Conditional genomic rearrangement by designed meiotic recombination using VDE (PI-SceI) in yeast

Molecular Genetics and Genomics

Volumn 278, Issue 4, 2007, Pages 467-478

  Fukuda, Tomoyuki ^a   Ohya, Yoshikazu ^b   Ohta, Kunihiro ^a  

^a RIKEN   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

Author keywords

Genetic rearrangement; Homing endonuclease; Meiosis; PI SceI; Recombination; VDE

Indexed keywords

ENDONUCLEASE; UNCLASSIFIED DRUG; VMA1 DERIVED ENDONUCLEASE;

ANALYTIC METHOD; ARTICLE; CELL VIABILITY; CONTROLLED STUDY; DNA FLANKING REGION; FUNGAL STRAIN; GENE CONVERSION; GENE REARRANGEMENT; GENE SEQUENCE; GENETIC RECOMBINATION; KNOCKOUT GENE; MEIOSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; YEAST;

CELL SURVIVAL; DNA BREAKS, DOUBLE-STRANDED; DNA SHUFFLING; GENE TARGETING; GENOME, FUNGAL; GENOMIC INSTABILITY; MEIOSIS; MODELS, BIOLOGICAL; MUTAGENESIS, INSERTIONAL; ORGANISMS, GENETICALLY MODIFIED; PROTON-TRANSLOCATING ATPASES; RECOMBINATION, GENETIC; SACCHAROMYCES CEREVISIAE PROTEINS; SPORES, FUNGAL; YEASTS;

EID: 34548756727     PISSN: 16174615     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00438-007-0264-7     Document Type: Article

References (34)

