Microarray profiling of phage-display selections for rapid mapping of transcription factor-DNA interactions

PLoS Genetics

Volumn 5, Issue 4, 2009, Pages

  Freckleton, Gordon ^a   Lippman, Soyeon I ^a   Broach, James R ^a   Tavazoie, Saeed ^a  

^a PRINCETON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; MADS DOMAIN PROTEIN; PROTEIN MYB; PROTEOME; TRANSCRIPTION FACTOR; ZINC FINGER PROTEIN; FUNGAL PROTEIN;

ARTICLE; BINDING SITE; DNA BINDING; GENE IDENTIFICATION; GENE INTERACTION; GENE MAPPING; GENE SEQUENCE; MICROARRAY ANALYSIS; NONHUMAN; PHAGE DISPLAY; REGULATORY DNA SEQUENCE; YEAST; BACTERIOPHAGE; CHEMISTRY; DNA MICROARRAY; EVALUATION; GENE LIBRARY; GENETICS; METABOLISM; METHODOLOGY; PROTEIN BINDING; PROTEIN TERTIARY STRUCTURE;

BACTERIOPHAGES; BINDING SITES; DNA; FUNGAL PROTEINS; GENE LIBRARY; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; TRANSCRIPTION FACTORS; YEASTS;

EID: 66149105187     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1000449     Document Type: Article

References (52)

