Detection of RAG Protein-V(D)J Recombination Signal Interactions Near the Site of DNA Cleavage by UV Cross-Linking

REFERENCES

• Agrawal, A., and J. Schatz 1997. RAG1 and RAG2 form a stable post-cleavage synaptic complex with DNA containing signal ends in V(D)J recombination. Cell 89:43–53.
   PubMed Web of Science ®Google Scholar
• Akamatsu, Y., and J. Oettinger 1998. Distinct roles of RAG1 and RAG2 in binding the V(D)J recombination signal sequences. Mol. Cell. Biol. 18:4670–4678.
   PubMedGoogle Scholar
• Baker, T. A., and J. Luo 1994. Identification of residues in the Mu transposase essential for catalysis. Proc. Natl. Acad. Sci. USA 91:6654–6658.
   PubMedGoogle Scholar
• Bianchi, M. E., M. Beltrame, and J. Paonessa 1989. Specific recognition of cruciform DNA by nuclear protein HMG1. Science 243:1056–1059.
   PubMed Web of Science ®Google Scholar
• Bolland, S., and J. Kleckner 1996. The three chemical steps of Tn 10/IS 10 transposition involve repeated utilization of a single active site. Cell 84:223–233.
   PubMedGoogle Scholar
• Cheung, S., K. Arndt, and J. Lu 1984. Correlation of the lac operator imino exchange kinetics with its function. Proc. Natl. Acad. Sci. USA 81:3665–3669.
   PubMed Web of Science ®Google Scholar
• Cuomo, C. A., C. L. Mundy, and J. Oettinger 1996. DNA sequence and structure requirements for cleavage of V(D)J recombination signal sequences. Mol. Cell. Biol. 16:5683–5690.
   PubMedGoogle Scholar
• Difilippantonio, M. J., C. J. McMahan, Q. M. Eastman, E. Spanopoulou, and J. Schatz 1996. RAG1 mediates signal sequence recognition and recruitment of RAG2 in V(D)J recombination. Cell 87:253–262.
   PubMedGoogle Scholar
• Donlan, M., and J. Lu 1992. Transcriptional enhancer related DNA sequences: anomalous 1H NMR NOE crosspeaks. Nucleic Acids Res. 20:525–532.
   PubMedGoogle Scholar
• Eastman, Q. M., T. M. J. Leu, and J. Schatz 1996. Initiation of V(D)J recombination in vitro obeying the 12/23 rule. Nature 380:85–88.
   PubMedGoogle Scholar
• Eastman, Q. M., and J. Schatz 1997. Nicking is asynchronous and stimulated by synapsis in 12/23-rule regulated V(D)J recombination. Nucleic Acids Res. 25:4370–4378.
   PubMedGoogle Scholar
• Folta-Stogniew, E., and J. Russu 1994. Sequence dependence of base-pair opening in a DNA dodecamer containing the CACA/GTGT sequence motif. Biochemistry 33:11016–11024.
   PubMedGoogle Scholar
• Hesse, J. E., M. R. Lieber, K. Mizuuchi, and J. Gellert 1989. V(D)J recombination: a functional definition of the joining signals. Genes Dev. 3:1053–1061.
   PubMed Web of Science ®Google Scholar
• Hiom, K., and J. Gellert 1998. Assembly of a 12/23 paired signal complex: a critical control point in V(D)J recombination. Mol. Cell 1:1011–1019.
   PubMed Web of Science ®Google Scholar
• Hiom, K., and J. Gellert 1997. A stable RAG1-RAG2-DNA complex that is active in V(D)J cleavage. Cell 88:65–72.
   PubMedGoogle Scholar
• Kennedy, A. K., A. Guhathakurta, N. Kleckner, and J. Haniford 1998. Tn 10 excision via a DNA hairpin intermediate. Cell 95:125–134.
   PubMedGoogle Scholar
• Koradi, R., M. Billeter, and J. Wuthrich 1996. MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 14:51–55.
   PubMedGoogle Scholar
• Lavoie, B. D., B. S. Chan, R. G. Allison, and J. Chaconas 1991. Structural aspects of a higher order nucleoprotein complex: induction of an altered DNA structure at the Mu-host junction of the Mu type 1 transpososome. EMBO J. 10:3051–3059.
   PubMedGoogle Scholar
• Leu, T. M. J., and J. Schatz 1995. rag-1 and rag-2 are components of a high-molecular-weight complex, and association of rag-2 with this complex is rag-1 dependent. Mol. Cell. Biol. 15:5657–5670.
   PubMed Web of Science ®Google Scholar
• Lewis, S. M. 1994. The mechanism of V(D)J joining: lessons from molecular, immunological, and comparative analyses. Adv. Immunol. 56:27–150.
