Enabling a Community to Dissect an Organism: Overview of the Neurospora Functional Genomics Project

Advances in Genetics

Volumn 57, Issue , 2007, Pages 49-96

  Dunlap, Jay C ^a   Borkovich, Katherine A ^b   Henn, Matthew R ^c   Turner, Gloria E ^d   Sachs, Matthew S ^e   Glass, N Louise ^f   McCluskey, Kevin ^g   Plamann, Michael ^g   Galagan, James E ^c   Birren, Bruce W ^c   Weiss, Richard L ^d   Townsend, Jeffrey P ^h   Loros, Jennifer J ^a   Nelson, Mary Anne ⁱ   Lambreghts, Randy ^a   Colot, Hildur V ^a   Park, Gyungsoon ^b   Collopy, Patrick ^a   Ringelberg, Carol ^a   Crew, Christopher ^b   Litvinkova, Liubov ^b   DeCaprio, Dave ^c   Hood, Heather M ^e   Curilla, Susan ^a   Shi, Mi ^a   Crawford, Matthew ^c   Koerhsen, Michael ^c   Montgomery, Phil ^c   Larson, Lisa ^c   Pearson, Matthew ^c   Kasuga, Takao ^f   Tian, Chaoguang ^f   Baştürkmen, Meray ^e   Altamirano, Lorena ^b   Xu, Junhuan ⁱ   more..

^a DARTMOUTH MEDICAL SCHOOL   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

^f UNIVERSITY OF CALIFORNIA   (United States)

^g UNIVERSITY OF MISSOURI KANSAS CITY   (United States)

^h YALE UNIVERSITY   (United States)

ⁱ UNIVERSITY OF NEW MEXICO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL DNA;

CHROMOSOME MAP; DNA MICROARRAY; GENE DELETION; GENE EXPRESSION PROFILING; GENE LIBRARY; GENETIC PROCEDURES; GENETICS; GENOME; GENOMICS; MUTATION; NEUROSPORA; NUCLEOTIDE SEQUENCE; PHENOTYPE; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM;

BASE SEQUENCE; CHROMOSOME MAPPING; DNA, FUNGAL; GENE DELETION; GENE EXPRESSION PROFILING; GENE LIBRARY; GENETIC TECHNIQUES; GENOME, FUNGAL; GENOMICS; MUTATION; NEUROSPORA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 33847665978     PISSN: 00652660     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0065-2660(06)57002-6     Document Type: Review

References (68)

