DNA-binding properties of the recombinant high-mobility-group-like AT-hook-containing region from human BRG1 protein

References

Abragam, A. (1961). Principles of Nuclear Magnetism. International Series of Monographs on Physics No. 32 (New York, USA: Oxford University Press).Search in Google Scholar

Agalioti, T., Chen, G., and Thanos, D. (2002). Deciphering the transcriptional histone acetylation code for a human gene. Cell111, 381–392.10.1016/S0092-8674(02)01077-2Search in Google Scholar

Aravind, L. and Landsman, D. (1998). AT-hook motifs identified in a wide variety of DNA-binding proteins. Nucleic Acids Res.26, 4413–4421.10.1093/nar/26.19.4413Search in Google Scholar

Bianchi, M.E. and Agresti, A. (2005). HMG proteins: dynamic players in gene regulation and differentiation. Curr. Opin. Genet. Dev.15, 496–506.10.1016/j.gde.2005.08.007Search in Google Scholar

Bianchi, M.E. (1988). Interaction of a protein from rat liver nuclei with cruciform DNA. EMBO J.7, 843–849.10.1002/j.1460-2075.1988.tb02883.xSearch in Google Scholar

Bourachot, B., Yaniv, M., and Muchardt, C. (1999). The activity of mammalian brm/SNF2α is dependent on a high-mobility-group protein I/Y-like DNA binding domain. Mol. Cell. Biol.19, 3931–3939.10.1128/MCB.19.6.3931Search in Google Scholar

Bultman, S., Gebuhr, T., Yee, D., La Mantia, C., Nicholson, J., Gilliam, A., Randazzo, F., Metzger, D., Chambon, P., Crabtree, G., and Magnuson, T. (2000). A Brg1 null mutation in the mouse reveals functional differences among mammalian SWI/SNF complexes. Mol. Cell6, 1287–1295.10.1016/S1097-2765(00)00127-1Search in Google Scholar

Côté, J., Quinn, J., Workman, L., and Peterson, C.L. (1994). Stimulation of GAL4 derivative binding to nucleosomal DNA by the yeast SWI/SNF complex. Science265, 53–60.10.1126/science.8016655Search in Google Scholar

Dhalluin, C., Carlson, J.E., Zeng, L., He, C., Aggarwal, A.K., and Zhou, M.M. (1999). Structure and ligand of a histone acetyltransferase bromodomain. Nature399, 491–496.10.1038/20974Search in Google Scholar

DiRenzo, J., Shang, Y., Phelan, M., Sif, S., Myers, M., Kingston, R., and Brown, M. (2000). BRG-1 is recruited to estrogen-responsive promoters and cooperates with factors involved in histone acetylation. Mol. Cell. Biol.20, 7541–7549.10.1128/MCB.20.20.7541-7549.2000Search in Google Scholar

Dragan, A.I., Liggins, J.R., Crane-Robinson, C., and Privalov, P.L. (2003). The energetics of specific binding of AT-hooks from HMGA1 to target DNA. J. Mol. Biol.327, 393–411.10.1016/S0022-2836(03)00050-0Search in Google Scholar

Falvo, J.V., Thanos, D.T., and Maniatis, T. (1995). Reversal of intrinsic DNA bends in the IFN β gene enhancer by transcription factors and the architectural protein HMG I(Y). Cell83, 1101–1111.10.1016/0092-8674(95)90137-XSearch in Google Scholar

Fan, H.Y., He, X., Kingston, R.E. and Narlikar, G.J. (2003). Distinct strategies to make nucleosomal DNA accessible. Mol. Cell11, 1311–1322.10.1016/S1097-2765(03)00192-8Search in Google Scholar

Flaus, A. and Owen-Hughes, T. (2001). Mechanisms for ATP-dependent chromatin remodeling. Curr. Opin. Genet. Dev.11, 148–154.10.1016/S0959-437X(00)00172-6Search in Google Scholar

Guidi, C.J., Sands, A.T., Zambrowicz, B.P., Turner, T.K., Demers, D.A., Webster, W., Smith, T.W., Imbalzano, A.N., and Jones, S.N. (2001). Disruption of Ini1 leads to peri-implantation lethality and tumorigenesis in mice. Mol. Cell. Biol.21, 3598–3603.10.1128/MCB.21.10.3598-3603.2001Search in Google Scholar

Henderson, A., Holloway, A., Reeves, R., and Tremethick, D.J. (2004). Recruitment of SWI/SNF to the human immunodeficiency virus type 1 promoter. Mol. Cell. Biol.24, 389–397.10.1128/MCB.24.1.389-397.2004Search in Google Scholar

