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Epigenomics Volume 2, 2010 - Issue 6
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Review

Epigenetic Control of Inducible Gene Expression in the Immune System

Pek Siew Lim1 Department of Genome Biology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT2601, AustraliaView further author information
,
M Frances Shannon1 Department of Genome Biology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT2601, AustraliaView further author information
&
Kristine Hardy1 Department of Genome Biology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT2601, AustraliaCorrespondence[email protected]
View further author information
Pages 775-795 | Published online: 15 Dec 2010

Bibliography

  • Geissmann F , ManzMG, JungS, SiewekeMH, MeradM, LeyK: Development of monocytes, macrophages, and dendritic cells.Science327(5966) , 656–661 (2010).
  • Sitnicka E : From the bone marrow to the thymus: the road map of early stages of T-cell development.Crit. Rev. Immunol.29(6) , 487–530 (2009).
  • Parra M : Epigenetic events during B lymphocyte development.Epigenetics4(7) , 462–468 (2009).
  • Bernstein BE , MeissnerA, LanderES: The mammalian epigenome.Cell128(4) , 669–681 (2007).
  • Navarro F , LiebermanJ: Small RNAs guide hematopoietic cell differentiation and function.J. Immunol.184(11) , 5939–5947 (2010).
  • Jacquier A : The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs.Nat. Rev. Genet.10(12) , 833–844 (2009).
  • Cedar H , BergmanY: Linking DNA methylation and histone modification: patterns and paradigms.Nat. Rev. Genet.10(5) , 295–304 (2009).
  • Kouzarides T : Chromatin modifications and their function.Cell128(4) , 693–705 (2007).
  • Lee BM , MahadevanLC: Stability of histone modifications across mammalian genomes: implications for ‘epigenetic‘ marking.J. Cell. Biochem.108(1) , 22–34 (2009).
  • Li B , CareyM, WorkmanJL: The role of chromatin during transcription.Cell128(4) , 707–719 (2007).
  • Talbert PB , HenikoffS: Histone variants – ancient wrap artists of the epigenome.Nat. Rev. Mol. Cell. Biol.11(4) , 264–275 (2010).
  • Clapier CR , CairnsBR: The biology of chromatin remodeling complexes.Annu. Rev. Biochem.78 , 273–304 (2009).
  • Barski A , CuddapahS, CuiK et al.: High-resolution profiling of histone methylations in the human genome.Cell129(4) , 823–837 (2007).
  • Cui K , ZangC, RohTY et al.: Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation.Cell Stem Cell4(1) , 80–93 (2009).
  • Mikkelsen TS , KuM, JaffeDB et al.: Genome-wide maps of chromatin state in pluripotent and lineage-committed cells.Nature448(7153) , 553–560 (2007).
  • Roh TY , NgauWC, CuiK, LandsmanD, ZhaoK: High-resolution genome-wide mapping of histone modifications.Nat. Biotechnol.22(8) , 1013–1016 (2004).
  • Wang Z , ZangC, RosenfeldJA et al.: Combinatorial patterns of histone acetylations and methylations in the human genome.Nat. Genet.40(7) , 897–903 (2008).
  • Heintzman ND , StuartRK, HonG et al.: Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome.Nat. Genet.39(3) , 311–318 (2007).
  • Roh TY , CuddapahS, CuiK, ZhaoK: The genomic landscape of histone modifications in human T cells.Proc. Natl Acad. Sci. USA103(43) , 15782–15787 (2006).
  • Roh TY , CuddapahS, ZhaoK: Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping.Genes Dev.19(5) , 542–552 (2005).
  • Schones DE , CuiK, CuddapahS et al.: Dynamic regulation of nucleosome positioning in the human genome.Cell132(5) , 887-898 (2008).
  • Azuara V , PerryP, SauerS et al.: Chromatin signatures of pluripotent cell lines.Nat. Cell Biol.8(5) , 532–538 (2006).
  • Pokholok DK , HarbisonCT, LevineS et al.: Genome-wide map of nucleosome acetylation and methylation in yeast.Cell122(4) , 517–527 (2005).
  • Sinha I , WirenM, EkwallK: Genome-wide patterns of histone modifications in fission yeast.Chromosome Res.14(1) , 95–105 (2006).
  • Schubeler D , MacAlpineDM, ScalzoD et al.: The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote.Genes Dev.18(11) , 1263–1271 (2004).
