Regulation of V(D)J recombination by nucleosome positioning at recombination signal sequences

EMBO Journal

Volumn 22, Issue 19, 2003, Pages 5197-5207

  Baumann, Matthias ^a   Mamais, Adamantios ^a   McBlane, Fraser ^b   Xiao, Hua ^c   Boyes, Joan ^a  

^a INSTITUTE OF CANCER RESEARCH   (United Kingdom)

^b EUROPEAN INSTITUTE OF ONCOLOGY   (Italy)

^c NATIONAL CANCER INSTITUTE   (United States)

Author keywords

Chromatin remodelling; Chromosomal translocation; Nucleosome positioning; RAGs; V(D)J recombination

Indexed keywords

RAG1 PROTEIN; SIGNAL PEPTIDE;

ANIMAL CELL; ARTICLE; ASSAY; CHROMATIN; CHROMOSOME TRANSLOCATION; CONTROLLED STUDY; EMBRYO; FEMALE; GENETIC RECOMBINATION; HUMAN; HUMAN CELL; IN VITRO STUDY; IN VIVO STUDY; MOUSE; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; REGULATORY MECHANISM;

3T3 CELLS; ANIMALS; GENE EXPRESSION REGULATION; GENE REARRANGEMENT; IMMUNOGLOBULIN VARIABLE REGION; MICE; NUCLEOSOMES; RECOMBINATION, GENETIC;

ANIMALIA;

EID: 0141753136     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/cdg487     Document Type: Article

References (46)

