Large-scale chromatin remodeling at the immunoglobulin heavy chain locus: Aparadigm for multigene regulation

Advances in Experimental Medicine and Biology

Volumn 650, Issue , 2009, Pages 59-72

  Bolland, Daniel J ^a   Wood, Andrew L ^a   Corcoran, Anne E ^a  

^a BABRAHAM INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

IMMUNOGLOBULIN HEAVY CHAIN; T LYMPHOCYTE RECEPTOR;

ARTICLE; B LYMPHOCYTE; CELL MATURATION; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMATIN STRUCTURE; DOUBLE STRANDED DNA BREAK; GENE EXPRESSION REGULATION; GENE FREQUENCY; GENE LOCUS; GENETIC RECOMBINATION; GENETIC TRANSCRIPTION; HISTONE MODIFICATION; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN CONFORMATION; T LYMPHOCYTE; VDJ EXON; ALLELE; ANIMAL; CHROMATIN; GENE REARRANGEMENT; GENETICS; IMMUNOLOGY; METABOLISM; PHYSIOLOGY; REVIEW; ULTRASTRUCTURE;

MAMMALIA;

ALLELES; ANIMALS; B-LYMPHOCYTES; CHROMATIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; GENE EXPRESSION REGULATION; GENE REARRANGEMENT; IMMUNOGLOBULIN HEAVY CHAINS; RECOMBINATION, GENETIC; TRANSCRIPTION, GENETIC;

EID: 70349581224     PISSN: 00652598     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4419-0296-2_5     Document Type: Article

References (89)