  • Bernstein BE , KamalM, Lindblad-TohK et al.: Genomic maps and comparative analysis of histone modifications in human and mouse.Cell120(2) , 169–181 (2005).
  • Guenther MG , LevineSS, BoyerLA, JaenischR, YoungRA: A chromatin landmark and transcription initiation at most promoters in human cells.Cell130(1) , 77–88 (2007).
  • Koch CM , AndrewsRM, FlicekP et al.: The landscape of histone modifications across 1% of the human genome in five human cell lines.Genome Res.17(6) , 691–707 (2007).
  • Kim TH , BarreraLO, ZhengM et al.: A high-resolution map of active promoters in the human genome.Nature436(7052) , 876–880 (2005).
  • Liu CL , KaplanT, KimM et al.: Single-nucleosome mapping of histone modifications in S. cerevisiae. PLoS Biol.3(10) , E328 (2005).
  • Martens JH , O‘SullivanRJ, BraunschweigU et al.: The profile of repeat-associated histone lysine methylation states in the mouse epigenome.EMBO J.24(4) , 800–812 (2005).
  • Rosenfeld JA , WangZ, SchonesDE, ZhaoK, DeSalleR, ZhangMQ: Determination of enriched histone modifications in non-genic portions of the human genome.BMC Genomics10 , 143 (2009).
  • Bernstein BE , MikkelsenTS, XieX et al.: A bivalent chromatin structure marks key developmental genes in embryonic stem cells.Cell125(2) , 315–326 (2006).
  • Delaval K , GovinJ, CerqueiraF, RousseauxS, KhochbinS, FeilR: Differential histone modifications mark mouse imprinting control regions during spermatogenesis.EMBO J.26(3) , 720–729 (2007).
  • Strahl BD , AllisCD: The language of covalent histone modifications.Nature403(6765) , 41–45 (2000).
  • Vakoc CR , MandatSA, OlenchockBA, BlobelGA: Histone H3 lysine 9 methylation and HP1γ are associated with transcription elongation through mammalian chromatin.Mol. Cell19(3) , 381–391 (2005).
  • Bannister AJ , SchneiderR, MyersFA, ThorneAW, Crane-RobinsonC, KouzaridesT: Spatial distribution of di- and tri-methyl lysine 36 of histone H3 at active genes.J. Biol. Chem.280(18) , 17732–17736 (2005).
  • Farris SD , RubioED, MoonJJ, GombertWM, NelsonBH, KrummA: Transcription-induced chromatin remodeling at the c-myc gene involves the local exchange of histone H2A.Z.J. Biol. Chem.280(26) , 25298–25303 (2005).
  • Rao B , ShibataY, StrahlBD, LiebJD: Dimethylation of histone H3 at lysine 36 demarcates regulatory and nonregulatory chromatin genome-wide.Mol. Cell. Biol.25(21) , 9447–9459 (2005).
  • Vakoc CR , SachdevaMM, WangH, BlobelGA: Profile of histone lysine methylation across transcribed mammalian chromatin.Mol. Cell. Biol.26(24) , 9185–9195 (2006).
  • Edmunds JW , MahadevanLC, ClaytonAL: Dynamic histone H3 methylation during gene induction: HYPB/Setd2 mediates all H3K36 trimethylation.EMBO J.27(2) , 406–420 (2008).
  • Carrozza MJ , LiB, FlorensL et al.: Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription.Cell123(4) , 581–592 (2005).
  • Wang Z , ZangC, CuiK et al.: Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes.Cell138(5) , 1019–1031 (2009).
  • Bird A : DNA methylation patterns and epigenetic memory.Genes Dev.16(1) , 6–21 (2002).
  • Suzuki MM , BirdA: DNA methylation landscapes: provocative insights from epigenomics.Nat. Rev. Genet.9(6) , 465–476 (2008).
  • Khulan B , ThompsonRF, YeK et al.: Comparative isoschizomer profiling of cytosine methylation: the HELP assay.Genome Res.16(8) , 1046–1055 (2006).
  • Blackledge NP , ZhouJC, TolstorukovMY, FarcasAM, ParkPJ, KloseRJ: CpG islands recruit a histone H3 lysine 36 demethylase.Mol. Cell38(2) , 179–190 (2010).
