DNA helicase gene interaction network defined using synthetic lethality analyzed by microarray

Nature Genetics

Volumn 35, Issue 3, 2003, Pages 277-286

  Ooi, Siew Loon ^a   Shoemaker, Daniel D ^b   Boeke, Jef D ^a  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b MERCK RESEARCH LABORATORIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HELICASE; PROTEIN MRC1; PROTEIN RAD9; PROTEIN RRM3; RAD51 PROTEIN; RIBOSOME DNA; UNCLASSIFIED DRUG;

ALLELE; ANALYTIC METHOD; ANIMAL CELL; ARTICLE; CONTROLLED STUDY; DNA DAMAGE; DNA MICROARRAY; DNA REPLICATION; GENE; GENE DUPLICATION; GENE INTERACTION; GENE MUTATION; GENETIC RECOMBINATION; GENETIC STABILITY; LETHALITY; NONHUMAN; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; SGS1 GENE; SRS2 GENE; SYNTHETIC LETHALITY ANALYSIS BY MICROARRAY;

DNA HELICASES; DNA REPLICATION; GENES, LETHAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RECOMBINATION, GENETIC; SACCHAROMYCES CEREVISIAE;

ANIMALIA; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 0242298316     PISSN: 10614036     EISSN: None     Source Type: Journal    
DOI: 10.1038/ng1258     Document Type: Article

References (36)

