TRANSCompel™ - Documentation
References
Brass,A.L., Kehrli,E., Eisenbeis,C.F., Storb,U., and Singh,H. (1996) Pip, a lymphoid-restricted IRF, contains a regulatory domain that is important for autoinhibition and ternary complex formation with Ets factor PU.1. Genes Dev., 10, 2335-2347.
Butscher,W.G., Powers,C., Olive,M., Vinson,C., and Gardner,K. (1998) Coordinate transactivation of the interleukin-2 CD28 response element by c-Rel and ATF-1/CREB2. J. Biol. Chem., 273, 552-560.
Cantwell,C.A., Sterneck,E., and Johnson,P.F. (1998) Interleukin-6-specific activation of the C/EBPdelta gene in hepatocytes is mediated by Stat3 and Sp1. Mol. Cell. Biol., 18, 2108-2117.Casolaro,V., Georas,S.N., Song,Z., Zubkoff,I.D., Abdulkadir,S.A., Thanos,D., and Ono,S.J. (1995)
Inhibition of NF-AT-dependent transcription by NF-kappaB: implications for differential gene expression in T helper cell subsets. Proc. Natl. Acad. Sci. USA, 92, 11623-11627.
Chen,L., Glover,J.N.M., Hogan,P.G., Rao,A., and Harrison,S.C. (1998) Structure of the DNA-binding domains from NFAT, Fos and Jun bound specifically to DNA. Nature, 392, 42-48.
Diamond,M.I., Miner,J.N., Yoshinaga,S.K., and Yamamoto K.R. (1990) Transcription factor interactions: selectors of positive or negative regulation from a single DNA element. Science,249, 1266-1272.
Du,W., Thanos,D., and Maniatis,T. (1993) Mechanism of transcriptional synergism between distinct virus-inducible enhancer elements. Cell, 74, 887-898.
Gutman,A. and Wasylyk,B. (1990) The collagenase gene promoter contains a TPA and oncogen responsive unit encompassing the PEA3 and AP-1 binding sites. EMBO J., 9, 2241-2246.
Heinemeyer,T., Wingender,E., Reuter,I., Hermjakob,H., Kel,A.E., Kel,O.V., Ignatieva,E.V., Ananko,E.A., Podkolodnaya,O.A., Kolpakov,F.A., Podkolodny,N.L., and Kolchanov,N.A. (1998)
Databases on transcription regulation: TRANSFAC,TRRD and TRANSCompel. Nucleic Acids Res., 26, 362-367.
Jackson,D.A., Rowader,K.E., Stevens,K.Y., Jiang,C., Milos,P., and Zaret,K.S. (1993) Modulation of liver-specific transcription by interaction between Hepatocyte Nuclear Factor 3 and Nuclear Factor 1 binding DNA in close apposition. Mol.Cell.Biol., 13, 2401-2410.
Karas,H., Kel,A.E., Kel,O.V., Kolchanov,N.A., and Wingender,E. (1997) Integrating the knowledge on gene regulation. Mol. Biol. (Mosk)., 31, 531-539.
Kel,A.E., Kolchanov,N.A., Kel,O.V., Romashencko,A.G., Ananko,E.A., Ignatieva,E.V., Merkulova,T.I., Podkolodnaya,O.A., Stepanenko,I.L., Kochetov,A.V., Kolpakov,F.A., Podkolodnyi,N.L., and Naumochkin,A.N. (1997) TRRD: Database on Transcription Regulatory Regions of Eukaryotic Genes. Mol. Biol. (Mosk)., 31, 626-636.
Kel,A., Kel-Margoulis,O., Babenko,V., and Wingender,E. Recognition of NFATp/AP-1 composite elements within genes induced upon the activation of immune cells. J. Mol. Biol., submited.
Kel,O.V., Romaschenko,A.G., Kel,A.E., Naumochkin,A.N., and Kolchanov,N.A. (1995a) Data representation in the TRRD - a database of transcription regulatory regions of the eukaryotic genomes. Proceedings of the 28th Annual Hawaii International Conference on System Scienses [HICSS]. Biotechnology Computing, IEE Computer Society Press, Los Alamitos, California, 5, 42 -51.
Kel,O.V., Romaschenko,A.G., Kel,A.E., Wingender,E., and Kolchanov,N.A. (1995b) A compilation of composite regulatory elements affecting gene transcription in vertebrates. Nucleic Acids Res., 23, 4097-4103.
Kel,O.V., Romaschenko,A.G., Kel,A.E., Wingender,E., and Kolchanov,N.A. (1997) Composite regulatory elements: classification and description in the TRANSCompel database. Mol. Biol. (Mosk)., 31, 498-512.
