A BAF-centred view of the immune system (original) (raw)
Felsenfeld, G. & Groudine, M. Controlling the double helix. Nature421, 448–453 (2003). PubMed Google Scholar
Kornberg, R. D. & Lorch, Y. Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell98, 285–294 (1999). CASPubMed Google Scholar
Katsani, K. R., Mahmoudi, T. & Verrijzer, C. P. Selective gene regulation by SWI/SNF-related chromatin remodeling factors. Curr. Top. Microbiol. Immunol.274, 113–141 (2003). CASPubMed Google Scholar
Cheung, P., Allis, C. D. & Sassone-Corsi, P. Signaling to chromatin through histone modifications. Cell103, 263–271 (2000). CASPubMed Google Scholar
Kikyo, N., Wade, P. A., Guschin, D., Ge, H. & Wolffe, A. P. Active remodeling of somatic nuclei in egg cytoplasm by the nucleosomal ATPase ISWI. Science289, 2360–2362 (2000). CASPubMed Google Scholar
Muller, C. & Leutz, A. Chromatin remodeling in development and differentiation. Curr. Opin. Genet. Dev.11, 167–174 (2001). CASPubMed Google Scholar
Fisher, A. G. Cellular identity and lineage choice. Nature Rev. Immunol.2, 977–982 (2002). CAS Google Scholar
Agarwal, S., Viola, J. P. & Rao, A. Chromatin-based regulatory mechanisms governing cytokine gene transcription. J. Allergy Clin. Immunol.103, 990–999 (1999). CASPubMed Google Scholar
Lohning, M., Richter, A. & Radbruch, A. Cytokine memory of T helper lymphocytes. Adv. Immunol.80, 115–181 (2002). CASPubMed Google Scholar
Narlikar, G. J., Fan, H. Y. & Kingston, R. E. Cooperation between complexes that regulate chromatin structure and transcription. Cell108, 475–487 (2002). CASPubMed Google Scholar
Fry, C. J. & Peterson, C. L. Chromatin remodeling enzymes: who's on first? Curr. Biol.11, R185–R197 (2001). CASPubMed Google Scholar
Khavari, P. A., Peterson, C. L., Tamkun, J. W., Mendel, D. B. & Crabtree, G. R. BRG1 contains a conserved domain of the SWI2/SNF2 family necessary for normal mitotic growth and transcription. Nature366, 170–174 (1993). CASPubMed Google Scholar
Muchardt, C. & Yaniv, M. A human homologue of Saccharomyces cerevisiae SNF2/SWI2 and Drosophila brm genes potentiates transcriptional activation by the glucocorticoid receptor. EMBO J.12, 4279–4290 (1993). CASPubMedPubMed Central Google Scholar
Wang, W. et al. Purification and biochemical heterogeneity of the mammalian SWI–SNF complex. EMBO J.15, 5370–5382 (1996). CASPubMedPubMed Central Google Scholar
Strobeck, M. W. et al. Compensation of BRG-1 function by Brm: insight into the role of the core SWI–SNF subunits in retinoblastoma tumor suppressor signaling. J. Biol. Chem.277, 4782–4789 (2002). CASPubMed Google Scholar
Bultman, S. et al. A Brg1 null mutation in the mouse reveals functional differences among mammalian SWI/SNF complexes. Mol. Cell6, 1287–1295 (2000). CASPubMed Google Scholar
Chi, T. H. et al. Sequential roles of Brg, the ATPase subunit of BAF chromatin remodeling complexes, in thymocyte development. Immunity19, 169–182 (2003). References 17 and 19 use T-cell development as a model system to carry out the first in-depth genetic analysis of BRG in animals. CASPubMed Google Scholar
Reyes, J. C. et al. Altered control of cellular proliferation in the absence of mammalian brahma (SNF2α). EMBO J.17, 6979–6991 (1998). CASPubMedPubMed Central Google Scholar
Gebuhr, T. C. et al. The role of Brg1, a catalytic subunit of mammalian chromatin-remodeling complexes, in T cell development. J. Exp. Med.198, 1937–1949 (2003). CASPubMedPubMed Central Google Scholar
