SEARCH

SEARCH BY CITATION

References

  • Adlam M, Siu G (2003) Hierarchical interactions control CD4 gene expression during thymocyte development. Immunity 18: 173184
  • Anderson MK (2006) At the crossroads: diverse roles of early thymocyte transcriptional regulators. Immunol Rev 209: 191211
  • Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K (2007) High-resolution profiling of histone methylations in the human genome. Cell 129: 823837
  • Benoukraf T, Cauchy P, Fenouil R, Jeanniard A, Koch F, Jaeger S, Thieffry D, Imbert J, Andrau JC, Spicuglia S, Ferrier P (2009) CoCAS: a ChIP-on-chip analysis suite. Bioinformatics (Oxford, England) 25: 954955
  • Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, Fry B, Meissner A, Wernig M, Plath K, Jaenisch R, Wagschal A, Feil R, Schreiber SL, Lander ES (2006) A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125: 315326
  • Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P et al (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799816
  • Bonnet M, Huang F, Benoukraf T, Cabaud O, Verthuy C, Boucher A, Jaeger S, Ferrier P, Spicuglia S (2009) Duality of enhancer functioning mode revealed in a reduced TCRβ gene enhancer knockin mouse model. J Immunol 183: 79397948
  • Boyer LA, Lee TI, Cole MF, Johnstone SE, Levine SS, Zucker JP, Guenther MG, Kumar RM, Murray HL, Jenner RG, Gifford DK, Melton DA, Jaenisch R, Young RA (2005) Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122: 947956
  • Bulger M, Groudine M (2011) Functional and mechanistic diversity of distal transcription enhancers. Cell 144: 327339
  • Buratowski S (2009) Progression through the RNA polymerase II CTD cycle. Mol Cell 36: 541546
  • Capone M, Watrin F, Fernex C, Horvat B, Krippl B, Scollay R, Ferrier P (1993) TCRα and TCRβ gene enhancers confer tissue- and stage-specificity on V(D)J recombination events. EMBO J 12: 43354346
  • Chattopadhyay S, Whitehurst CE, Schwenk F, Chen J (1998) Biochemical and functional analyses of chromatin changes at the TCRβ gene locus during CD4−CD8− to CD4+CD8+ thymocyte differentiation. J Immunol 160: 12561267
  • Cherrier M, D'Andon MF, Rougeon F, Doyen N (2008) Identification of a new cis-regulatory element of the terminal deoxynucleotidyl transferase gene in the 5′ region of the murine locus. Mol Immunol 45: 10091017
  • Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, Steine EJ, Hanna J, Lodato MA, Frampton GM, Sharp PA, Boyer LA, Young RA, Jaenisch R (2010) Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci USA 107: 2193121936
  • Cui K, Zang C, Roh TY, Schones DE, Childs RW, Peng W, Zhao K (2009) Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation. Cell Stem Cell 4: 8093
  • De Santa F, Barozzi I, Mietton F, Ghisletti S, Polletti S, Tusi BK, Muller H, Ragoussis J, Wei CL, Natoli G (2010) A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol 8: e1000384
  • Georgopoulos K, van den Elsen P, Bier E, Maxam A, Terhorst C (1988) A T cell-specific enhancer is located in a DNase I-hypersensitive area at the 3′ end of the CD3-delta gene. EMBO J 7: 24012407
  • Ghisletti S, Barozzi I, Mietton F, Polletti S, De Santa F, Venturini E, Gregory L, Lonie L, Chew A, Wei CL, Ragoussis J, Natoli G (2010) Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages. Immunity 32: 317328
  • Guenther MG, Levine SS, Boyer LA, Jaenisch R, Young RA (2007) A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130: 7788
  • Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP, Cabili MN, Jaenisch R, Mikkelsen TS, Jacks T, Hacohen N, Bernstein BE, Kellis M, Regev A, Rinn JL, Lander ES (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458: 223227
  • Hayday AC, Pennington DJ (2007) Key factors in the organized chaos of early T cell development. Nat Immunol 8: 137144
  • He HH, Meyer CA, Shin H, Bailey ST, Wei G, Wang Q, Zhang Y, Xu K, Ni M, Lupien M, Mieczkowski P, Lieb JD, Zhao K, Brown M, Liu XS (2010) Nucleosome dynamics define transcriptional enhancers. Nat Genet 42: 343347
  • Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW, Ching KA, ntosiewicz-Bourget JE, Liu H, Zhang X, Green RD, Lobanenkov VV, Stewart R, Thomson JA, Crawford GE, Kellis M et al (2009) Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459: 108112
  • Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA, Wang W, Weng Z, Green RD, Crawford GE, Ren B (2007) Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet 39: 311318
  • Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK (2010) Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell 38: 576589
  • Hernandez-Munain C, Sleckman BP, Krangel MS (1999) A developmental switch from TCRδ enhancer to TCRα enhancer function during thymocyte maturation. Immunity 10: 723733
  • Hoffman BG, Robertson G, Zavaglia B, Beach M, Cullum R, Lee S, Soukhatcheva G, Li L, Wederell ED, Thiessen N, Bilenky M, Cezard T, Tam A, Kamoh B, Birol I, Dai D, Zhao Y, Hirst M, Verchere CB, Helgason CD et al (2010) Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver. Genome Res 20: 10371051
  • Hoffmann R, Bruno L, Seidl T, Rolink A, Melchers F (2003) Rules for gene usage inferred from a comparison of large-scale gene expression profiles of T and B lymphocyte development. J Immunol 170: 13391353
  • Hon G, Wang W, Ren B (2009) Discovery and annotation of functional chromatin signatures in the human genome. PLoS Comput Biol 5: e1000566
  • Hosoya-Ohmura S, Lin YH, Herrmann M, Kuroha T, Rao A, Moriguchi T, Lim KC, Hosoya T, Engel JD (2011) An NK and T cell enhancer lies 280 kilobase pairs 3′ to the gata3 structural gene. Mol Cell Biol 31: 18941904
  • Huber W, von Heydebreck A, Sultmann H, Poustka A, Vingron M (2002) Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics (Oxford, England) 18(Suppl 1): S96S104
  • Jenuwein T, Allis CD (2001) Translating the histone code. Science (New York, NY) 293: 10741080
  • Jiang H, Zhang F, Kurosu T, Peterlin BM (2005) Runx1 binds positive transcription elongation factor b and represses transcriptional elongation by RNA polymerase II: possible mechanism of CD4 silencing. Mol Cell Biol 25: 1067510683
  • Kaufmann C, Yoshida T, Perotti EA, Landhuis E, Wu P, Georgopoulos K (2003) A complex network of regulatory elements in Ikaros and their activity during hemo-lymphopoiesis. EMBO J 22: 22112223
  • Kim TK, Hemberg M, Gray JM, Costa AM, Bear DM, Wu J, Harmin DA, Laptewicz M, Barbara-Haley K, Kuersten S, Markenscoff-Papadimitriou E, Kuhl D, Bito H, Worley PF, Kreiman G, Greenberg ME (2010) Widespread transcription at neuronal activity-regulated enhancers. Nature 465: 182187
  • Koch F, Jourquin F, Ferrier P, Andrau JC (2008) Genome-wide RNA polymerase II: not genes only!. Trends Biochem Sci 33: 265273
  • Krangel MS (2007) T cell development: better living through chromatin. Nat Immunol 7: 687694
  • Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25
  • Lauzurica P, Krangel MS (1994) Temporal and lineage-specific control of T cell receptor α/δ gene rearrangement by T cell receptor α and δ enhancers. J Exp Med 179: 19131921
  • Li B, Carey M, Workman JL (2007) The role of chromatin during transcription. Cell 128: 707719
  • Lin YC, Jhunjhunwala S, Benner C, Heinz S, Welinder E, Mansson R, Sigvardsson M, Hagman J, Espinoza CA, Dutkowski J, Ideker T, Glass CK, Murre C (2010) A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate. Nat Immunol 11: 635643
  • Lupien M, Eeckhoute J, Meyer CA, Wang Q, Zhang Y, Li W, Carroll JS, Liu XS, Brown M (2008) FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. Cell 132: 958970
  • Marenduzzo D, Faro-Trindade I, Cook PR (2007) What are the molecular ties that maintain genomic loops? Trends Genet 23: 126133
  • Medlin J, Scurry A, Taylor A, Zhang F, Peterlin BM, Murphy S (2005) P-TEFb is not an essential elongation factor for the intronless human U2 snRNA and histone H2b genes. EMBO J 24: 41544165
  • Mellor J, Dudek P, Clynes D (2008) A glimpse into the epigenetic landscape of gene regulation. Curr Opin Genet Dev 18: 116122
  • Mendenhall EM, Bernstein BE (2008) Chromatin state maps: new technologies, new insights. Curr Opin Genet Dev 18: 109115
  • Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, Lee W, Mendenhall E, O'Donovan A, Presser A, Russ C, Xie X, Meissner A, Wernig M, Jaenisch R, Nusbaum C et al (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448: 553560
  • Mombaerts P, Terhorst C, Jacks T, Tonegawa S, Sancho J (1995) Characterization of immature thymocyte lines derived from T-cell receptor or recombination activating gene 1 and p53 double mutant mice. Proc Natl Acad Sci USA 92: 74207424
  • Natoli G (2010) Maintaining cell identity through global control of genomic organization. Immunity 33: 1224
  • Ng HH, Robert F, Young RA, Struhl K (2003) Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity. Mol Cell 11: 709719
  • Nicol JW, Helt GA, Blanchard Jr SG, Raja A, Loraine AE (2009) The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. Bioinformatics (Oxford, England) 25: 27302731