Kerppola,T.K. and Curran,T. (1991) Fos-Jun heterodimers and Jun homodimers bend DNA in opposite orientations: implications for transcription factor cooperativity. Cell, 66, 317-326.
Klein-Hessling,S., Schneider,G., Heinfling,A., Chuvpilo,S., and Serfling,E. (1996) HMG I(Y) interferes with the DNA binding of NF-AT factors and the induction of the interleukin 4 promoter in T cells. Proc. Natl. Acad. Sci. USA, 93, 15311-15316.
Kolchanov,N.A., Ananko,E.A., Podkolodnaya,O.A., Ignatieva,E.V., StepanenkoI.L., O.V. Kel-Margoulis, Kel,A.E., Merkulova,T.I., Goryachkovskaya,T.N., Busigina,T.N., Kolpakov,F.A., Podkolodny,N.L., Naumochkin,A.N., Romashchenko,A.G. (1999) Transcription regulatory regions database (TRRD): its status in 1999. Nucleic Acids Res., 27, in press.
Linhoff,M.W., Wright,K.L., and Ting,J.P.-Y. (1997) CCAAT-binding factor NF-Y and RFX are required for in vivo assembly of a nucleoprotein complex that spans 250 base pairs: the invariant chain promoter as a model. Mol. Cell. Biol., 17, 4589-4596.
Moreno,C.S., Emery,P., West,J.E., Durand,B., Reith,W., Mach,B., and Boss,M. (1995) Purified X2 binding protein (X2BP) cooperatively binds the class II MHC X box region in the presence of purified RFX, the X box factor deficient in the Bare Lymphocyte Syndrom. J. Immunol., 155, 4313-4321.
Moulton,K.S., Semple,K., Wu,H., and Glass,C.K. (1994) Cell-specific expression of the macrophage scavenger receptor gene is dependent on PU.1 and composite AP-1/ets motif. Mol. Cell. Biol., 14, 4408-4418.
Muhlethaler-Mottet,A., Berardino,W.D., Otten,L.A., and Mach,B. (1998) Activation of the MHC Class II Transactivator CIITA by interferon-gamma requires cooperative interaction between Stat1 and USF-1. Immunity, 8, 157-166.
Ohmori,Y., Schreiber,R.D., Hamilton,T.A. (1997) Synergy between interferon-gamma and tumor necrosis factor alpha in transcriptional activation is mediated by cooperation between Signal Transducer and Activator of Transcription 1 and Nuclear Factor kappaB. J. Biol. Chem., 272, 14899-14907.
Quandt,K., Frech,K., Karas,H., Wingender,E., and Werner,T. (1995) New fast and versatile tools for detection of consensus matches in nucleotide sequence data. Nucleic Acids Res., 23, 4878-4884.
Perier, R.C., Junier, Th., and Bucher, P. (1998) The Eukaryotic Promoter Database EPD. Nucleic Acids Res., 26, 353-357.
Rao,A., Luo,C., and Hogan,P.G. (1997) Transcription factors of the NFAT family: regulation and function. Annu. Rev. Immunol., 15, 707-747.
Rooney,J.W., Sun,Y.-L., Glimcher,L.H., and Hoey,T. (1995) Novel NFAT sites that mediate activation of the interleukin-2 promoter in response to T-cell receptor stimulation. Mol. Cell. Biol., 15, 6299-6310.
Stros,M., Stokrova,J., and O'Thomas,J. (1994) DNA looping by the HMG-box domains of HMG1 and modulation of DNA binding by the acidic C-terminal domain. Nucleic Acids Res., 22, 1044-1051.
Takeuchi,A., Reddy,G.S., Kobayashi,T., Okano,T., Park,J., and Sharma,S. (1998) Nuclear Factor of Activated T cells (NFAT) as a molecular target for 1alpha,25-dihydroxyvitamin D3-mediated effects. J. Immunol., 160, 209-218.
Wingender,E. (1997) Classification scheme of eukaryotic transcription factors. Mol. Biol. (Mosk).,31, 483-497.
Wingender,E., Kel,A.E., Kel,O.V., Karas,H., Heinemeyer,T., Dietze,P., Knüppel,R., Romaschenko,A.G., and Kolchanov,N.A. (1997) TRANSFAC, TRRD and TRANSCompel: Towards a federated database system on transcriptional regulation. Nucleic Acids Res., 25, 265-268.
Zaiman,A.L. and Lenz,J. (1996) Transcriptional activation of a retrovirus enhancer by CBF (AML1) requires a second factor: evidence for cooperativity with c-Myb. J. Virol., 8, 5618-5629.
back
