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Science 22 December 2000: Vol. 290. no. 5500, pp. 2306 - 2309 DOI: 10.1126/science.290.5500.2306
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Reports
Genome-Wide Location and Function of DNA Binding Proteins
Bing Ren,1*
François Robert,1*
John
J. Wyrick,12*
Oscar Aparicio,24
Ezra G. Jennings,12
Itamar Simon,1
Julia Zeitlinger,1
Jörg Schreiber,1
Nancy Hannett,1
Elenita Kanin,1
Thomas L. Volkert,1
Christopher J. Wilson,5
Stephen P. Bell,23
Richard A. Young12
Understanding how DNA binding proteins control global gene
expression and chromosomal maintenance requires knowledge of the chromosomal locations at which these proteins function in vivo. We
developed a microarray method that reveals the genome-wide location of
DNA-bound proteins and used this method to monitor binding of
gene-specific transcription activators in yeast. A combination of
location and expression profiles was used to identify genes whose
expression is directly controlled by Gal4 and Ste12 as cells respond to
changes in carbon source and mating pheromone, respectively. The
results identify pathways that are coordinately regulated by each of
the two activators and reveal previously unknown functions for Gal4 and
Ste12. Genome-wide location analysis will facilitate investigation of
gene regulatory networks, gene function, and genome maintenance.
1 Whitehead Institute for Biomedical Research,
Nine Cambridge Center, Cambridge, MA 02142, USA.
2 Department of Biology, Massachusetts Institute of
Technology, Cambridge, MA 02139, USA.
3 Howard
Hughes Medical Institute, Massachusetts Institute of Technology,
Cambridge, MA 02139, USA.
4 Program in Molecular
Biology University of Southern California, Los Angeles, CA 90089-1340,
USA.
5 Corning, Inc., Corning, NY 14834, USA.
*
These authors contributed equally to this work.
To whom correspondence should be addressed. E-mail:
young{at}wi.mit.edu
Read the Full Text
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| Abstract »
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| PDF »
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| Abstract »
| Full Text »
| PDF »
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| Abstract »
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| Full Text »
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| Abstract »
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- O. L. Griffith, S. B. Montgomery, B. Bernier, B. Chu, K. Kasaian, S. Aerts, S. Mahony, M. C. Sleumer, M. Bilenky, M. Haeussler, et al. (2008)
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| PDF »
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| Abstract »
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| Abstract »
| Full Text »
| PDF »
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- A. R. Borneman, T. A. Gianoulis, Z. D. Zhang, H. Yu, J. Rozowsky, M. R. Seringhaus, L. Y. Wang, M. Gerstein, and M. Snyder (2007)
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| Abstract »
| Full Text »
| PDF »
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134, 1977-1989
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282, 13854-13863
| Abstract »
| Full Text »
| PDF »
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6, 786-796
| Abstract »
| Full Text »
| PDF »
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- A. V. Morozov and E. D. Siggia (2007)
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104, 7068-7073
| Abstract »
| Full Text »
| PDF »
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- S. Kundu, P. J. Horn, and C. L. Peterson (2007)
Genes & Dev.
21, 997-1004
| Abstract »
| Full Text »
| PDF »
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- R. K. Gupta, N. Gao, R. K. Gorski, P. White, O. T. Hardy, K. Rafiq, J. E. Brestelli, G. Chen, C. J. Stoeckert Jr., and K. H. Kaestner (2007)
Genes & Dev.
21, 756-769
| Abstract »
| Full Text »
| PDF »
- Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae.
- Y. Hu, A. Rolfs, B. Bhullar, T. V. S. Murthy, C. Zhu, M. F. Berger, A. A. Camargo, F. Kelley, S. McCarron, D. Jepson, et al. (2007)
Genome Res.
17, 536-543
| Abstract »
| Full Text »
| PDF »
- Identification of Genes Directly Regulated by the Oncogene ZNF217 Using Chromatin Immunoprecipitation (ChIP)-Chip Assays.
