DOI: 10.1073/pnas.111163698. Exploring the DNA-binding specificities of zinc fingers with DNA microarrays

Exploring the DNA-binding specificities of zinc fingers with DNA microarrays

10.1073/pnas.111163698

Crossref journal-article

Proceedings of the National Academy of Sciences

Proceedings of the National Academy of Sciences (341)

Abstract

A key step in the regulation of networks that control gene expression is the sequence-specific binding of transcription factors to their DNA recognition sites. A more complete understanding of these DNA–protein interactions will permit a more comprehensive and quantitative mapping of the regulatory pathways within cells, as well as a deeper understanding of the potential functions of individual genes regulated by newly identified DNA-binding sites. Here we describe a DNA microarray-based method to characterize sequence-specific DNA recognition by zinc-finger proteins. A phage display library, prepared by randomizing critical amino acid residues in the second of three fingers of the mouse Zif268 domain, provided a rich source of zinc-finger proteins with variant DNA-binding specificities. Microarrays containing all possible 3-bp binding sites for the variable zinc fingers permitted the quantitation of the binding site preferences of the entire library, pools of zinc fingers corresponding to different rounds of selection from this library, as well as individual Zif268 variants that were isolated from the library by using specific DNA sequences. The results demonstrate the feasibility of using DNA microarrays for genome-wide identification of putative transcription factor-binding sites.

Bibliography

Bulyk, M. L., Huang, X., Choo, Y., & Church, G. M. (2001). Exploring the DNA-binding specificities of zinc fingers with DNA microarrays. Proceedings of the National Academy of Sciences, 98(13), 7158â7163.

Authors 4

Martha L. Bulyk (first)
Xiaohua Huang (additional)
Yen Choo (additional)
George M. Church (additional)

References 29 Referenced 222

10.1074/jbc.274.27.19281
10.1002/prot.340120202
10.1073/pnas.89.16.7345
10.1073/pnas.91.23.11168
10.1073/pnas.91.23.11163
10.1016/S0959-440X(97)80015-2
10.1126/science.8303274
10.1021/bi00185a004
10.1073/pnas.92.2.344
10.1021/bi00289a018
10.1093/nar/9.13.3047
10.1093/nar/21.15.3341
10.1093/nar/8.1.1
10.1126/science.1671176
10.1128/mcb.9.7.2944-2949.1989
10.1126/science.270.5235.467
10.1038/9878
10.1126/science.2028256
10.1016/S0969-2126(96)00125-6
10.1002/j.1460-2075.1994.tb06626.x
10.1016/0022-2836(86)90165-8
10.1093/nar/27.4.1182
10.1128/JB.182.10.2973-2977.2000
10.1002/pro.5560071111
10.1016/0378-1119(93)90253-Y
10.1074/jbc.274.33.23591
A Goffeau, B Barrell, H Bussey, R Davis, B Dujon, H Feldmann, F Galibert, J Hoheisel, C Jacq, M Johnston, et al. Science 546, 563–567 (1996). / Science by Goffeau A (1996)
10.1126/science.287.5461.2185
10.1126/science.288.5469.1146

Dates

Type	When
Created	23 years, 1 month ago (July 26, 2002, 10:45 a.m.)
Deposited	3 years, 4 months ago (April 25, 2022, 8:06 p.m.)
Indexed	3 weeks, 5 days ago (Aug. 5, 2025, 8:44 a.m.)
Issued	24 years, 2 months ago (June 12, 2001)
Published	24 years, 2 months ago (June 12, 2001)
Published Online	24 years, 2 months ago (June 12, 2001)
Published Print	24 years, 2 months ago (June 19, 2001)

Funders 0

None

BibTeX

@article{Bulyk_2001, title={Exploring the DNA-binding specificities of zinc fingers with DNA microarrays}, volume={98}, ISSN={1091-6490}, url={http://dx.doi.org/10.1073/pnas.111163698}, DOI={10.1073/pnas.111163698}, number={13}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Bulyk, Martha L. and Huang, Xiaohua and Choo, Yen and Church, George M.}, year={2001}, month=jun, pages={7158–7163} }

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