SATB1 packages densely looped, transcriptionally active chromatin for coordinated expression of cytokine genes (original) (raw)
References
Jenuwein, T. & Allis, C.D. Translating the histone code. Science293, 1074–1080 (2001). ArticleCAS Google Scholar
Wilson, C.B., Makar, K.W., Shnyreva, M. & Fitzpatrick, D.R. DNA methylation and the expanding epigenetics of T cell lineage commitment. Semin. Immunol.17, 105–119 (2005). ArticleCAS Google Scholar
Kosak, S.T. & Groudine, M. Form follows function: The genomic organization of cellular differentiation. Genes Dev.18, 1371–1384 (2004). ArticleCAS Google Scholar
Dekker, J., Rippe, K., Dekker, M. & Kleckner, N. Capturing chromosome conformation. Science295, 1306–1311 (2002). ArticleCAS Google Scholar
Horike, S., Cai, S., Miyano, M., Cheng, J.F. & Kohwi-Shigematsu, T. Loss of silent-chromatin looping and impaired imprinting of DLX5 in Rett syndrome. Nat. Genet.37, 31–40 (2005). ArticleCAS Google Scholar
Tolhuis, B., Palstra, R.J., Splinter, E., Grosveld, F. & de-Laat, W. Looping and interaction between hypersensitive sites in the active beta-globin locus. Mol. Cell10, 1453–1465 (2002). ArticleCAS Google Scholar
Carter, D., Chakalova, L., Osborne, C.S., Dai, Y.F. & Fraser, P. Long-range chromatin regulatory interactions in vivo. Nat. Genet.32, 623–626 (2002). ArticleCAS Google Scholar
Palstra, R.J. et al. The beta-globin nuclear compartment in development and erythroid differentiation. Nat. Genet.35, 190–194 (2003). ArticleCAS Google Scholar
Drissen, R. et al. The active spatial organization of the beta-globin locus requires the transcription factor EKLF. Genes Dev.18, 2485–2490 (2004). ArticleCAS Google Scholar
Vakoc, C.R. et al. Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1. Mol. Cell17, 453–462 (2005). ArticleCAS Google Scholar
Murrell, A., Heeson, S. & Reik, W. Interaction between differentially methylated regions partitions the imprinted genes Igf2 and H19 into parent-specific chromatin loops. Nat. Genet.36, 889–893 (2004). ArticleCAS Google Scholar
Kurukuti, S. et al. CTCF binding at the H19 imprinting control region mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to Igf2. Proc. Natl. Acad. Sci. USA103, 10684–10689 (2006). ArticleCAS Google Scholar
Ling, J.Q. et al. CTCF mediates interchromosomal colocalization between Igf2/H19 and Wsb1/Nf1. Science312, 269–272 (2006). ArticleCAS Google Scholar
Liu, Z. & Garrard, W.T. Long-range interactions between three transcriptional enhancers, active Vkappa gene promoters, and a 3′ boundary sequence spanning 46 kilobases. Mol. Cell. Biol.25, 3220–3231 (2005). ArticleCAS Google Scholar
Wurtele, H. & Chartrand, P. Genome-wide scanning of HoxB1-associated loci in mouse ES cells using an open-ended Chromosome Conformation Capture methodology. Chromosome Res.14, 477–495 (2006). Article Google Scholar
Spilianakis, C.G. & Flavell, R.A. Long-range intrachromosomal interactions in the T helper type 2 cytokine locus. Nat. Immunol.5, 1017–1027 (2004). ArticleCAS Google Scholar
Dickinson, L.A., Joh, T., Kohwi, Y. & Kohwi-Shigematsu, T. A tissue-specific MAR/SAR DNA-binding protein with unusual binding site recognition. Cell70, 631–645 (1992). ArticleCAS Google Scholar
Alvarez, J.D. et al. The MAR-binding protein SATB1 orchestrates temporal and spatial expression of multiple genes during T-cell development. Genes Dev.14, 521–535 (2000). CASPubMedPubMed Central Google Scholar
de Belle, I., Cai, S. & Kohwi-Shigematsu, T. The genomic sequences bound to special AT-rich sequence-binding protein 1 (SATB1) in vivo in Jurkat T cells are tightly associated with the nuclear matrix at the bases of the chromatin loops. J. Cell Biol.141, 335–348 (1998). ArticleCAS Google Scholar
Cai, S., Han, H.J. & Kohwi-Shigematsu, T. Tissue-specific nuclear architecture and gene expression regulated by SATB1. Nat. Genet.34, 42–51 (2003). ArticleCAS Google Scholar
Yasui, D., Miyano, M., Cai, S., Varga-Weisz, P. & Kohwi-Shigematsu, T. SATB1 targets chromatin remodelling to regulate genes over long distances. Nature419, 641–645 (2002). ArticleCAS Google Scholar
Kohwi-Shigematsu, T. & Kohwi, Y. Torsional stress stabilizes extended base unpairing in suppressor sites flanking immunoglobulin heavy chain enhancer. Biochemistry29, 9551–9560 (1990). ArticleCAS Google Scholar
Wen, J. et al. SATB1 family protein expressed during early erythroid differentiation modifies globin gene expression. Blood105, 3330–3339 (2005). ArticleCAS Google Scholar
Britanova, O., Akopov, S., Lukyanov, S., Gruss, P. & Tarabykin, V. Novel transcription factor Satb2 interacts with matrix attachment region DNA elements in a tissue-specific manner and demonstrates cell-type-dependent expression in the developing mouse CNS. Eur. J. Neurosci.21, 658–668 (2005). Article Google Scholar
