The DOI matches its Crossref record; 10 of the 10 references it cites were found in a registry or an index.
Genome-Wide Analysis of Protein-DNA Interactions
Abstract
The human genome is predominantly composed of nonprotein-coding sequences whose function remains largely undefined. A significant portion of the noncoding DNA is believed to serve as transcriptional regulatory elements that control gene expression in specific cell types at appropriate developmental stages. Identifying these regulatory sequences and determining the mechanisms by which they act present a great challenge in the postgenomic era. Previous investigations using genetic, molecular, and biochemical approaches have uncovered a large number of proteins involved in regulating transcription. Knowledge of the genomic locations of DNA binding for these proteins in the nucleus should define the identity and nature of the transcriptional regulatory sequences and reveal the gene regulatory networks in cells. Chromatin immunoprecipitation (ChIP) is a common method for detecting interactions between a protein and a DNA sequence in vivo. In recent years, this method has been combined with DNA microarrays and other high-throughput technologies to enable genome-wide identification of DNA-binding sites for various nuclear proteins. Here, we review recent advances in ChIP-based methods for genome-wide detection of protein-DNA interactions, and discuss their significance in enhancing our knowledge of the gene regulatory networks and epigenetic mechanisms in cells.
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Cites
Capturing Chromosome Conformation
Dekker, J., Rippe, K., Dekker, M., & Kleckner, N. (2002) · Science · doi:10.1126/science.1067799 · Cited by 3,652
Transcriptional Regulatory Networks in Saccharomyces cerevisiae
Lee, T. I., Rinaldi, N. J., Robert, F., Odom, D. T., Bar-Joseph, Z., Gerber, G. K., Hannett, N. M., Harbison, C. T., Thompson, C. M., Simon, I., et al. (2002) · Science · doi:10.1126/science.1075090 · Cited by 2,956
Self-citationA DNA damage checkpoint response in telomere-initiated senescence
Fagagna, F. D. D., Reaper, P. M., Clay-Farrace, L., Fiegler, H., Carr, P., von Zglinicki, T., Saretzki, G., Carter, N. P., & Jackson, S. P. (2003) · Nature · doi:10.1038/nature02118 · Cited by 2,917
A genomic regulatory network for development
Davidson, E. H., Rast, J. P., Oliveri, P., Ransick, A., Calestani, C., Yuh, C.-H., Minokawa, T., Amore, G., Hinman, V., Arenas-Mena, C., et al. (2002) · Science · doi:10.1126/science.1069883 · Cited by 1,567
A Global Map of p53 Transcription-Factor Binding Sites in the Human Genome
Wei, C.-L., Wu, Q., Vega, V. B., Chiu, K. P., Ng, P., Zhang, T., Shahab, A., Yong, H. C., Fu, Y., Weng, Z., et al. (2006) · Cell · doi:10.1016/j.cell.2005.10.043 · Cited by 1,141
E2F integrates cell cycle progression with DNA repair, replication, and G 2 /M checkpoints
Ren, B., Cam, H., Takahashi, Y., Volkert, T., Terragni, J., Young, R. A., & Dynlacht, B. D. (2002) · Genes & Development · doi:10.1101/gad.949802 · Cited by 1,125
Self-citationCawley, S., Bekiranov, S., Ng, H. H., Kapranov, P., Sekinger, E. A., Kampa, D., Piccolboni, A., Sementchenko, V., Cheng, J., Williams, A. J., et al. (2004) · Cell · doi:10.1016/s0092-8674(04)00127-8 · Cited by 1,095
Evidence for nucleosome depletion at active regulatory regions genome-wide
Lee, C.-K., Shibata, Y., Rao, B., Strahl, B. D., & Lieb, J. D. (2004) · Nature Genetics · doi:10.1038/ng1400 · Cited by 738
Using the transcriptome to annotate the genome
Saha, S., Sparks, A. B., Rago, C., Akmaev, V., Wang, C. J., Vogelstein, B., Kinzler, K. W., & Velculescu, V. E. (2002) · Nature Biotechnology · doi:10.1038/nbt0502-508 · Cited by 630
Genome-wide binding map of the histone deacetylase Rpd3 in yeast
Kurdistani, S. K., Robyr, D., Tavazoie, S., & Grunstein, M. (2002) · Nature Genetics · doi:10.1038/ng907 · Cited by 279
Cited by
Model-based Analysis of ChIP-Seq (MACS)
Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W., et al. (2008) · Genome Biology · doi:10.1186/gb-2008-9-9-r137 · Cited by 18,386
Heintzman, N. D., Stuart, R. K., Hon, G., Fu, Y., Ching, C. W., Hawkins, R. D., Barrera, L. O., Van Calcar, S., Qu, C., Ching, K. A., et al. (2007) · Nature Genetics · doi:10.1038/ng1966 · Cited by 3,398
Self-citationGenome-Wide Mapping of in Vivo Protein-DNA Interactions
Johnson, D. S., Mortazavi, A., Myers, R. M., & Wold, B. (2007) · Science · doi:10.1126/science.1141319 · Cited by 2,927
Design and analysis of ChIP-seq experiments for DNA-binding proteins
Kharchenko, P. V., Tolstorukov, M. Y., & Park, P. J. (2008) · Nature Biotechnology · doi:10.1038/nbt.1508 · Cited by 916
Chromatin structure analyses identify miRNA promoters
Ozsolak, F., Poling, L. L., Wang, Z., Liu, H., Liu, X. S., Roeder, R. G., Zhang, X., Song, J. S., & Fisher, D. E. (2008) · Genes & Development · doi:10.1101/gad.1706508 · Cited by 678
Metadata
- Authors
- Kim, T. H., & Ren, B.
- Venue
- Annual Review of Genomics and Human Genetics
- Publisher
- Annual Reviews
- Published
- 2006-09-01
- Volume
- 7
- Issue
- 1
- Pages
- 81-102
- ISSN
- 1527-8204 (ISSN-L)
- 1545-293X
- OpenAlex
- W2152556351
- Cited by
- 171
- References
- 10
- FWCI
- 1.23
- Type
- journal article
- Language
- en
- Open access
- closed
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- Kim, T. H., & Ren, B. (2006). Genome-Wide Analysis of Protein-DNA Interactions. Annual Review of Genomics and Human Genetics. https://doi.org/10.1146/annurev.genom.7.080505.115634
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