Target DNA structure plays a critical role in RAG transposition

PLoS Biology

Volumn 4, Issue 11, 2006, Pages 1934-1946

  Posey, Jennifer E ^a,b   Pytlos, Malgorzata J ^c,d   Sinden, Richard R ^c,d   Roth, David B ^b  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

^b NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c TEXAS A AND M HEALTH SCIENCE CENTER   (United States)

^d Florida Institute of Technology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RAG1 PROTEIN; RAG2 PROTEIN; DNA; DNA BINDING PROTEIN; HOMEODOMAIN PROTEIN; OLIGODEOXYRIBONUCLEOTIDE; RAG 1 PROTEIN; RAG-1 PROTEIN; RAG2 PROTEIN, MOUSE; RECOMBINANT PROTEIN; TRANSPOSASE;

ARTICLE; DNA STRUCTURE; DNA TRANSPOSITION; GC RICH SEQUENCE; GENE TARGETING; NUCLEOTIDE SEQUENCE; PLASMID; ANIMAL; GENETIC RECOMBINATION; GENETICS; HUMAN; METABOLISM; MOLECULAR GENETICS; MOUSE; TRANSPOSON;

ANIMALS; BASE SEQUENCE; DNA; DNA TRANSPOSABLE ELEMENTS; DNA-BINDING PROTEINS; HOMEODOMAIN PROTEINS; HUMANS; MICE; MOLECULAR SEQUENCE DATA; OLIGODEOXYRIBONUCLEOTIDES; RECOMBINANT PROTEINS; RECOMBINATION, GENETIC; TRANSPOSASES;

EID: 33751050807     PISSN: 15457885     EISSN: 15457885     Source Type: Journal    
DOI: 10.1371/journal.pbio.0040350     Document Type: Article

References (49)