  • Pekowska A, Benoukraf T, Ferrier P, Spicuglia S (2010) A unique H3K4me2 profile marks tissue-specific gene regulation. Genome Res 20: 14931502
  • Phatnani HP, Greenleaf AL (2006) Phosphorylation and functions of the RNA polymerase II CTD. Genes Dev 20: 29222936
  • Puthier D, Joly F, Irla M, Saade M, Victorero G, Loriod B, Nguyen C (2004) A general survey of thymocyte differentiation by transcriptional analysis of knockout mouse models. J Immunol 173: 61096118
  • Rada-Iglesias A, Bajpai R, Swigut T, Brugmann SA, Flynn RA, Wysocka J (2011) A unique chromatin signature uncovers early developmental enhancers in humans. Nature 470: 279283
  • Rahl PB, Lin CY, Seila AC, Flynn RA, McCuine S, Burge CB, Sharp PA, Young RA (2010) c-Myc regulates transcriptional pause release. Cell 141: 432445
  • Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, Simon I, Zeitlinger J, Schreiber J, Hannett N, Kanin E, Volkert TL, Wilson CJ, Bell SP, Young RA (2000) Genome-wide location and function of DNA binding proteins. Science 290: 23062309
  • Robertson AG, Bilenky M, Tam A, Zhao Y, Zeng T, Thiessen N, Cezard T, Fejes AP, Wederell ED, Cullum R, Euskirchen G, Krzywinski M, Birol I, Snyder M, Hoodless PA, Hirst M, Marra MA, Jones SJ (2008) Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding. Genome Res 18: 19061917
  • Schmidl C, Klug M, Boeld TJ, Andreesen R, Hoffmann P, Edinger M, Rehli M (2009) Lineage-specific DNA methylation in T cells correlates with histone methylation and enhancer activity. Genome Res 19: 11651174
  • Selth LA, Sigurdsson S, Svejstrup JQ (2010) Transcript elongation by RNA polymerase II. Annu Rev Biochem 79: 271293
  • Senoo M, Shinkai Y (1998) Regulation of Vβ germline transcription in RAG-deficient mice by the CD3epsilon-mediated signals: implication of Vβ transcriptional regulation in TCRβ allelic exclusion. Int Immunol 10: 553560
  • Shinkai Y, Rathbun G, Lam KP, Oltz EM, Stewart V, Mendelsohn M, Charron J, Datta M, Young K, Stall AL, Alt FW (1992) RAG-2 deficient mice lack mature lymphocytes owing to inability to initiate V(D)J rearrangement. Cell 68: 855867
  • Sleckman BP, Bardon CG, Ferrini R, Davidson L, Alt FW (1997) Function of the TCRα enhancer in αβ and γδ T cells. Immunity 7: 505515
  • Smyth GK (2004) Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3: Article3
  • Spicuglia S, Kumar S, Yeh JH, Vachez E, Chasson L, Gorbatch S, Cautres J, Ferrier P (2002) Promoter activation by enhancer-dependent and -independent loading of activator and coactivator complexes. Mol Cell 10: 14791487
  • Spicuglia S, Payet D, Tripathi RK, Rameil P, Verthuy C, Imbert J, Ferrier P, Hempel WM (2000) TCRα enhancer activation occurs via a conformational change of a pre-assembled nucleo-protein complex. EMBO J 19: 20342045
  • Taniuchi I, Ellmeier W, Littman DR (2004) The CD4/CD8 lineage choice: new insights into epigenetic regulation during T cell development. Adv Immunol 83: 5589
  • Tan-Wong SM, French JD, Proudfoot NJ, Brown MA (2008) Dynamic interactions between the promoter and terminator regions of the mammalian BRCA1 gene. Proc Natl Acad Sci USA 105: 51605165
  • Toedling J, Skylar O, Krueger T, Fischer JJ, Sperling S, Huber W (2007) Ringo--an R/Bioconductor package for analyzing ChIP-chip readouts. BMC Bioinformatics 8: 221
  • Umlauf D, Goto Y, Feil R (2004) Site-specific analysis of histone methylation and acetylation. Methods Mol Biol 287: 99120
  • Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F, Afzal V, Ren B, Rubin EM, Pennacchio LA (2009) ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457: 854858
  • von Boehmer H (2005) Unique features of the pre-T-cell receptor alpha-chain: not just a surrogate. Nat Rev Immunol 5: 571577
  • Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY, Peng W, Zhang MQ, Zhao K (2008) Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet 40: 897903
  • Xu J, Pope SD, Jazirehi AR, Attema JL, Papathanasiou P, Watts JA, Zaret KS, Weissman IL, Smale ST (2007) Pioneer factor interactions and unmethylated CpG dinucleotides mark silent tissue-specific enhancers in embryonic stem cells. Proc Natl Acad Sci USA 104: 1237712382
  • Xu J, Watts JA, Pope SD, Gadue P, Kamps M, Plath K, Zaret KS, Smale ST (2009) Transcriptional competence and the active marking of tissue-specific enhancers by defined transcription factors in embryonic and induced pluripotent stem cells. Genes Dev 23: 28242838