1. Winzeler, E.A. et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285, 901-906 (1999).
2. Giaever, G. et al. Functional profiling of the Saccharomyces cerevisiae genome. Nature 418, 387-391 (2002).
3. Dobzhansky, T. Genetics of natural populations. XIII. Recombination and variability in populations of Drosophila pseudoobscura. Genetics 31, 269-290 (1946).
4. Novick, P., Osmond, B.C. & Botstein, D. Suppressors of yeast actin mutations. Genetics 121, 659-674 (1989).
5. Bender, A. & Pringle, J.R. Use of a screen for synthetic lethal and multicopy suppressee mutants to identify two new genes involved in morphogenesis in Saccharomyces cerevisiae. Mol. Cell. Biol. 11, 1295-1305 (1991).
6. Hartman, J., Garvik, B. & Hartwell, L. Principles for the buffering of genetic variation. Science 291, 1001-1004 (2001).
7. Tong, A.H. et al. Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294, 2364-2368 (2001).
8. Ooi, S.L., Shoemaker, D.D. & Boeke, J.D. A DNA microarray-based genetic screen for nonhomologous end-joining mutants in Saccharomyces cerevisiae. Science 294, 2552-2556 (2001).
9. Rong, L. & Klein, H.L. Purification and characterization of the SRS2 DNA helicase of the yeast Saccharomyces cerevisiae. J. Biol. Chem. 268, 1252-1259 (1993).
10. Lu, J. et al. Human homologues of yeast helicase. Nature 383, 678-679 (1996).
11. Bennett, R.J., Sharp, J.A. & Wang, J.C. Purification and characterization of the Sgs1 DNA helicase activity of Saccharomyces cerevisiae. J. Biol. Chem. 273, 9644-9650 (1998).
12. Hickson, I.D. RecQ helicases: caretakers of the genome. Nat. Rev. Cancer 3, 169-178 (2003).
13. Aboussekhra, A. et al. RADH, a gene of Saccharomyces cerevisiae encoding a putative DNA helicase involved in DNA repair. Characteristics of radH mutants and sequence of the gene. Nucleic Acids Res. 17, 7211-7219 (1989).
14. Lee, S.K., Johnson, R.E., Yu, S.L., Prakash, L. & Prakash, S. Requirement of yeast SGS1 and SRS2 genes for replication and transcription. Science 286, 2339-2342 (1999).
15. Aguilera, A. & Klein, H.L. Genetic control of intrachromosomal recombination in Saccharomyces cerevisiae. I. Isolation and genetic characterization of hyper-recombination mutations. Genetics 119, 779-790 (1988).
16. Gangloff, S., Soustelle, C. & Fabre, F. Homologous recombination is responsible for cell death in the absence of the Sgs1 and Srs2 helicases. Nat. Genet. 25, 192-194 (2000).
17. Yamagata, K. et al. Bloom's and Werner's syndrome genes suppress hyperrecombination in yeast sgs1 mutant: implication for genomic instability in human diseases. Proc. Natl. Acad. Sci. USA 95, 8733-8738 (1998).
18. Aylon, Y., Liefshitz, B., Bitan-Banin, G. & Kupiec, M. Molecular dissection of mitotic recombination in the yeast Saccharomyces cerevisiae. Mol. Cell. Biol. 23, 1403-1417 (2003).
19. Vaze, M.B. et al. Recovery from checkpoint-mediated arrest after repair of a double-strand break requires Srs2 helicase. Mol. Cell 10, 373-385 (2002).
20. Frei, C. & Gasser, S.M. The yeast Sgs1p helicase acts upstream of Rad53p in the DNA replication checkpoint and colocalizes with Rad53p in S-phase-specific foci. Genes Dev. 14, 81-96 (2000).
21. Bennett, C.B. et al. Genes required for ionizing radiation resistance in yeast. Nat. Genet. 29, 426-434 (2001).
22. Mankouri, H.W., Craig, T.J. & Morgan, A. SGS1 is a multicopy suppressor of srs2: functional overlap between DNA helicases. Nucleic Acids Res. 30, 1103-1113 (2002).
23. Mullen, J.R., Kaliraman, V., Ibrahim, S.S. & Brill, S.J. Requirement for three novel protein complexes in the absence of the Sgs1 DNA helicase in Saccharomyces cerevisiae. Genetics 157, 103-118 (2001).
24. Debrauwere, H., Loeillet, S., Lin, W., Lopes, J. & Nicolas, A. Links between replication and recombination in Saccharomyces cerevisiae: a hypersensitive requirement for homologous recombination in the absence of Rad27 activity. Proc. Natl. Acad. Sci. USA 98, 8263-8269 (2001).
25. Ogawa, T. et al. RecA-like recombination proteins in eukaryotes: functions and structures of RAD51 genes. Cold Spring Harb. Symp. Quant. Biol. 58, 567-576 (1993).
26. Sung, P., Trujillo, K.M. & Van Komen, S. Recombination factors of Saccharomyces cerevisiae. Mutat. Res. 451, 257-275 (2000).
27. Fabre, F., Chan, A., Heyer, W.D. & Gangloff, S. Alternate pathways involving Sgs1/Top3, Mus81/Mms4 and Srs2 prevent formation of toxic recombination intermediates from single-stranded gaps created by DNA replication. Proc. Natl. Acad. Sci. USA 99, 16887-16892 (2002).
28. Morrow, D.M., Connelly, C. & Hieter, P. "Break copy" duplication: a model for chromosome fragment formation in Saccharomyces cerevisiae. Genetics 147, 371-382 (1997).
29. Alcasabas, A.A. et al. Mrc1 transduces signals of DNA replication stress to activate Rad53. Nat. Cell Biol. 3, 958-965 (2001).
30. Qiu, J., Qian, Y., Frank, P., Wintersberger, U. & Shen, B. Saccharomyces cerevisiae RNase H(35) functions in RNA primer removal during lagging-strand DNA synthesis, most efficiently in cooperation with Rad27 nuclease. Mol. Cell. Biol. 19, 8361-8371 (1999).
31. Uetz, P. et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623-627 (2000).
32. Schmidt, K.H., Derry, K.L. & Kolodner, R.D. Saccharomyces cerevisiae RRM3, a 5′ to 3′ DNA helicase, physically interacts with proliferating cell nuclear antigen. J. Biol. Chem. 277, 45331-45337 (2002).
33. Ivessa, A.S., Zhou, J.Q. & Zakian, V.A. The Saccharomyces Pif1p DNA helicase and the highly related Rrm3p have opposite effects on replication fork progression in ribosornal DNA. Cell 100, 479-489 (2000).
34. Ivessa, A.S., Zhou, J.Q., Schulz, V.P., Monson, E.K. & Zakian, V.A. Saccharomyces Rrm3p, a 5′ to 3′ DNA helicase that promotes replication fork progression through telomeric and subtelomeric DNA. Genes Dev. 16, 1383-1396 (2002).
35. Hughes, T.R. et al. Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat. Biotechnol. 19, 342-347 (2001).
36. Breitkreutz, B.J., Stark, C. & Tyers, M. Osprey: a network visualization system. Genome Biol. 4, R22 (2003).