Novel nucleotide sequence motifs that produce hotspots of meiotic recombination in Schizosaccharomyces pombe

Genetics

Volumn 182, Issue 2, 2009, Pages 459-469

  Steiner, Walter W ^a   Steiner, Estelle M ^a   Girvin, Angela R ^a   Plewik, Lauren E ^a  

^a NIAGARA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

ARTICLE; CONSENSUS SEQUENCE; CONTROLLED STUDY; DNA STRAND BREAKAGE; GENETIC RECOMBINATION; GENOME; MEIOSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SCHIZOSACCHAROMYCES POMBE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; CYTOLOGY; FUNGAL GENOME; GENETICS; SCHIZOSACCHAROMYCES;

SCHIZOSACCHAROMYCES POMBE; SCHIZOSACCHAROMYCETACEAE;

BASE SEQUENCE; GENOME, FUNGAL; MEIOSIS; RECOMBINATION, GENETIC; SCHIZOSACCHAROMYCES;

EID: 68949206286     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.109.101253     Document Type: Article

References (55)

1. BAGSHAW, A. T., J. P. PITT and N. J. GEMMEL, 2006 Association of poly-purine/poly-pyrimidine sequences with meiotic recombination hotspots. BMC Genomics 7: 179-188.
2. BAILEY, T. L., N. WILLIAMS, C. MISLEH and W. W. LI, 1996 MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res. 34: W369-W373.
3. BAKER, B. S., A. T. C. CARPENTER, M. S. ESPOSITO, R. E. ESPOSITO and L. Sandler, 1976 The genetic control of meiosis. Annu. Rev. Genet. 10: 53-134.
4. BAUDAT, F., and A. NICOLAS, 1997 Clustering of meiotic double-strand breaks on yeast chromosome III. Proc. Natl. Acad. Sci. USA 94: 5213-5218.
5. BÄHLER, J., J.-Q. WU, M. S. LONGTINE, N. G. SHAH, A. MCKENZIE, III et al., 1998 Heterologous modules for efficient and versatile PCR-based gene targeting in Schizosaccharomyces pombe. Yeast 14: 943-951.
6. CAO, L., E. ALANI and N. KLECKNER, 1990 A pathway for generation and processing of double-strand breaks during meiotic recombination in S. cerevisiae. Cell 61: 1089-1101. (Pubitemid 20203491)
7. CERVANTES, M. D., J. A. FARAH and G. R. SMITH, 2000 Meiotic DNA breaks associated with recombination in S. pombe. Mol. Cell 5: 883-888.
8. COTTAREL, G., D. BEACH and U. DEUSCHLE, 1993 Two new multi-purpose multicopy Schizosaccharomyces pombe shuttle vectors, pSP1 and pSP2. Curr. Genet. 23: 547-548.
9. CROMIE, G. A., R. W. HYPPA, H. P. CAM, J. A. FARAH, S. I. S. GREWAL et al., 2007 A discrete class of intergenic DNA dictates meiotic DNA break hotspots in fission yeast. PLoS Genet. 3: 1496-1507.
10. CROMIE, G. A., C. A. RUBIO, R. W. HYPPA and G. R. SMITH, 2005 A natural meiotic DNA break site in Schizosaccharomyces pombe is a hotspot of gene conversion, highly associated with crossing over. Genetics 169: 595-605.
11. EGEL, R., 1977 Selective spore survival during replica-plating of fission yeast. Arch. Microbiol. 112: 109-110.
12. ESPOSITO, M. S., and J. E. WAGSTAFF, 1981 Mechanisms of mitotic recombination, pp. 341-370 in The Molecular Biology of the Yeast Saccharomyces, edited by J. N. STRATHERN, E. W. JONES and J. R. BROACH. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
13. FAN, Q., F. XU and T. D. PETES, 1995 Meiosis-specific double-strand DNA breaks at the HIS4 recombination hot spot in the yeast Saccharomyces cerevisiae: control in cis and trans. Mol. Cell. Biol. 15: 1679-1688.
14. FOX, M. E., J. B. VIRGIN, J. METZGER and G. R. SMITH, 1997 Position- and orientation-independent activity of the Schizosaccharomyces pombe meiotic recombination hot spot M26. Proc. Natl. Acad. Sci. USA 94: 7446-7451.
15. FOX, M. F., T. YAMADA, K. OHTA and G. R. SMITH, 2000 A family of CRE-related DNA sequences with meiotic recombination hotspot activity in Schizosaccharomyces pombe. Genetics 156: 59-68.
