Abstract
The bromodomain is a structurally conserved protein module that is present in a large number of chromatin-associated proteins and in many nuclear histone acetyltransferases. The bromodomain functions as an acetyl-lysine binding domain and has recently been shown to play an important role in regulating protein-protein interactions in chromatin-mediated cellular gene transcription as well as in viral transcriptional activation. Recent structural analyses of bromodomains in complex with acetyl-lysine-containing biological ligands provide insights into the molecular basis of differences in ligand selectivity of the bromodomain family, and reinforce the concept that functional diversity of a conserved protein structure is achieved by evolutionary changes of amino acid sequences in the ligand binding site.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Aasland, R., Gibson, T.J., and Stewart, A.F. (1995). The PHD finger: implications for chromatin-mediated transcriptional regulation. Trends Biochem. Sci. 20:56–59.
Adams, M., Sharmeen, L., Kimpton, J., Romeo, J.M., Garcia, J.V., Peterlin, B.M., Groudine, M., and Emerman, M. (1994). Cellular latency in human immunodeficiency virus-infected individuals with high CD4 levels can be detected by the presence of promoter-proximal transcripts. Proc. Natl. Acad. Sci. USA 91:3862–3866.
Agalioti, T., Chen, G., and Thanos, D. (2002). Deciphering the transcriptional histone acetylation code for a human gene. Cell 111:381–392.
An, W., Palhan, V.B., Karymov, M.A., Leuba, S.H., and Roeder, R.G. (2002). Selective requirements for histone H3 and H4 N termini in p300-dependent transcriptional activation from chromatin. Mol. Cell 9:811–821.
Baltimore, D. (1981). Gene conversion: some implications for immunoglobulin genes. Cell 24:592–594.
Barlev, N.A., Liu, L., Chehab, N.H., Mansfield, K., Harris, K.G., Halazonetis, T.D., and Berger, S.L. (2001). Acetylation of p53 activates transcription through recruitment of coactivators/histone acetyltransferases. Mol. Cell 8:1243–1254.
Benkirane, M., Chun, R.F., Xiao, H., Ogryzko, V.V., Howard, B.H., Nakatani, Y., and Jeang, K.-T. (1998). Activation of integrated provirus requires histone acetyltransferase: p300 and P/CAF are co-activators for HIV-1 Tat. J. Biol. Chem. 273:24898–24905.
Bochar, D.A., Savard, J., Wang, W., Lafleur, D.W., Moore, P., Cote, J., and Shiekhattar, R. (2000). A family of chromatin remodeling factors related to Williams syndrome transcription factor. Proc. Natl. Acad. Sci. USA 97:1038–1043.
Brown, C.E., Howe, L., Sousa, K., Alley, S.C., Carozza, M.J., Tan, S., and Workman, J.L. (2001). Recruitment of HAT complexes by direct activator interactions with the ATM-related Tra1 subunit. Science 292:2333–2337.
Brownell, J.E., and Allis, C.D. (1996). Special HATs for special occasions: linking histone acetylation to chromatin assembly and gene activation. Curr. Opin. Genet. Dev. 6:176–184.
Brownell, J.E., Zhou, J., Ranalli, T., Kobayashi, R., Edmondson, D.G., Roth, S.Y., and Allis, C.D. (1996). Tetrahymena histone acetyltransferase A: a homolog to yeast Gcn5p linking histone acetylation to gene activation. Cell 84:843–851.
Cairns, B.R., Schlichter, A., Erdjument-Bromage, H., Tempst, P., Kornberg, R.D., and Winston, F. (1999). Two functionally distinct forms of the RSC nucleosome-remodeling complex, containing essential AT hook, BAH, and bromodomains. Mol. Cell 4:715–723.
Callebaut, I., Courvalin, J.C., and Mornon, J.P. (1999). The BAH (bromo-adjacent homology) domain: a link between DNA methylation, replication and transcriptional regulation. FEBS Lett. 446:189–193.
Chang, L., and Karin, M. (2001). Mammalian MAP kinase signaling cascades. Nature 410:37–40.
Chua, P., and Roeder, G.S. (1995). Bdf1, a yeast chromosomal protein required for sporulation. Mol. Cell Biol. 15:3685–3696.
Cullen, B.R. (1998). HIV-1 auxiliary proteins: making connections in a dying cell. Cell 93:685–692.
Deng, L., Fuente, C.d.l., Fu, P., Wang, L., Donnelly, R., Wade, J.D., Lambert, P., Li, H., Lee, C.-G., and Kashanchi, F. (2000). Acetylation of HIV-1 Tat by CBP/P300 increases transcription of integrated HIV-1 genome and enhances binding to core histones. Virology 277:278–295.