1. Hesslein DG, Schatz DG. Factors and forces controlling V(D)J recombination. Adv Immunol 2001; 78:169-232. (Pubitemid 32566020)
2. Corcoran AE, Immunoglobulin locus silencing and allelic exclusion. Sernin Immunol 2005; 17(2):141-154. (Pubitemid 40289217)
3. Johnston CM, Wood AL, Bolland OJ et al. Complete sequence assembly and characterization of the C57BLl6 mouseIgheavy chainV region. J Immunol2006; 176(7):4221-4234. (Pubitemid 44264401)
4. Brekke KM, Garrard WT. Assembly and analysis of the mouse immunoglobulin kappa gene sequence. Immunogenetics 2004; 56(7):490-505. (Pubitemid 39517831)
5. Ye J, The immunoglobulin IGHD gene locus in C57BL/6 mice. Immunogenetics 2004; 56(6):399-404. (Pubitemid 39349882)
6. Atkinson MJ, Michnick DA, PaigeCJ et al. Iggenerearrangements on individual alleles of Abelson murine leukemia cell lines from (C57BL/6 × BALB/c) Fl fetal livers. J Immunoll991; 146(8):2805-2812.
7. Jeong HD, Komisar JL, Kraig E et al. Strain-dependentexpression of VH genefamilies.J Immunol 1988; 140(7):2436-2441.
8. MalynnBA, Yancopoulos GO, BarthJE et aL Biased expression of JH-proximal VH genesoccursin the newlygeneratedrepertoire of neonataland adult mice. J Exp Med 1990; 171(3):843-859. (Pubitemid 20088986)
9. MatsudaF, IshiiK, Bourvagnet P et al. The complete nucleotidesequence of the human immunoglobulin heavy chain variable regionlocus. J Exp Med 1998; 188(11):2151-2162. (Pubitemid 28562531)
10. Hiom K, MelekM, GellertM. DNA transposition by the RAG1 and RAG2proteins: a possible source of oncogenic translocarions, Cell 1998; 94(4):463-470. (Pubitemid 28391862)
11. JonesJM, GellertM. Thetamingof a transposon: V(D)Jrecombination and the immunesystem. Immunol Rev 2004; 200:233-248.
12. Retter I, Chevillard C, Scharfe M et al. Sequence and Characterization of the Ig Heavy Chain Constant and Partial Variable Region of the Mouse Strain 129S1. J Immunol 2007; 179(4):2419-2427.
13. McBlane F, Boyes J. Stimulation of V(D)J recombination by histone acetylation. Curr Bioi 2000; 10(8):483-486. (Pubitemid 30247339)
14. Mattick JS, The functional genomics of noncodingRNA. Science 2005; 309(5740):1527-1528. (Pubitemid 41266470)
15. Lennon GG, Perry RP. C mu-containing transcripts initiate heterogeneously within the IgH enhancer region and contain a novel 5′-snontranslatable exon. Narure 1985;318(6045):475-478. (Pubitemid 16195850)
16. Thompson A, Timmers E, Schuurman RK et al. Immunoglobulin heavy chain germ-line JH-C mu transcription in human precursor B.lymphocytes initiates in a unique region upstream of DQ52. Eur J Immuno11995; 25(1):257-261.
17. Reth MG, Ale FW: Novel immunoglobulin heavy chains are produced from DJH genesegment rearrangements in lymphoid cells. Nature 1984; 312(5993):418-423. (Pubitemid 15217834)
18. Yancopoulos GO, Alt FW:Developmentally controlledand tissue-specific expression of unrearranged VH gene segments. Cell 1985; 40(2):271-281. (Pubitemid 15138455)
19. Corcoran AE, Riddell A, Krooshoop 0 et al. Impaired immunoglobulin gene rearrangement in mice lacking the IL-7 receptor. Nature 1998; 391(6670):904-907. (Pubitemid 28157669)
20. Krangel MS, Gene segment selection in V(D)J recombination: accessibility and beyond. Nat Immunol 2003; 4(7):624-630. (Pubitemid 36874434)
21. Stanhope-Baker P, Hudson KM, Shaffer AL et al, Cell type-specific chromatin structure determines the targeting of V(D)J recombinase activity in vitro. Cell 1996; 85(6):887-897. (Pubitemid 26192139)
22. Bolland OJ, Wood AL, Johnston CM et al. Antisense intergenic transcription in V(D)J recombination. Nat Immunol2004; 5(6):630-637. (Pubitemid 38811888)
23. Osborne CS, Chakalova L, Mitchell JA et al. Myc dynamically and preferentially relocates to a transcription factoty occupiedby lgh, PLoS Bioi 2007; 5(8):e192.
24. Fraser P, Transcriptional control thrown for a loop. CUrt Opin Genet Dev 2006; 16(5):490-495. (Pubitemid 44345199)
