Abstract
A number of important cellular processes, such as transcriptional regulation, recombination, replication, repair, and DNA modification, are performed by DNA binding proteins. Of particular interest are transcription factors (TFs) which, through their sequence-specific interactions with DNA binding sites, modulate gene expression in a manner required for normal cellular growth and differentiation, and also for response to environmental stimuli. Despite their importance, the DNA binding specificities of most DNA binding proteins still remain unknown, since prior technologies aimed at identifying DNA–protein interactions have been laborious, not highly scalable, or have required limiting biological reagents. Recently a new DNA microarray-based technology, termed protein binding microarrays (PBMs), has been developed that allows rapid, high-throughput characterization of the in vitro DNA binding site sequence specificities of TFs, other DNA binding proteins, or synthetic compounds. DNA binding site data from PBMs combined with gene annotation data, comparative sequence analysis, and gene expression profiling, can be used to predict what genes are regulated by a given TF, what the functions are of a given TF and its predicted target genes, and how that TF may fit into the cell's transcriptional regulatory network.
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Abbreviations
- ChIP:
-
Chromatin immunoprecipitation
- Dam:
-
DNA adenine methyltransferase
- dsDNA:
-
Double-stranded DNA
- GST:
-
glutathione S-transferase
- PBM:
-
Protein binding microarray
- TF:
-
Transcription factor
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Acknowledgments
I thank Michael F. Berger and Tom Volkert for technical assistance. This work was supported in part by National Institutes of Health grants from the National Human Genome Research Institute to M.L.B. (R01 HG002966, R01 HG003420, and R01 HG003985).
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Bulyk, M.L. (2006). Protein Binding Microarrays for the Characterization of DNA–Protein Interactions. In: Seitz, H. (eds) Analytics of Protein–DNA Interactions. Advances in Biochemical Engineering/Biotechnology, vol 104. Springer, Berlin, Heidelberg . https://doi.org/10.1007/10_025
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DOI: https://doi.org/10.1007/10_025
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