Abstract
Recent advances in the understanding of eukaryotic gene regulation have produced an extensive body of transcriptionally-related sequence information in the biological literature, and have created a need for computing structures that organize and manage this information. The 'relational model' represents an approach that is finding increasing application in the design of biological databases. This report describes the compilation of information regarding eukaryotic transcription factors, the organization of this information into five tables, the computational applications of the resultant relational database that are of theoretical as well as experimental interest, and possible avenues of further development.
Full text
PDF![1749](https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c578/330592/e967630394ee/nar00191-0074.png)
![1750](https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c578/330592/17aba5c5a0ac/nar00191-0075.png)
![1751](https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c578/330592/41cd08b2dc6a/nar00191-0076.png)
![1752](https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c578/330592/ad013872018f/nar00191-0077.png)
![1753](https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c578/330592/f1fb75d48994/nar00191-0078.png)
![1754](https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c578/330592/17ee85ce2dfe/nar00191-0079.png)
![1755](https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c578/330592/9d38b4d789d4/nar00191-0080.png)
![1756](https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c578/330592/45bae9f90eb4/nar00191-0081.png)
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Beato M. Gene regulation by steroid hormones. Cell. 1989 Feb 10;56(3):335–344. doi: 10.1016/0092-8674(89)90237-7. [DOI] [PubMed] [Google Scholar]
- Ben-Hattar J., Beard P., Jiricny J. Cytosine methylation in CTF and Sp1 recognition sites of an HSV tk promoter: effects on transcription in vivo and on factor binding in vitro. Nucleic Acids Res. 1989 Dec 25;17(24):10179–10190. doi: 10.1093/nar/17.24.10179. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bicknell E. J., Rada R., Davidson S., Stander R. Mapping from GenBank to MEDLINE. Nucleic Acids Res. 1988 Mar 11;16(5):1667–1680. doi: 10.1093/nar/16.5.1667. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Blundell T. L., Sibanda B. L., Sternberg M. J., Thornton J. M. Knowledge-based prediction of protein structures and the design of novel molecules. 1987 Mar 26-Apr 1Nature. 326(6111):347–352. doi: 10.1038/326347a0. [DOI] [PubMed] [Google Scholar]
- Burks C., Tomlinson L. J. Submission of data to GenBank. Proc Natl Acad Sci U S A. 1989 Jan;86(2):408–408. doi: 10.1073/pnas.86.2.408. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Böni J., Coen D. M. Examination of the roles of transcription factor Sp1-binding sites and an octamer motif in trans induction of the herpes simplex virus thymidine kinase gene. J Virol. 1989 Sep;63(9):4088–4092. doi: 10.1128/jvi.63.9.4088-4092.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Carlberg K., Ryden T. A., Beemon K. Localization and footprinting of an enhancer within the avian sarcoma virus gag gene. J Virol. 1988 May;62(5):1617–1624. doi: 10.1128/jvi.62.5.1617-1624.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Chiu R., Angel P., Karin M. Jun-B differs in its biological properties from, and is a negative regulator of, c-Jun. Cell. 1989 Dec 22;59(6):979–986. doi: 10.1016/0092-8674(89)90754-x. [DOI] [PubMed] [Google Scholar]