25. Johnson K, Pough DL, Yu O et al. B-cell-specific lossof histone3 lysine 9 methylation in the V(H) locus depends on Pax5. Nat Immunol2004; 5(8):853-861. (Pubitemid 39172979)
26. GribnauJ, Diderich K, Pruzina S et al. Intergenic transcription and developmental remodeling of chromarin subdomains in the human beta-globin locus. Mol Cell 2000; 5(2):377-386. (Pubitemid 30628094)
27. DrewellRA, BaeE, BurrJ et al. Transcription defines the embryonic domainsof cis-regulatory activity at the Drosophilabithorax complex. Proc Nad AcadSci USA2002; 99(26):16853-16858. (Pubitemid 36034062)
28. Masternak K, Peyraud N, Krawczyk M et al. Chromatin remodeling and extragenic transcription at the MHC class II locus control region. Nat Immunol 2003; 4(2):132-137. (Pubitemid 36193014)
29. Bernstein BE, KamalM, Lindblad-Toh K et al. Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 2005; 120(2):169-181. (Pubitemid 40174761)
30. Wilson CJ, ChaoOM, Imbalzano AN et al. RNApolymerase II holoenzyme containsSWI/SNF regula-tors involved in chromatinremodeling. Cell 1996; 84(2):235-244. (Pubitemid 26040843)
31. Cho H, OrphanidesG, SunX et al.A humanRNApolymerase II complex containingfactors that modify chromatin structure. Mol Cell Bioi 1998; 18(9):5355-5363. (Pubitemid 28388118)
32. WittschiebenBO, Otero G, de Bizemont T et al. A novelhistone acetyltransfcrase is an integralsubunit of elongating RNA polymerase II holoenzyme. Mol Cell 1999;4(l):123-128. (Pubitemid 29386138)
33. KroganNJ, KimM, TongA et al. Methylation of histoneH3 bySet2 in Saccharomyces cerevisiae is linked to rranscriptional elongation by RNA polymerase II. Mol Cell Bioi2003; 23(12):4207-4218. (Pubitemid 36666424)
34. Ng HH, Robert F, Young RA et al Targeted recruitment of Setl histone methylase by elongating Pol II provides a localized mark and memoryof recent transcriptional activity. Mol Cell 2003; 11(3):709-719. (Pubitemid 36385124)
35. Schwartz BE,Ahmad K. Transcriptional activation triggers deposition and removal of the histonevariant H3.3. GenesDev 2005; 19(7):804-814.
36. Mito Y,HenikoffJG, HenikoffS.Genome-scaleprofiling of histoneH3.3 replacement patterns.Nat Genet 2005.
37. Orphanides G, Rcinberg D. RNA polymerase II elongation through chromatin . Nature 2000; 407(6803):471-475.
38. Chakalova L, Debrand E, MitchellJA et al. Replication and rranscription: shaping the landscape of the genome. Nat RevGenet 2005; 6(9):669-677. (Pubitemid 41192318)
39. Mahy NL, PerryPE, Bickmore WA. Genedensityand transcription influence the localization of chromatin outsideof chromosome territories detectableby FISH.J Cell Bioi2002; 159(5):753-763. (Pubitemid 36008358)
40. MullerWG, Walker D, HagerGLet al. Large-scale chromatin dccondcnsation and recondensation regulated by transcription from a natural promoter.J Cell Bioi2001; 154(1):33-48. (Pubitemid 34289276)
41. Volpi EY, Chevret E, JonesT et al. Large-scale chromatin organization of the major histocompatibility complex and other regions of humanchromosome 6 and its response to interferonin interphase nuclei. J Cell Sci 2000; 113 ( Pt 9):1565-1576. (Pubitemid 30312505)
42. Chambeyron S, Da Silva NR, Lawson KA et al, Nuclear re-organisation of the Hoxb complex during mouseembryonic development. Development 2005; 132(9):2215-2223. (Pubitemid 40744480)
43. Schmitt S, Prestel M, Paro R. Ineergenic transcription through a polycomb group response element counteracts silencing.Genes Dev 2005; 19(6):697-708. (Pubitemid 40395081)
44. Ho Y, Elefant F, Liebhaber SAet al. Locusconrrol region transcription plays an active role in long-range gene activation. Mol Cell 2006; 23(3):365-375. (Pubitemid 44128843)
45. Sleutels F, Zwart R, Barlow DP. The noncodingAir RNA is required for silencing autosomal imprinted genes. Nature 2002; 415(6873):810-813. (Pubitemid 34150505)
46. Grewal SI, Jia S. Heterochromatin revisited. Nat RevGenet 2007; 8(1):35-46. (Pubitemid 46006048)
47. SlotkinRK, Martienssen R. Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet 2007; 8(4):272-285. (Pubitemid 46439291)