  • Bouwman P , PhilipsenS: Regulation of the activity of Sp1-related transcription factors.Mol. Cell. Endocrinol.195(1–2) , 27–38 (2002).
  • Zelko IN , MuellerMR, FolzRJ: CpG methylation attenuates Sp1 and Sp3 binding to the human extracellular superoxide dismutase promoter and regulates its cell-specific expression.Free Radic. Biol. Med.48(7) , 895–904 (2010).
  • Orford K , KharchenkoP, LaiW et al.: Differential H3K4 methylation identifies developmentally poised hematopoietic genes.Dev. Cell14(5) , 798–809 (2008).
  • Hargreaves DC , HorngT, MedzhitovR: Control of inducible gene expression by signal-dependent transcriptional elongation.Cell138(1) , 129–145 (2009).
  • Kuo CT , LeidenJM: Transcriptional regulation of T lymphocyte development and function.Annu. Rev. Immunol.17 , 149–187 (1999).
  • Santana MA , Esquivel-GuadarramaF: Cell biology of T cell activation and differentiation.Int. Rev. Cytol.250 , 217–274 (2006).
  • Ullman KS , NorthropJP, VerweijCL, CrabtreeGR: Transmission of signals from the T lymphocyte antigen receptor to the genes responsible for cell proliferation and immune function: the missing link.Annu. Rev. Immunol.8 , 421–452 (1990).
  • Herschman HR : Primary response genes induced by growth factors and tumor promoters.Annu. Rev. Biochem.60 , 281–319 (1991).
  • Lim PS , HardyK, BuntingKL et al.: Defining the chromatin signature of inducible genes in T cells.Genome Biol.10(10) , R107 (2009).
  • Barski A , JothiR, CuddapahS et al.: Chromatin poises miRNA- and protein-coding genes for expression.Genome Res.19(10) , 1742–1751 (2009).
  • Ramirez-Carrozzi VR , BraasD, BhattDM et al.: A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling.Cell138(1) , 114–128 (2009).
  • Roh TY , ZhaoK: High-resolution, genome-wide mapping of chromatin modifications by GMAT.Methods Mol. Biol.387 , 95–108 (2008).
  • Muse GW , GilchristDA, NechaevS et al.: RNA polymerase is poised for activation across the genome.Nat. Genet.39(12) , 1507–1511 (2007).
  • Radonjic M , AndrauJC, LijnzaadP et al.: Genome-wide analyses reveal RNA polymerase II located upstream of genes poised for rapid response upon S. cerevisiae stationary phase exit.Mol. Cell18(2) , 171–183 (2005).
  • Zeitlinger J , StarkA, KellisM et al.: RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo.Nat. Genet.39(12) , 1512–1516 (2007).
  • O‘Brien T , LisJT: RNA polymerase II pauses at the 5´ end of the transcriptionally induced Drosophila hsp70 gene.Mol. Cell. Biol.11(10) , 5285–5290 (1991).
  • Rougvie AE , LisJT: The RNA polymerase II molecule at the 5´ end of the uninduced hsp70 gene of D. melanogaster is transcriptionally engaged.Cell54(6) , 795–804 (1988).
  • Lis J : Promoter-associated pausing in promoter architecture and postinitiation transcriptional regulation.Cold Spring Harb. Symp. Quant. Biol.63 , 347–356 (1998).
  • Margaritis T , HolstegeFC: Poised RNA polymerase II gives pause for thought.Cell133(4) , 581–584 (2008).
  • Price DH : Poised polymerases: on your mark…get set…go!Mol. Cell30(1) , 7–10 (2008).
  • Saunders A , CoreLJ, LisJT: Breaking barriers to transcription elongation.Nat. Rev. Mol. Cell Biol.7(8) , 557–567 (2006).
  • Gilchrist DA , NechaevS, LeeC et al.: NELF-mediated stalling of Pol II can enhance gene expression by blocking promoter-proximal nucleosome assembly.Genes Dev.22(14) , 1921–1933 (2008).
  • Lee C , LiX, HechmerA et al.: NELF and GAGA factor are linked to promoter-proximal pausing at many genes in Drosophila. Mol. Cell. Biol.28(10) , 3290–3300 (2008).
  • Hendrix DA , HongJW, ZeitlingerJ, RokhsarDS, LevineMS: Promoter elements associated with RNA Pol II stalling in the Drosophila embryo.Proc. Natl Acad. Sci. USA105(22) , 7762–7767 (2008).