16. GERTON, J. L., J. DERISI, R. SHROFF, M. LICHTEN, P. O. BROWN et al., 2000 Global mapping of meiotic recombination hotspots and coldspots in the yeast Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 97: 11383-11390.
17. GUTZ, H., 1971 Site specific induction of gene conversion in Schizosaccharomyces pombe. Genetics 69: 317-337.
18. GUTZ, H., H. HESLOT, U. LEUPOLD and N. LOPRIENO, 1974 Schizosaccharomyces pombe, pp. 395-446 in Handbook of Genetics, edited by R. C. KING. Plenum, New York.
19. HEY, J., 2004 What's so hot about recombination hotspots? PLoS Biol. 2: 0730-0733.
20. HIROTA, K., W. W. STEINER, T. SHIBATA and K. OHTA, 2007 Chromatin configuration at natural meiotic recombination hot spots in fission yeast. Eukaryot. Cell 6: 2072-2080.
21. KEENEY, S., C. N. GIROUX and N. KLECKNER, 1997 Meiosis-specific DNA double-strand breaks are catalyzed by Spo11, a member of a widely conserved protein family. Cell 88: 375-384.
22. KIRKPATRICK, D. T., Y. H. WANG, M. DOMINSKA, J. D. GRIFFITH and T. D. PETES, 1999 Control of meiotic recombination and gene expression in yeast by a simple repetitive DNA sequence that excludes nucleosomes. Mol. Cell. Biol. 19: 7661-7671.
23. KON, N., M. D. KRAWCHUK, B. G. WARREN, G. R. SMITH and W. P. WAHLS, 1997 Transcription factor Mts1/Mts2 (Atf1/Pcr1, Gad7/Pcr1) activates the M26 meiotic recombination hotspot in Schizosaccharomyces pombe. Proc. Natl. Acad. Sci. USA 94: 13756-13770.
24. MAHADEVAIAH, S. K., J. M. A. TURNER, F. BAUDAT, E. P. ROGAKOU, P. DEBOER et al., 2001 Recombinational DNA double strand breaks in mice precede synapsis. Nat. Genet. 27: 271-276.
25. MALIK, S.-B., M. A. RAMESH, A. M. HULSTRAND and J. M. LOGSDON JR., 2007 Protist homologs of the meiotic Spo11 gene and topoisomerase VI reveal an evolutionary history of gene duplication and lineage-specific loss. Mol. Biol. Evol. 24: 2827-2841.
26. MCNABB, D. S., K. A.-S. TSENG and L. GUARENTE, 1997 The Saccharomyces cerevisiae Hap5p homolog from fission yeast reveals two conserved domains that are essential for assembly of heterotetrameric CCAAT-binding factor. Mol. Cell. Biol. 17: 7008-7018.
27. MERCIER, A., B. PELLETIER and S. LABBÉ, 2006 A transcription factor cascade involving Fep1 and the CCAAT-binding factor Php4 regulates gene expression in response to iron deficiency in the fission yeast Schizosaccharomyces pombe. Eukaryotic Cell 5: 1866-1881.
28. MIECZKOWSKI, P. A., M. DOMINSKA, M. J. BUCK, J. L. GERTON, J. D. LIEB et al., 2006 A global analysis of the relationship between the binding of the Bas1p transcription factor and meiosis-specific double-strand DNA breaks in Saccharomyces cerevisiae. Mol. Cell. Biol. 26: 1014-1027.
29. MIZUNO, K.-I., Y. EMURA, M. BAUR, J. KOHLI, K. OHTA et al., 1997 Remodeling of chromatin structure around a single nucleotide mutation in ade6-M26 that creates meiotic recombination hotspot in fission yeast. Genes Dev. 11: 876-886.
30. MYERS, S., L. BOTTOLO, C. FREEMAN, G. MCVEAN and P. DONNELLY, 2005 A fine-scale map of recombination rates and hotspots across the human genome. Science 310: 321-324.
31. MYERS, S., C. FREEMAN, A. AUTON, P. DONNELLY and G. MCVEAN, 2008 A common sequence motif associated with recombination hot spots and genome instability in humans. Nat. Genet. 40: 1124-1129.
32. NISHANT, K. T., and M. R. S. RAO, 2005 Molecular features of meiotic recombination hotspots. Bioessays 28: 45-56.
33. PEARSON, W., and D. LIPMAN, 1988 Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA 85: 2444-2448.
34. PETES, T. D., 2001 Meiotic recombination hot spots and cold spots. Nat. Rev. Genet. 2: 360-370.
35. PÂQUES, F., and J. E. HABER, 1999 Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev. 63: 349-404.