- S. R. Krig, V. X. Jin, M. C. Bieda, H. O'Geen, P. Yaswen, R. Green, and P. J. Farnham (2007)
J. Biol. Chem.
282, 9703-9712
| Abstract »
| Full Text »
| PDF »
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- Y.-S. Kwon, I. Garcia-Bassets, K. R. Hutt, C. S. Cheng, M. Jin, D. Liu, C. Benner, D. Wang, Z. Ye, M. Bibikova, et al. (2007)
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104, 4852-4857
| Abstract »
| Full Text »
| PDF »
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- C. Girardot, O. Sklyar, S. Grosz, W. Huber, and E. E. M. Furlong (2007)
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23, 771-773
| Abstract »
| Full Text »
| PDF »
- General transcription factor specified global gene regulation in archaea.
- M. T. Facciotti, D. J. Reiss, M. Pan, A. Kaur, M. Vuthoori, R. Bonneau, P. Shannon, A. Srivastava, S. M. Donohoe, L. E. Hood, et al. (2007)
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104, 4630-4635
| Abstract »
| Full Text »
| PDF »
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- S. Rodrigue, J. Brodeur, P.-E. Jacques, A. L. Gervais, R. Brzezinski, and L. Gaudreau (2007)
J. Bacteriol.
189, 1505-1513
| Abstract »
| Full Text »
| PDF »
- Genome-Wide Redistribution of Meiotic Double-Strand Breaks in Saccharomyces cerevisiae.
- N. Robine, N. Uematsu, F. Amiot, X. Gidrol, E. Barillot, A. Nicolas, and V. Borde (2007)
Mol. Cell. Biol.
27, 1868-1880
| Abstract »
| Full Text »
| PDF »
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- F. Parisi, P. Wirapati, and F. Naef (2007)
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| Abstract »
| Full Text »
| PDF »
- Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry.
- T. W. Siggers and B. Honig (2007)
Nucleic Acids Res.
35, 1085-1097
| Abstract »
| Full Text »
| PDF »
- Meiotic association between Spo11 regulated by Rec102, Rec104 and Rec114.
- H. Sasanuma, H. Murakami, T. Fukuda, T. Shibata, A. Nicolas, and K. Ohta (2007)
Nucleic Acids Res.
35, 1119-1133
| Abstract »
| Full Text »
| PDF »
- Quantifying DNA-protein binding specificities by using oligonucleotide mass tags and mass spectroscopy.
- L. Zhang, S. Kasif, and a. C. R. Cantor (2007)
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104, 3061-3066
| Abstract »
| Full Text »
| PDF »
- In vitro analysis of DNA-protein interactions by proximity ligation.
- S. M. Gustafsdottir, J. Schlingemann, A. Rada-Iglesias, E. Schallmeiner, M. Kamali-Moghaddam, C. Wadelius, and U. Landegren (2007)
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104, 3067-3072
| Abstract »
| Full Text »
| PDF »
- A core transcriptional network for early mesoderm development in Drosophila melanogaster.
- T. Sandmann, C. Girardot, M. Brehme, W. Tongprasit, V. Stolc, and E. E.M. Furlong (2007)
Genes & Dev.
21, 436-449
| Abstract »
| Full Text »
| PDF »
- HOXA5 is targeted by cell-type-specific CpG island methylation in normal cells and during the development of acute myeloid leukaemia.
- G. Strathdee, A. Sim, R. Soutar, T. L. Holyoake, and R. Brown (2007)
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28, 299-309
| Abstract »
| Full Text »
| PDF »
- Functional genomics via multiscale analysis: application to gene expression and ChIP-on-chip data.
- G. Lerman, J. McQuown, A. Blais, B. D. Dynlacht, G. Chen, and B. Mishra (2007)
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23, 314-320
| Abstract »
| Full Text »
| PDF »
- Transcriptional regulation of protein complexes within and across species.
- K. Tan, T. Shlomi, H. Feizi, T. Ideker, and R. Sharan (2007)
PNAS
104, 1283-1288
| Abstract »
| Full Text »
| PDF »
- Ctk Complex-Mediated Regulation of Histone Methylation by COMPASS.
- A. Wood, A. Shukla, J. Schneider, J. S. Lee, J. D. Stanton, T. Dzuiba, S. K. Swanson, L. Florens, M. P. Washburn, J. Wyrick, et al. (2007)
Mol. Cell. Biol.