   PubMed Web of Science ®Google Scholar
• Li, W., P. Swanson, and J. Desiderio 1997. RAG-1 and RAG-2-dependent assembly of functional complexes with V(D)J recombination substrates in solution. Mol. Cell. Biol. 17:6932–6939.
   PubMedGoogle Scholar
• Lykke-Andersen, J., R. Garrett, and J. Kjems 1997. Mapping metal ions at the catalytic centres of two intron-encoded endonucleases. EMBO J. 16:3272–3281.
   PubMedGoogle Scholar
• May, E. W., and J. Craig 1996. Switching from cut-and-paste to replicative Tn 7 transposition. Science 272:401–404.
   PubMedGoogle Scholar
• McBlane, J. F., D. C. van Gent, D. A. Ramsden, C. Romeo, C. A. Cuomo, M. Gellert, and J. Oettinger 1995. Cleavage at a V(D)J recombination signal requires only RAG1 and RAG2 proteins and occurs in two steps. Cell 83:387–395.
   PubMed Web of Science ®Google Scholar
• McMahan, C. J., M. J. Difilippantonio, N. Rao, E. S. Spanopoulou, and J. Schatz 1997. A basic motif in the N-terminal region of RAG1 enhances recombination activity. Mol. Cell. Biol. 17:4544–4552.
   PubMedGoogle Scholar
• McMahan, C. J., M. J. Sadofsky, and J. Schatz 1997. Definition of a large region of RAG1 that is important for co-immunoprecipitation of RAG2. J. Immunol. 158:2202–2210.
   PubMedGoogle Scholar
• Meisenheimer, K. M., and J. Koch 1997. Photocross-linking of nucleic acids to associated proteins. Crit. Rev. Biochem. Mol. Biol. 32:101–140.
   PubMed Web of Science ®Google Scholar
• Mizuuchi, M., T. A. Baker, and J. Mizuuchi 1991. DNase protection analysis of the stable synaptic complexes involved in Mu transposition. Proc. Natl. Acad. Sci. USA 88:9031–9035.
   PubMedGoogle Scholar
• Mombaerts, P., J. Iacomini, R. S. Johnson, K. Herrup, S. Tonegawa, and J. Papaioannou 1992. RAG-1-deficient mice have no mature B and T lymphocytes. Cell 68:869–877.
   PubMed Web of Science ®Google Scholar
• Nagawa, F., K. Ishiguro, A. Tsuboi, T. Yoshida, A. Ishikawa, T. Takemori, A. Otsuka, and J. Sakano 1998. Footprint analysis of the RAG protein recombination signal sequence complex for V(D)J type recombination. Mol. Cell. Biol. 18:655–663.
   PubMedGoogle Scholar
• Ramsden, D. A., K. Baetz, and J. Wu 1994. Conservation of sequence in recombination signal sequence spacers. Nucleic Acids Res. 22:1785–1796.
   PubMedGoogle Scholar
• Ramsden, D. A., J. F. McBlane, D. C. van Gent, and J. Gellert 1996. Distinct DNA sequence and structure requirements for the two steps of V(D)J recombination signal cleavage. EMBO J. 15:3197–3206.
   PubMedGoogle Scholar
• Rodgers, K. K., Z. Bu, K. G. Fleming, D. G. Schatz, D. M. Engelman, and J. Coleman 1996. A unique zinc-binding dimerization motif domain in RAG-1 includes the C3HC4 motif. J. Mol. Biol. 260:70–84.
   PubMedGoogle Scholar
• Rodgers, K. K., I. J. Villey, E. Corbett, D. G. Schatz, and J. E. Coleman. A dimer of RAG1 recognizes the recombination signal sequence and the complex stably incorporates HMG2. Submitted for publication.
   Google Scholar
• Roman, C. A. J., and J. Baltimore 1996. Genetic evidence that the RAG1 protein directly participates in V(D)J recombination through substrate recognition. Proc. Natl. Acad. Sci. USA 93:2333–2338.
   PubMedGoogle Scholar
• Sadofsky, M. J., J. E. Hesse, and J. Gellert 1994. Definition of a core region of RAG-2 that is functional in V(D)J recombination. Nucleic Acids Res. 22:1805–1809.
   PubMed Web of Science ®Google Scholar
• Sadofsky, M. J., J. E. Hesse, J. F. McBlane, and J. Gellert 1993. Expression and V(D)J recombination activity of mutated RAG-1 proteins. Nucleic Acids Res. 22:5644–5650.
   Google Scholar
• Sadofsky, M. J., J. E. Hesse, D. C. Vangent, and J. Gellert 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.
   PubMedGoogle Scholar
• Santagata, S., V. Aidinis, and J. Spanopoulou 1998. The effect of Me++ cofactors at the initial stages of V(D)J recombination. J. Biol. Chem. 273:16325–16331.
   PubMedGoogle Scholar
• Sarnovsky, R. J., E. W. May, and J. Craig 1996. The Tn 7 transposase is a heteromeric complex in which DNA breakage and joining activities are distributed between different gene products. EMBO J. 15:6348–6361.