Kadam, S. & Emerson, B. M. Transcriptional specificity of human SWI/SNF BRG1 and BRM chromatin remodeling complexes. Mol. Cell11, 377–389 (2003). CASPubMed Google Scholar
Nie, Z. et al. A specificity and targeting subunit of a human SWI/SNF family-related chromatin-remodeling complex. Mol. Cell. Biol.20, 8879–8888 (2000). CASPubMedPubMed Central Google Scholar
Lemon, B., Inouye, C., King, D. S. & Tjian, R. Selectivity of chromatin-remodelling cofactors for ligand-activated transcription. Nature414, 924–928 (2001). CASPubMed Google Scholar
Wang, W. et al. Diversity and specialization of mammalian SWI/SNF complexes. Genes Dev.10, 2117–2130 (1996). CASPubMed Google Scholar
Olave, I., Wang, W., Xue, Y., Kuo, A. & Crabtree, G. R. Identification of a polymorphic, neuron-specific chromatin remodeling complex. Genes Dev.16, 2509–2517 (2002). CASPubMedPubMed Central Google Scholar
Tong, J. K., Hassig, C. A., Schnitzler, G. R., Kingston, R. E. & Schreiber, S. L. Chromatin deacetylation by an ATP-dependent nucleosome remodelling complex. Nature395, 917–921 (1998). CASPubMed Google Scholar
Xue, Y. et al. NURD, a novel complex with both ATP-dependent chromatin-remodeling and histone deacetylase activities. Mol. Cell2, 851–861 (1998). CASPubMed Google Scholar
Zhang, Y., LeRoy, G., Seelig, H. P., Lane, W. S. & Reinberg, D. The dermatomyositis-specific autoantigen Mi2 is a component of a complex containing histone deacetylase and nucleosome remodeling activities. Cell95, 279–289 (1998). CASPubMed Google Scholar
Chi, T. H. et al. Reciprocal regulation of CD4/CD8 expression by SWI/SNF-like BAF complexes. Nature418, 195–199 (2002). This paper shows that BAF57, a subunit dispensable for chromatin remodellingin vitro, has essential functionsin vivo. It establishes BAF complexes as the key regulator of CD4 and CD8 expression. CASPubMed Google Scholar
Morshead, K. B., Ciccone, D. N., Taverna, S. D., Allis, C. D. & Oettinger, M. A. Antigen receptor loci poised for V(D)J rearrangement are broadly associated with BRG1 and flanked by peaks of histone H3 dimethylated at lysine 4. Proc. Natl Acad. Sci. USA100, 11577–11582 (2003). CASPubMedPubMed Central Google Scholar
Kwon, J., Morshead, K. B., Guyon, J. R., Kingston, R. E. & Oettinger, M. A. Histone acetylation and hSWI/SNF remodeling act in concert to stimulate V(D)J cleavage of nucleosomal DNA. Mol. Cell6, 1037–1048 (2000). CASPubMed Google Scholar
Patenge, N., Elkin, S. K. & Oettinger, M. A. ATP-dependent remodeling by SWI/SNF and ISWI proteins stimulates V(D)J cleavage of 5 S arrays. J. Biol. Chem.279, 35360–35367 (2004). CASPubMed Google Scholar
Golding, A., Chandler, S., Ballestar, E., Wolffe, A. P. & Schlissel, M. S. Nucleosome structure completely inhibits in vitro cleavage by the V(D)J recombinase. EMBO J.18, 3712–3723 (1999). CASPubMedPubMed Central Google Scholar
Spicuglia, S. et al. Promoter activation by enhancer-dependent and -independent loading of activator and coactivator complexes. Mol. Cell10, 1479–1487 (2002). CASPubMed Google Scholar
Agalioti, T. et al. Ordered recruitment of chromatin modifying and general transcription factors to the IFN-β promoter. Cell103, 667–678 (2000). CASPubMed Google Scholar
Lomvardas, S. & Thanos, D. Nucleosome sliding via TBP DNA binding in vivo. Cell106, 685–696 (2001). CASPubMed Google Scholar
Lomvardas, S. & Thanos, D. Modifying gene expression programs by altering core promoter chromatin architecture. Cell110, 261–271 (2002). ArticleCASPubMed Google Scholar
