Antisense intergenic transcription in V(D)J recombination

Nature Immunology

Volumn 5, Issue 6, 2004, Pages 630-637

  Bolland, Daniel J ^a   Wood, Andrew L ^a   Johnston, Colette M ^a   Bunting, Sam F ^a   Morgan, Geoff ^a   Chakalova, Lyubomira ^a   Fraser, Peter J ^a   Corcoran, Anne E ^a  

^a BABRAHAM INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ANTISENSE OLIGONUCLEOTIDE; IMMUNOGLOBULIN HEAVY CHAIN; LYMPHOCYTE ANTIGEN RECEPTOR; COMPLEMENTARY DNA; HOMEODOMAIN PROTEIN; RAG 1 PROTEIN; RAG-1 PROTEIN; RNA; SPACER DNA;

ALLELE; ANIMAL CELL; ARTICLE; CELL SELECTION; CHROMATIN; CONTROLLED STUDY; FLUORESCENCE IN SITU HYBRIDIZATION; GENE AMPLIFICATION; GENE CONTROL; GENE IDENTIFICATION; GENE LOCUS; GENE REARRANGEMENT; GENE SEQUENCE; GENETIC RECOMBINATION; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; LYMPHOCYTE SUBPOPULATION; MOUSE; NONHUMAN; PRIORITY JOURNAL; REGULATORY MECHANISM; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA HYBRIDIZATION; ANIMAL; C57BL MOUSE; GENETICS; IMMUNOGLOBULIN GENE; METABOLISM; PHYSIOLOGY;

ANIMALS; DNA, ANTISENSE; DNA, INTERGENIC; GENE REARRANGEMENT; GENES, IMMUNOGLOBULIN; HOMEODOMAIN PROTEINS; IN SITU HYBRIDIZATION, FLUORESCENCE; MICE; MICE, INBRED C57BL; RNA; TRANSCRIPTION, GENETIC;

EID: 2942691957     PISSN: 15292908     EISSN: None     Source Type: Journal    
DOI: 10.1038/ni1068     Document Type: Article

References (52)