48. Katayama S,Tomaru Y,Kasukawa T et al. Antisense transcription in the mammalian transcriptome, Science 2005; 309(5740):1564-1566.
49. RinnJL, Kertesz M, WangJK et al. Functional Demarcation of Active and SilentChromatin Domains in Human HOX Loci by NoncodingRNAs. Cell 2007; 129(7):1311-1323. (Pubitemid 46962090)
50. Uhler JP, Hertel C, Svejstrup JQ, A role for noncoding transcription in activation of the yeast PH05 gene. Proc Natl Acad Sci USA 2007;104(19) :8011-8016. (Pubitemid 47185867)
51. Sessa L, Breiling A, Lavorgna G et al. NoncodingRNA synthesis and lossof Polycomb group repression accompanies the colinear activation of the human HOXA cluster. RNA 2007; 13(2):223-239. (Pubitemid 46147898)
52. Chowdhury D, Sen R. Stepwise activation of the immunoglobulin mu heavychain gene locus. EMBOJ 2001; 20(22):6394-6403. (Pubitemid 33078712)
53. MaesJ, O'Neill LP, Cavelier P et aLChromatin remodeling at the Ig loci prior to V(D)J recombination. J Immunol2001; 167(2):866-874. (Pubitemid 32660842)
54. Johnson K, Angelin-Duclos C, Park S et al. Changes in histone acetylation are associated with differences in accessibility of V(H) gene segments to V-DJ recombination during B-cellontogenyand development. Mol Cell Bioi 2003; 23(7):2438-2450. (Pubitemid 36351025)
55. Su IH, Basavaraj A, Krurchinsky AN et al. Ezh2 controls B-cc11 development throughhistone H3 methylation and Igh rearrangement. Nat Immunol 2003; 4(2):124-131. (Pubitemid 36193013)
56. Bolland DJ, Wood AL, Afshar R et al. Antisense intergenic transcription precedes Jgh Dvro-J recombination and is controlled by the intronic enhancer Emu. Mol Cell Bioi2007; 27(15):5523-5533. (Pubitemid 47124404)
57. SakaiE, BottaroA, Davidson L et al. Recombination and transcription of the endogenous Ig heavy chain locus is effected by the lg heavy chain inrronic enhancercore region in the absence of the matrixattachment regions. Proc Natl Acad Sci USA 1999; 96(4):1526-1531. (Pubitemid 29098484)
58. Serwe M, Sablitzky F.V(D)J recombination in B-cells is impairedbut not blocked by targeted deletion of the immunoglobulin heavy chain intron enhancer. EMBOJ 1993; 12(6):2321-2327. (Pubitemid 23194182)
59. Perlor T, Alr FW,Bassing CH et al. Elucidation of IgH intronic enhancer functions viagerm-line deletion. Proc Natl Acad Sci USA 2005; 102(40):14362-14367. (Pubitemid 41429703)
60. Afshar R, Pierce S, Bolland DJ et al. Regulation of IgH Gene Assembly: Role of the Intronic Enhancer and 5′DQ52 Regionin Targeting DHJH Recombination.J Immunol 2006; 176(4):2439-2447. (Pubitemid 43201694)
61. Morshead KB,Ciccone DN. Taverna SD et al. Antigen receptor locipoisedfor V(D)J rearrangement are broadly associated with BRG1 and Aanked by peaks of histoneH3 dimethylated at lysine 4. Proc Natl Acad SciUSA2003: 100(20):11577-11582. (Pubitemid 37205978)
62. Maes J, Chappaz S. Cavelier P et al. Activation of V(D)J Recombination at the IgHChainJH Locus Occurswithina 6-Kilobase ChromatinDomainand IsAssociated with Nucleosomal Remodelmg.J hnmunol 2006; 176(9):5409-5417.
63. Bangs LA, SanzIE. Teale JM. Comparison of D.JH and junctionaldiversity in the fetal. adult and aged Bvcell reperroires.J hnmuno11991: 146(6):1996-2004.
64. Chakraborty T, Chowdhury D. Keyes A et al. Repeat organization and epigenetic regulation of the DH-Cmu domain of the immunoglobulin heavy-chain genelocus. Mol Cell 2007;27(5):842-850. (Pubitemid 47333226)
65. Abarrategui I, Krangel MS. Regulation of T-cell receptor-alpha gene recombination by transcription. Nat ImmunoI 2006: 7(10):1109-1115.
66. Chowdhury D, Sen R. Stepwise activation of the immunoglobulin mu heavy chain gene locus. EMBO J 2001: 20(22):6394-6403. (Pubitemid 33078712)
67. Hesslein DG,PAugh DL. Chowdhury D et al. paxs isrequired for recombination of transcribed. acerylared, 5′ IgH V genesegments. Genes Dev 2003: 17(1):37-42. (Pubitemid 36062506)
68. Maes J, Chappaz S. Cavelier P et al. Activation of V(D)J recombination at the IgH chainJH locus occurs within a 6-kilobase chromatin domainand is associated with nucleosomal remodeling.J Immunol 2006; 176(9):5409-5417.