  • Krumm A , HickeyLB, GroudineM: Promoter-proximal pausing of RNA polymerase II defines a general rate-limiting step after transcription initiation.Genes Dev.9(5) , 559–572 (1995).
  • Wu CH , YamaguchiY, BenjaminLR et al.: NELF and DSIF cause promoter proximal pausing on the hsp70 promoter in Drosophila. Genes Dev.17(11) , 1402–1414 (2003).
  • Yamaguchi Y , TakagiT, WadaT et al.: NELF, a multisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation.Cell97(1) , 41–51 (1999).
  • Fuda NJ , ArdehaliMB, LisJT: Defining mechanisms that regulate RNA polymerase II transcription in vivo. Nature461(7261) , 186–192 (2009).
  • Barboric M , NissenRM, KanazawaS, Jabrane-FerratN, PeterlinBM: NF-κB binds P-TEFb to stimulate transcriptional elongation by RNA polymerase II.Mol. Cell8(2) , 327–337 (2001).
  • Eberhardy SR , FarnhamPJ: Myc recruits P-TEFb to mediate the final step in the transcriptional activation of the cad promoter.J. Biol. Chem.277(42) , 40156–40162 (2002).
  • Kanazawa S , OkamotoT, PeterlinBM: Tat competes with CIITA for the binding to P-TEFb and blocks the expression of MHC class II genes in HIV infection.Immunity12(1) , 61–70 (2000).
  • Simone C , StieglerP, BagellaL et al.: Activation of MyoD-dependent transcription by cdk9/cyclin T2.Oncogene21(26) , 4137–4148 (2002).
  • Anderson P : Post-transcriptional regulons coordinate the initiation and resolution of inflammation.Nat. Rev. Immunol.10(1) , 24–35 (2010).
  • Curtale G , CitarellaF, CarissimiC et al.: An emerging player in the adaptive immune response: microRNA-146a is a modulator of IL-2 expression and activation-induced cell death in T lymphocytes.Blood115(2) , 265–273 (2010).
  • Androulidaki A , IliopoulosD, ArranzA et al.: The kinase Akt1 controls macrophage response to lipopolysaccharide by regulating microRNAs.Immunity31(2) , 220–231 (2009).
  • Gan Q , YoshidaT, McDonaldOG, OwensGK: Concise review: epigenetic mechanisms contribute to pluripotency and cell lineage determination of embryonic stem cells.Stem Cells25(1) , 2–9 (2007).
  • Byun JS , WongMM, CuiW et al.: Dynamic bookmarking of primary response genes by p300 and RNA polymerase II complexes.Proc. Natl Acad. Sci. USA106(46) , 19286–19291 (2009).
  • Juelich T , SutcliffeE, DentonA et al.: Interplay between chromatin remodeling and epigenetic changes during lineage-specific commitment to granzyme B expression.J. Immunol.183(11) , 7063–7072 (2009).
  • Smith JL , FreebernWJ, CollinsI et al.: Kinetic profiles of p300 occupancy in vivo predict common features of promoter structure and coactivator recruitment.Proc. Natl Acad. Sci. USA101(32) , 11554–11559 (2004).
  • Aung HT , SchroderK, HimesSR et al.: LPS regulates proinflammatory gene expression in macrophages by altering histone deacetylase expression.FASEB J.20(9) , 1315–1327 (2006).
  • Ghisletti S , BarozziI, MiettonF et al.: Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages.Immunity32(3) , 317–328 (2010).
  • Smith AE , ChronisC, ChristodoulakisM et al.: Epigenetics of human T cells during the G0–>G1 transition.Genome Res.19(8) , 1325–1337 (2009).
  • Liang MD , ZhangY, McDevitD, MareckiS, NikolajczykBS: The interleukin-1β gene is transcribed from a poised promoter architecture in monocytes.J. Biol. Chem.281(14) , 9227–9237 (2006).
  • Saccani S , PantanoS, NatoliG: p38-dependent marking of inflammatory genes for increased NF-κ B recruitment.Nat. Immunol.3(1) , 69–75 (2002).
  • De Santa F , TotaroMG, ProsperiniE, NotarbartoloS, TestaG, NatoliG: The histone H3 lysine-27 demethylase Jmjd3 links inflammation to inhibition of polycomb-mediated gene silencing.Cell130(6) , 1083–1094 (2007).