1. Adams A, Gottschling D, Kaiser C, Stearns T (1997) Methods in yeast genetics. Cold Spring Harbor Laboratory Press, New York
2. Arnould S, Chames P, Perez C, Lacroix E, Duclert A, Epinat JC, Stricher F, Petit AS, Patin A, Guillier S, Rolland S, Prieto J, Blanco FJ, Bravo J, Montoya G, Serrano L, Duchateau P, Paques F (2006) Engineering of large numbers of highly specific homing endonucleases that induce recombination on novel DNA targets. J Mol Biol 355:443-458
3. Ashworth J, Havranek JJ, Duarte CM, Sussman D, Monnat RJ Jr, Stoddard BL, Baker D (2006) Computational redesign of endonuclease DNA binding and cleavage specificity. Nature 441:656-659
4. Baudat F, Nicolas A (1997) Clustering of meiotic double-strand breaks on yeast chromosome III. Proc Natl Acad Sci USA 94:5213-5218
5. Baudin A, Ozier-Kalogeropoulos O, Denouel A, Lacroute F, Cullin C (1993) A simple and efficient method for direct gene deletion in Saccharomyces cerevisiae. Nucleic Acids Res 21:3329-3330
6. Bishop DK, Zickler D (2004) Early decision; meiotic crossover interference prior to stable strand exchange and synapsis. Cell 117:9-15
7. Church GM, Gilbert W (1984) Genomic sequencing. Proc Natl Acad Sci USA 81:1991-1995
8. Cromie GA, Rubio CA, Hyppa RW, Smith GR (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
9. Fukuda T, Ohya Y (2006) Recruitment of RecA homologs Dmc1p and Rad51p to the double-strand break repair site initiated by meiosis-specific endonuclease VDE (PI-SceI). Mol Genet Genomics 275:204-214
10. Fukuda T, Nogami S, Ohya Y (2003) VDE-initiated intein homing in Saccharomyces cerevisiae proceeds in a meiotic recombination-like manner. Genes Cells 8:587-602
11. Fukuda T, Nagai Y, Ohya Y (2004) Molecular mechanism of VDE-initiated intein homing in yeast nuclear genome. Adv Biophys 38:215-232
12. Fukuda T, Ohta K, Ohya Y (2006) Investigation of the mechanism of meiotic DNA cleavage by VMA1-derived endonuclease uncovers a meiotic alteration in chromatin structure around the target site. Eukaryot Cell 5:981-990
13. Gerton JL, DeRisi J, Shroff R, Lichten M, Brown PO, Petes TD (2000) Inaugural article: global mapping of meiotic recombination hotspots and coldspots in the yeast Saccharomyces cerevisiae. Proc Natl Acad Sci USA 97:11383-11390
14. Gimble FS, Thorner J (1992) Homing of a DNA endonuclease gene by meiotic gene conversion in Saccharomyces cerevisiae. Nature 357:301-306
15. Herman PK, Rine J (1997) Yeast spore germination: a requirement for Ras protein activity during re-entry into the cell cycle. EMBO J 16:6171-6181
16. Hillers KJ (2004) Crossover interference. Curr Biol 14:R1036-1037
17. Hirata R, Ohsumk Y, Nakano A, Kawasaki H, Suzuki K, Anraku Y (1990) Molecular structure of a gene, VMA1, encoding the catalytic subunit of H(+)-translocating adenosine triphosphatase from vacuolar membranes of Saccharomyces cerevisiae. J Biol Chem 265:6726-6733
18. Huang ME, Cadieu E, Souciet JL, Galibert F (1997) Disruption of six novel yeast genes reveals three genes essential for vegetative growth and one required for growth at low temperature. Yeast 13:1181-1194
19. Kane PM, Yamashiro CT, Wolczyk DF, Neff N, Goebl M, Stevens TH (1990) Protein splicing converts the yeast TFP1 gene product to the 69-kD subunit of the vacuolar H+-adenosine triphosphatase. Science 250:651-657
20. Keeney S (2001) Mechanism and control of meiotic recombination initiation. Curr Top Dev Biol 52:1-53
21. Kelly TJ, Martin GS, Forsburg SL, Stephen RJ, Russo A, Nurse P (1993) The fission yeast cdc18+ gene product couples S phase to START and mitosis. Cell 74:371-382
22. Kono K, Matsunaga R, Hirata A, Suzuki G, Abe M, Ohya Y (2005) Involvement of actin and polarisome in morphological change during spore germination of Saccharomyces cerevisiae. Yeast 22:129-139
23. Malkova A, Klein F, Leung WY, Haber JE (2000) HO endonuclease-induced recombination in yeast meiosis resembles Spo11-induced events. Proc Natl Acad Sci USA 97:14500-14505
24. Martini E, Diaz RL, Hunter N, Keeney S (2006) Crossover homeostasis in yeast meiosis. Cell 126:285-295
25. Neale MJ, Ramachandran M, Trelles-Sticken E, Scherthan H, Goldman AS (2002) Wild-type levels of Spo11-induced DSBs are required for normal single-strand resection during meiosis. Mol Cell 9:835-846
26. Niu H, Wan L, Baumgartner B, Schaefer D, Loidl J, Hollingsworth NM (2005) Partner choice during meiosis is regulated by Hop1-promoted dimerization of Mek1. Mol Biol Cell 16:5804-5818
27. Nogami S, Fukuda T, Nagai Y, Yabe S, Sugiura M, Mizutani R, Satow Y, Anraku Y, Ohya Y (2002) Homing at an extragenic locus mediated by VDE (PI-SceI) in Saccharomyces cerevisiae. Yeast 19:773-782
28. Ohta K, Nicolas A, Furuse M, Nabetani A, Ogawa H, Shibata T (1998) Mutations in the MRE11, RAD50, XRS2, and MRE2 genes alter chromatin configuration at meiotic DNA double-stranded break sites in premeiotic and meiotic cells. Proc Natl Acad Sci USA 95:646-51
29. Pecina A, Smith KN, Mezard C, Murakami H, Ohta K, Nicolas A (2002) Targeted stimulation of meiotic recombination. Cell 111:173-184
30. Petronczki M, Siomos MF, Nasmyth K (2003) Un menage a quatre: the molecular biology of chromosome segregation in meiosis. Cell 112:423-440
31. Sakumoto N, Mukai Y, Uchida K, Kouchi T, Kuwajima J, Nakagawa Y, Sugioka S, Yamamoto E, Furuyama T, Mizubuchi H, Ohsugi N, Sakuno T, Kikuchi K, Matsuoka I, Ogawa N, Kaneko Y, Harashima S (1999) A series of protein phosphatase gene disruptants in Saccharomyces cerevisiae. Yeast 15:1669-1679
32. Schwacha A, Kleckner N (1997) Interhomolog bias during meiotic recombination: meiotic functions promote a highly differentiated interhomolog-only pathway. Cell 90:1123-1135
33. Tye BK (1999) MCM proteins in DNA replication. Annu Rev Biochem 68:649-86
34. Urnov FD, Miller JC, Lee YL, Beausejour CM, Rock JM, Augustus S, Jamieson AC, Porteus MH, Gregory PD, Holmes MC (2005) Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature 435:646-651