Analysis of the distribution of binding sites for a tissue-specific transcription factor in the vertebrate genome

Journal of Molecular Biology

Volumn 266, Issue 2, 1997, Pages 231-245

  Tronche, François ^a   Ringeisen, François ^a   Blumenfeld, Marta ^b   Yaniv, Moshe ^a   Pontoglio, Marco ^a  

^a CNRS   (France)

^b Genset 1 ^*  (France)

Author keywords

DNA binding prediction; Genome analysis; HNF1; Promoter; Tissue specificity

Indexed keywords

NUCLEAR FACTOR I; TRANSCRIPTION FACTOR;

ANIMAL TISSUE; ARTICLE; BINDING SITE; CELL TYPE; COMPUTER ANALYSIS; CONTROLLED STUDY; DATA BASE; DNA SEQUENCE; EPITHELIUM CELL; GENE CLUSTER; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENOME; LIVER CELL; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN DNA BINDING; RAT; VERTEBRATE;

ANIMALIA; VERTEBRATA;

EID: 0031581855     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0760     Document Type: Article

References (34)

1. Arenzana N., Rodriguez d. C. S., Rey C. J. Expression of the human gene coding for the alpha-chain of C4b-binding protein, C4BPA, is controlled by an HNF1-dependent hepatic-specific promoter. Biochem. J. 308:1995;613-621.
2. Benson D. A., Boguski M., Lipman D. J., Ostell J. GenBank. Nucl. Acids Res. 22:1994;3441-3444.
3. Berg O. G., von Hippel P. Selection of DNA binding sites by regulatory proteins. II. The binding specificity of cyclic AMP receptor protein to recognition sites. J. Mol. Biol. 200:1988;709-723.
4. Bicknell E. J., Rada R., Davidson S., Stander R. Mapping from GenBank to MEDLINE. Nucl. Acids Res. 16:1988;1667-1680.
5. Blumenfeld M., Maury M., Chouard T., Yaniv M., Condamine H. Hepatic nuclear factor 1 (HNF1) shows a wider distribution than products of its known target genes in developing mouse. Development. 113:1991;589-599.
6. Bucher P. Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. J. Mol. Biol. 212:1990;563-578.
7. Cereghini S., Blumenfeld M., Yaniv M. A liver-specific factor essential for albumin transcription differs between differentiated and dedifferentiated rat hepatoma cells. Genes Dev. 2:1988;957-974.
8. Ceska T. A., Lamers M., Monaci P., Nicosia A., Cortese R., Suck D. The X-ray structure of an atypical homeodomain present in the rat liver transcription factor LFB1/HNF1 and implications for DNA binding. EMBO J. 12:1993;1805-1810.
9. Chouard T., Blumenfeld M., Bach I., Vandekerckhove J., Cereghini S., Yaniv M. A distal dimerization domain is essential for DNA-binding by the atypical HNF1 homeodomain. Nucl. Acids Res. 18:1990;5853-5863.
10. Claverie J. M., Sauvaget I. Assessing the biological significance of primary structure consensus patterns using sequence databanks. I. Heat-shock and glucocorticoid control elements in eukaryotic promoters. Comput. Appl. Biosci. 1:1985;95-104.
11. Costa R. H. Hepatocyte Nuclear Factor 3/ Forkhead protein family: mammalian transcription factors that possess divergent cellular expression patterns and binding specificities. Liver Gene Expression. 1994;R. G. Landes, Austin, TX.
12. Falvey E., Schibler U. How are the regulators regulated? FASEB J. 5:1991;309-314.
13. Frain M., Swart G., Monaci P., Nicosia A., Stampfli S., Frank R., Cortese R. The liver-specific transcription factor LF-B1 contains a highly diverged homeobox DNA binding domain. Cell. 59:1989;145-157.
14. Frech K., Herrmann G., Werner T. Computer-assisted prediction, classification, and delimitation of protein binding sites in nucleic acids. Nucl. Acids Res. 21:1993;1655-1664.