  • Attema JL , ReevesR, MurrayV et al.: The human IL-2 gene promoter can assemble a positioned nucleosome that becomes remodeled upon T-cell activation.J. Immunol.169(5) , 2466–2476 (2002).
  • Brettingham-Moore KH , SprodOR, ChenX, OakfordP, ShannonMF, HollowayAF: Determinants of a transcriptionally competent environment at the GM-CSF promoter.Nucleic Acids Res.36(8) , 2639–2653 (2008).
  • Chen X , WangJ, WoltringD, GerondakisS, ShannonMF: Histone dynamics on the interleukin-2 gene in response to T-cell activation.Mol. Cell. Biol.25(8) , 3209–3219 (2005).
  • Rao A , AvniO: Molecular aspects of T-cell differentiation.Br. Med. Bull.56(4) , 969–984 (2000).
  • Rao S , ProckoE, ShannonMF: Chromatin remodeling, measured by a novel real-time polymerase chain reaction assay, across the proximal promoter region of the IL-2 gene.J. Immunol.167(8) , 4494–4503 (2001).
  • Zhao K , WangW, RandoOJ et al.: Rapid and phosphoinositol-dependent binding of the SWI/SNF-like BAF complex to chromatin after T lymphocyte receptor signaling.Cell95(5) , 625–636 (1998).
  • Ishihara S , VarmaR, SchwartzRH: A new fractionation assay, based on the size of formaldehyde-crosslinked, mildly sheared chromatin, delineates the chromatin structure at promoter regions.Nucleic Acids Res.38(11) , E124 (2010).
  • Liu H , MulhollandN, FuH, ZhaoK: Cooperative activity of BRG1 and Z-DNA formation in chromatin remodeling.Mol. Cell. Biol.26(7) , 2550–2559 (2006).
  • Sutcliffe EL , ParishIA, HeYQ et al.: Dynamic histone variant exchange accompanies gene induction in T cells.Mol. Cell. Biol.29(7) , 1972–1986 (2009).
  • Tamura T , SmithM, KannoT, DasenbrockH, NishiyamaA, OzatoK: Inducible deposition of the histone variant H3.3 in interferon-stimulated genes.J. Biol. Chem.284(18) , 12217–12225 (2009).
  • Schwartz BE , AhmadK: Transcriptional activation triggers deposition and removal of the histone variant H3.3.Genes Dev.19(7) , 804–814 (2005).
  • Jin C , FelsenfeldG: Nucleosome stability mediated by histone variants H3.3 and H2A.Z.Genes Dev.21(12) , 1519–1529 (2007).
  • Lau LF , NathansD: Expression of a set of growth-related immediate early genes in BALB/c 3T3 cells: coordinate regulation with c-fos or c-myc.Proc. Natl Acad. Sci. USA84(5) , 1182–1186 (1987).
  • Heintzman ND , HonGC, HawkinsRD et al.: Histone modifications at human enhancers reflect global cell-type-specific gene expression.Nature459(7243) , 108–112 (2009).
  • Kouskouti A , TalianidisI: Histone modifications defining active genes persist after transcriptional and mitotic inactivation.EMBO J.24(2) , 347–357 (2005).
  • Northrop JK , WellsAD, ShenH: Cutting edge: chromatin remodeling as a molecular basis for the enhanced functionality of memory CD8 T cells.J. Immunol.181(2) , 865–868 (2008).
  • Araki Y , WangZ, ZangC et al.: Genome-wide analysis of histone methylation reveals chromatin state-based regulation of gene transcription and function of memory CD8(+) T cells.Immunity30(6) , 912–925 (2009).
  • Mirabella F , BaxterEW, BoissinotM, JamesSR, CockerillPN: The human IL-3/granulocyte-macrophage colony-stimulating factor locus is epigenetically silent in immature thymocytes and is progressively activated during T-cell development.J. Immunol.184(6) , 3043–3054 (2010).
  • Cuddapah S , BarskiA, ZhaoK: Epigenomics of T-cell activation, differentiation, and memory.Curr. Opin. Immunol.22 , 1–7 (2010).