- Coen D. M., Weinheimer S. P., McKnight S. L. A genetic approach to promoter recognition during trans induction of viral gene expression. Science. 1986 Oct 3;234(4772):53–59. doi: 10.1126/science.3018926. [DOI] [PubMed] [Google Scholar]
- Corton J. C., Johnston S. A. Altering DNA-binding specificity of GAL4 requires sequences adjacent to the zinc finger. Nature. 1989 Aug 31;340(6236):724–727. doi: 10.1038/340724a0. [DOI] [PubMed] [Google Scholar]
- Devereux J., Haeberli P., Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387–395. doi: 10.1093/nar/12.1part1.387. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Evans R. M., Hollenberg S. M. Zinc fingers: gilt by association. Cell. 1988 Jan 15;52(1):1–3. doi: 10.1016/0092-8674(88)90522-3. [DOI] [PubMed] [Google Scholar]
- Gil G., Smith J. R., Goldstein J. L., Slaughter C. A., Orth K., Brown M. S., Osborne T. F. Multiple genes encode nuclear factor 1-like proteins that bind to the promoter for 3-hydroxy-3-methylglutaryl-coenzyme A reductase. Proc Natl Acad Sci U S A. 1988 Dec;85(23):8963–8967. doi: 10.1073/pnas.85.23.8963. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Gribskov M., McLachlan A. D., Eisenberg D. Profile analysis: detection of distantly related proteins. Proc Natl Acad Sci U S A. 1987 Jul;84(13):4355–4358. doi: 10.1073/pnas.84.13.4355. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hamm G. H., Cameron G. N. The EMBL data library. Nucleic Acids Res. 1986 Jan 10;14(1):5–9. doi: 10.1093/nar/14.1.5. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Herr W., Sturm R. A., Clerc R. G., Corcoran L. M., Baltimore D., Sharp P. A., Ingraham H. A., Rosenfeld M. G., Finney M., Ruvkun G. The POU domain: a large conserved region in the mammalian pit-1, oct-1, oct-2, and Caenorhabditis elegans unc-86 gene products. Genes Dev. 1988 Dec;2(12A):1513–1516. doi: 10.1101/gad.2.12a.1513. [DOI] [PubMed] [Google Scholar]
- Hirai S. I., Ryseck R. P., Mechta F., Bravo R., Yaniv M. Characterization of junD: a new member of the jun proto-oncogene family. EMBO J. 1989 May;8(5):1433–1439. doi: 10.1002/j.1460-2075.1989.tb03525.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hoeffler J. P., Meyer T. E., Yun Y., Jameson J. L., Habener J. F. Cyclic AMP-responsive DNA-binding protein: structure based on a cloned placental cDNA. Science. 1988 Dec 9;242(4884):1430–1433. doi: 10.1126/science.2974179. [DOI] [PubMed] [Google Scholar]
- Honess R. W., Gompels U. A., Barrell B. G., Craxton M., Cameron K. R., Staden R., Chang Y. N., Hayward G. S. Deviations from expected frequencies of CpG dinucleotides in herpesvirus DNAs may be diagnostic of differences in the states of their latent genomes. J Gen Virol. 1989 Apr;70(Pt 4):837–855. doi: 10.1099/0022-1317-70-4-837. [DOI] [PubMed] [Google Scholar]
- Hurst H. C., Jones N. C. Identification of factors that interact with the E1A-inducible adenovirus E3 promoter. Genes Dev. 1987 Dec;1(10):1132–1146. doi: 10.1101/gad.1.10.1132. [DOI] [PubMed] [Google Scholar]
- Islam S. A., Sternberg M. J. A relational database of protein structures designed for flexible enquiries about conformation. Protein Eng. 1989 Mar;2(6):431–442. doi: 10.1093/protein/2.6.431. [DOI] [PubMed] [Google Scholar]
- Johnson P. F., McKnight S. L. Eukaryotic transcriptional regulatory proteins. Annu Rev Biochem. 1989;58:799–839. doi: 10.1146/annurev.bi.58.070189.004055. [DOI] [PubMed] [Google Scholar]