Dey, A., Chitsaz, F., Abbasi, A., Misteli, T., and Ozato, K. (2003). The double bromodomain protein Brd4 binds to acetylated chromatin during interphase and mitosis. Proc. Natl. Acad. Sci. USA 100:8758–8763.
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. Nature 399:491–496.
Du, J., Nasir, I., Benton, B.K., Kladde, M.P., and Laurent, B.C. (1998). Sth1p, a Saccharomyces cerevisiae Snf2p/Swi2p homolog, is an essential ATPase in RSC and differs from Snf/Swi in its interactions with histones and chromatin-associated proteins. Genetics 150:987–1005.
Filetici, P., Aranda, C., Gonzalez, A., and Ballario, P. (1998). GCN5, a yeast transcriptional co-activator, induces chromatin reconfiguration of HIS3 promotor in vivo. Biochem. Biophys. Res. Commun. 242:84–87.
Fischle, W., Wang, Y., and Allis, C.D. (2003). Binary switches and modification cassettes in histone biology and beyond. Nature 425:475–479.
Garber, M.E., and Jones, K.A. (1999). HIV-1 Tat: coping with negative elongation factors. Curr. Opin. Immunol. 11:460–465.
Georgakopoulos, T., Gounalaki, N., and Thireos, G. (1995). Gentic evidence for the interaction of the yeast transcriptional co-activator proteins GCN5 and ADA2. Mol. Gen. Genet. 246:723–728.
Greenwald, R.J., Tumang, J.R., Sinha, A., Currier, N., Cardiff, R.D., Rothstein, T.L., Faller, D.V., and Denis, G.V. (2004). E mu-RD2 transgenic mice develop B-cell lymphoma and leukemia. Blood 103:1475–1484.
Grunstein, M. (1997). Histone acetylation in chromatin structure and transcription. Nature 389:349–352.
Gu, W., and Roeder, R.G. (1997). Activation of p53 sequence-specific DNA binding by acetylation of the p53 C-terminal domain. Cell 90:595–606.
Hajduk, P.J., Measdows, R.P., and Fesik, S.W. (1999). NMR-based screening in drug discovery. Q. Rev. Biophys. 32:211–240.
Hassan, A.H., Prochasson, P., Neely, K.E., Galasinski, S.C., Chandy, M., Carrozza, M.J., and Workman, J.L. (2002). Function and selectivity of bromodomains in anchoring chromatin-modifying complexes to promoter nucleosomes. Cell 111:369–379.
Haynes, S.R., Dollard, C., Winston, F., Beck, S., Trowsdale, J., and Dawid, I.B. (1992). The bromodomain: a conserved sequence found in human, Drosophia and yeast proteins. Nucleic Acids Res. 20:2603–2603.
Hottiger, M.O., and Nabel, G.J. (1998). Interaction of human immunodeficiency virus type 1 Tat with the transcriptional coactivators p300 and CREB binding protein. J. Virol. 72:8252–8256.
Hudson, B.P., Martinez-Yamout, M.A., Dyson, H.J., and Wright, P.E. (2000). Solution structure and acetyllysine binding activity of the GCN5 bromodomain. J. Mol. Biol. 304:355–370.
Ito, A., Lai, C.H., Zhao, X., Saito, S., Hamilton, M.H., Appella, E., and Yao, T.P. (2001). p300/CBP-mediated p53 acetylation is commonly induced by p53-activating agents and inhibited by MDM2. EMBO J. 20:1331–1340.
Ito, A., Kawaguchi, Y., Lai, C.H., Kovacs, J.J., Higashimoto, Y., Appella, E., and Yao, T.P. (2002). MDM2-HDAC1-mediated deacetylation of p53 is required for its degradation. EMBO J. 21:6236–6245.
Jacobson, R.H., Ladurner, A.G., King, D.S., and Tjian, R. (2000). Structure and function of a human TAFII250 double bromodomain module. Science 288:1422–1425.
Jeang, K.-T., Xiao, H., and Rich, E.A. (1999). Multifaceted activities of the HIV-1 transactivator of transcription, Tat. J. Biol. Chem. 274:28837–28840.
Jeanmougin, F., Wurtz, J.M., Le Douarin, B., Chambon, P., and Losson, R. (1997). The bromodomain revisited. Trends Biochem. Sci. 22:151–153.
Jenuwein, T., and Allis, C.D. (2001). Translating the histone code. Science 293:1074–1080.
John, S., and Workman, J.L. (1998). Just the facts of chromatin transcription. Science 282:1836–1837.
Johnson, G.L., and Lapadat, R. (2002). Mitogen-activated protein kinase pathways mediated by ERK, JNK, and p38 protein kinases. Science 298:1911–1912.