1. Elemento O, Tavazoie S (2005) Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach. Genome biology 6: R18.
2. Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423: 241-254.
3. Elemento O, Slonim N, Tavazoie S (2007) A universal framework for regulatory element discovery across all genomes and data types. Molecular cell 28: 337-350.
4. Kadonaga JT, Tjian R (1986) Affinity purification of sequence-specific DNA binding proteins. Proceedings of the National Academy of Sciences of the United States of America 83: 5889-5893.
5. Ammerer G (1990) Identification, purification, and cloning of a polypeptide (PRTF/GRM) that binds to mating-specific promoter elements in yeast. Genes & development 4: 299-312.
6. Gadgil H, Jurado LA, Jarrett HW (2001) DNA affinity chromatography of transcription factors. Analytical biochemistry 290: 147-178.
7. Parthun MR, Jaehning JA (1990) Purification and characterization of the yeast transcriptional activator GAL4. The Journal of biological chemistry 265: 209-213.
8. Shore D, Nasmyth K (1987) Purification and cloning of a DNA binding protein from yeast that binds to both silencer and activator elements. Cell 51: 721-732.
9. Sze JY, Kohlhaw GB (1993) Purification and structural characterization of transcriptional regulator Leu3 of yeast. The Journal of biological chemistry 268: 2505-2512.
10. Fields S, Song O (1989) A novel genetic system to detect protein-protein interactions. Nature 340: 245-246.
11. Alexander MK, Bourns BD, Zakian VA (2001) One-hybrid systems for detecting protein-DNA interactions. Methods Mol Biol 177: 241-259.
12. Ito T, Ota K, Kubota H, Yamaguchi Y, Chiba T, et al. (2002) Roles for the twohybrid system in exploration of the yeast protein interactome. Mol Cell Proteomics 1: 561-566.
13. De Silva EK, Gehrke AR, Olszewski K, Leon I, Chahal JS, et al. (2008) Specific DNA-binding by apicomplexan AP2 transcription factors. Proceedings of the National Academy of Sciences of the United States of America 105: 8393-8398.
14. Mukherjee S, Berger MF, Jona G, Wang XS, Muzzey D, et al. (2004) Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nature genetics 36: 1331-1339.
15. Bulyk ML, Huang X, Choo Y, Church GM (2001) Exploring the DNA-binding specificities of zinc fingers with DNA microarrays. Proceedings of the National Academy of Sciences of the United States of America 98: 7158-7163.
16. Dreier B, Fuller RP, Segal DJ, Lund CV, Blancafort P, et al. (2005) Development of zinc finger domains for recognition of the 5'-CNN-3' family DNA sequences and their use in the construction of artificial transcription factors. The Journal of biological chemistry 280: 35588-35597.
17. Moore M, Klug A, Choo Y (2001) Improved DNA binding specificity from polyzinc finger peptides by using strings of two-finger units. Proceedings of the National Academy of Sciences of the United States of America 98: 1437-1441.
18. Wolfe SA, Greisman HA, Ramm EI, Pabo CO (1999) Analysis of zinc fingers optimized via phage display: evaluating the utility of a recognition code. Journal of molecular biology 285: 1917-1934.
19. Cicchini C, Ansuini H, Amicone L, Alonzi T, Nicosia A, et al. (2002) Searching for DNA-protein interactions by lambda phage display. Journal of molecular biology 322: 697-706.
20. Danner S, Belasco JG (2001) T7 phage display: a novel genetic selection system for cloning RNA- binding proteins from cDNA libraries. Proceedings of the National Academy of Sciences of the United States of America 98: 12954-12959.
21. Zhang Y, Pak JW, Maruyama IN, Machida M (2000) Affinity selection of DNAbinding proteins displayed on bacteriophage lambda. J Biochem (Tokyo) 127: 1057-1063.
22. Butteroni C, De Felici M, Scholer HR, Pesce M (2000) Phage display screening reveals an association between germline- specific transcription factor Oct-4 and multiple cellular proteins. Journal of molecular biology 304: 529-540.
23. Cheng X, Kay BK, Juliano RL (1996) Identification of a biologically significant DNA-binding peptide motif by use of a random phage display library. Gene 171: 1-8.
24. Hertveldt K, Dechassa ML, Robben J, Volckaert G (2003) Identification of Gal80p-interacting proteins by Saccharomyces cerevisiae whole genome phage display. Gene 307: 141-149.
25. Rodi DJ, Makowski L (1999) Phage-display technology-finding a needle in a vast molecular haystack. Curr Opin Biotechnol 10: 87-93.
26. Rosenberg A, Griffin K, Studier FW, McCormick M, Berg J, et al. (1996) T7Select® Phage Display System: A powerful new protein display system based on bacteriophage T7. inNovations 6: 1-6.
27. Dequard-Chablat M, Riva M, Carles C, Sentenac A (1991) RPC19, the gene for a subunit common to yeast RNA polymerases A (I) and C (III). The Journal of biological chemistry 266: 15300-15307.
28. Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM (1999) Systematic determination of genetic network architecture. Nature genetics 22: 281-285.
29. Cliften PF, Hillier LW, Fulton L, Graves T, Miner T, et al. (2001) Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis. Genome research 11: 1175-1186.
30. Pritsker M, Liu YC, Beer MA, Tavazoie S (2004) Whole-genome discovery of transcription factor binding sites by network-level conservation. Genome research 14: 99-108.
31. Beer MA, Tavazoie S (2004) Predicting gene expression from sequence. Cell 117: 185-198.
32. Liko D, Slattery MG, Heideman W (2007) Stb3 binds to RRPE motifs that control transcriptional responses to growth in Saccharomyces cerevisiae. The Journal of biological chemistry.
33. Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, et al. (2004) Transcriptional regulatory code of a eukaryotic genome. Nature 431: 99-104.
34. Jorgensen P, Nishikawa JL, Breitkreutz BJ, Tyers M (2002) Systematic identification of pathways that couple cell growth and division in yeast. Science (New York, N Y 297: 395-400.
35. Kuo MH, Grayhack E (1994) A library of yeast genomic MCM1 binding sites contains genes involved in cell cycle control, cell wall and membrane structure, and metabolism. Molecular and cellular biology 14: 348-359.
36. Lieb JD, Liu X, Botstein D, Brown PO (2001) Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nature genetics 28: 327-334.
37. Isalan M, Choo Y, Klug A (1997) Synergy between adjacent zinc fingers in sequence-specific DNA recognition. Proceedings of the National Academy of Sciences of the United States of America 94: 5617-5621.
38. Tan S, Ammerer G, Richmond TJ (1988) Interactions of purified transcription factors: binding of yeast MAT alpha 1 and PRTF to cell type-specific, upstream activating sequences. The EMBO journal 7: 4255-4264.
39. Vignais ML, Woudt LP, Wassenaar GM, Mager WH, Sentenac A, et al. (1987) Specific binding of TUF factor to upstream activation sites of yeast ribosomal protein genes. The EMBO journal 6: 1451-1457.
40. Bruhn L, Hwang-Shum JJ, Sprague GF Jr (1992) The N-terminal 96 residues of MCM1, a regulator of cell type-specific genes in Saccharomyces cerevisiae, are sufficient for DNA binding, transcription activation, and interaction with alpha 1. Molecular and cellular biology 12: 3563-3572.
41. Graham IR, Haw RA, Spink KG, Halden KA, Chambers A (1999) In vivo analysis of functional regions within yeast Rap1p. Molecular and cellular biology 19: 7481-7490.
42. Konig P, Giraldo R, Chapman L, Rhodes D (1996) The crystal structure of the DNA-binding domain of yeast RAP1 in complex with telomeric DNA. Cell 85: 125-136.
43. Tan S, Richmond TJ (1998) Crystal structure of the yeast MATalpha2/MCM1/DNA ternary complex. Nature 391: 660-666.
44. Thompson M, Woodbury NW (2001) Thermodynamics of specific and nonspecific DNA binding by two DNA-binding domains conjugated to fluorescent probes. Biophysical journal 81: 1793-1804.
45. Singer MS, Kahana A, Wolf AJ, Meisinger LL, Peterson SE, et al. (1998) Identification of high-copy disruptors of telomeric silencing in Saccharomyces cerevisiae. Genetics 150: 613-632.
46. Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415: 141-147.
47. Kasten MM, Stillman DJ (1997) Identification of the Saccharomyces cerevisiae genes STB1-STB5 encoding Sin3p binding proteins. Mol Gen Genet 256: 376-386.
48. Kurdistani SK, Robyr D, Tavazoie S, Grunstein M (2002) Genome-wide binding map of the histone deacetylase Rpd3 in yeast. Nature genetics 31: 248-254.
49. Fingerman I, Nagaraj V, Norris D, Vershon AK (2003) Sfp1 plays a key role in yeast ribosome biogenesis. Eukaryotic cell 2: 1061-1068.
50. Novagen (1998) DNase Shotgun Cleavage Kit Manual TB05B. Madison, WI: Novagen.
51. Hegde P, Qi R, Abernathy K, Gay C, Dharap S, et al. (2000) A concise guide to cDNA microarray analysis. Biotechniques 29: 548-50, 552.
52. Iscove NN, Barbara M, Gu M, Gibson M, Modi C, Winegarden N (2002) Representation is faithfully preserved in global cDNA amplified exponentially from sub-picogram quantities of mRNA. Nature biotechnology 20: 940-943.