1. Bassing, C.H., Swat, W. and Alt, F.W. (2002) The mechanism and regulation of chromosomal V(D)J recombination. Cell, 109 Suppl., S45-S55.
2. Boyes, J. (1999) Preparation of chromatin templates for transcription studies. In Latchman, D.S. (ed.), Transcription Factors: A Practical Approach. Oxford University Press, Oxford, UK, pp. 229-260.
3. Boyes, J. and Felsenfeld, G. (1996) Tissue-specific factors additively increase the probability of the all-or-none formation of a hypersensitive site. EMBO J., 15, 2496-2507.
4. Cairns, B.R. and Kingston, R.E. (2000) The SWI/SNF family of remodelling complexes. In Elgin, S.C.R. and Workman,J.L. (eds), Chromatin Structure and Gene Expression. Oxford University Press, New York, NY, pp. 97-113.
5. Clark, D.J. and Felsenfeld, G. (1991) Formation of nucleosomes on positively supercoiled DNA. EMBO J., 10, 387-395.
6. Di Croce, L., Koop, R., Venditti, P., Westphal, H.M., Nightingale, K.P., Corona, D.F., Becker, P.B. and Beato, M. (1999) Two-step synergism between the progesterone receptor and the DNA-binding domain of nuclear factor I on MMTV minichromosomes. Mol. Cell, 4, 45-54.
7. Drew, H.R. and Travers, A.A. (1985) DNA bending and its relation to nucleosome positioning. J. Mol. Biol., 186, 773-790.
8. Fascher, K.-D., Schmitz, J. and Horz, W. (1993) Structural and functional requirements for the chromatin transition at the PH05 promoter in Saccharomyces cerevisiae upon PHO5 activation. J. Mol. Biol., 231, 658-667.
9. Fragoso, G., John, S., Roberts, M.S. and Hager, G.L. (1995) Nucleosome positioning on the MMTV LTR results from the frequency-biased occupancy of multiple frames. Genes Dev., 9, 1933-1947.
10. Golding, A., Chandler, S., Ballestar, E., Wolffe, A.P. and Schlissel, M.S. (1999) Nucleosome structure completely inhibits in vitro cleavage by the V(D)J recombinase. EMBO J., 18, 3712-3723.
11. Hamiche, A., Sandaltzopoulos, R., Gdula, D.A. and Wu, C. (1999) ATP-dependent histone octamer sliding mediated by the chromatin remodeling complex NURF. Cell, 97, 833-842.
12. Herrera, R.E., Nordheim, A. and Stewart, A.F. (1997) Chromatin structure analysis of the human c-fos promoter reveals a centrally positioned nucleosome. Chromosoma, 106, 284-292.
13. Kang, J.G., Hamiche, A. and Wu, C. (2002) GAL4 directs nucleosome sliding induced by NURF. EMBO J., 21, 1406-1413.
14. Kosak, S.T., Skok, J.A., Medina, K.L., Riblet, R., Le Beau, M.M., Fisher, A.G. and Singh, H. (2002) Subnuclear compartmentalization of immunoglobulin loci during lymphocyte development. Science, 296, 158-162.
15. Krajewski, W.A. (2002) Histone acetylation status and DNA sequence modulate ATP-dependent nucleosome repositioning. J. Biol. Chem., 277, 14509-14513.
16. Kwon, J., Imbalzano, A.N., Matthews, A. and Oettinger, M.A. (1998) Accessibility of nucleosomal DNA to V(D)J cleavage is modulated by RSS positioning and HMG1. Mol. Cell, 2, 829-839.
17. Kwon, J., Morshead, K.B., Guyon, J.R., Kingston, R.E. and Oettinger, M.A. (2000) Histone acetylation and hSWI/SNF remodeling act in concert to stimulate V(D)J cleavage of nucleosomal DNA. Mol. Cell, 6, 1037-1048.
18. Langst, G., Bonte, E.J., Corona, D.F. and Becker, P.B. (1999) Nucleosome movement by CHRAC and ISWI without disruption or transdisplacement of the histone octamer. Cell, 97, 843-852.
19. Lewis, S.M. (1994) The mechanism of V(D)J joining: lessons from molecular, immunological and comparative analyses. Adv. Immunol., 56, 27-150.
20. Lewis, S.M., Agard, E., Suh, S. and Czyzyk, L. (1997) Cryptic signals and the fidelity of V(D)J joining. Mol. Cell. Biol., 17, 3125-3136.
21. Lieber, M.R., Hesse, J.E., Mizuuchi, K. and Gellert, M. (1987) Developmental stage specificity of the lymphoid V(D)J recombination activity. Genes Dev., 1, 751-761.
22. Linxweiler, W. and Horz, W. (1984) Reconstitution of mononucleosomes: characterization of distinct particles that differ in the position of the histone core. Nucleic Acids Res., 12, 9395-9413.
23. Lu, Q., Wallrath, L.L. and Elgin, S.C. (1995) The role of a positioned nucleosome at the Drosophila melanogaster hsp26 promoter. EMBO J., 14, 4738-4746.