Kanno, T., Kanno, Y., Siegel, R.M., Jang, M.K., Lenardo, M.J., and Ozato, K. (2004). Selective recognition of acetylated histones by bromodomain proteins visualized in living cells. Mol. Cell 13:33–43.
Karn, J. (1999). Tackling Tat. J. Mol. Biol. 293:235–254.
Keyse, S.M. (2000). Protein phosphatases and the regulation of mitogen-activated protein kinase signalling. Curr. Opin. Cell. Biol. 12:186–192.
Kiernan, R.E., Vanhulle, C., Schiltz, L., Adam, E., Xiao, H., Maudoux, F., Calomme, C., Burny, A., Nakatani, Y., Jeang, K.-T., and Van Lint. C. (1999). HIV-1 Tat transcriptional activity is regulated by acetylation. EMBO J. 18:6106–6118.
Ladurner, A.G., Inouye, C., Jain, R., and Tjian, R. (2003). Bromodomains mediate an acetyl-histone encoded antisilencing function at heterochromatin boundaries. Mol. Cell 11:365–376.
Letunic, I., Goodstadt, L., Dickens, N.J., Doerks, T., Schultz, J., Mott, R., Ciccarelli, F., Copley, R.R., Ponting, C.P., and Bork, P. (2002). Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Res 30:242–244.
Li, M., Luo, J., Brooks, C.L., and Gu, W. (2002). Acetylation of p53 inhibits its ubiquitination by Mdm2. J. Biol. Chem. 277:50607–50611.
Liu, L., Scolnick, D.M., Trievel, R.C., Zhang, H.B., Marmorstein, R., Halazonetis, T.D., and Berger, S.L. (1999). p53 sites acetylated in vitro by P/CAF and p300 are acetylated in vivo in response to DNA damage. Mol. Cell Biol. 19:1202–1209.
Lu, X., Meng, X., Morris, C.A., and Keating, M.T. (1998). A novel human gene, WSTF, is deleted in Williams syndrome. Genomics 54:241–249.
Luger, K., Mäder, A.W., Richmond, R.K., Sargent, D.F., and Richmond, T.J. (1997). Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389:251–260.
Manning, E.T., Ikehara, T., Ito, T., Kadonaga, J.T., and Kraus, W.L. (2001). p300 forms a stable, templatecommitted complex with chromatin: role for the bromodomain. Mol. Cell Biol. 21:3876–3887.
Marcus, G.A., Silverman, N., Berger, S.L., Horiuchi, J., and Guarente, L. (1994). Functional similarity and physical association between GCN5 and ADA2: putative transcriptional adaptors. EMBO J. 13:4807–4815.
Matangkasombut, O., and Buratowski, S. (2003). Different sensitivities of bromodomain factors 1 and 2 to histone H4 acetylation. Mol. Cell 11:353–363.
Matangkasombut, O., Buratowski, R.M., Swilling, N.W., and Buratowski, S. (2000). Bromodomain factor 1 corresponds to a missing piece of yeast TFIID. Genes Dev. 14:951–962.
Mizzen, C., Kuo, M.-H., Smith, E., Brownell, J., Zhou, J., Ohba, R., Wei, Y., Monaco, L., Sassone-Corsi, P., and Allis, C.D. (1998). Signaling to chromatin through histone modifications: How clear is the signal? Cold Spring Harbor Symp. Quant. Biol. LXIII:469–481.
Muchardt, C., and Yaniv, M. (1999). The mammalian SWI/SNF complex and the control of cell growth. Semin. Cell Dev. Biol. 10:189–195.
Muchardt, C., Bourachot, B., Reyes, J.C., and Yaniv, M. (1998). ras transformation is associated with decreased expression of the brm/SNF2alpha ATPase from the mammalian SWI-SNF complex. EMBO J. 17:223–231.
Mujtaba, S., He, Y., Zeng, L., Farooq, A., Carlson, J.E., M. Ott, Verdin, E., and Zhou, M.-M. (2002). Structural basis of lysine-acetylated HIV-1 Tat recognition by P/CAF bromodomain. Mol. Cell 9:575–586.
Mujtaba, S., He, Y., Zeng, L., Yan, S., Plotnikova, O., Sanchez, R., Zeleznik-Le, N., Ronai, Z., and Zhou, M.-M. (2004). Structural mechanism of the bromodomain of the coactivator CBP in p53 transcriptional activation. Mol. Cell 13:251–263.
Ott, M., Schnolzer, M., Garnica, J., Fischle, W., Emiliani, S., Rackwitz, H.-R., and Verdin, E. (1999). Acetylation of the HIV-1 Tat protein by p300 is important for its transcriptional activity. Curr. Biol. 9:1489–1492.