36. PONTICELLI, A. S., and G. R. SMITH, 1989 Meiotic recombination deficient mutants of Schizosaccharomyces pombe. Genetics 123: 45-54. (Pubitemid 19233889)
37. SCHUCHERT, P., M. LANGSFORD, E. KÄSLIN and J. KOHLI, 1991 A specific DNA sequence is required for high frequency of recombination in the ade6 gene of fission yeast. EMBO J. 10: 2157-2163.
38. SINHA, S., and N. TOMPA, 2002 Discovery of novel transcription factor binding sites by statistical overrepresentation. Nucleic Acids Res. 30: 5549-5560. (Pubitemid 36113932)
39. SINHA, S., and N. TOMPA, 2003 YMF: a program for discovery of novel transcription factor binding sites by statistical overrepresentation. Nucleic Acids Res. 31: 3586-3588.
40. STEINER, W. W., R. W. SCHRECKHISE and G. R. SMITH, 2002 Meiotic DNA breaks at the S. pombe recombination hotspot M26. Mol. Cell 9: 847-855. (Pubitemid 34454894)
41. STEINER, W. W., and G. R. SMITH, 2005a Natural meiotic recombination hotspots in the S. pombe genome successfully predicted from the simple sequence motif M26. Mol. Cell. Biol. 25: 9054-9062.
42. STEINER, W. W., and G. R. SMITH, 2005b Optimizing the nucleotide sequence of a meiotic recombination hotspot in Schizosaccharomyces pombe. Genetics 169: 1973-1983. (Pubitemid 40695612)
43. STORICI, F., L. K. LEWIS and M. A. RESNICK, 2001 In vivo site-directed mutagenesis using oligonucleotides. Nat. Biotechnol. 19: 773-776.
44. SUN, H., D. TRECO, N. P. SCHULTES and J. W. SZOSTAK, 1989 Double-strand breaks at an initiation site for meiotic gene conversion. Nature 338: 87-90. (Pubitemid 19076790)
45. SZANKASI, P., W. D. HEYER, P. SCHUCHERT and J. KOHLI, 1988 DNA sequence analysis of the ade6 gene of Schizosaccharomyces pombe: wild-type and mutant alleles including the recombination hotspot allele ade6-M26. J. Mol. Biol. 204: 917-925.
46. VALLEJO, A. N., R. J. POGULIS and L. R. PEASE, 1995 Mutagenesis by PCR, pp. 603-612 in PCR Primer: A Laboratory Manual, edited by C. W. DIEFFENBACH and G. S. DVEKSLER. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
47. VIRGIN, J. B., J. METZGER and G. R. SMITH, 1995 Active and inactive transplacement of the M26 recombination hotspot in Schizosaccharomyces pombe. Genetics 141: 33-48.
48. WAHLS, W. P., E. R. SIEGEL and M. K. DAVISDSON, 2008 Meiotic recombination hotspots of fission yeast are directed to loci that express non-coding RNA. PLoS ONE 3: e2887.
49. WHITE, M. A., M. DOMINSKA and T. D. PETES, 1993 Transcription factors are required for the meiotic recombination hotspot at the HIS4 locus in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 90: 6621-6625.
50. WOOD, V., R. G. WILLIAM, M.-A. RAJANDREAM, M. LYNE, R. LYNE et al., 2002 The genome sequence of the eukaryote fission yeast Schizosaccharomyces pombe. Nature 415: 871-880.
51. WU, T.-C., and M. LICHTEN, 1994 Meiosis-induced double-strand break sites determined by yeast chromatin structure. Science 263: 515-518. (Pubitemid 24082749)
52. YAMADA, T., K. MIZUNO, K. HIROTA, N. KON, W. P. WAHLS, et al., 2004 Roles of histone acetylation and chromatin remodeling factor in a meiotic recombination hotspot. EMBO J. 23: 1792-1803.
53. YOUNG, J. A., R. W. SCHRECKHISE, W. W. STEINER and G. R. SMITH, 2002 Meiotic recombination remote from prominent DNA break sites in S. pombe. Mol. Cell 9: 253-263. (Pubitemid 34195552)
54. ZAHN-ZABAL, M., E. LEHMANN and J. KOHLI, 1995 Hot spots of recombination in fission yeast: inactivation of the M26 hot spot by deletion of the ade6 promoter and the novel hotspot ura4-aim. Genetics 140: 469-478.
55. ZHANG, J., F. LI, J. LI, M. Q. ZHANG and X. ZHANG, 2004 Evidence and characteristics of putative human alpha recombination hotspots. Hum. Mol. Genet. 13: 2823-2828.