Agalioti, T., Chen, G. & Thanos, D. Deciphering the transcriptional histone acetylation code for a human gene. Cell111, 381–392 (2002). References 35–38 set up a paradigm for dissecting the mechanisms of regulation of a natural promoter. They show the biological significance of the chromatin configuration of a promoter, how signalling pathways mobilize both BRG and HAT, and how these two enzymes cooperate to reconfigure the chromatin to allow gene induction. CASPubMed Google Scholar
Cui, K. et al. The chromatin-remodeling BAF complex mediates cellular antiviral activities by promoter priming. Mol. Cell. Biol.24, 4476–4486 (2004). This paper shows that BAF complexes use a unique strategy to regulate an IFN-α-responsive promoter. CASPubMedPubMed Central Google Scholar
Huang, M. et al. Chromatin-remodelling factor BRG1 selectively activates a subset of interferon-α-inducible genes. Nature Cell Biol.4, 774–781 (2002). CASPubMed Google Scholar
Liu, H., Kang, H., Liu, R., Chen, X. & Zhao, K. Maximal induction of a subset of interferon target genes requires the chromatin-remodeling activity of the BAF complex. Mol. Cell. Biol.22, 6471–6479 (2002). CASPubMedPubMed Central Google Scholar
Zhao, K. et al. Rapid and phosphoinositol-dependent binding of the SWI/SNF-like BAF complex to chromatin after T lymphocyte receptor signaling. Cell95, 625–636 (1998). This is the first paper that links nuclear inositol signalling to chromatin remodelling. It indicates that BRG functions downstream of TCR signalling to decondense chromatin during T-cell activation. CASPubMed Google Scholar
Hakelien, A. M., Landsverk, H. B., Robl, J. M., Skalhegg, B. S. & Collas, P. Reprogramming fibroblasts to express T-cell functions using cell extracts. Nature Biotechnol.20, 460–466 (2002). CAS Google Scholar
Goodbourn, S., Didcock, L. & Randall, R. E. Interferons: cell signalling, immune modulation, antiviral response and virus countermeasures. J. Gen. Virol.81, 2341–2364 (2000). CASPubMed Google Scholar
Munshi, N. et al. Acetylation of HMG I(Y) by CBP turns off IFN β expression by disrupting the enhanceosome. Mol. Cell2, 457–467 (1998). CASPubMed Google Scholar
Gyory, I., Wu, J., Fejer, G., Seto, E. & Wright, K. L. PRDI-BF1 recruits the histone H3 methyltransferase G9a in transcriptional silencing. Nature Immunol.5, 299–308 (2004). CAS Google Scholar
Wack, A., Coles, M., Norton, T., Hostert, A. & Kioussis, D. Early onset of CD8 transgene expression inhibits the transition from DN3 to DP thymocytes. J. Immunol.165, 1236–1242 (2000). CASPubMed Google Scholar
Bhattacharya, S. et al. Cooperation of Stat2 and p300/CBP in signalling induced by interferon-α. Nature383, 344–347 (1996). CASPubMed Google Scholar
Ting, J. P. & Trowsdale, J. Genetic control of MHC class II expression. Cell109, S21–S33 (2002). CASPubMed Google Scholar
Pattenden, S. G., Klose, R., Karaskov, E. & Bremner, R. Interferon-γ-induced chromatin remodeling at the CIITA locus is BRG1 dependent. EMBO J.21, 1978–1986 (2002). This is the first paper that links BAF complexes to cytokine-mediated signalling. CASPubMedPubMed Central Google Scholar
Mudhasani, R. & Fontes, J. D. The class II transactivator requires brahma-related gene 1 to activate transcription of major histocompatibility complex class II genes. Mol. Cell. Biol.22, 5019–5026 (2002). CASPubMedPubMed Central Google Scholar