- Jones K. A., Kadonaga J. T., Luciw P. A., Tjian R. Activation of the AIDS retrovirus promoter by the cellular transcription factor, Sp1. Science. 1986 May 9;232(4751):755–759. doi: 10.1126/science.3008338. [DOI] [PubMed] [Google Scholar]
- Jones K. A., Kadonaga J. T., Rosenfeld P. J., Kelly T. J., Tjian R. A cellular DNA-binding protein that activates eukaryotic transcription and DNA replication. Cell. 1987 Jan 16;48(1):79–89. doi: 10.1016/0092-8674(87)90358-8. [DOI] [PubMed] [Google Scholar]
- Jones K. A., Yamamoto K. R., Tjian R. Two distinct transcription factors bind to the HSV thymidine kinase promoter in vitro. Cell. 1985 Sep;42(2):559–572. doi: 10.1016/0092-8674(85)90113-8. [DOI] [PubMed] [Google Scholar]
- Jones N. C., Rigby P. W., Ziff E. B. Trans-acting protein factors and the regulation of eukaryotic transcription: lessons from studies on DNA tumor viruses. Genes Dev. 1988 Mar;2(3):267–281. doi: 10.1101/gad.2.3.267. [DOI] [PubMed] [Google Scholar]
- Kadonaga J. T., Carner K. R., Masiarz F. R., Tjian R. Isolation of cDNA encoding transcription factor Sp1 and functional analysis of the DNA binding domain. Cell. 1987 Dec 24;51(6):1079–1090. doi: 10.1016/0092-8674(87)90594-0. [DOI] [PubMed] [Google Scholar]
- Kanehisa M., Fickett J. W., Goad W. B. A relational database system for the maintenance and verification of the Los Alamos sequence library. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):149–158. doi: 10.1093/nar/12.1part1.149. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kanehisa M., Klein P., Greif P., DeLisi C. Computer analysis and structure prediction of nucleic acids and proteins. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):417–428. doi: 10.1093/nar/12.1part1.417. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Landschulz W. H., Johnson P. F., Adashi E. Y., Graves B. J., McKnight S. L. Isolation of a recombinant copy of the gene encoding C/EBP. Genes Dev. 1988 Jul;2(7):786–800. doi: 10.1101/gad.2.7.786. [DOI] [PubMed] [Google Scholar]
- Landschulz W. H., Johnson P. F., McKnight S. L. The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins. Science. 1988 Jun 24;240(4860):1759–1764. doi: 10.1126/science.3289117. [DOI] [PubMed] [Google Scholar]
- Lawton J. R., Martinez F. A., Burks C. Overview of the LiMB database. Nucleic Acids Res. 1989 Aug 11;17(15):5885–5899. doi: 10.1093/nar/17.15.5885. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lee M. S., Gippert G. P., Soman K. V., Case D. A., Wright P. E. Three-dimensional solution structure of a single zinc finger DNA-binding domain. Science. 1989 Aug 11;245(4918):635–637. doi: 10.1126/science.2503871. [DOI] [PubMed] [Google Scholar]
- Lesk A. M., Boswell D. R., Lesk V. I., Lesk V. E., Bairoch A. A cross-reference table between the Protein Data Bank of macromolecular structures and the National Biomedical Research Foundation-Protein Identification Resource amino acid sequence data bank. Protein Seq Data Anal. 1989 Jul;2(4):295–308. [PubMed] [Google Scholar]
- Mader S., Kumar V., de Verneuil H., Chambon P. Three amino acids of the oestrogen receptor are essential to its ability to distinguish an oestrogen from a glucocorticoid-responsive element. Nature. 1989 Mar 16;338(6212):271–274. doi: 10.1038/338271a0. [DOI] [PubMed] [Google Scholar]
- Maniatis T., Goodbourn S., Fischer J. A. Regulation of inducible and tissue-specific gene expression. Science. 1987 Jun 5;236(4806):1237–1245. doi: 10.1126/science.3296191. [DOI] [PubMed] [Google Scholar]