1. Chevillard, C., Ozaki, J., Herring, C.D. & Riblet, R. A three-megabase yeast artificial chromosome contig spanning the C57BL mouse Igh locus. J. Immunol. 168, 5659-5666(2002).
2. Krangel, M.S. Gene segment selection in V(D)J recombination: accessibility and beyond. Nat. Immunol. 4, 624-630 (2003).
3. Yancopoulos, G.D. & Alt, F.W. Developmentally controlled and tissue-specific expression of unrearranged VH gene segments. Cell 40, 271-281 (1985).
4. Corcoran, A.E., Riddell, A., Krooshoop, D. & Venkitaraman, A.R. Impaired immunoglobulin gene rearrangement in mice lacking the IL-7 receptor. Nature 391, 904-907 (1998).
5. H-DJ recombination does not require germ line transcription of the recombining variable gene segment. Mol. Cell. Biol. 18, 6253-6264 (1998).
6. Haines, B.B. & Brodeur, P.H. Accessibility changes across the mouse Igh-V locus during B cell development. Eur. J. Immunol. 28, 4228-4235 (1998).
7. Nelson, K.J., Haimovich, J. & Perry, R.P. Characterization of productive and sterile transcripts from the immunoglobulin heavy-chain locus: processing of micron and μS mRNA. Mol. Cell. Biol. 3, 1317-1332 (1983).
8. Schlissel, M.S., Corcoran, L.M. & Baltimore, D. Virus-transformed pre-B cells show ordered activation but not inactivation of immunoglobulin gene rearrangement and transcription. J. Exp. Med. 173, 711-720 (1991).
9. Duber, S., Engel, H., Rolink, A., Kretschmer, K. & Weiss, S. Germline transcripts of immunoglobulin light chain variable regions are structurally diverse and differentially expressed. Mol. Immunol. 40, 509-516 (2003).
10. Goldman, J.P., Spencer, D.M. & Raulet, D.H. Ordered rearrangement of variable region genes of the T cell receptor γ locus correlates with transcription of the unrearranged genes. J. Exp. Med. 177, 729-739 (1993).
11. Sleckman, B.P., Gorman, J.R. & Alt, F.W. Accessibility control of antigen-receptor variable-region gene assembly: role of cis-acting elements. Annu. Rev. Immunol. 14, 459-481 (1996).
12. Stanhope-Baker, P., Hudson, K.M., Shaffer, A.L., Constantinescu, A. & Schlissel, M.S. Cell type-specific chromatin structure determines the targeting of V(D)J recombinase activity in vitro. Cell 85, 887-897. (1996).
13. Mostoslavsky, R. et al. κ chain monoallelic demethylation and the establishment of allelic exclusion. Genes Dev. 12, 1801-1811 (1998).
14. McBlane, F. & Boyes, J. Stimulation of V(D)J recombination by histone acetylation. Curr. Biol. 10, 483-486 (2000).
15. McMurry, M.T. & Krangel, M.S. A role for histone acetylation in the developmental regulation of VDJ recombination. Science 287, 495-498 (2000).
16. Chowdhury, D. & Sen, R. Stepwise activation of the immunoglobulin μ heavy chain gene locus. EMBO J. 20, 6394-6403 (2001).
17. Johnson, K., Angelin-Duclos, C., Park, S. & Calame, K.L. Changes in histone acetylation are associated with differences in accessibility of V(H) gene segments to V-DJ recombination during B-cell ontogeny and development. Mol. Cell. Biol. 23, 2438-2450 (2003).
18. Morshead, K.B., Ciccone, D.N., Taverna, S.D., Allis, C.D. & Oettinger, M.A. Antigen receptor loci poised for V(D)J rearrangement are broadly associated with BRG1 and flanked by peaks of histone H3 dimethylated at lysine 4. Proc. Natl. Acad. Sci. USA 100, 11577-11582 (2003).
19. Maes, J. et al. Chromatin remodeling at the Ig loci prior to V(D)J recombination. J. Immunol. 167, 866-874 (2001).
20. Golding, A., Chandler, S., Ballestar, E., Wolffe, A.P. & Schlissel, M.S. Nucleosome structure completely inhibits in vitro cleavage by the V(D)J recombinase. EMBO J. 18, 3712-3723 (1999).
21. Kwon, J., Morshead, K.B., Guyon, J.R., Kingston, R.E. & Oettinger, M.A. Histone acetylation and hSWI/SNF remodeling act in concert to stimulate V(D)J cleavage of nucleosomal DNA. Mol. Cell 6, 1037-1048 (2000).
22. Gribnau, J., Diderich, K., Pruzina, S., Calzolari, R. & Fraser, P. Intergenic transcription and developmental remodeling of chromatin subdomains in the human β-globin locus. Mol. Cell 5, 377-386 (2000).
23. Li, Y.S., Hayakawa, K. & Hardy, R.R. The regulated expression of B lineage associated genes during B cell differentiation in bone marrow and fetal liver. J. Exp. Med. 178, 951-960 (1993).
24. H recombination. J. Exp. Med. 189, 735-740 (1999).