  • Messi M , GiacchettoI, NagataK, LanzavecchiaA, NatoliG, SallustoF: Memory and flexibility of cytokine gene expression as separable properties of human T(h)1 and T(h)2 lymphocytes.Nat. Immunol.4(1) , 78–86 (2003).
  • Avni O , RaoA: T cell differentiation: a mechanistic view.Curr. Opin. Immunol.12(6) , 654–659 (2000).
  • Fujita N , JayeDL, GeigermanC et al.: MTA3 and the Mi-2/NuRD complex regulate cell fate during B lymphocyte differentiation.Cell119(1) , 75–86 (2004).
  • Gao H , LukinK, RamirezJ, FieldsS, LopezD, HagmanJ: Opposing effects of SWI/SNF and Mi-2/NuRD chromatin remodeling complexes on epigenetic reprogramming by EBF and Pax5.Proc. Natl Acad. Sci. USA106(27) , 11258–11263 (2009).
  • Chi TH , WanM, LeePP et al.: Sequential roles of Brg, the ATPase subunit of BAF chromatin remodeling complexes, in thymocyte development.Immunity19(2) , 169–182 (2003).
  • Jani A , WanM, ZhangJ et al.: A novel genetic strategy reveals unexpected roles of the Swi-Snf-like chromatin-remodeling BAF complex in thymocyte development.J. Exp. Med.205(12) , 2813–2825 (2008).
  • Williams CJ , NaitoT, ArcoPG et al.: The chromatin remodeler Mi-2β is required for CD4 expression and T-cell development.Immunity20(6) , 719–733 (2004).
  • Gebuhr TC , KovalevGI, BultmanS, GodfreyV, SuL, MagnusonT: The role of Brg1, a catalytic subunit of mammalian chromatin-remodeling complexes, in T cell development.J. Exp. Med.198(12) , 1937–1949 (2003).
  • Zhang F , BoothbyM: T helper type 1-specific Brg1 recruitment and remodeling of nucleosomes positioned at the IFN-γ promoter are Stat4 dependent.J. Exp. Med.203(6) , 1493–1505 (2006).
  • Wurster AL , PazinMJ: BRG1-mediated chromatin remodeling regulates differentiation and gene expression of T helper cells.Mol. Cell. Biol.28(24) , 7274–7285 (2008).
  • Gyory I , WuJ, FejerG, SetoE, WrightKL: PRDI-BF1 recruits the histone H3 methyltransferase G9a in transcriptional silencing.Nat. Immunol.5(3) , 299–308 (2004).
  • Tachibana M , SugimotoK, FukushimaT, ShinkaiY: Set domain-containing protein, G9a, is a novel lysine-preferring mammalian histone methyltransferase with hyperactivity and specific selectivity to lysines 9 and 27 of histone H3.J. Biol. Chem.276(27) , 25309–25317 (2001).
  • Agarwal S , RaoA: Modulation of chromatin structure regulates cytokine gene expression during T cell differentiation.Immunity9(6) , 765–775 (1998).
  • Agarwal S , ViolaJP, RaoA: Chromatin-based regulatory mechanisms governing cytokine gene transcription.J. Allergy Clin. Immunol.103(6) , 990–999 (1999).
  • Agarwal S , AvniO, RaoA: Cell-type-restricted binding of the transcription factor NFAT to a distal IL-4 enhancer in vivo.Immunity12(6) , 643–652 (2000).
  • Schoenborn JR , DorschnerMO, SekimataM et al.: Comprehensive epigenetic profiling identifies multiple distal regulatory elements directing transcription of the gene encoding interferon-γ.Nat. Immunol.8(7) , 732–742 (2007).
  • Miller SA , HuangAC, MiazgowiczMM, BrassilMM, WeinmannAS: Coordinated but physically separable interaction with H3K27-demethylase and H3K4-methyltransferase activities are required for T-box protein-mediated activation of developmental gene expression.Genes Dev.22(21) , 2980–2993 (2008).
  • Tong Y , AuneT, BoothbyM: T-bet antagonizes mSin3a recruitment and transactivates a fully methylated IFN-γ promoter via a conserved T-box half-site.Proc. Natl Acad. Sci. USA102(6) , 2034–2039 (2005).
  • Spilianakis CG , LaliotiMD, TownT, LeeGR, FlavellRA: Interchromosomal associations between alternatively expressed loci.Nature435(7042) , 637–645 (2005).
