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Cited by 355

The DOI matches its Crossref record; 53 of the 53 references it cites were found in a registry or an index.

Genomic Regions Flanking E-Box Binding Sites Influence DNA Binding Specificity of bHLH Transcription Factors through DNA Shape

Open access
Gordân, Raluca, Shen, Ning, Dror, Iris, Zhou, Tianyin, Horton, John, Rohs, Remo, Bulyk, Martha L.·2013·Cell Reports
DOI 10.1016/j.celrep.2013.03.014
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Abstract

DNA sequence is a major determinant of the binding specificity of transcription factors (TFs) for their genomic targets. However, eukaryotic cells often express, at the same time, TFs with highly similar DNA binding motifs but distinct in vivo targets. Currently, it is not well understood how TFs with seemingly identical DNA motifs achieve unique specificities in vivo. Here, we used custom protein-binding microarrays to analyze TF specificity for putative binding sites in their genomic sequence context. Using yeast TFs Cbf1 and Tye7 as our case studies, we found that binding sites of these bHLH TFs (i.e., E-boxes) are bound differently in vitro and in vivo, depending on their genomic context. Computational analyses suggest that nucleotides outside E-box binding sites contribute to specificity by influencing the three-dimensional structure of DNA binding sites. Thus, the local shape of target sites might play a widespread role in achieving regulatory specificity within TF families.

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Metadata

Authors
Gordân, R., Shen, N., Dror, I., Zhou, T., Horton, J., Rohs, R., & Bulyk, M. L.
Venue
Cell Reports
Publisher
Elsevier BV
Published
2013-04
Volume
3
Issue
4
Pages
1093-1104
ISSN
2211-1247 (ISSN-L)
DOI
10.1016/j.celrep.2013.03.014
OpenAlex
W2087058596
Cited by
355
References
53
FWCI
11.83
Type
journal article
Language
en
Open access
gold

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