Global H4 acetylation analysis by ChIP-chip in systemic lupus erythematosus monocytes
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Baechler EC, Batliwalla FM, Karypis G, Gaffney PM, Ortmann WA, Espe KJ et al. Interferon-inducible gene expression signature in peripheral blood cells of patients with severe lupus. Proc Natl Acad Sci USA 2003; 100: 2610–2615.
Bennett L, Palucka AK, Arce E, Cantrell V, Borvak J, Banchereau J et al. Interferon and granulopoiesis signatures in systemic lupus erythematosus blood. J Exp Med 2003; 197: 711–723.
Bengtsson AA, Sturfelt G, Truedsson L, Blomberg J, Alm G, Vallin H et al. Activation of type I interferon system in systemic lupus erythematosus correlates with disease activity but not with antiretroviral antibodies. Lupus 2000; 9: 664–671.
Cunninghame Graham DS, Manku H, Wagner S, Reid J, Timms K, Gutin A et al. Association of IRF5 in UK SLE families identifies a variant involved in polyadenylation. Hum Mol Genet 2007; 16: 579–591.
Demirci FY, Manzi S, Ramsey-Goldman R, Minster RL, Kenney M, Shaw PS et al. Association of a common interferon regulatory factor 5 (IRF5) variant with increased risk of systemic lupus erythematosus (SLE). Ann Hum Genet 2007; 71 (Pt 3): 308–311.
Garnier S, Dieude P, Michou L, Barbet S, Tan A, Lasbleiz S et al. IRF5 rs2004640-T allele, the new genetic factor for systemic lupus erythematosus, is not associated with rheumatoid arthritis. Ann Rheum Dis 2007; 66: 828–831.
Urowitz MB, Ibanez D, Gladman DD . Atherosclerotic vascular events in a single large lupus cohort: prevalence and risk factors. J Rheumatol 2007; 34: 70–75.
Asanuma Y, Oeser A, Shintani AK, Turner E, Olsen N, Fazio S et al. Premature coronary-artery atherosclerosis in systemic lupus erythematosus. N Engl J Med 2003; 349: 2407–2415.
Hill GS, Delahousse M, Nochy D, Remy P, Mignon F, Mery JP et al. Predictive power of the second renal biopsy in lupus nephritis: significance of macrophages. Kidney Int 2001; 59: 304–316.
Schubeler D, MacAlpine DM, Scalzo D, Wirbelauer C, Kooperberg C, van Leeuwen F et al. The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. Genes Dev 2004; 18: 1263–1271.
Chang S, Aune TM . Dynamic changes in histone-methylation ‘marks’ across the locus encoding interferon-gamma during the differentiation of T helper type 2 cells. Nat Immunol 2007; 8: 723–731.
Sullivan KE, Reddy AB, Dietzmann K, Suriano AR, Kocieda VP, Stewart M et al. Epigenetic regulation of tumor necrosis factor alpha. Mol Cell Biol 2007; 27: 5147–5160.
Ramirez-Carrozzi VR, Nazarian AA, Li CC, Gore SL, Sridharan R, Imbalzano AN et al. Selective and antagonistic functions of SWI/SNF and Mi-2beta nucleosome remodeling complexes during an inflammatory response. Genes Dev 2006; 20: 282–296.
Widschwendter M, Fiegl H, Egle D, Mueller-Holzner E, Spizzo G, Marth C et al. Epigenetic stem cell signature in cancer. Nat Genet 2007; 39: 157–158.
Mellor J, Dudek P, Clynes D . A glimpse into the epigenetic landscape of gene regulation. Curr Opin Genet Dev 2008; 18: 116–122.
Sullivan KE, Suriano A, Dietzmann K, Lin J, Goldman D, Petri MA . The TNFalpha locus is altered in monocytes from patients with systemic lupus erythematosus. Clin Immunol 2007; 123: 74–81.
