
  25. Hashimoto S., Schmid W., Schütz G. Transcriptional activation of the rat liver tyrosine aminotransferase gene by cAMP. Proc Natl Acad Sci U S A. 1984 Nov;81(21):6637–6641. doi: 10.1073/pnas.81.21.6637. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Heard J. M., Herbomel P., Ott M. O., Mottura-Rollier A., Weiss M., Yaniv M. Determinants of rat albumin promoter tissue specificity analyzed by an improved transient expression system. Mol Cell Biol. 1987 Jul;7(7):2425–2434. doi: 10.1128/mcb.7.7.2425. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Jantzen H. M., Strähle U., Gloss B., Stewart F., Schmid W., Boshart M., Miksicek R., Schütz G. Cooperativity of glucocorticoid response elements located far upstream of the tyrosine aminotransferase gene. Cell. 1987 Apr 10;49(1):29–38. doi: 10.1016/0092-8674(87)90752-5. [DOI] [PubMed] [Google Scholar]
  28. 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 Sep;38(2):523–534. doi: 10.1016/0092-8674(84)90507-5. [DOI] [PubMed] [Google Scholar]
  29. Leach R. J., Thayer M. J., Schafer A. J., Fournier R. E. Physical mapping of human chromosome 17 using fragment-containing microcell hybrids. Genomics. 1989 Aug;5(2):167–176. doi: 10.1016/0888-7543(89)90043-8. [DOI] [PubMed] [Google Scholar]
  30. Lem J., Chin A. C., Thayer M. J., Leach R. J., Fournier R. E. Coordinate regulation of two genes encoding gluconeogenic enzymes by the trans-dominant locus Tse-1. Proc Natl Acad Sci U S A. 1988 Oct;85(19):7302–7306. doi: 10.1073/pnas.85.19.7302. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Melton D. A., Krieg P. A., Rebagliati M. R., Maniatis T., Zinn K., Green M. R. Efficient in vitro synthesis of biologically active RNA and RNA hybridization probes from plasmids containing a bacteriophage SP6 promoter. Nucleic Acids Res. 1984 Sep 25;12(18):7035–7056. doi: 10.1093/nar/12.18.7035. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Müller G., Ruppert S., Schmid E., Schütz G. Functional analysis of alternatively spliced tyrosinase gene transcripts. EMBO J. 1988 Sep;7(9):2723–2730. doi: 10.1002/j.1460-2075.1988.tb03126.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Oliviero S., Morrone G., Cortese R. The human haptoglobin gene: transcriptional regulation during development and acute phase induction. EMBO J. 1987 Jul;6(7):1905–1912. doi: 10.1002/j.1460-2075.1987.tb02450.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Ott M. O., Sperling L., Herbomel P., Yaniv M., Weiss M. C. Tissue-specific expression is conferred by a sequence from the 5' end of the rat albumin gene. EMBO J. 1984 Nov;3(11):2505–2510. doi: 10.1002/j.1460-2075.1984.tb02164.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Pinkert C. A., Ornitz D. M., Brinster R. L., Palmiter R. D. An albumin enhancer located 10 kb upstream functions along with its promoter to direct efficient, liver-specific expression in transgenic mice. Genes Dev. 1987 May;1(3):268–276. doi: 10.1101/gad.1.3.268. [DOI] [PubMed] [Google Scholar]
  36. Ruiz-Bravo N., Ernest M. J. Induction of tyrosine aminotransferase mRNA by glucocorticoids and cAMP in fetal rat liver. Proc Natl Acad Sci U S A. 1982 Jan;79(2):365–368. doi: 10.1073/pnas.79.2.365. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. SVOBODA J. Presence of chicken tumour virus in the sarcoma of the adult rat inoculated after birth with Rous sarcoma tissue. Nature. 1960 Jun 18;186:980–981. doi: 10.1038/186980b0. [DOI] [PubMed] [Google Scholar]
  38. Scherer G., Schmid W., Strange C. M., Röwekamp W., Schütz G. Isolation of cDNA clones coding for rat tyrosine aminotransferase. Proc Natl Acad Sci U S A. 1982 Dec;79(23):7205–7208. doi: 10.1073/pnas.79.23.7205. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Schmid E., Schmid W., Jantzen M., Mayer D., Jastorff B., Schütz G. Transcription activation of the tyrosine aminotransferase gene by glucocorticoids and cAMP in primary hepatocytes. Eur J Biochem. 1987 Jun 15;165(3):499–506. doi: 10.1111/j.1432-1033.1987.tb11467.x. [DOI] [PubMed] [Google Scholar]
  40. Schneider J. A., Weiss M. C. Expression of differentiated functions in hepatoma cell hybrids. I. Tyrosine aminotransferase in hepatoma-fibroblast hybrids. Proc Natl Acad Sci U S A. 1971 Jan;68(1):127–131. doi: 10.1073/pnas.68.1.127. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Shinomiya T., Scherer G., Schmid W., Zentgraf H., Schütz G. Isolation and characterization of the rat tyrosine aminotransferase gene. Proc Natl Acad Sci U S A. 1984 Mar;81(5):1346–1350. doi: 10.1073/pnas.81.5.1346. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Stewart A. F., Schütz G. Camptothecin-induced in vivo topoisomerase I cleavages in the transcriptionally active tyrosine aminotransferase gene. Cell. 1987 Sep 25;50(7):1109–1117. doi: 10.1016/0092-8674(87)90177-2. [DOI] [PubMed] [Google Scholar]
  43. Thompson E. B., Tomkins G. M., Curran J. F. Induction of tyrosine alpha-ketoglutarate transaminase by steroid hormones in a newly established tissue culture cell line. Proc Natl Acad Sci U S A. 1966 Jul;56(1):296–303. doi: 10.1073/pnas.56.1.296. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Tuan D., Solomon W., Li Q., London I. M. The "beta-like-globin" gene domain in human erythroid cells. Proc Natl Acad Sci U S A. 1985 Oct;82(19):6384–6388. doi: 10.1073/pnas.82.19.6384. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. de Wet J. R., Wood K. V., DeLuca M., Helinski D. R., Subramani S. Firefly luciferase gene: structure and expression in mammalian cells. Mol Cell Biol. 1987 Feb;7(2):725–737. doi: 10.1128/mcb.7.2.725. [DOI] [PMC free article] [PubMed] [Google Scholar]

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