Masternak, K. et al. CIITA is a transcriptional coactivator that is recruited to MHC class II promoters by multiple synergistic interactions with an enhanceosome complex. Genes Dev.14, 1156–1166 (2000). CASPubMedPubMed Central Google Scholar
Kara, C. J. & Glimcher, L. H. Developmental and cytokine-mediated regulation of MHC class II gene promoter occupancy in vivo. J. Immunol.150, 4934–4942 (1993). CASPubMed Google Scholar
Beresford, G. W. & Boss, J. M. CIITA coordinates multiple histone acetylation modifications at the HLA-DRA promoter. Nature Immunol.2, 652–657 (2001). CAS Google Scholar
Smale, S. T. The establishment and maintenance of lymphocyte identity through gene silencing. Nature Immunol.4, 607–615 (2003). CAS Google Scholar
Fisher, A. G. & Merkenschlager, M. Gene silencing, cell fate and nuclear organisation. Curr. Opin. Genet. Dev.12, 193–197 (2002). CASPubMed Google Scholar
Ellmeier, W., Sawada, S. & Littman, D. R. The regulation of CD4 and CD8 coreceptor gene expression during T cell development. Annu. Rev. Immunol.17, 523–554 (1999). CASPubMed Google Scholar
Zou, Y. R. et al. Epigenetic silencing of CD4 in T cells committed to the cytotoxic lineage. Nature Genet.29, 332–336 (2001). CASPubMed Google Scholar
Taniuchi, I. et al. Differential requirements for Runx proteins in CD4 repression and epigenetic silencing during T lymphocyte development. Cell111, 621–633 (2002). This paper shows that theCD4silencer has two distinct functions at different stages of T-cell development. CASPubMed Google Scholar
Coisy, M. et al. Cyclin A repression in quiescent cells is associated with chromatin remodeling of its promoter and requires Brahma/SNF2α. Mol. Cell15, 43–56 (2004). CASPubMed Google Scholar
Sif, S., Saurin, A. J., Imbalzano, A. N. & Kingston, R. E. Purification and characterization of mSin3A-containing Brg1 and hBrm chromatin remodeling complexes. Genes Dev.15, 603–618 (2001). CASPubMedPubMed Central Google Scholar
Pal, S. et al. mSin3A/histone deacetylase 2- and PRMT5-containing Brg1 complex is involved in transcriptional repression of the Myc target gene cad. Mol. Cell. Biol.23, 7475–7487 (2003). CASPubMedPubMed Central Google Scholar
Williams, C. J. et al. The chromatin remodeler Mi-2β is required for CD4 expression and T cell development. Immunity20, 719–733 (2004). CASPubMed Google Scholar
Simone, C. et al. p38 pathway targets SWI–SNF chromatin-remodeling complex to muscle-specific loci. Nature Genet.36, 738–743 (2004). CASPubMed Google Scholar
Bourachot, B., Yaniv, M. & Muchardt, C. Growth inhibition by the mammalian SWI–SNF subunit Brm is regulated by acetylation. EMBO J.22, 6505–6515 (2003). CASPubMedPubMed Central Google Scholar
Steger, D. J., Haswell, E. S., Miller, A. L., Wente, S. R. & O'Shea, E. K. Regulation of chromatin remodeling by inositol polyphosphates. Science299, 114–116 (2003). CASPubMed Google Scholar
Shen, X., Xiao, H., Ranallo, R., Wu, W. H. & Wu, C. Modulation of ATP-dependent chromatin-remodeling complexes by inositol polyphosphates. Science299, 112–114 (2003). CASPubMed Google Scholar
Martelli, A. M., Manzoli, L. & Cocco, L. Nuclear inositides: facts and perspectives. Pharmacol. Ther.101, 47–64 (2004). CASPubMed Google Scholar
Cocco, L., Maraldi, N. M. & Manzoli, F. A. New frontiers of inositide-specific phospholipase C in nuclear signalling. Eur. J. Histochem.48, 83–88 (2004). CASPubMed Google Scholar
Irvine, R. F. Nuclear lipid signaling. Sci STKE2002, re13 (2002).