Nambiar MP, Warke VG, Fisher CU, Tsokos GC . Effect of trichostatin A on human T cells resembles signaling abnormalities in T cells of patients with systemic lupus erythematosus: a new mechanism for TCR zeta chain deficiency and abnormal signaling. J Cell Biochem 2002; 85: 459–469.
Garcia BA, Busby SA, Shabanowitz J, Hunt DF, Mishra N . Resetting the epigenetic histone code in the MRL-lpr/lpr mouse model of lupus by histone deacetylase inhibition. J Proteome Res 2005; 4: 2032–2042.
Mishra N, Brown DR, Olorenshaw IM, Kammer GM . Trichostatin A reverses skewed expression of CD154, interleukin-10, and interferon-gamma gene and protein expression in lupus T cells. Proc Natl Acad Sci USA 2001; 98: 2628–2633.
Richardson BC, Strahler JR, Pivirotto TS, Quddus J, Bayliss GE, Gross LA et al. Phenotypic and functional similarities between 5-azacytidine-treated T cells and a T cell subset in patients with active systemic lupus erythematosus. Arthritis Rheum 1992; 35: 647–662.
Richardson B, Scheinbart L, Strahler J, Gross L, Hanash S, Johnson M . Evidence for impaired T cell DNA methylation in systemic lupus erythematosus and rheumatoid arthritis. Arthritis Rheum 1990; 33: 1665–1673.
Hu N, Qiu X, Luo Y, Yuan J, Li Y, Lei W et al. Abnormal histone modification patterns in lupus CD4+ T cells. J Rheumatol 2008; 35: 804–810.
Mishra N, Reilly CM, Brown DR, Ruiz P, Gilkeson GS . Histone deacetylase inhibitors modulate renal disease in the MRL-lpr/lpr mouse. J Clin Invest 2003; 111: 539–552.
Clayton AL, Hazzalin CA, Mahadevan LC . Enhanced histone acetylation and transcription: a dynamic perspective. Mol Cell 2006; 23: 289–296.
Koch CM, Andrews RM, Flicek P, Dillon SC, Karaoz U, Clelland GK et al. The landscape of histone modifications across 1% of the human genome in five human cell lines. Genome Res 2007; 17: 691–707.
O’Neill LP, Turner BM . Histone H4 acetylation distinguishes coding regions of the human genome from heterochromatin in a differentiation-dependent but transcription-independent manner. EMBO J 1995; 14: 3946–3957.
Garrett S, Dietzmann-Maurer K, Song L, Sullivan KE . Polarization of primary human monocytes by IFN-gamma induces chromatin changes and recruits RNA Pol II to the TNF-alpha promoter. J Immunol 2008; 180: 5257–5266.
Johnson WE, Li W, Meyer CA, Gottardo R, Carroll JS, Brown M et al. Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci USA 2006; 103: 12457–12462.
Ji H, Jiang H, Ma W, Johnson DS, Myers RM, Wong WH . An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol 2008; 26: 1293–1300.
Liu H, Zeeberg BR, Qu G, Koru AG, Ferrucci A, Kahn A et al. AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets. Bioinformatics (Oxford, England) 2007; 23: 2385–2390.
Loots GG, Ovcharenko I, Pachter L, Dubchak I, Rubin EM . rVista for comparative sequence-based discovery of functional transcription factor binding sites. Genome Res 2002; 12: 832–839.
Dennis Jr G, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC et al. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 2003; 4: P3.
Shoshan Y, Shapira I, Toubi E, Frolkis I, Yaron M, Mevorach D . Accelerated Fas-mediated apoptosis of monocytes and maturing macrophages from patients with systemic lupus erythematosus: relevance to in vitro impairment of interaction with iC3b-opsonized apoptotic cells. J Immunol 2001; 167: 5963–5969.
Baumann I, Kolowos W, Voll RE, Manger B, Gaipl U, Neuhuber WL et al. Impaired uptake of apoptotic cells into tingible body macrophages in germinal centers of patients with systemic lupus erythematosus. Arthritis Rheum 2002; 46: 191–201.
