Germline transcription: A key regulator of accessibility and recombination

Advances in Experimental Medicine and Biology

Volumn 650, Issue , 2009, Pages 93-102

  Abarrategui, Lratxe ^a   Krangel, Michael S ^a  

^a DUKE UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DEXAMETHASONE; HISTONE H3; HISTONE H4; LIPOPOLYSACCHARIDE; RECOMBINASE;

ARTICLE; CHROMATIN STRUCTURE; GENE DISRUPTION; GENE EXPRESSION; GENE FUNCTION; GENETIC RECOMBINATION; GENETIC REGULATION; GENETIC TRANSCRIPTION; GERM LINE; HISTONE ACETYLATION; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; SIGNAL TRANSDUCTION; ANIMAL; CHEMISTRY; CHROMATIN; GENE REARRANGEMENT; GERM CELL; IMMUNOGLOBULIN GENE; METABOLISM; PHYSIOLOGY; REVIEW; T LYMPHOCYTE RECEPTOR GENE;

ANIMALS; CHROMATIN; GENE REARRANGEMENT, B-LYMPHOCYTE; GENE REARRANGEMENT, T-LYMPHOCYTE; GENES, IMMUNOGLOBULIN; GENES, T-CELL RECEPTOR; GERM CELLS; RECOMBINATION, GENETIC; TRANSCRIPTION, GENETIC; VDJ RECOMBINASES;

EID: 70349570163     PISSN: 00652598     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4419-0296-2_8     Document Type: Article

References (79)

