Analysis of Spontaneous Gene Conversion Tracts within and between Mammalian Chromosomes

Journal of Molecular Biology

Volumn 377, Issue 2, 2008, Pages 337-351

  Rukść, Ania ^a   Bell Rogers, Patricia L ^b   Smith, Jillian D L ^a   Baker, Mark D ^a  

^a UNIVERSITY OF GUELPH   (Canada)

^b UNIVERSITY OF GUELPH   (Canada)

Author keywords

gene conversion; gene targeting; homologous recombination; intrachromosomal recombination; mammalian cells

Indexed keywords

ANIMAL CELL; ARTICLE; CELL CULTURE; CHROMOSOME; CHROMOSOME TRANSLOCATION; CONTROLLED STUDY; DNA REPAIR; DNA REPLICATION; GENE CONVERSION; GENE DELETION; GENE LOCUS; GENE MUTATION; GENE SEQUENCE; GENE STRUCTURE; GENE TARGETING; GENETIC POLYMORPHISM; HOMOLOGOUS RECOMBINATION; MAMMAL CELL; MOLECULAR WEIGHT; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SOMATIC CELL; SOUTHERN BLOTTING;

MAMMALIA;

EID: 40049091001     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2008.01.036     Document Type: Article

References (61)

1. F. Paques J.E. Haber Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae Microbiol. Mol. Biol. Rev. 63 1999 349 404
2. L.S. Symington Role of Rad52 epistasis group genes in homologous recombination and double-strand break repair Microbiol. Mol. Biol. Rev. 66 2002 630 670
3. S. Keeney C.N. Giroux N. Kleckner Meiosis-specific DNA double-strand breaks are catalyzed by Spo11, a member of a widely conserved protein family Cell 88 1997 375 384
4. S.R. Judd T.D. Petes Physical lengths of meiotic and mitotic gene conversion tracts in Saccharomyces cerevisiae Genetics 118 1988 401 410
5. C.B. McGill B.K. Shafer D.R. Higgins J.N. Strathern Analysis of interchromosomal mitotic recombination Curr. Genet. 18 1990 29 39
6. R.H. Borts J.E. Haber Meiotic recombination in yeast: alteration by multiple heterozygosities Science 237 1987 1459 1465
7. R.H. Borts J.E. Haber Length and distribution of meiotic gene conversion tracts and crossovers in Saccharomyces cerevisiae Genetics 123 1989 69 80
8. P. Detloff T.D. Petes Measurements of excision repair tracts formed during meiotic recombination in Saccharomyces cerevisiae Mol. Cell Biol. 12 1992 1805 1814
9. T.L. Orr-Weaver A. Nicolas J.W. Szostak Gene conversion adjacent to regions of double-strand break repair Mol. Cell. Biol. 8 1988 5292 5298
10. S. Palmer E. Schildkraut R. Lazarin J. Nguyen J.A. Nickoloff Gene conversion tracts in Saccharomyces cerevisiae can be extremely short and highly directional Nucleic Acids Res. 31 2003 1164 1173
11. D.B. Sweetser H. Hough J.F. Whelden M. Arbuckle J.A. Nickoloff Fine-resolution mapping of spontaneous and double-strand break-induced gene conversion tracts in Saccharomyces cerevisiae reveals reversible mitotic conversion polarity Mol. Cell Biol. 14 1994 3863 3875
12. J.A. Nickoloff D.B. Sweetzer J.A. Clikeman G.J. Khalsa S.L. Wheeler Multiple heterologies increase mitotic double-strand break induced allelic gene conversion tract lengths in yeast Genetics 153 1999 665 679
13. T.G. Taghian J.A. Nickoloff Chromosomal double-strand breaks induce gene conversion at high frequency in mammalian cells Mol. Cell Biol. 17 1997 6386 6393
14. B. Elliott C. Richardson J. Winderbaum J.A. Nickoloff M. Jasin Gene conversion tracts from double-strand break repair in mammalian cells Mol. Cell Biol. 18 1998 93 101
15. R.D. Johnson M. Jasin Sister chromatid gene conversion is a prominent double-strand break repair pathway in mammalian cells EMBO J. 19 2000 3398 3407
16. C. Richardson M.E. Moynahan M. Jasin Double-strand break repair by interchromosomal recombination: suppression of chromosomal translocations Genes Dev. 12 1998 3831 3842