Tas SW, Quartier P, Botto M, Fossati-Jimack L . Macrophages from patients with SLE and rheumatoid arthritis have defective adhesion in vitro, while only SLE macrophages have impaired uptake of apoptotic cells. Ann Rheum Dis 2006; 65: 216–221.
Bijl M, Reefman E, Horst G, Limburg PC, Kallenberg CG . Reduced uptake of apoptotic cells by macrophages in systemic lupus erythematosus: correlates with decreased serum levels of complement. Ann Rheum Dis 2006; 65: 57–63.
Figueroa-Vega N, Galindo-Rodriguez G, Bajana S, Portales-Perez D, Abud-Mendoza C, Sanchez-Torres C et al. Phenotypic analysis of IL-10-treated, monocyte-derived dendritic cells in patients with systemic lupus erythematosus. Scand J Immunol 2006; 64: 668–676.
Koller M, Zwolfer B, Steiner G, Smolen JS, Scheinecker C . Phenotypic and functional deficiencies of monocyte-derived dendritic cells in systemic lupus erythematosus (SLE) patients. Int Immunol 2004; 16: 1595–1604.
Nossent J, Cikes N, Kiss E, Marchesoni A, Nassonova V, Mosca M et al. Current causes of death in systemic lupus erythematosus in Europe, 2000–2004: relation to disease activity and damage accrual. Lupus 2007; 16: 309–317.
Roman MJ, Shanker BA, Davis A, Lockshin MD, Sammaritano L, Simantov R et al. Prevalence and correlates of accelerated atherosclerosis in systemic lupus erythematosus. N Engl J Med 2003; 349: 2399–2406.
Foote A, Briganti EM, Kipen Y, Santos L, Leech M, Morand EF . Macrophage migration inhibitory factor in systemic lupus erythematosus. J Rheumatol 2004; 31: 268–273.
Neubert K, Meister S, Moser K, Weisel F, Maseda D, Amann K et al. The proteasome inhibitor bortezomib depletes plasma cells and protects mice with lupus-like disease from nephritis. Nat Med 2008; 14: 748–755.
Majetschak M, Perez M, Sorell LT, Lam J, Maldonado ME, Hoffman RW . Circulating 20S proteasome levels in patients with mixed connective tissue disease and systemic lupus erythematosus. Clin Vaccine Immunol 2008; 15: 1489–1493.
Chang DH, Angelin-Duclos C, Calame K . BLIMP-1: trigger for differentiation of myeloid lineage. Nat Immunol 2000; 1: 169–176.
Otero K, Turnbull IR, Poliani PL, Vermi W, Cerutti E, Aoshi T et al. Macrophage colony-stimulating factor induces the proliferation and survival of macrophages via a pathway involving DAP12 and beta-catenin. Nat Immunol 2009; 10: 734–743.
Kroger A, Koster M, Schroeder K, Hauser H, Mueller PP . Activities of IRF-1. J Interferon Cytokine Res 2002; 22: 5–14.
Reilly CM, Olgun S, Goodwin D, Gogal Jr RM, Santo A, Romesburg JW et al. Interferon regulatory factor-1 gene deletion decreases glomerulonephritis in MRL/lpr mice. Eur J Immunol 2006; 36: 1296–1308.
Eklund EA, Kakar R . Recruitment of CREB-binding protein by PU.1, IFN-regulatory factor-1, and the IFN consensus sequence-binding protein is necessary for IFN-gamma-induced p67phox and gp91phox expression. J Immunol 1999; 163: 6095–6105.
James JA, Kaufman KM, Farris AD, Taylor-ALbert E, Lehman TJA, Harley JB . An increased prevalence of Epstein-Barr virus infection in young patients suggests a possible etiology for systemic lupus erythematosus. J Clin Invest 1997; 100: 3019–3026.