1. Cobb RM, Oestreich KJ. Osipovich OA et al. Accessibility control of V(D)J recombination. Adv Immunol 2006: 91:45-109. (Pubitemid 44286994)
2. Yancopoulos GD, Alt FW Developmentally controlled and tissue-specific expression of unrearranged VH gene segments. Cell 1985: 40:271-281. (Pubitemid 15138455)
3. Fondell JD, Marcu KB. Transcription of germ line Va segments correlates with ongoing T-cell receptor a-chain rearrangement. Mol Cell Bioi 1992: 12:1480-1489.
4. Goldman JP, Spencer DM, Raulet DH. Ordered rearrangement of variable region genes of the T-cell receptor y locus correlates with transcription of the unrearranged genes. J Exp Med 1993; 177:729-739. (Pubitemid 23104284)
5. Schlissel MS, Corcoran LM. Baltimore D. Virus-transformed prell-cells show ordered activation but not inactivation of immunoglobulin gene rearrangement and transcription.JExp Med 1991; 173:711-20.
6. Bolland D,J. Wood AL. Johnston CM et al. Antisense intergenic transcription in V(D)Jrecombination. Nat Immunol 2004; 5:630-637.
7. BlackwellTK. Moore MW; Yancopoulos GD et al. Recombination between immunoglobulin variable region gene segments is enhanced by transcription. Nature 1986; 324:585-589. (Pubitemid 17185076)
8. Schlissel MS, Baltimore D. Activation of immunoglobulin kappa gene rearrangement correlates with induction of germline kappa gene transcription. Cell 1989; 58:1001-1007. (Pubitemid 19227905)
9. Olrz EM, Alt FW; Lin WC et al. A V(D)J rccombinase-inducible B-celliine: role of transcriptional enhancer elements in directing V(D)Jrecombination . Mol Cell Bioi 1993; 13:6223-6230. (Pubitemid 23292616)
10. Sun T, Storb U. Insertion of phosphoglycerine kinase (PGK)-neo 5' ofJA.l dramatically enhances VJA.l rearrangemenr, JExp Med 2001; 193:699-712.
11. Romanow W,J. Langerak AW;Goebel P et al. E2A and EBF act in synergy with the V(D)J recombinase to generate a diverse immunoglobulin repertoire in nonlymphoid cells. Mol Cell 2000; 5:343-353. (Pubitemid 30636005)
12. Ghosh J,K. Romanow W.J. Murre C. Induction of a diverse T-cell receptor ψδ repertoire by the helix-loop-helix proteins E2A and HEB in nonlymphoid cells. JExp Med 2001; 193:769-775. (Pubitemid 32524469)
13. Casellas R, JankovicM. Meyer G et al. OcaB is required for normal transcription and V(D)J recombination of a subset of immunoglobulin kappa genes. Cell 2002; 110:575-585. (Pubitemid 35247838)
14. Bertolino E, Reddy K. Medina KL et al. Regulation of interleukin 7-dependent immunoglobulin heavy-chain variable gen e rearrangements by transcription factor STAT5. Nat Immunol 2005; 6:836-843. (Pubitemid 43090470)
15. YeSK. Agata Y, Lee HC et al. The IL-7 receptor controls the accessibility of the TCRy locus by Stat5 and histone acetylation. Immunity 2001; 15:813-823. (Pubitemid 34008508)
16. Zhao H, Nguyen H. Kang J. Interleukin 15 controls the generation of the restricted T-cell receptor repertoire of γδ intestinal intraepitheliallymphocytes. Nat Immunol 2005; 6:1263-1271. (Pubitemid 43045638)
17. Hesslein DG, Pflugh DL. Chowdhury D et al. Pax5 is required for recombination of transcribed. acerylated, 5' IgH V gene segments. Genes Dev 2003; 17:37-42. (Pubitemid 36062506)
18. Fuxa M, Skok J, Souabni A et al. Pax5 induces V-to-DJrearrangements and locus contraction of the immunoglobulin heavy-chain gene. Genes Dev 2004; 18:411-422. (Pubitemid 38316348)
19. H rearrangement of immunoglobulin genes. Nat Immunol 2006; 7:616-624. (Pubitemid 43797343)
20. Okada A, Mendelsohn M. Alt F. Differential activation of transcription versus recombination of transgenic T-cell receptor β variable region gene segments in B and T lineage cells. J Exp Med 1994; 180:261-272. (Pubitemid 24181075)
21. Fernex C, Capone M. Ferrier P. The V(D)J recombinational and transcriptional activities of the immunoglobulin heavy-chain intronic enhancer can be mediated through distinct protein-binding sites in a transgenic substrate. Mol Cell Bioi 1995; 15:3217-3226.
22. Tripathi RK, Mathieu N. Spicuglia S et al.. Definition of a T-cell receptor β gene core enhancer of V(D) J recombination by transgenic mapping. Mol Cell Biol 2000; 20:42-53. (Pubitemid 30002546)
23. Jia J, Kondo M. Zhuang Y. Germline transcription from T-cell receptor Vβ gene is uncoupled from allelic exclusion. EMBO J 2007; 26:2387-2399 . (Pubitemid 46685854)
24. Jackson A, Kondilis HD. Khor B et al. Regulation of T-cell receptor β allelic exclusion at a level beyond accessibility. Nat Immuno12005; 6:189-197. (Pubitemid 40268200)
25. Senoo M, Wang L. Suzuki D et al.. Increase of TCR Vβ accessibility within Eβ regulatory region influences its recombination frequency but not allelic exclusion.JImmunol 2003; 171:829-835.