17. G. Donoho M. Jasin P. Berg Analysis of gene targeting and intrachromosomal homologous recombination stimulated by genomic double-strand breaks in mouse embryonic stem cells Mol. Cell Biol. 18 1998 4070 4078
18. E.A.H. Neuwirth M. Honma A.J. Grosovsky Interchromosomal crossing-over in human cells is associated with long gene conversion tracts Mol. Cell. Biol. 27 2007 5261 5274
19. M.D. Baker High frequency homologous recombination between duplicate chromosomal immunoglobulin mu heavy-chain constant regions Mol. Cell Biol. 9 1989 5500 5507
20. M.D. Baker L.R. Read Ectopic recombination within homologous immunoglobulin mu gene constant regions in a mouse hybridoma cell line Mol. Cell Biol. 12 1992 4422 4432
21. R.M. Liskay J.L. Stachelek Evidence for intrachromosomal gene conversion in cultured mouse cells Cell 35 1983 157 165
22. R.M. Liskay J.L. Stachelek A. Letsou Homologous recombination between repeated chromosomal sequences in mouse cells Cold Spring Harbor Symp. Quant. Biol. 49 1984 183 189
23. M.J. Shulman C. Collins A. Connor L.R. Read M.D. Baker Interchromosomal recombination is suppressed in mammalian somatic cells EMBO J. 14 1995 4102 4107
24. A.J. Smith P. Berg Homologous recombination between defective neo genes in mouse 3T6 cells Cold Spring Harbor. Symp. Quant. Biol. 49 1984 171 181
25. M.D. Baker N. Pennell L. Bosnoyan M.J. Shulman Homologous recombination can restore normal immunoglobulin production in a mutant hybridoma cell line Proc. Natl Acad. Sci. USA 85 1988 6432 6436
26. J. Ellis A. Bernstein Gene targeting with retroviral vectors: recombination by gene conversion into regions of nonhomology Mol. Cell Biol. 9 1989 1621 1627
27. K.R. Thomas M.R. Capecchi Introduction of homologous DNA sequences into mammalian cells induces mutations in the cognate gene Nature 324 1986 34 38
28. J.R. Murti M. Bumbulis J.C. Schimenti High-frequency germline gene conversion in transgenic mice Mol. Cell. Biol. 12 1992 2545 2552
29. J.R. Murti M. Bumbulis J.C. Schimenti Gene conversion between unlinked sequences in the germline of mice Genetics 137 1994 837 843
30. R.M. Liskay J.L. Stachelek Information transfer between duplicated chromosomal sequences in mammalian cells involves contiguous regions of DNA Proc. Natl Acad. Sci. USA 83 1986 1802 1806
31. E.C. Birmingham S.A. Lee R.D. McCulloch M.D. Baker Testing predictions of the double-strand break repair model relating to crossing over in mammalian cells Genetics 168 2001 1539 1555
32. G. Köhler M.J. Potash H. Lehrach M.J. Shulman Deletions in immunoglobulin mu chains EMBO J. 1 1982 555 563
33. P. Ng M.D. Baker Mechanisms of double-strand-break repair during gene targeting in mammalian cells Genetics 151 1999 1127 1141
34. G.I. Goldberg E.F. Vanin A.M. Zrolka F.R. Blattner Sequence of the gene for the constant region of the μ chain of Balb/c mouse immunoglobulin Gene 15 1981 33 42
35. M.D. Baker L.R. Read B.G. Beatty P. Ng Requirements for ectopic homologous recombination in mammalian somatic cells Mol. Cell Biol. 1 1996 7122 7132
36. P. Hasty R. Ramirez-Solis R. Krumlauf A. Bradley Introduction of a subtle mutation into the Hox-2.6 locus in embryonic stem cells Nature 350 1991 243 246
37. G. Kõhler M.J. Shulman Immunoglobulin M mutants Eur. J. Immunol. 10 1980 467 476
38. A.J. Hilliker G. Harauz A.G. Reaume M. Gray S.H. Clark A. Chovnick Meiotic gene conversion tract length distribution within the rosy locus of Drosophila melanogaster Genetics 137 1994 1019 1026
39. C.R. Preston W.R. Engels P-element-induced male recombination and gene conversion in Drosophila Genetics 144 1996 1611 1622
