Calling Cards enable multiplexed identification of the genomic targets of DNA-binding proteins

Genome Research

Volumn 21, Issue 5, 2011, Pages 748-755

  Wang, Haoyi ^a,c   Mayhew, David ^a   Chen, Xuhua ^a   Johnston, Mark ^b   Mitra, Robi David ^a  

^a WASHINGTON UNIVERSITY   (United States)

^b UNIVERSITY OF COLORADO   (United States)

^c WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA BINDING PROTEIN;

ARTICLE; DNA FLANKING REGION; DNA SEQUENCE; GENE SEQUENCE; GENETIC ANALYSIS; GENOME; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; TRANSPOSON;

BINDING SITES; CHROMOSOME MAPPING; DNA TRANSPOSABLE ELEMENTS; DNA-BINDING PROTEINS; GENOME, FUNGAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MUTAGENESIS, INSERTIONAL; SACCHAROMYCES CEREVISIAE; SILENT INFORMATION REGULATOR PROTEINS, SACCHAROMYCES CEREVISIAE; TRANSCRIPTION FACTORS;

EID: 79955562246     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.114850.110     Document Type: Article

References (23)

1. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. 2000. Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29. (Pubitemid 30257031)
2. Badis G, Chan ET, van Bakel H, Pena-Castillo L, Tillo D, Tsui K, Carlson CD, Gossett AJ, Hasinoff MJ, Warren CL, et al. 2008. A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol Cell 32: 878-887.
3. Granek JA, Clarke ND. 2005. Explicit equilibrium modeling of transcription-factor binding and gene regulation. Genome Biol 6: R87. doi: 10.1186/gb-2005-6-10-r87.
4. Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, MacIsaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, et al. 2004. Transcriptional regulatory code of a eukaryotic genome. Nature 431: 99-104. (Pubitemid 39215116)
5. Johnston M, Davis RW. 1984. Sequences that regulate the divergent GAL1-GAL10 promoter in Saccharomyces cerevisiae. Mol Cell Biol 4: 1440-1448.
6. Kharchenko PV, Tolstorukov MY, Park PJ. 2008. Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol 26: 1351-1359.
7. Kurihara LJ, Stewart BG, Gammie AE, Rose MD. 1996. Kar4p, a karyogamy-specific component of the yeast pheromone response pathway. Mol Cell Biol 16: 3990-4002. (Pubitemid 26251198)
8. Lahav R, Gammie A, Tavazoie S, Rose MD. 2007. Role of transcription factor Kar4 in regulating downstream events in the Saccharomyces cerevisiae pheromone response pathway. Mol Cell Biol 27: 818-829. (Pubitemid 46174548)
9. Liu X, Noll DM, Lieb JD, Clarke ND. 2005. DIP-chip: Rapid and accurate determination of DNA-binding specificity. Genome Res 15: 421-427. (Pubitemid 40467783)
10. Liu X, Lee CK, Granek JA, Clarke ND, Lieb JD. 2006. Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosomeoccupancy in target site selection. Genome Res 16: 1517-1528. (Pubitemid 44878490)
11. Lucau-Danila A, Delaveau T, Lelandais G, Devaux F, Jacq C. 2003. Competitive promoter occupancy by two yeast paralogous transcription factors controlling the multidrug resistance phenomenon. J Biol Chem 278: 52641-52650. (Pubitemid 38035861)
12. Lusted LB. 1971. Decision-making studies in patient management. N Engl J Med 284: 416-424.
13. Ma H, Kunes S, Schatz PJ, Botstein D. 1987. Plasmid construction by homologous recombination in yeast. Gene 58: 201-216. (Pubitemid 17164063)
14. MacIsaac KD, Wang T, Gordon DB, Gifford DK, Stormo GD, Fraenkel E. 2006. An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics 7: 113. doi: 10.1186/1471-2105-7-113.
15. Meng X, Brodsky MH, Wolfe SA. 2005. A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors. Nat Biotechnol 23: 988-994. (Pubitemid 41114033)
16. Pokholok DK, Harbison CT, Levine S, Cole M, Hannett NM, Lee TI, Bell GW, Walker K, Rolfe PA, Herbolsheimer E, et al. 2005. Genome-wide map of nucleosome acetylation and methylation in yeast. Cell 122: 517-527. (Pubitemid 41191151)
17. Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, Simon I, Zeitlinger J, Schreiber J, Hannett N, Kanin E, et al. 2000. Genome-wide location and function of DNA binding proteins. Science 290: 2306-2309. (Pubitemid 32041573)
18. Roth FP, Hughes JD, Estep PW, Church GM. 1998. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat Biotechnol 16: 939-945. (Pubitemid 28483622)
19. Wach A, Brachat A, Pohlmann R, Philippsen P. 1994. New heterologous modules for classical or PCR-based gene disruptions in Saccharomyces cerevisiae. Yeast 10: 1793-1808.
20. Wang H, Johnston M, Mitra RD. 2007. Calling cards for DNA-binding proteins. Genome Res 17: 1202-1209. (Pubitemid 47204864)
21. Wang H, Heinz ME, Crosby SD, Johnston M, Mitra RD. 2008. 'Calling Cards' method for high-throughput identification of targets of yeast DNA-binding proteins. Nat Protoc 3: 1569-1577.
22. Zhu Y, Dai J, Fuerst PG, Voytas DF. 2003. Controlling integration specificity of a yeast retrotransposon. Proc Natl Acad Sci 100: 5891-5895. (Pubitemid 36576903)
23. Zhu C, Byers K, McCord R, Shi Z, Berger M, Newburger D, Saulrieta K, Smith Z, Shah M, Radhakrishnan M, et al. 2009. High-resolution DNA binding specificity analysis of yeast transcription factors. Genome Res 19: 556-566.