24. Marculescu, R., Le, T., Simon, P., Jaeger, U. and Nadel, B. (2002) V(D)J-mediated translocations in lymphoid neoplasms: a functional assessment of genomic instability by cryptic sites. J. Exp. Med., 195, 85-98.
25. McBlane, F. and Boyes, J. (2000) Stimulation of V(D)J recombination by histone acetylation. Curr. Biol., 10, 483-486.
26. McBlane, J.F., van Gent, D.C., Ramsden, D.A., Romeo, C., Cuomo, C.A., Gellert, M. and Oettinger, M.A. (1995) Cleavage at a V(D)J recombination signal requires only RAG1 and RAG2 proteins and occurs in two steps. Cell, 83, 387-395.
27. McMurry, M.T. and Krangel, M.S. (2000) A role for histone acetylation in the developmental regulation of VDJ recombination. Science, 287, 495-498.
28. Mostoslavsky, R., Singh, N., Kirillov, A., Pelanda, R., Cedar, H., Chess, A. and Bergman, Y. (1998) Kappa chain monoallelic demethylation and the establishment of allelic exclusion. Genes Dev., 12, 1801-1811.
29. Muegge, K., West, M. and Durum, S.K. (1993) Recombination sequence-binding protein in thymocytes undergoing T-cell receptor gene rearrangement. Proc. Natl Acad. Sci. USA, 90, 4151-4155.
30. Narlikar, G.J., Fan, H.Y. and Kingston, R.E. (2002) Cooperation between complexes that regulate chromatin structure and transcription. Cell, 108, 475-487.
31. Oettinger, M.A., Schatz, D.G., Gorka, C. and Baltimore, D. (1990) RAG-1 and RAG-2, adjacent genes that synergistically activate V(D)J recombination. Science, 248, 1517-1523.
32. Raghavan, S.C., Kirsch, I.R. and Lieber, M.R. (2001) Analysis of the V(D)J recombination efficiency at lymphoid chromosomal translocation breakpoints. J. Biol. Chem., 276, 29126-29133.
33. Richmond, T.J. and Widom, J. (2000) Nucleosome and chromatin structure. In Elgin, S.C.R. and Workman, J.L. (eds), Chromatin Structure and Gene Expression. Oxford University Press, New York, NY, pp. 1-23.
34. Roth, D.B. and Roth, S.Y. (2000) Unequal access: regulating V(D)J recombination through chromatin remodeling. Cell, 103, 699-702.
35. Sadofsky, M.J., Hesse, J.E., van Gent, D.C. and Gellert, M. (1995) RAG-1 mutations that affect the target specificity of V(D)J recombination: a possible direct role of RAG-1 in site recognition. Genes Dev., 9, 2193-2199.
36. Schild, C., Claret, F.X., Wahli, W. and Wolffe, A.P. (1993) A nucleosome-dependent static loop potentiates estrogen-regulated transcription from the Xenopus vitellogenin B1 promoter in vitro. EMBO J., 12, 423-433.
37. Shinkai, Y. et al. (1992) RAG-2-deficient mice lack mature lymphocytes owing to inability to initiate V(D)J rearrangement. Cell, 68, 855-867.
38. Shockett, P., Difilippantonio, M., Hellman, N. and Schatz, D.G. (1995) A modified tetracycline-regulated system provides autoregulatory, inducible gene expression in cultured cells and transgenic mice. Proc. Natl Acad. Sci. USA, 92, 6522-6526.
39. Shrader, T.E. and Crothers, D.M. (1989) Artificial nucleosome positioning sequences. Proc. Natl Acad. Sci. USA, 86, 7418-7422.
40. Sleckman, B.P., Gorman, J.R. and Alt, F.W. (1996) Accessibility control of antigen-receptor variable-region gene assembly: role of cis-acting elements. Annu. Rev. Immunol., 14, 459-481.
41. Stanhope-Baker, P., Hudson, K.M., Shaffer, A.L., Constantinescu, A. and Schlissel, M.S. (1996) Cell type-specific chromatin structure determines the targeting of V(D)J recombinase activity in vitro. Cell, 85, 887-897.
42. Svaren, J. and Horz, W. (1997) Transcription factors vs nucleosomes: regulation of the PH05 promoter in yeast. Trends Biochem. Sci., 22, 93-97.
43. van Gent, D.C., McBlane, J.F., Ramsden, D.A., Sadofsky, M.J., Hesse, J.E. and Gellert, M. (1995) Initiation of V(D)J recombination in a cell-free system. Cell, 81, 925-934.
44. van Gent, D.C., Hiom, K., Paull, T.T. and Gellert, M. (1997) Stimulation of V(D)J cleavage by high mobility group proteins. EMBO J., 16, 2665-2670.
45. Wang, Y.H., Amirhaeri, S., Kang, S., Wells, R.D. and Griffith, J.D. (1994) Preferential nucleosome assembly at DNA triplet repeats from the myotonic dystrophy gene. Science, 265, 669-671.
46. Wu, C., Becker, P.B. and Tsukiyama, T. (2000) ATP-dependent chromatin remodelling by the ISWI complexes. In Elgin, S.C.R. and Workman, J.L. (eds), Chromatin Structure and Gene Expression. Oxford University Press, New York, NY, pp. 114-134.