69. Kosak ST, SkokJA. MedinaKL et al. Subnuclear compartmentalization of immunoglobulin loci during lymphocyte development. Science 2002: 296(5565):158-162. (Pubitemid 34280078)
70. Yang Q,Riblee R. Schildkraut CL. Sites that direct nuclear compartmentalization are near the 5′ end of the mouse immunoglobulin heavy-chain locus. Mol Cell Bioi2005; 25(14):6021-6030. (Pubitemid 40946555)
71. Fuxa M, SkokJ, Souabni A et al. Pax5 induces V-to-DJ rearrangements and locus contraction of the immunoglobulin heavy-chain gene. Genes Dev 2004; 18(4):411-422. (Pubitemid 38316348)
72. Roldan E, Fuxa M. ChongWet al. Locus 'decontracrion' and centromeric recruitment contribute to allelic exclusion of the immunoglobulin heavy-chain gene. Nat Immunol 2005;6(1):31-41. (Pubitemid 40136693)
73. Sayegh C, Jhunjhunwala S. Riblet R et al. Visualization of looping involving the immunoglobulin heavy-chainlocus in developing Bscells. Genes Dev 2005; 19(3):322-327. (Pubitemid 40189295)
74. Cobaleda C, Schebesta A. DeloguAet al. Pax5: the guardian of B-cell identity and function. Nat hnmunol 2007: 8(5):463-470. (Pubitemid 46605911)
75. Liu H, Schmidt-Supprian M. Shi Y et al. Yin Yang 1 is a critical regulator ofB-cell development. Genes Dev 2007: 21(10):1179-1189. (Pubitemid 46789876)
76. Ibarra FJ,Pombo A.Jackson DAet al.Active RNApolymerases arelocalizedwithindiscrete transcription 'factories' in humannuclei.J Cell Sci 1996: 109 (Pt 6):1427-1436. (Pubitemid 26190492)
77. Faro-Trindade I. Cook PRo Transcription factories: structures conserved durin gdifferentiation and evolution. Biochem Soc Trans 2006: 34(Pt 6):1133-1137. (Pubitemid 46769004)
78. Osborne CS, Chakalova L. Brown KE et al. Active genes dynamically colocalize to sharedsites of ongoing transcription. Nat Genet 2004: 36(10):1065-1071. (Pubitemid 41184467)
79. TrimbomT. GribnauJ. Grosveld F et al. Mechanisms of developmental control of transcription in the murinealpha- and beta-globin loci, Genes Dev 1999: 13(1):112-124. (Pubitemid 29045120)
80. Ragoczy T, Bender MA. Telling A et al. Thelocus controlregion is required for association of the murine beta-globin locus with engaged transcription factories during erythroid marurarion. Genes Dev 2006; 20(11):1447-1457. (Pubitemid 43830652)
81. Chowdhury D, Sen R. Transient IL-7/IL-7Rsignaling provides a mechanism for feedback inhibition of immunoglobulin heavy chain generearrangements. Immunity 2003: 18(2):229-241. (Pubitemid 36262998)
82. SkokJA. Brown KE. Azuara V et al. Nonequivalenr nuclear location of immunoglobulin alleles in B-lymphocytes. Nat ImmunoI2001: 2(9):848-854.
83. DalyJ. Licence S. NanouA et al. Transcription of productive and nonproductive VOJ-recombined alleles afterIgH allelic exclusion. EMBOJ 2007: 26(19):4273-4282. (Pubitemid 47525158)
84. HainesBB. Brodeur PH. Accessibility changes across the mouse Igh-Vlocus during B-cell development. EurJ Immuno11998; 28(12):4228-4235. (Pubitemid 28558654)
85. SkokJA. Gisler R. Novatchkova M et al. Reversible contraction by loopingof the Tcra and Tcrbloci in rearranging thymocytes, Nat Immunol 2007; 8(4):378-387. (Pubitemid 46745413)
86. Mosroslavsky R, SinghN. Kirillov A et al. Kappachain monoallelic demethylarion and the establishment of allelic exclusion. Genes Dev 1998: 12(12):1801-1811. (Pubitemid 28304333)
87. Goldmit M,Ji Y, SkokJ et al. Epigenetic ontogeny of the Igk locus during B-cell development. Nat ImmunoI 2005; 6(2):198-203. (Pubitemid 40268201)
88. Kouzarides T, Chromatinmodifications and their function. Cell 2007; 128(4):693-705. (Pubitemid 46273577)
89. Pawlirzky I, Angeles Cv. Siegel AM et al. Identification of a candidate regulatory dement within the 5′ flanking region of the mouse Igh locus defined by pro-B-cell-specific hypersensitivity associated with bindingof PUI. pax5 and E2A.J Immunol 2006: 176(11):6839-6851. (Pubitemid 43791970)