504
Views
3
CrossRef citations to date
0
Altmetric
Point of View

Illuminating transcription pathways using fluorescent reporter genes and yeast functional genomics

&
Pages 76-80 | Published online: 01 Sep 2010

References

  • Barrera LO, Ren B. The transcriptional regulatory code of eukaryotic cells—insights from genome-wide analysis of chromatin organization and transcription factor binding. Curr Opin Cell Biol 2006; 18:291 - 298
  • Veitia RA. One thousand and one ways of making functionally similar transcriptional enhancers. Bioessays 2008; 30:1052 - 1057
  • Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, et al. Evolutionarily conserved elements in vertebrate, insect, worm and yeast genomes. Genome Res 2005; 15:1034 - 1050
  • Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, et al. Initial sequencing and comparative analysis of the mouse genome. Nature 2002; 420:520 - 562
  • Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J. Initial sequencing and analysis of the human genome. Nature 2001; 409:860 - 921
  • Larroux C, Luke GN, Koopman P, Rokhsar DS, Shimeld SM, Degnan BM. Genesis and expansion of metazoan transcription factor gene classes. Mol Biol Evol 2008; 25:980 - 996
  • Megraw M, Pereira F, Jensen ST, Ohler U, Hatzigeorgiou AG. A transcription factor affinity-based code for mammalian transcription initiation. Genome Res 2009; 19:644 - 656
  • Kainth P, Andrews B. Quantitative cell array screening to identify regulators of gene expression. Brief Funct Genomics 2010; 9:13 - 23
  • Kainth P, Sassi HE, Peña-Castillo L, Chua G, Hughes TR, Andrews B. Comprehensive genetic analysis of transcription factor pathways using a dual reporter gene system in budding yeast. Methods 2009; 48:258 - 264
  • Tong AH, Evangelista M, Parsons AB, Xu H, Bader GD, Pagé N, et al. Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 2001; 294:2364 - 2368
  • Tong AH, Lesage G, Bader GD, Ding H, Xu H, Xin X, et al. Global mapping of the yeast genetic interaction network. Science 2004; 303:808 - 813
  • Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, et al. The genetic landscape of a cell. Science 2010; 327:425 - 431
  • Fillingham J, Kainth P, Lambert JP, van Bakel H, Tsui K, Peña-Castillo L, et al. Two-color cell array screen reveals interdependent roles for histone chaperones and a chromatin boundary regulator in histone gene repression. Mol Cell 2009; 35:340 - 351
  • Gunjan A, Verreault A. A Rad53 kinase-dependent surveillance mechanism that regulates histone protein levels in S. cerevisiae. Cell 2003; 115:537 - 549
  • Gunjan A, Paik J, Verreault A. Regulation of histone synthesis and nucleosome assembly. Biochimie 2005; 87:625 - 635
  • Hereford LM, Osley MA, Ludwig TR 2nd, McLaughlin CS. Cell cycle regulation of yeast histone mRNA. Cell 1981; 24:367 - 375
  • Osley MA, Lycan D. Trans-acting regulatory mutations that alter transcription of Saccharomyces cerevisiae histone genes. Mol Cell Biol 1987; 7:4204 - 4210
  • Green EM, Antczak AJ, Bailey AO, Franco AA, Wu KJ, Yates JR 3rd, et al. Replication-independent histone deposition by the HIR complex and Asf1. Curr Biol 2005; 15:2044 - 2049
  • Prochasson P, Florens L, Swanson SK, Washburn MP, Workman JL. The HIR corepressor complex binds to nucleosomes generating a distinct protein/DNA complex resistant to remodeling by SWI/SNF. Genes Dev 2005; 19:2534 - 2539
  • De Koning L, Corpet A, Haber JE, Almouzni G. Histone chaperones: an escort network regulating histone traffic. Nat Struct Mol Biol 2007; 14:997 - 1007
  • Mujtaba S, Zeng L, Zhou MM. Structure and acetyllysine recognition of the bromodomain. Oncogene 2007; 26:5521 - 5527