40. G.B. Gloor N.A. Nassif D.M. Johnson-Schlitz C.R. Preston W.R. Engels Targeted gene replacement in Drosophila via P element-induced gap repair Science 253 1991 1110 1117
41. J.W. Cho G.J. Khalsa J.A. Nickoloff Gene-conversion tract directionality is influenced by the chromosome environment Curr. Genet. 34 1998 269 279
42. P.J. Yeadon D.E. Catcheside Long, interrupted conversion tracts initiated by cog in Neurospora crassa Genetics 148 1998 113 122
43. F.J. Bowring D.E. Catcheside Analysis of conversion tracts associated with recombination events at the am locus of Neurospora crassa Curr. Genet. 34 1998 43 49
44. R.J. Bollag R.M. Liskay Direct-repeat analysis of chromatid interactions during intrachromosomal recombination in mouse cells Mol. Cell Biol. 11 1991 4839 4845
45. L.C. Kadyk L.H. Hartwell Sister chromatids are preferred over homologs as substrates for recombinational repair in Saccharomyces cerevisiae Genetics 132 1992 387 402
46. J.L. Stachelek R.M. Liskay Accuracy of intrachromosomal gene conversion in mouse cells Nucleic Acids Res. 16 1988 4069 4076
47. F. Liang M. Han P.J. Romanienko M. Jasin Homology-directed repair is a major double-strand break repair pathway in mammalian cells Proc. Natl Acad. Sci. USA 95 1998 5172 5177
48. M.E. Moynahan M. Jasin Loss of heterozygosity induced by a chromosomal double-strand break Proc. Natl Acad. Sci. USA 94 1997 8988 8993
49. R.G. Sargent M.A. Brenneman J.H. Wilson Repair of site-specific double-strand breaks in a mammalian chromosome by homologous and illegitimate recombination Mol. Cell Biol. 17 1997 267 277
50. Y. Lin T. Lukacsovich A.S. Waldman Multiple pathways for repair of DNA double-strand breaks in mammalian chromosomes Mol. Cell Biol. 19 1999 8353 8360
51. P. Modrich Mechanisms in eukaryotic mismatch repair J. Biol. Chem. 281 2006 30305 30309
52. G. Lettier Q. Feng A.A. de Mayolo N. Erdeniz R.J. Reid M. Lisby The role of DNA double-strand breaks in spontaneous homologous recombination in S. cerevisiae PLoS Genet. 2 2006 e194
53. S.J. Raynard L.R. Read M.D. Baker Evidence for the murine IgH μ locus acting as a hot spot for intrachromosomal homologous recombination J. Immunol. 168 2002 2332 2339
54. B.S. Chevalier B.L. Stoddard Homing endonucleases: structural and functional insight into the catalysts of intron/intein mobility Nucleic Acids Res. 29 2001 3757 3774
55. A. Perrin M. Buckle B. Dujon Asymmetrical recognition and activity of the I-SceI endonuclease on its site and on intron–exon junctions EMBO J. 12 1993 2939 2947
56. G.S. Lee M.B. Neiditch S.S. Salus D.B. Roth RAG proteins shepherd double-strand breaks to a specific pathway, suppressing error-prone repair, but RAG nicking initiates homologous recombination Cell 117 2004 171 184
57. A. Aguilera H.L. Klein Yeast intrachromosomal recombination: long gene conversion tracts are preferentially associated with reciprocal exchange and require RAD1 and RAD3 gene products Genetics 123 1989 683 694
58. M.D. Baker L.R. Read B.G. Beatty P. Ng Requirements for ectopic homologous recombination in mammalian somatic cells Mol. Cell. Biol. 16 1996 7122 7133
59. J. Li M.D. Baker Use of a small palindrome genetic marker to investigate mechanisms of double-strand-break repair in mammalian cells Genetics 154 2000 1281 1289
60. M. Gross-Bellard P. Oudet P. Chambon Isolation of high-molecular weight DNA from mammalian cells Eur. J. Biochem. 36 1973 32 38
61. J. Sambrook E.F. Fritsch T. Maniatis Analysis and cloning of eukaryotic genomic DNA N. Ford C. Nolan M. Ferguson Molecular Cloning: A Laboratory Manual 2nd edit. 1989 Cold Spring Harbor Laboratory Press Cold Spring Harbor, NY 31 55