1. van Gent DC, Mizuuchi K, Gellert M (1996) Similarities between initiation of V(D)J recombination and retroviral integration. Science 271: 1592-1594.
2. Roth DB, Craig NL (1998) VDJ recombination: A transposase goes to work. Cell 94: 411-414.
3. Brandt VL, Roth DB (2004) How to tame a transposase. Immunol Rev 200: 249-260.
4. Zhou L, Mitra R, Atkinson PW, Hickman AB, Dyda F, et al. (2004) Transposition of hAT elements links transposable elements and V(D)J recombination. Nature 432: 995-1001.
5. Agrawal A, Eastman QM, Schatz DG (1998) Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system. Nature 394: 744-751.
6. Hiom K, Melek M, Gellert M (1998) DNA transposition by the RAG1 and RAG2 proteins: A possible source of oncogenic translocations. Cell 94: 463-470.
7. Melek M, Gellert M (2000) RAG1/2-mediated resolution of transposition intermediates: Two pathways and possible consequences. Cell 101: 625-633.
8. Shih IH, Melek M, Jayaratne ND, Gellert M (2002) Inverse transposition by the RAG1 and RAG2 proteins: Role reversal of donor and target DNA. EMBO J 21: 6625-6633.
9. Messier TL, O'Neill JP, Hou SM, Nicklas JA, Finette BA (2003) In vivo transposition mediated by V(D)J recombinase in human T lymphocytes. EMBO J 22: 1381-1388.
10. Chatterji M, Tsai CL, Schatz DG (2006) Mobilization of RAG-generated signal ends by transposition and insertion in vivo. Mol Cell Biol 26: 1558-1568.
11. Reddy YV, Perkins EJ, Ramsden DA (2006) Genomic instability due to V(D)J recombination-associated transposition. Genes Dev 20: 1575-1582.
12. Elkin SK, Matthews AG, Oettinger MA (2003) The C-terminal portion of RAG2 protects against transposition in vitro. EMBO J 22: 1931-1938.
13. Tsai CL, Schatz DG (2003) Regulation of RAG1/RAG2-mediated transposition by GTP and the C-terminal region of RAG2. EMBO J 22: 1922-1930.
14. Swanson PC, Volkmer D, Wang L (2004) Full-length RAG-2, and not full-length RAG-1, specifically suppresses RAG-mediated transposition, but not hybrid joint formation or disintegration. J Biol Chem 279: 4034-4044.
15. Neiditch MB, Lee GS, Landree MA, Roth DB (2001) RAG transposase can capture and commit to target DNA before or after donor cleavage. Mol Cell Biol 21: 4302-4310.
16. Lee GS, Neiditch MB, Sinden RR, Roth DB (2002) Targeted transposition by the V(D)J recombinase. Mol Cell Biol 22: 2068-2077.
17. Tsai CL, Chatterji M, Schatz DG (2003) DNA mismatches and GC-rich motifs target transposition by the RAG1/RAG2 transposase. Nucleic Acids Res 31: 6180-6190.
18. Kabotyanski EB, Zhu C, Kallick DA, Roth DB (1995) Hairpin opening by single-strand specific nucleases. Nucleic Acids Res 23: 3872-3881.
19. Sinden RR (1994) DNA structure and function. San Diego: Academic Press. 398 p.
20. Oussatcheva EA, Shlyakhtenko LS, Glass R, Sinden RR, Lyubchenko YL, et al. (1999) Structure of branched DNA molecules: Gel retardation and atomic force microscopy studies. J Mol Biol 292: 75-86.
21. Germond JE, Hirt B, Oudet P, Gross-Bellark M, Chambon P (1975) Folding of the DNA double helix in chromatin-like structures from simian virus 40. Proc Natl Acad Sci U S A 72: 1843-1847.
22. Keller W, Wendel I (1975) Stepwise relaxation of supercoiled SV40 DNA. Cold Spring Harb Symp Quant Biol 39: 199-208.
23. Sinden RR, Pettijohn DE (1984) Cruciform transitions in DNA. J Biol Chem 259: 6593-6600.
24. Xodo LE, Manzini G, Quadrifoglio F, van der Marel G, van Boom J (1991) DNA hairpin loops in solution: Correlation between primary structure, thermostability, and reactivity with single-strand-specific nuclease from mung bean. Nucleic Acids Res 19: 1505-1511.
25. Van de Ven FJM, Hilbers CW (1988) Nucleic acids and nuclear magnetic resonance. Eur J Biochem 178: 1-38.
26. Varani G (1995) Exceptionally stable nucleic acid hairpins. Annu Rev Biophys Biomol Struct 24: 379-404.
27. Blommers MJJ, Walters JALI, Haasnoot CAG, Aelen JMA, van der Marel GA, et al. (1989) Effects of base sequence on loop folding in DNA hairpins. Biochemistry 28: 7491-7498.
28. Davison A, Leach DRF (1994) Two-base DNA hairpin-loop structures in vivo. Nucleic Acids Res 22: 4361-4363.
29. Mariappan SVS, Garcia AE, Gupta G (1996) Structure and dynamics of the DNA hairpins formed by tandemly repeated CTG triplets associated with myotonic dystrophy. Nucleic Acids Res 24: 775-783.
30. Mariappan SVS, Catasti P, Chen X, Ratliff R, Moyzis RK, et al. (1996) Solution structures of the individual single strands of the fragile X DNA triplets (GCC)n.(GGC)n. Nucleic Acids Res 24: 784-792.
31. Darlow JM, Leach DR (1998) Secondary structures in d(CGG) and d(CCG) repeat tracts. J Mol Biol 275: 3-16.
32. Pearson CE, Sinden RR (1998) Trinucleotide repeat DNA structures: Dynamic mutations from dynamic DNA. Curr Opin Struct Biol 8: 321-330.
33. Dere R, Napierala M, Ranum LP, Wells RD (2004) Hairpin structure-forming propensity of the (CCTG.CAGG) tetranucleotide repeats contributes to the genetic instability associated with myotonic dystrophy type 2. J Biol Chem 279: 41715-41726.
34. Boehm T, Mengle-Gaw L, Kees UR, Spurr N, Lavenir I, et al. (1989) Alternating purine-pyrimidine tracts may promote chromosomal translocations seen in a variety of human lymphoid tumours. EMBO J 8: 2621-2631.
35. Adachi M, Tsujimoto Y (1990) Potential Z-DNA elements surround the breakpoints of chromosome translocation within the 5′ flanking region of bcl-2 gene. Oncogene 5: 1653-1657.
36. Aplan PD, Raimondi SC, Kirsch IR (1992) Disruption of the SCL gene by a t(1;3) translocation in a patient with T cell acute lymphoblastic leukemia. J Exp Med 176: 1303-1310.
37. Lu M, Zhang N, Raimondi S, Ho AD (1992) S1 nuclease hypersensitive sites in an oligopurine/oligopyrimidine DNA from the t(10;14) breakpoint cluster region. Nucleic Acids Res 20: 263-266.
38. Seite P, Hillion J, Leroux D, Berger R, Larsen CJ (1993) Common sequence in chromosome translocations affecting B- and T-cell malignancies: a novel recombination site? Genes Chromosomes Cancer 6: 253-254.
39. Raghavan SC, Swanson PC, Wu X, Hsieh CL, Lieber MR (2004) A non-B-DNA structure at the Bcl-2 major breakpoint region is cleaved by the RAG complex. Nature 428: 88-93.
40. Spanopoulou E, Cortes P, Shih C, Huang C-M, Silver DP, et al. (1995) Localization, interaction, and RNA binding properties of the V(D)J recombination-activating proteins RAG1 and RAG2. Immunity 3: 715-726.
41. Yarnall Schultz H, Landree MA, Qiu JX, Kale SB, Roth DB (2001) Joining-deficient RAG1 mutants block V(D)J recombination in vivo and hairpin opening in vitro. Mol Cell 7: 65-75.
42. Kale SB, Landree MA, Roth DB (2001) Conditional RAG-1 mutants block the hairpin formation step of V(D)J recombination. Mol Cell Biol 21: 459-466.
43. McBlane JF, van Gent DC, Ramsden DA, Romeo C, Cuomo CA, et al. (1995) Cleavage at a V(D)J recombination signal requires only RAG1 and RAG2 proteins and occurs in two steps. Cell 83: 387-395.
44. Potaman VN, Bissler JJ, Hashem VI, Oussatcheva EA, Lu L, et al. (2003) Unpaired structures in SCA10 (ATTCT)n.(AGAAT)n repeats. J Mol Biol 326: 1095-1111.
45. Sinden RR, Zheng GX, Brankamp RG, Allen KN (1991) On the deletion of inverted repeated DNA in Escherichia coli: Effects of length, thermal stability, and cruciform formation in vivo. Genetics 129: 991-1005.
46. Lewis SM, Hesse JE, Mizuuchi K, Gellert M (1988) Novel strand exchanges in V(D)J recombination. Cell 55: 1099-1107.
47. Hesse JE, Lieber MR, Mizuuchi K, Gellert M (1989) V(D)J recombination: A functional definition of the joining signals. Genes Dev 3: 1053-1061.
48. Steen SB, Gomelsky L, Speidel SL, Roth DB (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.
49. Han J-O, Steen SB, Roth DB (1997) Ku86 is not required for protection of signal ends or for formation of nonstandard V(D)J recombination products. Mol Cell Biol 17: 2226-2234.