Abstract
DNA binding proteins play a number of key roles in cells,in processes including transcriptional regulation,recombination,genome rearrangements,and DNA replication, repair,and modification.Of particular interest are the interactions between transcription factors and their DNA binding sites,as they are an integral part of the transcriptional regulatory networks that control gene expression.Despite their importance,the DNA binding specificities of most DNA binding proteins remain unknown,as earlier technologies aimed at characterizing DNA-protein interactions have been time consuming and not highly scalable.We have developed a new DNA microarray-based technology,termed protein binding microarrays (PBMs),that allows rapid,high-throughput characterization of the in vitro DNA binding site sequence specificities of transcription factors in a single day. The resulting DNA binding site data can be used in a number of ways,including for the prediction of the genes regulated by a given transcription factor,annotation of transcription factor function,and functional annotation of the predicted target genes.
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References
Bulyk, M.(2003)Computational prediction of transcription-factor binding site locations. Genome Biol. 5, 201.
Mukherjee, S., Berger, M.F., Jona, G., et al. (2004) Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nat. Genet. 36, 1331–1339.
Sambrook, J., Fritsch, E.,and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual 2nd ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor,NY.
Liu, X., Brutlag, D.,and Liu, J. (2001) BioProspector:discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac. Symp. Biocomput. 127–138.
Hughes, J.D., Estep, P.W., Tavazoie, S.,and Church, G.M. (2000) Computational identification of cisegulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae J. Mol. Biol. 296, 1205–1214.
Bulyk, M.L., Huang, X., Choo, Y.,and Church, G.M. (2001) Exploring the DNA-binding specificities of zinc fingers with DNA microarrays. Proc. Natl. Acad. Sci. USA 98, 7158–7163.
Dudley, A., Aach, J., Steffen, M.,and Church, G. (2002) Measuring absolute expres-sion with microarrays with a calibrated reference sample and an extended signal intensity range. Proc. Natl. Acad. Sci. USA 99, 7554–7559.
Cleveland, W.and Devlin, S. (1988) Locally weighted regression:An approach to regression analysis by local fitting.J. Am. Stat. Assoc. 83, 596–610.
Taylor, J. (1997) An Introduction to Error Analysis 2nd ed., University Science Books, Sausalito,CA.
Bulyk, M., Johnson, P.,and Church, G. (2002) Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Res. 30, 1255–1261.
Sokal, R.and Rohlf, R.(1995)Biometry: The Principles and Practice of Statistics in Biological Research 3rd ed.,W.H.Freeman and Company, New York.
Huber, B.R.and Bulyk, M.L.(in review)Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data.
Roth, F.P., Hughes, J.D., Estep, P.W., and Church, G.M. (1998) Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat. Biotechnol. 16, 939–945.
Bailey, T. and Elkan, C. (1995) The value of prior knowledge in discovering motifs with MEME. Proc. Int. Conf. Intell. Syst. Mol. Biol. 3, 21–29.
Liu, X., Brutlag, D., and Liu, J. (2002) An algorithm for finding protein-DNA bind-ing sites with applications to chromatin-immunoprecipitation microarray experi-ments. Nat. Biotechnol. 20, 835–839.
Schneider, T.D. and Stephens, R.M. (1990) Sequence logos:a new way to display consensus sequences. Nucleic Acids Res. 18, 6097–6100.
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Berger, M.F., Bulyk, M.L. (2006). Protein Binding Microarrays (PBMs) for Rapid, High-Throughput Characterization of the Sequence Specificities of DNA Binding Proteins. In: Bina, M. (eds) Gene Mapping, Discovery, and Expression. Methods in Molecular Biology, vol 338. Humana Press. https://doi.org/10.1385/1-59745-097-9:245
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DOI: https://doi.org/10.1385/1-59745-097-9:245
Publisher Name: Humana Press
Print ISBN: 978-1-58829-575-0
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