Dobreva, G. et al. SATB2 is a multifunctional determinant of craniofacial patterning and osteoblast differentiation. Cell125, 971–986 (2006). ArticleCAS Google Scholar
Pavan Kumar, P. et al. Phosphorylation of SATB1, a global gene regulator, acts as a molecular switch regulating its transcriptional activity in vivo. Mol. Cell22, 231–243 (2006). ArticleCAS Google Scholar
Dobreva, G., Dambacher, J. & Grosschedl, R. SUMO modification of a novel MAR-binding protein, SATB2, modulates immunoglobulin mu gene expression. Genes Dev.17, 3048–3061 (2003). ArticleCAS Google Scholar
Glimcher, L.H. & Murphy, K.M. Lineage commitment in the immune system: the T helper lymphocyte grows up. Genes Dev.14, 1693–1711 (2000). CASPubMed Google Scholar
Smale, S.T. & Fisher, A.G. Chromatin structure and gene regulation in the immune system. Annu. Rev. Immunol.20, 427–462 (2002). ArticleCAS Google Scholar
Ansel, K.M., Lee, D.U. & Rao, A. An epigenetic view of helper T cell differentiation. Nat. Immunol.4, 616–623 (2003). ArticleCAS Google Scholar
Fields, P.E., Kim, S.T. & Flavell, R.A. Cutting edge: changes in histone acetylation at the IL-4 and IFN-gamma loci accompany Th1/Th2 differentiation. J. Immunol.169, 647–650 (2002). ArticleCAS Google Scholar
Avni, O. et al. T(H) cell differentiation is accompanied by dynamic changes in histone acetylation of cytokine genes. Nat. Immunol.3, 643–651 (2002). ArticleCAS Google Scholar
Baguet, A. & Bix, M. Chromatin landscape dynamics of the Il4-Il13 locus during T helper 1 and 2 development. Proc. Natl. Acad. Sci. USA101, 11410–11415 (2004). ArticleCAS Google Scholar
Makar, K.W. et al. Active recruitment of DNA methyltransferases regulates interleukin 4 in thymocytes and T cells. Nat. Immunol.4, 1183–1190 (2003). ArticleCAS Google Scholar
Fields, P.E., Lee, G.R., Kim, S.T., Bartsevich, V.V. & Flavell, R.A. Th2-specific chromatin remodeling and enhancer activity in the Th2 cytokine locus control region. Immunity21, 865–876 (2004). ArticleCAS Google Scholar
Grosveld, F., van Assendelft, G.B., Greaves, D.R. & Kollias, G. Position-independent, high-level expression of the human beta-globin gene in transgenic mice. Cell51, 975–985 (1987). ArticleCAS Google Scholar
Lee, G.R., Fields, P.E., Griffin, T.J. & Flavell, R.A. Regulation of the Th2 cytokine locus by a locus control region. Immunity19, 145–153 (2003). ArticleCAS Google Scholar
Lee, G.R., Spilianakis, C.G. & Flavell, R.A. Hypersensitive site 7 of the TH2 locus control region is essential for expressing TH2 cytokine genes and for long-range intrachromosomal interactions. Nat. Immunol.6, 42–48 (2005). ArticleCAS Google Scholar
Kohwi-Shigematsu, T., deBelle, I., Dickinson, L.A., Galande, S. & Kohwi, Y. Identification of base-unpairing region-binding proteins and characterization of their in vivo binding sequences. Methods Cell Biol.53, 323–354 (1998). ArticleCAS Google Scholar
Loots, G.G. et al. Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. Science288, 136–140 (2000). ArticleCAS Google Scholar
Zheng, W. & Flavell, R.A. The transcription factor GATA-3 is necessary and sufficient for Th2 cytokine gene expression in CD4 T cells. Cell89, 587–596 (1997). ArticleCAS Google Scholar
Zhu, J., Guo, L., Watson, C.J., Hu-Li, J. & Paul, W.E. Stat6 is necessary and sufficient for IL-4's role in Th2 differentiation and cell expansion. J. Immunol.166, 7276–7281 (2001). ArticleCAS Google Scholar
Kurata, H., Lee, H.J., O'Garra, A. & Arai, N. Ectopic expression of activated Stat6 induces the expression of Th2-specific cytokines and transcription factors in developing Th1 cells. Immunity11, 677–688 (1999). ArticleCAS Google Scholar
Ho, I.C., Hodge, M.R., Rooney, J.W. & Glimcher, L.H. The proto-oncogene c-maf is responsible for tissue-specific expression of interleukin-4. Cell85, 973–983 (1996). ArticleCAS 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). ArticleCAS Google Scholar
Paddison, P.J. et al. Cloning of short hairpin RNAs for gene knockdown in mammalian cells. Nat. Methods1, 163–167 (2004). ArticleCAS Google Scholar
Cook, P.R. Predicting three-dimensional genome structure from transcriptional activity. Nat. Genet.32, 347–352 (2002). ArticleCAS Google Scholar
Hager, G.L. et al. Chromatin dynamics and the evolution of alternate promoter states. Chromosome Res.14, 107–116 (2006). ArticleCAS Google Scholar
Kaye, J., Porcelli, S., Tite, J., Jones, B. & Janeway, C.A., Jr. Both a monoclonal antibody and antisera specific for determinants unique to individual cloned helper T cell lines can substitute for antigen and antigen-presenting cells in the activation of T cells. J. Exp. Med.158, 836–856 (1983). ArticleCAS Google Scholar