- McGeoch D. J., Dalrymple M. A., Davison A. J., Dolan A., Frame M. C., McNab D., Perry L. J., Scott J. E., Taylor P. The complete DNA sequence of the long unique region in the genome of herpes simplex virus type 1. J Gen Virol. 1988 Jul;69(Pt 7):1531–1574. doi: 10.1099/0022-1317-69-7-1531. [DOI] [PubMed] [Google Scholar]
- McGregor M. J., Islam S. A., Sternberg M. J. Analysis of the relationship between side-chain conformation and secondary structure in globular proteins. J Mol Biol. 1987 Nov 20;198(2):295–310. doi: 10.1016/0022-2836(87)90314-7. [DOI] [PubMed] [Google Scholar]
- Meisterernst M., Rogge L., Donath C., Gander I., Lottspeich F., Mertz R., Dobner T., Föckler R., Stelzer G., Winnacker E. L. Isolation and characterization of the porcine nuclear factor I (NFI) gene. FEBS Lett. 1988 Aug 15;236(1):27–32. doi: 10.1016/0014-5793(88)80279-5. [DOI] [PubMed] [Google Scholar]
- Miller J., McLachlan A. D., Klug A. Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. EMBO J. 1985 Jun;4(6):1609–1614. doi: 10.1002/j.1460-2075.1985.tb03825.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Mitchell P. J., Tjian R. Transcriptional regulation in mammalian cells by sequence-specific DNA binding proteins. Science. 1989 Jul 28;245(4916):371–378. doi: 10.1126/science.2667136. [DOI] [PubMed] [Google Scholar]
- Mitchell P. J., Wang C., Tjian R. Positive and negative regulation of transcription in vitro: enhancer-binding protein AP-2 is inhibited by SV40 T antigen. Cell. 1987 Sep 11;50(6):847–861. doi: 10.1016/0092-8674(87)90512-5. [DOI] [PubMed] [Google Scholar]
- Nabel G., Baltimore D. An inducible transcription factor activates expression of human immunodeficiency virus in T cells. Nature. 1987 Apr 16;326(6114):711–713. doi: 10.1038/326711a0. [DOI] [PubMed] [Google Scholar]
- Nakabeppu Y., Ryder K., Nathans D. DNA binding activities of three murine Jun proteins: stimulation by Fos. Cell. 1988 Dec 2;55(5):907–915. doi: 10.1016/0092-8674(88)90146-8. [DOI] [PubMed] [Google Scholar]
- Paonessa G., Gounari F., Frank R., Cortese R. Purification of a NF1-like DNA-binding protein from rat liver and cloning of the corresponding cDNA. EMBO J. 1988 Oct;7(10):3115–3123. doi: 10.1002/j.1460-2075.1988.tb03178.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Pearson W. R., Lipman D. J. Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A. 1988 Apr;85(8):2444–2448. doi: 10.1073/pnas.85.8.2444. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Pericak-Vance M. A., Hung W. Y., Yamaoka L., Haynes C., Bartlett R. J., Vance J. M., Lee J., Siddique T., Gaskell P. C., Stajich J. Systematic gene mapping in man: data management considerations. Aust Paediatr J. 1988;24 (Suppl 1):87–89. [PubMed] [Google Scholar]
- Ptashne M. How eukaryotic transcriptional activators work. Nature. 1988 Oct 20;335(6192):683–689. doi: 10.1038/335683a0. [DOI] [PubMed] [Google Scholar]
- Queen C., Korn L. J. A comprehensive sequence analysis program for the IBM personal computer. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):581–599. doi: 10.1093/nar/12.1part2.581. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ristiniemi J., Oikarinen J. Histone H1 binds to the putative nuclear factor I recognition sequence in the mouse alpha 2(I) collagen promoter. J Biol Chem. 1989 Feb 5;264(4):2164–2174. [PubMed] [Google Scholar]