26. Stanhope-Baker P, Hudson KM. Shaffer AL et al. Cell type-specific chromatin structure determines the targeting of V(D)Jrecombinase activity in vitro. Cell 1996; 85:887-897. (Pubitemid 26192139)
27. Angelin-Duclos C, Calame K.Evidencethat immunoglobulin V"DJrecombination docs not require germ line transcription of the recombining variable gene segment. Mol Cell Biol 1998; 18:6253-6264. (Pubitemid 28500516)
28. Cherry SR, Baltimore D. Chromatin remodeling directly activates V(D)Jrecombination. Proc Nad Acad Sci USA 1999; 96:10788-10793. (Pubitemid 29442222)
29. Whitehurst CEoChattopadhyay S, Chen J. Control of V(D)Jrecombinational accessibility of the Dβ1 gene segment at the TCβ locus by a germline promoter. Immunity 1999; 10:313-322. (Pubitemid 29165286)
30. Mathieu N, Hempel WM. Spicuglia S et al. Chromatin remodeling by the Tscell receptor (TCR)-β gene enhancer during early T-cell development : Implications for the control ofTCR-β locus recombination. J Exp Med 2000; 192:625-636.
31. SpicugliaS. Kumar S. Yeh JH et al. Promoter activation by enhancer-dependent and -independent loading of activator and coactivator complexes. Mol Cell 2002; 10:1479-1487. (Pubitemid 36050887)
32. Oestreich KJ, Cobb RM. Pierce S et al. Regulation of TCβ gene assembly by a promoter/enhancer holocomplex. Immunity 2006; 24:381-391.
33. SikesML, Meade A, Tripathi Ret al. Regulation of V(D)J recombination: a dominant role for promoter positioning in gene segment accessibility. Proc Natl Acad Sci USA 2002; 99:12309-12314.
34. Osipovich O, Cobb RM, Oestreich KJ et al. Essential function for SWI-SNF chromatin remodeling complexes in the promoter-directed assembly of Tcrb genes. Nat Immunol 2007; 8:809-816. (Pubitemid 47099033)
35. Misteli T, Beyond the sequence: cellular organization of genome function . Cell 2007; 128:787-800. (Pubitemid 46273571)
36. Khorasanizadeh S, The nucleosome: from genomic organization to genomic regulation . Cell 2004; 116:259-272. (Pubitemid 38167316)
37. Tremethick DJ, Higher-order structures of chromatin : the elusive 30 nm fiber. Cell 2007; 128:651-654. (Pubitemid 46290574)
38. Kouzarides T, Chromatin modifications and their function . Cell 2007; 128:693-705. (Pubitemid 46273577)
39. Lee KK, Workman JL. Histone acetyltransferase complexes: one size doesn't fit all. Nat Rev Mol Cell Biol 2007; 8:284-295. (Pubitemid 46474661)
40. Shi Y,Whetstine JR . Dynamic regulation of histone lysine methylation by demethylases, Mol Cell 2007; 25:1-14. (Pubitemid 46049067)
41. Li B, Carey M. Workman JL. The role of chromatin during transcription. Cell 2007; 128:707-719. (Pubitemid 46273570)
42. Ruthenburg AJ, Allis CD, Wysocka J. Methylation of lysine 4 on histone H3: intricacy of writing and reading a single epigenetic mark. Mol Cell 2007; 25:15-30. (Pubitemid 46049068)
43. Shogren-Knaak M, Ishii H, Sun JM et al. Histone H4-KI6 acetylation controls chromatin structure and protein interactions.Science 2006; 311:844-847. (Pubitemid 43228847)
44. Lachner M, O'Carroll D. Rea S et al., Methylation of histone H3 lysine 9 creates a binding site for HP 1 proteins . Nature 2001; 410:116-120. (Pubitemid 32225847)
45. Shi X, Hong T, Walter KL et al. ING2 PHD domal.n links histone H3 lysine 4 methylation to active gene repression. Nature 2006; 442:96-99 . (Pubitemid 44064216)
46. Taverna SD, Llin S, Rogers RS et al. Yngl PHD finger binding to H3 trimethylaced at K4 promotes NuA3 HAT activity at K14 of H3 and transcription at a subset of targeted ORFs. Mol Cell 2006; 24:785-796. (Pubitemid 44839214)
47. Wysocka J, Swigut T. Xiao H et al, A PHD finger of NURF couples histone H3 lysine 4 trimethylation with chromatin remodelling. Nature 2006; 442:86-90. (Pubitemid 44064214)
48. Li B, Gogol M, Carey M et al. Combined action of PHD and Chromodomal.ns directs the Rpd3S HDAC to transcribed chromatin. Science 2007 ; 316:1050-1054. (Pubitemid 46799495)
49. Saha A, Wittmeyer J. Cairns BR. Chromatin remodelling : the industrial revolution of DNA around histories. Nat Rev Mol Cell Biol 2006; 7:437-447. (Pubitemid 44050097)
50. SO. Smith CL, Peterson CL. ATP-dependent chromatin remodeling. Curr Top Dev Biol 2005; 65:115-148 .
51. Bruno M, Flaus A. Stockdale C et al. Histone H2A/H2B dimer exchange by ATP-dependent chromatin remodeling activities. Mol Cell 2003; 12:1599-1606. (Pubitemid 38037026)
52. Workman JL, Nucleosome displacement in transcription. Genes Dev 2006; 20:2009-2017. (Pubitemid 44157452)
53. Hassan AH, Neely KE. Workman JL. Histone acetyltransferase complexes stabilize SWI/SNF binding to promoter nucleosomes. Cell 2001; 104:817-827. (Pubitemid 32289275)
54. Sims RJ3rd, Belotserkovskaya R. Reinberg D. Elongation by RNA polymerase 11 : the short and long of it. Genes Dev 2004; 18:2437-2468. (Pubitemid 39362887)