1. Altshuler D., Pollara V.J., Cowles C.R., Van Etten W.J., Baldwin J., Linton L., and Lander E.S. An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature 407 6803 (2000) 513-516
2. Aronson B.D., Johnson K., Loros J.J., and Dunlap J.C. Negative feedback defining a circadian clock: Autoregulation in the clock gene frequency. Science 263 (1994) 1578-1584
3. Aronson B.D., Lindgren K.M., Dunlap J.C., and Loros J.J. An efficient method of gene disruption in Neurospora crassa with potential for other filamentous fungi. Mol. Gen. Genet. 242 (1994) 490-494
4. Bailey T.L., and Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. "Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology," (1994), AAAI Press, Menlo Park, CA 28-36
5. Beadle G.W., and Tatum E.L. Neurospora II. Methods of producing and detecting mutations concerned with nutritional requirements. Am. J. Bot. 32 (1945) 678-686
6. Bell-Pedersen D., Shinohara M., Loros J., and Dunlap J.C. Circadian clock-controlled genes isolated from Neurospora crassa are late night to early morning specific. Proc. Nat. Acad. Sci. USA 93 (1996) 13096-13101
7. Berger J., Suzuki T., Senti K.A., Stubbs J., Schaffner G., and Dickson B.J. Genetic mapping with SNP markers in Drosophila. Nat. Genet. 29 4 (2001) 475-481
8. Bistis G.N., Perkins D.D., and Read N.D. Different cell types in Neurospora crassa. Fungal Genet. Newslett. 50 (2003) 17-19
9. Bonnen A., and Brambl R. Germination physiology of Neurospora crassa conidia. Exp. Mycol. 7 (1983) 197-207
10. Borkovich K., Alex L., Yarden O., Freitag M., Turner G., Read N., Seiler S., Bell-Pedersen D., Paietta J., Plesofsky N., Plamann M., Schulte U., et al. Lessons from the genome sequence of Neurospora crassa: Tracing the path from genomic blueprint to multicellular organism. Microbiol. Mol. Biol. Rev. 68 (2004) 1-108
11. Bozdech Z., Zhu J., Joachimiak M.P., Cohen F.E., Pulliam B., and DeRisi J.L. Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. Genome Biol. 4 2 (2003) R9
12. Brazma A. On the importance of standardisation in life sciences. Bioinformatics 17 2 (2001) 113-114
13. Catlett N.L., Lee B., Yoder O.C., and Turgeon B.G. Split-marker recombination for efficient targeted deletion of fungal genes. Fungal Genet. Newslett. 50 (2003) 9-11
14. Cogoni C., and Macino G. Isolation of quelling-defective (qde) mutants impaired in posttranscriptional transgene-induced gene silencing in Neurospora crassa. Proc. Natl. Acad. Sci. USA 94 (1997) 10233-10238
15. Colot H., Park G., Jones J., Turner G., Borkovich K., and Dunlap J.C. High throughput knockout of transcription factors in Neurospora reveals diverse phenotypes. Proc. Natl. Acad. Sci. USA 103 (2006) 10352-10357
16. Colot H.V., Loros J.J., and Dunlap J.C. Temperature-modulated alternative splicing and promoter use in the Circadian clock gene frequency. Mol. Biol. Cell 16 12 (2005) 5563-5571
17. Coulter K.R., and Marzluf G.A. Functional analysis of different regions of the positive-acting CYS3 regulatory protein of Neurospora crassa. Curr. Genet. 33 6 (1998) 395-405
18. Davis R.H. "Neurospora: Contributions of a Model Organism." (2000), Oxford University Press, Oxford, UK
19. Davis R.L., and deSerres D. Genetic and microbial research techniques for Neurospora crassa. Methods Enzymol. 27A (1970) 79-143
20. Denfert C. Fungal spore germination-insights from the molecular genetics of Aspergillus nidulans and Neurospora crassa. Fungal Genet. Biol. 21 2 (1997) 163-172
21. Derisi J.L., and Iyer V.R. Genomics and array technology. Curr. Opin Oncol. 11 1 (1999) 76-79
22. Dillon D., and Stadler D. Spontaneous mutation at the mtr locus in Neurospora: The molecular spectrum in wild-type and a mutator strain. Genetics 138 1 (1994) 61-74
23. Drenkard E., Richter B.G., Rozen S., Stutius L.M., Angell N.A., Mindrinos M., Cho R.J., Oefner P.J., Davis R.W., and Ausubel F.M. A simple procedure for the analysis of single nucleotide polymorphisms facilitates map-based cloning in Arabidopsis. Plant Physiol. 124 4 (2000) 1483-1492