Rando, O. J., Zhao, K., Janmey, P. & Crabtree, G. R. Phosphatidylinositol-dependent actin filament binding by the SWI/SNF-like BAF chromatin remodeling complex. Proc. Natl Acad. Sci. USA99, 2824–2829 (2002). CASPubMedPubMed Central Google Scholar
Gozani, O. et al. The PHD finger of the chromatin-associated protein ING2 functions as a nuclear phosphoinositide receptor. Cell114, 99–111 (2003). CASPubMed Google Scholar
Festenstein, R. et al. Modulation of heterochromatin protein 1 dynamics in primary mammalian cells. Science299, 719–721 (2003). CASPubMed Google Scholar
Sif, S., Stukenberg, P. T., Kirschner, M. W. & Kingston, R. E. Mitotic inactivation of a human SWI/SNF chromatin remodeling complex. Genes Dev.12, 2842–2851 (1998). CASPubMedPubMed Central Google Scholar
Reyes, J. C., Muchardt, C. & Yaniv, M. Components of the human SWI/SNF complex are enriched in active chromatin and are associated with the nuclear matrix. J. Cell Biol.137, 263–274 (1997). CASPubMedPubMed Central Google Scholar
Turelli, P. et al. Cytoplasmic recruitment of INI1 and PML on incoming HIV preintegration complexes: interference with early steps of viral replication. Mol. Cell7, 1245–1254 (2001). CASPubMed Google Scholar
Craig, E., Zhang, Z. K., Davies, K. P. & Kalpana, G. V. A masked NES in INI1/hSNF5 mediates hCRM1-dependent nuclear export: implications for tumorigenesis. EMBO J.21, 31–42 (2002). CASPubMedPubMed Central Google Scholar
Memedula, S. & Belmont, A. S. Sequential recruitment of HAT and SWI/SNF components to condensed chromatin by VP16. Curr. Biol.13, 241–246 (2003). CASPubMed Google Scholar
Madakamutil, L. T. et al. CD8αα-mediated survival and differentiation of CD8 memory T cell precursors. Science304, 590–593 (2004). CASPubMed Google Scholar
Kaech, S. M. et al. Selective expression of the interleukin 7 receptor identifies effector CD8 T cells that give rise to long-lived memory cells. Nature Immunol.4, 1191–1198 (2003). CAS Google Scholar
Belandia, B., Orford, R. L., Hurst, H. C. & Parker, M. G. Targeting of SWI/SNF chromatin remodelling complexes to estrogen-responsive genes. EMBO J.21, 4094–4103 (2002). CASPubMedPubMed Central Google Scholar
Hsiao, P. W., Fryer, C. J., Trotter, K. W., Wang, W. & Archer, T. K. BAF60a mediates critical interactions between nuclear receptors and the BRG1 chromatin-remodeling complex for transactivation. Mol. Cell. Biol.23, 6210–6220 (2003). CASPubMedPubMed Central Google Scholar
Inoue, H. et al. Largest subunits of the human SWI/SNF chromatin-remodeling complex promote transcriptional activation by steroid hormone receptors. J. Biol. Chem.277, 41674–41685 (2002). CASPubMed Google Scholar
Trotter, K. W. & Archer, T. K. Reconstitution of glucocorticoid receptor-dependent transcription in vivo. Mol. Cell. Biol.24, 3347–3358 (2004). CASPubMedPubMed Central Google Scholar
Kalpana, G. V., Marmon, S., Wang, W., Crabtree, G. R. & Goff, S. P. Binding and stimulation of HIV-1 integrase by a human homolog of yeast transcription factor SNF5. Science266, 2002–2006 (1994). CASPubMed Google Scholar
Strahl, B. D. & Allis, C. D. The language of covalent histone modifications. Nature403, 41–45 (2000). CASPubMed Google Scholar
Kurdistani, S. K., Tavazoie, S. & Grunstein, M. Mapping global histone acetylation patterns to gene expression. Cell117, 721–733 (2004). CASPubMed Google Scholar
Lusser, A. & Kadonaga, J. T. Chromatin remodeling by ATP-dependent molecular machines. Bioessays25, 1192–1200 (2003). CASPubMed Google Scholar
Martens, J. A. & Winston, F. Recent advances in understanding chromatin remodeling by Swi/Snf complexes. Curr. Opin. Genet. Dev.13, 136–142 (2003). CASPubMed Google Scholar
Fan, H. Y., He, X., Kingston, R. E. & Narlikar, G. J. Distinct strategies to make nucleosomal DNA accessible. Mol. Cell11, 1311–1322 (2003). CASPubMed Google Scholar
Stopka, T. & Skoultchi, A. I. The ISWI ATPase Snf2h is required for early mouse development. Proc. Natl Acad. Sci. USA100, 14097–14102 (2003). CASPubMedPubMed Central Google Scholar
Lickert, H. et al. Baf60c is essential for function of BAF chromatin remodelling complexes in heart development. Nature432, 107–112 (2004). CASPubMed Google Scholar