27, 709-720
| Abstract »
| Full Text »
| PDF »
- GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs.
- A. G. Jegga, J. Chen, S. Gowrisankar, M. A. Deshmukh, R. Gudivada, S. Kong, V. Kaimal, and B. J. Aronow (2007)
Nucleic Acids Res.
35, D116-D121
| Abstract »
| Full Text »
| PDF »
- Precise physical models of protein-DNA interaction from high-throughput data.
- J. B. Kinney, G. Tkacik, and C. G. Callan Jr. (2007)
PNAS
104, 501-506
| Abstract »
| Full Text »
| PDF »
- Large-scale production of SAGE libraries from microdissected tissues, flow-sorted cells, and cell lines.
- J. Khattra, A. D. Delaney, Y. Zhao, A. Siddiqui, J. Asano, H. McDonald, P. Pandoh, N. Dhalla, A.-l. Prabhu, K. Ma, et al. (2007)
Genome Res.
17, 108-116
| Abstract »
| Full Text »
| PDF »
- Pheromone-Induced Degradation of Ste12 Contributes to Signal Attenuation and the Specificity of Developmental Fate.
- R. K. Esch, Y. Wang, and B. Errede (2006)
Eukaryot. Cell
5, 2147-2160
| Abstract »
| Full Text »
| PDF »
- Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques.
- L. Elnitski, V. X. Jin, P. J. Farnham, and S. J.M. Jones (2006)
Genome Res.
16, 1455-1464
| Abstract »
| Full Text »
| PDF »
- Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection.
- X. Liu, C.-K. Lee, J. A. Granek, N. D. Clarke, and J. D. Lieb (2006)
Genome Res.
16, 1517-1528
| Abstract »
| Full Text »
| PDF »
- Role of the Transcription Activator Ste12p as a Repressor of PRY3 Expression.
- K. S. Bickel and D. R. Morris (2006)
Mol. Cell. Biol.
26, 7901-7912
| Abstract »
| Full Text »
| PDF »
- Singing Mice, Songbirds, and More: Models for FOXP2 Function and Dysfunction in Human Speech and Language.
- S. A. White, S. E. Fisher, D. H. Geschwind, C. Scharff, and T. E. Holy (2006)
J. Neurosci.
26, 10376-10379
| Abstract »
| Full Text »
| PDF »
- Distinct Functions of Dispersed GATA Factor Complexes at an Endogenous Gene Locus..
- J. A. Grass, H. Jing, S.-I. Kim, M. L. Martowicz, S. Pal, G. A. Blobel, and E. H. Bresnick (2006)
Mol. Cell. Biol.
26, 7056-7067
| Abstract »
| Full Text »
| PDF »
- TOS9 Regulates White-Opaque Switching in Candida albicans.
- T. Srikantha, A. R. Borneman, K. J. Daniels, C. Pujol, W. Wu, M. R. Seringhaus, M. Gerstein, S. Yi, M. Snyder, and D. R. Soll (2006)
Eukaryot. Cell
5, 1674-1687
| Abstract »
| Full Text »
| PDF »
- The Galactose Switch in Kluyveromyces lactis Depends on Nuclear Competition between Gal4 and Gal1 for Gal80 Binding.
- A. Anders, H. Lilie, K. Franke, L. Kapp, J. Stelling, E. D. Gilles, and K. D. Breunig (2006)
J. Biol. Chem.
281, 29337-29348
| Abstract »
| Full Text »
| PDF »
- Widespread, but Non-identical, Association of Proteasomal 19 and 20 S Proteins with Yeast Chromatin.
- D. Sikder, S. A. Johnston, and T. Kodadek (2006)
J. Biol. Chem.
281, 27346-27355
| Abstract »
| Full Text »
| PDF »
- Simple histone acetylation plays a complex role in the regulation of gene expression..
- H. Fukuda, N. Sano, S. Muto, and M. Horikoshi (2006)
Brief Funct Genomic Proteomic
5, 190-208
| Abstract »
| Full Text »
| PDF »
- Oxidative Stress-Activated Zinc Cluster Protein Stb5 Has Dual Activator/Repressor Functions Required for Pentose Phosphate Pathway Regulation and NADPH Production..