  • Spilianakis CG , FlavellRA: Long-range intrachromosomal interactions in the T helper type 2 cytokine locus.Nat. Immunol.5(10) , 1017–1027 (2004).
  • Cai S , LeeCC, Kohwi-ShigematsuT: SATB1 packages densely looped, transcriptionally active chromatin for coordinated expression of cytokine genes.Nat. Genet.38(11) , 1278–1288 (2006).
  • Stock JK , GiadrossiS, CasanovaM et al.: Ring1-mediated ubiquitination of H2A restrains poised RNA polymerase II at bivalent genes in mouse ES cells.Nat. Cell Biol.9(12) , 1428–1435 (2007).
  • Noer A , LindemanLC, CollasP: Histone H3 modifications associated with differentiation and long-term culture of mesenchymal adipose stem cells.Stem Cells Dev.18(5) , 725–736 (2009).
  • Rodriguez CR , ChoEJ, KeoghMC, MooreCL, GreenleafAL, BuratowskiS: Kin28, the TFIIH-associated carboxy-terminal domain kinase, facilitates the recruitment of mRNA processing machinery to RNA polymerase II.Mol. Cell. Biol.20(1) , 104–112 (2000).
  • Wei G , WeiL, ZhuJ et al.: Global mapping of H3K4me3 and H3K27me3 reveals specificity and plasticity in lineage fate determination of differentiating CD4+ T cells.Immunity30(1) , 155–167 (2009).
  • Weishaupt H , SigvardssonM, AttemaJL: Epigenetic chromatin states uniquely define the developmental plasticity of murine hematopoietic stem cells.Blood115(2) , 247–256 (2010).
  • Mukasa R , BalasubramaniA, LeeYK et al.: Epigenetic instability of cytokine and transcription factor gene loci underlies plasticity of the T helper 17 cell lineage.Immunity32(5) , 616–627 (2010).
  • Celniker SE , DillonLA, GersteinMB et al.: Unlocking the secrets of the genome.Nature459(7249) , 927–930 (2009).
  • Perales R , BentleyD: ‘Cotranscriptionality‘: the transcription elongation complex as a nexus for nuclear transactions.Mol. Cell36(2) , 178–191 (2009).
  • Massie CE , MillsIG: ChIPping away at gene regulation.EMBO Rep.9(4) , 337–343 (2008).
  • Impey S , McCorkleSR, Cha-MolstadH et al.: Defining the CREB regulon: a genome-wide analysis of transcription factor regulatory regions.Cell119(7) , 1041–1054 (2004).
  • Johnson DS , MortazaviA, MyersRM, WoldB: Genome-wide mapping of in vivo protein–DNA interactions.Science316(5830) , 1497–1502 (2007).
  • Robertson G , HirstM, BainbridgeM et al.: Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing.Nat. Methods4(8) , 651–657 (2007).
  • Schones DE , ZhaoK: Genome-wide approaches to studying chromatin modifications.Nat. Rev. Genet.9(3) , 179–191 (2008).
  • Wei CL , WuQ, VegaVB et al.: A global map of p53 transcription-factor binding sites in the human genome.Cell124(1) , 207–219 (2006).
  • Kaufmann SH : The contribution of immunology to the rational design of novel antibacterial vaccines.Nat. Rev. Microbiol.5(7) , 491–504 (2007).
  • Dong C : Diversification of T-helper-cell lineages: finding the family root of IL-17–producing cells.Nat. Rev. Immunol.6(4) , 329–333 (2006).
  • Weaver CT , HarringtonLE, ManganPR, GavrieliM, MurphyKM: Th17: an effector CD4 T cell lineage with regulatory T cell ties.Immunity24(6) , 677–688 (2006).
  • Mosmann TR , CoffmanRL: TH1 and TH2 cells: different patterns of lymphokine secretion lead to different functional properties.Annu. Rev. Immunol.7 , 145–173 (1989).
  • Korn T , BettelliE, OukkaM, KuchrooVK: IL-17 and Th17 Cells.Annu. Rev. Immunol.27 , 485–517 (2009).
  • Corthay A : How do regulatory T cells work?Scand. J. Immunol.70(4) , 326–336 (2009).
  • Santana MA , RosensteinY: What it takes to become an effector T cell: the process, the cells involved, and the mechanisms.J. Cell. Physiol.195(3) , 392–401 (2003).

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