55. Krogan NJ, Dover J. Wood A et al. The Pafl complex is required for histone H3 methylation by COMPASS and Dotlp: linking transcriptional elongation to histone methylation. Mol Cell 2003; 11:721-729. (Pubitemid 36385125)
56. Wood A, Schneider J. DoverJet al. The PafI complex is essential for histone monoubiquitination by the Rad6-Brel complex, which signals for histone methylation by COMPASS and Dorlp. J Biol Chern 2003; 278:34739-34742. (Pubitemid 37102230)
57. Xiao T, Hall H, Kizer KO ec al. Phosphorylation of RNA polymerase 11 CTD regulates H3 methylation in yeast. Genes Dev 2003; 17:654-663. (Pubitemid 36307549)
58. Govind CK, Zhang F,Qiu H et al . Gcn5 promotes acetylation, eviction and methylation of nucleosomes in transcribed coding regions. Mol Cell 2007; 25:31-42. (Pubitemid 46049060)
59. Pavri R, Zhu B. Li G et al. Histone H2B monoubiquitination functions cooperatively with FACT to regulate elongation by RNA polymerase 11. Cell 2006; 125:703-717. (Pubitemid 43732350)
60. Carrozza MJ, Li B. Florens L et al. Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 2005; 123:581-592. (Pubitemid 41608462)
61. Joshi AA, Strohl K.Eaf3 chromodomal.n interaction with methylated H3-K36 links histone deacerylation to Pol II elongation. Mol Cell 2005; 20:971-978. (Pubitemid 41814885)
62. Belotserkovskaya R, Oh S, Bondarenko VA et al. FACT facilitates transcription-dependent nucleosome alteration . Science 2003; 301:1090-1093. (Pubitemid 37022309)
63. Schwabish MA, Struhl K. AsfI mediates histone eviction and deposition during elongation by RNA polymerase 11. Mol Cell 2006; 22:415-422.
64. Carey M, Li B, Workman JL. RSC exploits histone acetylation to abrogate the nucleosomal block to RNA polymerase II elongation. Mol Cell 2006; 24:481-487. (Pubitemid 44647905)
65. Corey LL, Weirich CS, Benjamin IJ et al. Localized recruitment of a chromatin-remodeling activity by an activator in vivo drives transcriptional elongation . Genes Dev 2003; 17:1392-1401. (Pubitemid 36666008)
66. Krangel MS, Carabana J, Abarrategui I et al. Enforcing order within a complex locus: current perspectives on the control of V(D)J recombination at the murine T-cell receptor a/β locus. Immunol Rev 2004; 200:224-232. (Pubitemid 38998205)
67. Sleckman BP, Bardon CG. Ferrini R et al. Function of the TCRa enhancer in ap and yβ Tscells. Immunity 1997; 7:505-515.
68. Villey I, Caillol D, Selz F et al. Defect in rearrangement of the most 5' TCR-Ja following targeted deletion ofT early alpha (TEA) : implications for TCRa locus accessibility. Immunity 1996; 5:331-342. (Pubitemid 26366756)
69. Hawwari A, Bock C, Krangel MS. Regulation of T-cell receptor-a gene assemblyby a complex hierarchy of germline Ja promoters. Nat Immunol 2005; 6:481-489. (Pubitemid 41716761)
70. Buch T, Rieux-Laucat F, Forster I et al. Failure of Hr-speclfic rhymocytes to escape negative selection by receptor editing . Immunity 2002; 16:707-718. (Pubitemid 34626691)
71. Wang F, Huang CY, Kanagawa O. Rapid deletion of rearranged T-cell antigen receptor (TCR) Vα-Jα segment by secondary rearrangement in the thymus : role of continuous rearrangement of TCRa chal.n gene and positive selection in the T-cell repertoire formation . Proc Nad Acad Sci USA 1998; 95:11834-11839.
72. Hawwari A, Krangel MS. Role for rearranged variable gene segments in directing secondary T-cell receptor - A recombination. Proc Natl Acad Sci USA 2007; 104:903-907.
73. Mauvicux L, Villey I, de Villartay J-P. TEA regulates local TCR-Ja accessibilitythrough histone acetylation . Eur J Immunol 2003; 33:2216-2222. (Pubitemid 37010039)
74. Abarraeegui I, Krangel MS. Regulation of T-cell receptor-o gene recombination by transcription. Nat Immunol 2006; 7:1109-1115.
75. Abarrategui I, Krangel MS. Noncoding transcription controls downstream promoters to regulate T-cell receptor a recombination. EMBO J 2007; 26: 4380-4390. (Pubitemid 47587667)
76. Bolland DJ, Wood Al., Afshar R et al. Antisense intergcnic transcription precedes Igh D-co-J recombination and is controlled by the intronic enhancer Ell. Mol Cell Biol 2007; 27:5523-5533 . (Pubitemid 47124404)
77. Elkin SK, Ivanov D, Ewalt M et Al. A PHD finger motif in the C terminus of RAG2 modulates recombination activity. J Biol Chern 2005; 280:28701-28710. (Pubitemid 41105771)
78. West KL, Singha NC, De Ioannes P et Al. A direct interaction between the RAG2 C terminus and the core histones is required for efficient V(D)J recombination. Immunity 2005; 23:203-212. (Pubitemid 41169289)
79. Tanny JC, Erdjumenr-Bromage H. Tempst P et Al. Ubiquitylation of histone H2B controls RNA polymerase II transcription elongation Independently of histone H3 methylation. Genes Dev 2007; 21:835-847. (Pubitemid 46572362)