   PubMedGoogle Scholar
• Sawchuk, D., F. Weis-Garcia, S. Malik, E. Besmer, M. Bustin, M. Nussenzweig, and J. Cortes 1997. V(D)J recombination: modulation of RAG1 and RAG2 cleavage activity on 12/23 substrates by whole cell extract and DNA-bending proteins. J. Exp. Med. 185:2025–2032.
   PubMedGoogle Scholar
• Schultz, S., G. Shields, and J. Steitz 1991. Crystal structure of a CAP-DNA complex: the DNA is bent by 90°. Science 253:1001–1007.
   PubMed Web of Science ®Google Scholar
• Shinkai, Y., G. Rathbun, L. Kong-Peng, E. M. Oltz, V. Stewart, M. Mendelsohn, J. Charron, M. Datta, F. Young, A. M. Stall, and J. Alt 1992. RAG-2-deficient mice lack mature lymphocytes owing to inability to initiate V(D)J rearrangement. Cell 68:855–867.
   PubMed Web of Science ®Google Scholar
• Spanopoulou, E., P. Cortes, C. Shih, C. M. Huang, D. P. Silver, P. Svec, and J. Baltimore 1995. Localization, interaction, and RNA binding properties of the V(D)J recombination-activating proteins RAG1 and RAG2. Immunity 3:715–726.
   PubMedGoogle Scholar
• Spanopoulou, E., F. Zaitseva, F.-H. Wang, S. Santagata, D. Baltimore, and J. Panayotou 1996. The homeodomain of Rag-1 reveals the parallel mechanisms of bacterial and V(D)J recombination. Cell 87:263–276.
   PubMedGoogle Scholar
• Steen, S. B., L. Gomelsky, and J. Roth 1996. The 12/23 rule is enforced at the cleavage step of V(D)J recombination in vivo. Genes Cells 1:543–553.
   PubMedGoogle Scholar
• Steen, S. B., L. Gomelsky, S. L. Speidel, and J. Roth 1997. Initiation of V(D)J recombination in vivo: role of recombination signal sequences in formation of single and paired double-strand breaks. EMBO J. 16:2656–2664.
   PubMedGoogle Scholar
• Swanson, P., and J. Desiderio 1998. V(D)J recombination signal recognition: distinct, overlapping DNA-protein contacts in complexes containing RAG1 with and without RAG2. Immunity 9:115–125.
   PubMedGoogle Scholar
• Tari, L., and J. Secco 1995. Base-pair opening and spermine binding B-DNA features displayed in crystal structure of a gal operon fragment: implications for protein-DNA recognition. Nucleic Acids Res. 23:2065–2073.
   PubMed Web of Science ®Google Scholar
• Timsit, Y., E. Vilbois, and J. Moras 1991. Base-pairing shift in the major groove of (CA)n tracts by B-DNA crystal structures. Nature 354:167–170.
   PubMed Web of Science ®Google Scholar
• van Gent, D. C., K. Hiom, T. T. Paull, and J. Gellert 1997. Stimulation of V(D)J cleavage by high mobility group proteins. EMBO J. 16:2665–2670.
   PubMed Web of Science ®Google Scholar
• van Gent, D. C., J. F. McBlane, D. A. Ramsden, M. J. Sadofsky, J. E. Hesse, and J. Gellert 1995. Initiation of V(D)J recombination in a cell-free system. Cell 81:925–934.
   PubMed Web of Science ®Google Scholar
• van Gent, D. C., K. Mizuuchi, and J. Gellert 1996. Similarities between initiation of V(D)J recombination and retroviral integration. Science 271:1592–1594.
   PubMedGoogle Scholar
• van Gent, D. C., D. A. Ramsden, and J. Gellert 1996. The RAG1 and RAG2 proteins establish the 12/23 rule in V(D)J recombination. Cell 85:107–113.
   PubMed Web of Science ®Google Scholar
• Villa, A., S. Santagata, F. Bozzi, S. Giliani, A. Frattini, L. Imberti, L. Gatta, H. Ochs, S. Schwarz, L. Notarangelo, V. Vezzoni, and J. Spanopoulou 1998. Partial V(D)J recombination activity leads to Omenn’s syndrome. Cell 93:885–896.
   PubMed Web of Science ®Google Scholar
• Willis, M. C., B. J. Hicke, O. C. Uhlenbeck, T. R. Cech, and J. Koch 1993. Photocrosslinking of 5-iodouracil-substituted RNA and DNA to proteins. Science 262:1255–1257.
   PubMed Web of Science ®Google Scholar
• Zwilling, S., H. Konig, and J. Wirth 1995. High mobility group protein 2 functionally interacts with the POU domains of octamer transcription factors. EMBO J. 14:1198–1208.
   PubMedGoogle Scholar