25. + cells in murine bone marrow does not express CD19 and contains natural killer cell progenitors. J. Exp. Med. 163, 187-194 (1996).
26. Spanopoulou, E. et al. Functional immunoglobulin transgenes guide ordered B-cell differentiation in Rag-1-deficient mice. Genes Dev. 8, 1030-1042 (1994).
27. Lennon, G.G. & Perry, R.P. Cμ-containing transcripts initiate heterogeneously within the IgH enhancer region and contain a novel 5′-nontranslatable exon. Nature 318, 475-478 (1985).
28. de Krom, M., van de Corput, M., von Lindern, M., Grosveld, F. & Strouboulis, J. Stochastic patterns in globin gene expression are established prior to transcriptional activation and are clonally inherited. Mol. Cell 9, 1319-1326 (2002).
29. Kosak, S.T. et al. Subnuclear compartmentalization of immunoglobulin loci during lymphocyte development. Science 296, 158-162 (2002).
30. Li, Y.S., Wasserman, R., Hayakawa, K. & Hardy, R.R. Identification of the earliest B lineage stage in mouse bone marrow. Immunity 5, 527-535 (1996).
31. Ehlich, A., Martin, V., Muller, W. & Rajewsky, K. Analysis of the B-cell progenitor compartment at the level of single cells. Curr. Biol. 4, 573-583 (1994).
32. Mostoslavsky, R. et al. Asynchronous replication and allelic exclusion in the immune system. Nature 414, 221-225 (2001).
33. Skok, J. A. et al. Nonequivalent nuclear location of immunoglobulin alleles in B lymphocytes. Nat. Immunol. 2, 848-854 (2001).
34. Trimborn, T., Gribnau, J., Grosveld, F. & Fraser, P. Mechanisms of developmental control of transcription in the murine α- and β-globin loci. Genes Dev. 13, 112-124 (1999).
35. Allshire, R. Molecular biology. RNAi and heterochromatin - a hushed-up affair. Science 297, 1818-1819 (2002).
36. Vanhee-Brossollet, C. & Vaquero, C. Do natural antisense transcripts make sense in eukaryotes? Gene 211, 1-9 (1998).
37. Sleutels, F., Zwart, R. & Barlow, D.P. The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature 415, 810-813 (2002).
38. Hebbes, T.R., Clayton, A.L., Thorne, A.W. & Crane-Robinson, C. Core histone hyper-acetylation co-maps with generalized DNase I sensitivity in the chicken β-globin chromosomal domain. EMBO J. 13, 1823-1830 (1994).
39. Orphanides, G. & Reinberg, D. RNA polymerase II elongation through chromatin. Nature 407, 471-475 (2000).
40. Nambu, Y. et al. Transcription-coupled events associating with immunoglobulin switch region chromatin. Science 302, 2137-2140 (2003).
41. Schlissel, M.S. & Morrow, T. Ig heavy chain protein controls B cell development by regulating germ-line transcription and retargeting V(D)J recombination. J. Immunol. 153, 1645-1657 (1994).
42. Chowdhury, D. & Sen, R. Transient IL-7/IL-7R signaling provides a mechanism for feedback inhibition of immunoglobulin heavy chain gene rearrangements. Immunity 18, 229-241 (2003).
43. β chromatin associated with TCRβ allelic exclusion. J. Immunol. 168, 2316-2324 (2002).
44. Stevenson, D.S. & Jarvis, P. Chromatin silencing: RNA in the driving seat. Curr. Biol. 13, R13-R15 (2003).
45. Su, I.H. et al. Ezh2 controls B cell development through histone H3 methylation and Igh rearrangement. Nat. Immunol. 4, 124-131 (2003).
46. Urbanek, P., Wang, Z.Q., Fetka, I., Wagner, E.F. & Busslinger, M. Complete block of early B cell differentiation and altered patterning of the posterior midbrain in mice lacking Pax5/BSAP. Cell 79, 901-912 (1994).
47. Hesslein, D.G. et al. Pax5 is required for recombination of transcribed, acetylated, 5′ IgH V gene segments. Genes Dev. 17, 37-42 (2003).
48. Shendure, J. & Church, G.M. Computational discovery of sense-antisense transcription in the human and mouse genomes. Genome Biol. 3, 0044.1-0044.14 (2002).
49. Kiyosawa, H., Yamanaka, I., Osato, N., Kondo, S. & Hayashizaki, Y. Antisense transcripts with FANTOM2 clone set and their implications for gene regulation. Genome Res. 13, 1324-1334 (2003).
50. Kirch, S.A., Rathbun, G.A. & Oettinger, M.A. Dual role of RAG2 in V(D)J recombination: catalysis and regulation of ordered Ig gene assembly. EMBO J. 17, 4881-4886 (1998).
51. Gribnau, J. et al. Chromatin interaction mechanism of transcriptional control in vivo. EMBO J. 17, 6020-6027 (1998).
52. Chakalova, L., Carter, D. & Fraser, P. RNA fluorescence in situ hybridization tagging and recovery of associated proteins to analyze in vivo chromatin interactions. Methods Enzymol. 375, 479-493 (2004).