24. Dunlap J.C., and Loros J.J. Analysis of circadian rhythms in Neurospora: Overview of assays and genetic and molecular biological manipulation. Methods Enzymol. 393 (2005) 3-22
25. Eisen M.B., and Brown P.O. DNA arrays for analysis of gene expression. Methods Enzymol. 303 (1999) 179-205
26. Eisen M.B., Spellman P.T., Brown P.O., and Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95 (1998) 14863-14868
27. Fairhead C., Llorente B., Denis F., Soler M., and Dujon B. New vectors for combinatorial deletions in yeast chromosomes and for gap-repair cloning using "split-marker" recombination. Yeast 12 (1996) 1439-1457
28. Galagan J.E., Calvo S.E., Borkovich K.A., Selker E.U., Read N.D., Jaffe D., FitzHugh W., Ma L.J., Smirnov S., Purcell S., Rehman B., Elkins T., et al. The genome sequence of the filamentous fungus Neurospora crassa. Nature 422 (2003) 859-868
29. Gasch A.P., Moses A.M., Chiang D.Y., Fraser H.B., Berardini M., and Eisen M.B. Conservation and evolution of cis-regulatory systems in ascomycete fungi. PLoS Biol. 2 12 (2004) e398
30. Goldstein A.L., and McCusker J.H. Three new dominant drug resistance cassettes for gene disruption in Saccharomyces cerevisiae. Yeast 15 (1999) 1541-1543
31. Gritz L., and Davies J. Plasmid-encoded hygromycin B resistance: The sequence of the hygromycin B phosphotransferase gene and its expression in Escherichia coli and Saccharomyces cerevisiae. Gene 25 (1983) 179-188
32. Kasuga T., Townsend J.P., Tian C., Gilbert L.B., Mannhaupt G., Taylor J.W., and Glass N.L. Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germination. Nucleic Acids Res. 33 20 (2005) 6469-6485
33. Kerr M.K., and Churchill G.A. Statistical design and the analysis of gene expression microarray data. Genet. Res. 77 2 (2001) 123-128
34. Konieczny A., Voytas D.F., Cummings M.P., and Ausubel F.M. A superfamily of Arabidopsis thaliana retrotransposons. Genetics 127 4 (1991) 801-809
35. Kramer C., Loros J.J., Dunlap J.C., and Crosthwaite S.K. Role for antisense RNA in regulating circadian clock function in Neurospora crassa. Nature 421 (2003) 948-952
36. Liu X.S., Brutlag D.L., and Liu J.S. An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat. Biotechnol. 20 8 (2002) 835-839
37. Martin A.C., and Drubin D.G. Impact of genome-wide functional analyses on cell biology research. Curr. Opin. Cell Biol. 15 (2003) 6-13
38. McClung C.R., Fox B.A., and Dunlap J.C. The Neurospora clock gene frequency shares a sequence element with the Drosophila clock gene period. Nature 339 (1989) 558-562
39. McGuire A.M., Hughes J.D., and Church G.M. Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes. Genome Res. 10 6 (2000) 744-757
40. Metzenberg R.L., and Grotelueschen J. Restriction polymorphism maps of Neurospora crassa: Update. Fungal Genet. Newslett. 42 (1995) 82-90
41. Metzenberg R.L., Stevens J.N., Selker E.U., and Morzycka-Wroblewska E. A restriction fragment length polymorphism map for Neurospora crassa. Proc. Natl. Acad. Sci. USA 82 (1985) 2067-2071
42. Muller H.M., Kenny E.E., and Sternberg P.W. Textpresso: An ontology-based information retrieval and extraction system for biological literature. PLoS Biol. 2 (2004) e309
43. Nelson M.A., Kang S., Braun E.L., Crawford M.E., Dolan P.L., Leonard P.M., Mitchell J., Armijo A.M., Bean L., Blueyes E., Cushing T., Errett A., et al. Expressed sequences from conidial, mycelial, and sexual stages of Neurospora. Fungal Genet. Biol. 21 (1997) 348-363
44. Ninomiya Y., Suzuki K., Ishii C., and Inoue H. Highly efficient gene replacements in Neurospora strains deficient for nonhomologous end-joining. Proc. Natl. Acad. Sci. USA 101 33 (2004) 12248-12253
45. Oldenburg K.R., Vo K.T., Michaelis S., and Paddon C. Recombination-mediated PCR-directed plasmid construction in vivo in yeast. Nucleic Acids Res. 25 (1997) 451-452
46. Ooi S.L., Shoemaker D.D., and Boeke J.D. A DNA microarray-based genetic screen for nonhomologous end-joining mutants in Saccharomyces cerevisiae. Science 294 (2001) 2552-2556