- Rupp R. A., Sippel A. E. Chicken liver TGGCA protein purified by preparative mobility shift electrophoresis (PMSE) shows a 36.8 to 29.8 kd microheterogeneity. Nucleic Acids Res. 1987 Dec 10;15(23):9707–9726. doi: 10.1093/nar/15.23.9707. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ryden T. A., Beemon K. Avian retroviral long terminal repeats bind CCAAT/enhancer-binding protein. Mol Cell Biol. 1989 Mar;9(3):1155–1164. doi: 10.1128/mcb.9.3.1155. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Saltzman A. G., Weinmann R. Promoter specificity and modulation of RNA polymerase II transcription. FASEB J. 1989 Apr;3(6):1723–1733. doi: 10.1096/fasebj.3.6.2649403. [DOI] [PubMed] [Google Scholar]
- Sealey L., Chalkley R. At least two nuclear proteins bind specifically to the Rous sarcoma virus long terminal repeat enhancer. Mol Cell Biol. 1987 Feb;7(2):787–798. doi: 10.1128/mcb.7.2.787. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Sidman K. E., George D. G., Barker W. C., Hunt L. T. The protein identification resource (PIR). Nucleic Acids Res. 1988 Mar 11;16(5):1869–1871. doi: 10.1093/nar/16.5.1869. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Singh H., LeBowitz J. H., Baldwin A. S., Jr, Sharp P. A. Molecular cloning of an enhancer binding protein: isolation by screening of an expression library with a recognition site DNA. Cell. 1988 Feb 12;52(3):415–423. doi: 10.1016/s0092-8674(88)80034-5. [DOI] [PubMed] [Google Scholar]
- Smith T. F., Gruskin K., Tolman S., Faulkner D. The molecular biology computer research resource. Nucleic Acids Res. 1986 Jan 10;14(1):25–29. doi: 10.1093/nar/14.1.25. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Speck N. A., Baltimore D. Six distinct nuclear factors interact with the 75-base-pair repeat of the Moloney murine leukemia virus enhancer. Mol Cell Biol. 1987 Mar;7(3):1101–1110. doi: 10.1128/mcb.7.3.1101. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Staden R. The current status and portability of our sequence handling software. Nucleic Acids Res. 1986 Jan 10;14(1):217–231. doi: 10.1093/nar/14.1.217. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Starcich B., Ratner L., Josephs S. F., Okamoto T., Gallo R. C., Wong-Staal F. Characterization of long terminal repeat sequences of HTLV-III. Science. 1985 Feb 1;227(4686):538–540. doi: 10.1126/science.2981438. [DOI] [PubMed] [Google Scholar]
- Stormo G. D. Computer methods for analyzing sequence recognition of nucleic acids. Annu Rev Biophys Biophys Chem. 1988;17:241–263. doi: 10.1146/annurev.bb.17.060188.001325. [DOI] [PubMed] [Google Scholar]
- Struhl K. Helix-turn-helix, zinc-finger, and leucine-zipper motifs for eukaryotic transcriptional regulatory proteins. Trends Biochem Sci. 1989 Apr;14(4):137–140. doi: 10.1016/0968-0004(89)90145-X. [DOI] [PubMed] [Google Scholar]
- Turner R., Tjian R. Leucine repeats and an adjacent DNA binding domain mediate the formation of functional cFos-cJun heterodimers. Science. 1989 Mar 31;243(4899):1689–1694. doi: 10.1126/science.2494701. [DOI] [PubMed] [Google Scholar]
- Vinson C. R., LaMarco K. L., Johnson P. F., Landschulz W. H., McKnight S. L. In situ detection of sequence-specific DNA binding activity specified by a recombinant bacteriophage. Genes Dev. 1988 Jul;2(7):801–806. doi: 10.1101/gad.2.7.801. [DOI] [PubMed] [Google Scholar]
- Wasylyk B. Enhancers and transcription factors in the control of gene expression. Biochim Biophys Acta. 1988 Nov 10;951(1):17–35. doi: 10.1016/0167-4781(88)90021-8. [DOI] [PubMed] [Google Scholar]
- Wu F. K., Garcia J. A., Harrich D., Gaynor R. B. Purification of the human immunodeficiency virus type 1 enhancer and TAR binding proteins EBP-1 and UBP-1. EMBO J. 1988 Jul;7(7):2117–2130. doi: 10.1002/j.1460-2075.1988.tb03051.x. [DOI] [PMC free article] [PubMed] [Google Scholar]