- M. Larochelle, S. Drouin, F. Robert, and B. Turcotte (2006)
Mol. Cell. Biol.
26, 6690-6701
| Abstract »
| Full Text »
| PDF »
- 1,25-Dihydroxyvitamin D3 Regulates the Expression of Low-Density Lipoprotein Receptor-Related Protein 5 via Deoxyribonucleic Acid Sequence Elements Located Downstream of the Start Site of Transcription.
- J. A. Fretz, L. A. Zella, S. Kim, N. K. Shevde, and J. W. Pike (2006)
Mol. Endocrinol.
20, 2215-2230
| Abstract »
| Full Text »
| PDF »
- Strategies to unravel molecular codes essential for the development of meso-diencephalic dopaminergic neurons.
- F. M. J. Jacobs, S. M. Smits, K. J. M. Hornman, J. P. H. Burbach, and M. P. Smidt (2006)
J. Physiol.
575, 397-402
| Abstract »
| Full Text »
| PDF »
- Model-based analysis of tiling-arrays for ChIP-chip.
- W. E. Johnson, W. Li, C. A. Meyer, R. Gottardo, J. S. Carroll, M. Brown, and X. S. Liu (2006)
PNAS
103, 12457-12462
| Abstract »
| Full Text »
| PDF »
- Identifying transcription factor functions and targets by phenotypic activation.
- G. Chua, Q. D. Morris, R. Sopko, M. D. Robinson, O. Ryan, E. T. Chan, B. J. Frey, B. J. Andrews, C. Boone, and T. R. Hughes (2006)
PNAS
103, 12045-12050
| Abstract »
| Full Text »
| PDF »
- Extensive low-affinity transcriptional interactions in the yeast genome.
- A. Tanay (2006)
Genome Res.
16, 962-972
| Abstract »
| Full Text »
| PDF »
- ChIP-chip Comes of Age for Genome-wide Functional Analysis..
- J. Wu, L. T. Smith, C. Plass, and T. H-M. Huang (2006)
Cancer Res.
66, 6899-6902
| Abstract »
| Full Text »
| PDF »
- Transcription Factor STE12{alpha} Has Distinct Roles in Morphogenesis, Virulence, and Ecological Fitness of the Primary Pathogenic Yeast Cryptococcus gattii..
- P. Ren, D. J. Springer, M. J. Behr, W. A. Samsonoff, S. Chaturvedi, and V. Chaturvedi (2006)
Eukaryot. Cell
5, 1065-1080
| Abstract »
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| PDF »
- Linking DNA-binding proteins to their recognition sequences by using protein microarrays.
- S.-W. Ho, G. Jona, C. T. L. Chen, M. Johnston, and M. Snyder (2006)
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103, 9940-9945
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- L. A. Zella, S. Kim, N. K. Shevde, and J. W. Pike (2006)
Mol. Endocrinol.
20, 1231-1247
| Abstract »
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| PDF »
- Histone H1 of Saccharomyces cerevisiae Inhibits Transcriptional Silencing.
- M. Veron, Y. Zou, Q. Yu, X. Bi, A. Selmi, E. Gilson, and P.-A. Defossez (2006)
Genetics
173, 579-587
| Abstract »
| Full Text »
| PDF »
- Bayesian error analysis model for reconstructing transcriptional regulatory networks.
- N. Sun, R. J. Carroll, and H. Zhao (2006)
PNAS
103, 7988-7993
| Abstract »
| Full Text »
| PDF »
- Deciphering the Roles of the Histone H2B N-Terminal Domain in Genome-Wide Transcription.
- M. A. Parra, D. Kerr, D. Fahy, D. J. Pouchnik, and J. J. Wyrick (2006)
Mol. Cell. Biol.
26, 3842-3852
| Abstract »
| Full Text »
| PDF »
- Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression.
- M. Blanchette, A. R. Bataille, X. Chen, C. Poitras, J. Laganiere, C. Lefebvre, G. Deblois, V. Giguere, V. Ferretti, D. Bergeron, et al. (2006)
Genome Res.
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