47. Ooi S.L., Pan X., Peyser B.D., Ye P., Meluh P.B., Yuan D.S., Irizarry R.A., Bader J.S., Spencer F.A., and Boeke J.D. Global synthetic-lethality analysis and yeast functional profiling. Trends Genet. 22 1 (2006) 56-63
48. Pandit N.N., and Russo V.E. Reversible inactivation of a foreign gene, hph, during the asexual cycle in Neurospora crassa transformants. Mol. Gen. Genet. 234 (1992) 412-422
49. Perkins D.D., Radford A., and Sachs M.S. "The Neurospora Compendium." (2001), Academic Press, San Diego
50. Raymond C.K., Pownder T.A., and Sexson S.L. General method for plasmid construction using homologous recombination. Biotechniques 26 (1999) 134-141
51. Riquelme M., Reynaga-Peña C.G., Gierz G., and Bartnicki-García S. What determines growth direction in fungal hyphae?. Fungal Genet. Biol. 24 1-2 (1998) 101-109
52. Roca M.G., Arlt J., Jeffree C.E., and Read N.D. Cell biology of conidial anastomosis tubes in Neurospora crassa. Eukaryot. Cell 4 (2005) 911-919
53. Ruepp A., Zollner A., Maier D., Albermann K., Hani J., Mokrejs M., Tetko I., Guldener U., Mannhaupt G., Munsterkotter M., and Mewes H.W. The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res. 32 18 (2004) 5539-5545
54. Sachs M.S., and Yanofsky C. Development expression of genes involved in conidiation and amino acid biosynthesis in Neurospora crassa. Dev. Biol. 148 1 (1991) 117-128
55. Schmidt J.C., and Brody S. Biochemical genetics of Neurospora crassa conidial germination. Bacteriol. Rev. 40 (1976) 1-41
56. Selker E.U. Premeiotic instability of repeated sequences in Neurospora crassa. Annu. Rev. Genet. 24 (1990) 579-613
57. Selker E.U. Epigenetic phenomena in filamentous fungi. Trends Genet. 13 (1997) 296-301
58. Tey W.K., North A.J., Reyes J.L., Lu Y.F., and Jedd G. Polarized gene expression determines Woronin body formation at the leading edge of the fungal colony. Mol. Biol. Cell 16 6 (2005) 2651-2659
59. Townsend J.P. Multifactorial experimental design and the transitivity of ratios with spotted DNA microarrays. BMC Genomics 4 1 (2003) 41
60. Townsend J.P., and Hartl D.L. Bayesian analysis of gene expression levels: Statistical quantification of relative mRNA level across multiple strains or treatments. Genome Biol. 3 (2002) RESEARCH0071
61. Vinciotti V., Khanin R., D'Alimonte D., Liu X., Cattini N., Hotchkiss G., Bucca G., de Jesus O., Rasaiyaah J., Smith C.P., Kellam P., and Wit E. An experimental evaluation of a loop versus a reference design for two-channel microarrays. Bioinformatics 21 4 (2005) 492-501
62. Wicks S., Yeh R., Gish W., Waterson R., and Plasterk H. Rapid gene mapping in C. elegans using a high density polymorphism map. Nat. Genet. 28 (2001) 160-164
63. Winzeler E.A., Shoemaker D.D., Astromoff A., Liang H., Anderson K., Andre B., Bangham R., Benito R., Boeke J.D., Bussey H., Chu A.M., Connelly C., et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285 5429 (1999) 901-906
64. Wolfinger R.D., Gibson G., Wolfinger E.D., Bennett L., Hamadeh H., Bushel P., Afshari C., and Paules R.S. Assessing gene significance from cDNA microarray expression data via mixed models. J. Comput. Biol. 8 6 (2001) 625-637
65. Yang Y.H., and Speed T. Design issues for cDNA microarray experiments. Nat. Rev. Genet. 3 (2002) 579-588
66. Young J.L., and Marzluf G.A. Molecular comparison of the negative-acting nitrogen control gene, nmr, in Neurospora crassa and other Neurospora and fungal species. Biochem. Genet. 29 9-10 (1991) 447-459
67. Zeitlinger J., Simon I., Harbison C.T., Hannett N.M., Volkert T.L., Fink G.R., and Young R.A. Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling. Cell 113 3 (2003) 395-404
68. Zhu H., Nowrousian M., Kupfer D., Colot H., Berrocal-Tito G., Lai H., Bell-Pedersen D., Roe B., Loros J.J., and Dunlap J.C. Analysis of expressed sequence tags from two starvation, time-of-day-specific libraries of Neurospora crassa reveals novel clock-controlled genes. Genetics 157 (2001) 1057-1065