  • Lee W, Tillo D, Bray N, Morse RH, Davis RW, Hughes TR, et al. A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet 2007; 39:1235 - 1244
  • Fisk DG, Ball CA, Dolinski K, Engel SR, Hong EL, Issel-Tarver L, et al. Saccharomyces cerevisiae S288C genome annotation: a working hypothesis. Yeast 2006; 23:857 - 865
  • Scherens B, Goffeau A. The uses of genome-wide yeast mutant collections. Genome Biol 2004; 5:229
  • Giaever G, Chu AM, Ni L, Connelly C, Riles L, Véronneau S, et al. Functional profiling of the Saccharomyces cerevisiae genome. Nature 2002; 418:387 - 391
  • Mnaimneh S, Davierwala AP, Haynes J, Moffat J, Peng WT, Zhang W, et al. Exploration of essential gene functions via titratable promoter alleles. Cell 2004; 118:31 - 44
  • Davierwala AP, Haynes J, Li Z, Brost RL, Robinson MD, Yu L, et al. The synthetic genetic interaction spectrum of essential genes. Nat Genet 2005; 37:1147 - 1152
  • Ben-Aroya S, Coombes C, Kwok T, O'Donnell KA, Boeke JD, Hieter P. Toward a comprehensive temperature-sensitive mutant repository of the essential genes of Saccharomyces cerevisiae. Mol Cell 2008; 30:248 - 258
  • Sopko R, Huang D, Preston N, Chua G, Papp B, Kafadar K, et al. Mapping pathways and phenotypes by systematic gene overexpression. Mol Cell 2006; 21:319 - 330
  • Zhu H, Klemic JF, Chang S, Bertone P, Casamayor A, Klemic KG, et al. Analysis of yeast protein kinases using protein chips. Nat Genet 2000; 26:283 - 289
  • Sopko R, Papp B, Oliver SG, Andrews BJ. Phenotypic activation to discover biological pathways and kinase substrates. Cell Cycle 2006; 5:1397 - 1402
  • Huang D, Kaluarachchi S, van Dyk D, Friesen H, Sopko R, Ye W, et al. Dual regulation by pairs of cyclin-dependent protein kinases and histone deacetylases controls G1 transcription in budding yeast. PLoS Bio 2009; 7:1000188
  • Sopko R, Huang D, Smith JC, Figeys D, Andrews BJ. Activation of the Cdc42p GTPase by cyclindependent protein kinases in budding yeast. EMBO J 2007; 26:4487 - 4500
  • Chua G, Morris QD, Sopko R, Robinson MD, Ryan O, Chan ET, et al. Identifying transcription factor functions and targets by phenotypic activation. Proc Natl Acad Sci USA 2006; 103:12045 - 12050
  • Morley M, Molony CM, Weber TM, Devlin JL, Ewens KG, Spielman RS, et al. Genetic analysis of genome-wide variation in human gene expression. Nature 2004; 430:743 - 747
  • Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, Colinayo V, et al. Genetics of gene expression surveyed in maize, mouse and man. Nature 2003; 422:297 - 302
  • Brem RB, Yvert G, Clinton R, Kruglyak L. Genetic dissection of transcriptional regulation in budding yeast. Science 2002; 296:752 - 755
  • Yvert G, Brem RB, Whittle J, Akey JM, Foss E, Smith EN, et al. Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nat Genet 2003; 35:57 - 64
  • Ronald J, Brem RB, Whittle J, Kruglyak L. Local regulatory variation in Saccharomyces cerevisiae. PLoS Genet 2005; 1:25
  • Li Y, Alvarez OA, Gutteling EW, Tijsterman M, Fu J, Riksen JA, et al. Mapping determinants of gene expression plasticity by genetical genomics in C. elegans. PLoS Genet 2006; 2:222
  • Zheng W, Zhao H, Mancera E, Steinmetz LM, Snyder M. Genetic analysis of variation in transcription factor binding in yeast. Nature 2010; 464:1187 - 1191
  • Kasowski M, Grubert F, Heffelfinger C, Hariharan M, Asabere A, Waszak SM, et al. Variation in transcription factor binding among humans. Science 2010; 328:232 - 235
  • Smith AM, Heisler LE, Mellor J, Kaper F, Thompson MJ, Chee M, et al. Quantitative phenotyping via deep barcode sequencing. Genome Res 2009; 19:1836 - 1842