Owen, D.J., Ornaghi, P., Yang, J.C., Lowe, N., Evans, P.R., Ballario, P., Neuhaus, D., Eiletici, 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.
Pawson, T., and Nash, P. (2003). Assembly of cell regulatory systems through protein interaction domains. Science 300:445–452.
Polesskaya, A., Naguibneva, I., Duquet, A., Bengal, E., Robin, P., and Harel-Bellan, A. (2001). Interaction between acetylated MyoD and the bromodomain of CBP and/or p300. Mol. Cell Biol. 21:5312–5320.
Sakaguchi, K., Herrera, J.E., Saito, S., Miki, T., Bustin, M., Vassilev, A., Anderson, C.W., and Appella, E. (1998). DNA damage activates p53 through a phosphorylation-acetylation cascade. Genes Dev. 12:2831–2841.
Schlessinger, J., and Lemmon, M.A. (2003). SH2 and PTB domains in tyrosine kinase signaling. Sci. STKE 2003:RE12.
Schultz, D.C., Friedman, J.R., and Rauscher, F.J., 3rd (2001). Targeting histone deacetylase complexes via KRAB-zinc finger proteins: the PHD and bromodomains of KAP-1 form a cooperative unit that recruits a novel isoform of the Mi-2alpha subunit of NuRD. Genes Dev. 15:428–443.
Schultz, J., Milpetz, F., Bork, P., and Ponting, C.P. (1998). SMART, a simple modular architecture research tool: identification of signaling domains. Proc. Natl. Acad. Sci. USA 95:5857–5864.
Sterner, D.E., Grant, P.A., Roberts, S.M., Duggan, L.J., Belotserkovskaya, R., Pacella, L.A., Winston, F., Workman, J.L., and Berger, S.L. (1999). Functional organization of the yeast SAGA complex: distinct components involved in structural integrity, nucleosome acetylation, and TATA-binding protein interaction. Mol. Cell Biol. 19:86–98.
Strahl, B.D., and Allis, C.D. (2000). The language of covalent histone modifications. Nature 403:41–45.
Struhl, K. (1998). Histone acetylation and transcriptional regulatory mechanisms. Genes Dev. 12:599–606.
Syntichaki, P., Topalidou, I., and Thireos, G. (2000). The Gcn5 bromodomain coordinates nucleosome remodelling. Nature 404:414–417.
Tamkun, J.W., Deuring, R., Scott, M.P., Kissinger, M., Pattatucci, A.M., Kaufman, T.C., and Kennison, J.A. (1992). brahma: a regulator of Drosophila homeotic genes structurally related to the yeast transcriptional activator SNF2/SWI2. Cell 68:561–572.
Travers, A. (1999). Chromatin modification: how to put a HAT on the histones. Curr. Biol. 9:23–25.
Turner, B.M. (2002). Cellular memory and the histone code. Cell 111:285–291.
Wei, P., Garber, M.E., Fang, S.M., Fischer, W.H., and Jones, K.A. (1998). Anovel CDK9-associated C-type cyclin interacts with HIV-1 Tat and mediates its high-affinity, loop-specific binding to TAR RNA. Cell 92:451–462.
Winston, F., and Allis, C.D. (1999). The bromodomain: a chromatin-targeting module? Nat. Struct Biol. 6:601–604.
Wolffe, A.P., and Hayes, J.J. (1999). Chromatin disruption and modification. Nucleic Acids Res. 27:711–720.
Yan, K.S., Kuti, M., Mujtaba, S., Farooq, A., Goldfarb, M.P., and Zhou, M.-M. (2002a). SNT PTB domain conformation regulates interactions with divergent neurotrophic receptors. J. Biol. Chem. 277:17088–17094.
Yan, K.S., Kuti, M., and Zhou, M.-M. (2002b). PTB or not PTB—that is the question. FEBS Lett. 513:67–70.
Zeng, L., and Zhou, M.-M. (2001). Bromodomain: an acetyl-lysine binding domain. FEBS Lett. 513:124–128.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer Science+Business Media, Inc.
About this chapter
Cite this chapter
Yan, K.S., Zhou, MM. (2005). The Structure and Molecular Interactions of the Bromodomain. In: Waksman, G. (eds) Proteomics and Protein-Protein Interactions. Protein Reviews, vol 3. Springer, Boston, MA. https://doi.org/10.1007/0-387-24532-4_10
Download citation
DOI: https://doi.org/10.1007/0-387-24532-4_10
Publisher Name: Springer, Boston, MA
Print ISBN: 978-0-387-24531-7
Online ISBN: 978-0-387-24532-4
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)