Hudson, B.P., Martinez-Yamout, M.A., Dyson, H.J., and Wright, P.E. (2000). Solution structure and acetyl-lysine binding activity of the GCN5 bromodomain. J. Mol. Biol.304, 355–370.10.1006/jmbi.2000.4207Search in Google Scholar

Huth, J.R., Bewley, C.A., Nissen, M.S., Evans, J.N., Reeves, R., Gronenborn, A.M., and Clore, G.M. (1997). The solution structure of an HMG-I(Y)-DNA complex defines a new architectural minor groove binding motif. Nat. Struct. Biol.4, 657–665.10.1038/nsb0897-657Search in Google Scholar

Jacobson, R.H., Ladurner, A.G., King, D.S., and Tjian, R. (2000). Structure and function of a human TAFII250 double bromodomain module. Science288, 1422–1425.10.1126/science.288.5470.1422Search in Google Scholar

Jeanmougin, F., Wurtz, J.M., Le Douarin, B., Chambon, P., and Losson, R. (1997). The bromodomain revisited. Trends Biochem. Sci.22, 151–153.10.1016/S0968-0004(97)01042-6Search in Google Scholar

Klochendler-Yeivin, A., Fiette, L., Barra, J., Muchardt, C., Babinet, C., and Yaniv, M. (2000). The murine SNF5/INI1 chromatin remodeling factor is essential for embryonic development and tumor suppression. EMBO Rep.1, 500–506.10.1093/embo-reports/kvd129Search in Google Scholar PubMed PubMed Central

Kouzarides, T. (2002). Histone methylation in transcriptional control. Curr. Opin. Genet. Dev.12, 198–209.10.1016/S0959-437X(02)00287-3Search in Google Scholar

Meyer, B. and Peters, T. (2003). NMR spectroscopy techniques for screening and identifying ligand binding to protein receptors. Angew. Chem. Int. Ed. Engl.42, 864–890.10.1002/anie.200390233Search in Google Scholar

Muchardt, C. and Yaniv, M. (2001). When the SWI/SNF complex remodels … the cell cycle. Oncogene20, 3067–3075.10.1038/sj.onc.1204331Search in Google Scholar

Munshi, N., Merika, M., Yie, J., Senger, K., Chen, G., and Thanos, D. (1998). Acetylation of HMG I(Y) by CBP turns off IFNβ expression by disrupting the enhanceosome. Mol. Cell2, 457–467.10.1016/S1097-2765(00)80145-8Search in Google Scholar

Murphy, F.V. VI, Sweet, R.M., and Churchill, M.E. (1999). The structure of a chromosomal high mobility group protein-DNA complex reveals sequence-neutral mechanisms important for non-sequence-specific DNA recognition. EMBO J.18, 6610–6618.10.1093/emboj/18.23.6610Search in Google Scholar

Owen, D.J., Ornaghi, P., Yang, J.C., Lowe, N., Evans, P.R., Ballario, P., Neuhaus, D., Filetici, P., and Travers, A.A. (2000). The structural basis for the recognition of acetylated histone H4 by the bromodomain of histone acetyltransferase gcn5p. EMBO J.19, 6141–6149.10.1093/emboj/19.22.6141Search in Google Scholar

Peterson, C.L. and Herskowitz, I. (1992). Characterization of the yeast SWI1, SWI2, and SWI3 genes, which encode a global activator of transcription. Cell68, 573–583.10.1016/0092-8674(92)90192-FSearch in Google Scholar

Piotto, M., Saudek, V., and Sklenar, V. (1992). Gradient-tailored excitation for single quantum NMR spectroscopy in aqueous solution. J. Biomol. NMR6, 661–665.10.1007/BF02192855Search in Google Scholar

Quinn, J., Fyrberg, A.M., Ganster, R.W., Schmidt, M.C., and Peterson, C.L. (1996). DNA-binding properties of the yeast SWI/SNF complex. Nature379, 844–847.10.1038/379844a0Search in Google Scholar

Reeves, R. and Beckerbauer, L. (2001). HMGI/Y proteins: flexible regulators of transcription and chromatin structure. Biochim. Biophys. Acta1519, 13–29.10.1016/S0167-4781(01)00215-9Search in Google Scholar

Reeves, R. and Nissen, M.S. (1990). The AT-DNA-binding domain of mammalian high mobility group I chromosomal proteins. A novel peptide motif for recognizing DNA structure. J. Biol. Chem.265, 8573–8582.Search in Google Scholar

Reeves, R. (2001). Molecular biology of HMGA proteins: hubs of nuclear function. Gene277, 63–81.10.1016/S0378-1119(01)00689-8Search in Google Scholar