15. Ghosh D. TFD: the transcription factors database. Nucl. Acids Res. 20:1992;2091-2093.
16. Goomer R. S., Holst B. D., Wood I. C., Jones F. S., Edelman G. M. Regulation in vitro of an L-CAM enhancer by homeobox genes HoxD9 and HNF-1. Proc. Natl Acad. Sci. USA. 91:1994;7985-7989.
17. Hansen L. P., Crabtree G. R. Regulation of the HNF-1 homeodomain proteins by DCoH. Curr. Opin. Genet. Dev. 3:1993;246-253.
18. Johnson P. F., Williams S. C. CCAAT/enhancer binding (C/EBP) proteins. Tronche F., Yaniv M. Liver Gene Expression. 1994;R. G. Landes, Austin, TX.
19. Lavery D., Schibler U. DBP and related transcription factors of the PAR familly. Tronche F., Yaniv M. Liver Gene Expression. 1994;R. G. Landes, Austin, TX.
20. Lazzaro D., De S. V., De M. L., Lehtonen E., Cortese R. LFB1 and LFB3 homeoproteins are sequentially expressed during kidney development. Development. 114:1992;469-479.
21. Lichtsteiner S., Schibler U. A glycosylated liver-specific transcription factor stimulates transcription of the albumin gene. Cell. 57:1989;1179-1187.
22. Ott M. O., Rey C. J., Cereghini S., Yaniv M. vHNF1 is expressed in epithelial cells of distinct embryonic origin during development and precedes HNF1 expression. Mech. Dev. 36:1991;47-58.
23. Pollock R., Treisman R. A sensitive method for the determination of protein-DNA binding specificities. Nucl. Acids Res. 18:1990;6197-6204.
24. Rey-Campos J., Chouard T., Yaniv M., Cereghini S. vHNF1 is a homeoprotein that activates transcription and forms heterodimers with HNF1. EMBO J. 10:1991;1445-1457.
25. Rice C. M., Fuchs R., Higgins D. G., Stoehr P. J., Cameron G. N. The EMBL data library. Nucl. Acids Res. 21:1993;2967-2971.
26. Ringeisen F., Rey C. J., Yaniv M. The transactivation potential of variant hepatocyte nuclear factor 1 is modified by alternative splicing. J. Biol. Chem. 268:1993;25706-25711.
27. Ryffel G. U., Kugler W., Wagner U., Kaling M. Liver cell specific gene transcription in vitro: the promoter elements HP1 and TATA box are necessary and sufficient to generate a liver-specific promoter. Nucl. Acids Res. 17:1989;939-953.
28. Sladek F. M. Orphan receptor HNF-4 and liver-specific gene expression. Receptor. 4:1994;223-232.
29. Thiesen H. J., Bach C. Target detection assay (TDA): a versatile procedure to determine DNA binding sites as demonstrated on SP1 protein. Nucl. Acids Res. 18:1990;3203-3209.
30. Tronche F., Bach I., Chouard I., David-Wattine B., Pontoglio M., Ringeisen F., Sourdive D., Thepot D., Yaniv M. Hepatocyte nuclear factor 1 (HNF1) and liver gene expression. Tronche F., Yaniv M. Liver Gene Expression. 1994;R. G. Landes, Austin, TX.
31. Venijzer C. P., Alkema M. J., van Weperen W., van Leeuwen H., Strating M. J., van der Vliet P. The DNA binding specificity of the bipartite POU domain and its subdomains. EMBO J. 11:1992;4993-5003.
32. Wade D. P., Lindahl G. E., Lawn R. M. Apolipoprotein(a) gene transcription is regulated by liver-enriched trans-acting factor hepatocyte nuclear factor 1 alpha. J. Biol. Chem. 269:1994;19757-19765.
33. Wong J. M., Bateman E. TBP-DNA interactions in the minor groove discriminate between A:T and T:A base pairs. Nucl. Acids Res. 22:1994;1890-1896.
34. Wu G. D., Chen L., Forslund K., Traber P. G. Hepatocyte nuclear factor-1 alpha (HNF-1 alpha) and HNF-1 beta regulate transcription via two elements in an intestine-specific promoter. J. Biol. Chem. 269:1994;17080-17085.