Rehm, T., Huber, R., and Holak, T.A. (2002). Application of NMR in structural proteomics: screening for proteins amenable to structural analysis. Structure (Camb.)10, 1613–1618.10.1016/S0969-2126(02)00894-8Search in Google Scholar

Reyes, J.C., Barra, J., Muchardt, C., Camus, A., Babinet, C., and Yaniv, M. (1998). Altered control of cellular proliferation in the absence of mammalian brahma (SNF2α). EMBO J.17, 6979–6991.10.1093/emboj/17.23.6979Search in Google Scholar

Roberts, C.W. and Orkin, S.H. (2004). The SWI/SNF complex – chromatin and cancer. Nat. Rev. Cancer4, 133–142.10.1038/nrc1273Search in Google Scholar

Roberts, C.W., Galusha, S.A., McMenamin, M.E., Fletcher, C.D., and Orkin, S.H. (2000). Haploinsufficiency of Snf5 (integrase interactor 1) predisposes to malignant rhabdoid tumors in mice. Proc. Natl. Acad. Sci. USA97, 13796–13800.10.1073/pnas.250492697Search in Google Scholar

Sif, S., Saurin, A.J., Imbalzano, A.N., and Kingston, R.E. (2001). Purification and characterization of mSin3A-containing Brg1 and hBrm chromatin remodeling complexes. Genes Dev.15, 603–618.10.1101/gad.872801Search in Google Scholar

Strahl, B.D. and Allis, C.D. (2000). The language of covalent histone modifications. Nature403, 41–45.10.1038/47412Search in Google Scholar

Thanos, D. and Maniatis, T. (1992). The high mobility group protein HMGI(Y) is required for NF-κβ-dependent virus induction of the human IFN-β gene. Cell71, 777–789.10.1016/0092-8674(92)90554-PSearch in Google Scholar

Vignali, M., Hassan, A.H., Neely, K.E., and Workman, J.L. (2000). ATP-dependent chromatin-remodeling complexes. Mol. Cell. Biol.20, 1899–1910.10.1128/MCB.20.6.1899-1910.2000Search in Google Scholar PubMed PubMed Central

Wang, W., Cote, J., Xue, Y., Zhou, S., Khavari, P.A., Biggar, S.R., Muchardt, C., Kalpana, G.V., Goff, S.P., Yaniv, M., et al. (1996). Purification and biochemical heterogeneity of the mammalian SWI-SNF complex. EMBO J.15, 5370–5382.10.1002/j.1460-2075.1996.tb00921.xSearch in Google Scholar

Wang, W., Chi, T., Xue, Y., Zhou, S., Kuo, A., and Crabtree, G.R. (1998). Architectural DNA binding by a high-mobility-group/kinesin-like subunit in mammalian SWI/SNF-related complexes. Proc. Natl. Acad. Sci. USA95, 492–498.10.1073/pnas.95.2.492Search in Google Scholar

Wilson, C.J., Chao, D.M., Imbalzano, A.N., Schnitzler, G.R., Kingston, R.E., Young, R.A. (1996). RNA polymerase II holoenzyme contains SWI/SNF regulators involved in chromatin remodeling. Cell84, 235–244.10.1016/S0092-8674(00)80978-2Search in Google Scholar

Wong, A.K., Shanahan, F., Chen, Y., Lian, L., Ha, P., Hendricks, K., Ghaffari, S., Iliev, D., Penn, B., Woodland, A.M., et al. (2000). BRG1, a component of the SWI-SNF complex, is mutated in multiple human tumor cell lines. Cancer Res.60, 6171–6177.Search in Google Scholar

Wüthrich, K. (1986). NMR of Proteins and Nucleic Acids (New York, USA: John Wiley & Sons).10.1051/epn/19861701011Search in Google Scholar

Yang, X.J. (2004). Lysine acetylation and the bromodomain: a new partnership for signaling. Bioessays26, 1076–1087.10.1002/bies.20104Search in Google Scholar

Yoshinaga, S.K., Peterson, C.L., Herskowitz, I., Yamamoto, K.R. (1992). Roles of SWI1, SWI2, and SWI3 proteins for transcriptional enhancement by steroid receptors. Science258, 1598–1604.10.1126/science.1360703Search in Google Scholar

Zeng, L. and Zhou, M.M. (2002). Bromodomain: an acetyl-lysine binding domain. FEBS Lett.513, 124–128.10.1016/S0014-5793(01)03309-9Search in Google Scholar

Zhang, W., Wu, Q., Pwee, K.H., Jois, S.D., and Kini, R.M. (2003). Characterization of the interaction of wheat HMGa with linear and four-way junction DNAs. Biochemistry42, 6596–6607.10.1021/bi034280hSearch in Google Scholar PubMed