The DOI matches its Crossref record; 65 of the 65 references it cites were found in a registry or an index.
Cofactor Binding Evokes Latent Differences in DNA Binding Specificity between Hox Proteins
Open accessAbstract
Summary Members of transcription factor families typically have similar DNA binding specificities yet execute unique functions in vivo. Transcription factors often bind DNA as multiprotein complexes, raising the possibility that complex formation might modify their DNA binding specificities. To test this hypothesis, we developed an experimental and computational platform, SELEX-seq, that can be used to determine the relative affinities to any DNA sequence for any transcription factor complex. Applying this method to all eight Drosophila Hox proteins, we show that they obtain novel recognition properties when they bind DNA with the dimeric cofactor Extradenticle-Homothorax (Exd). Exd-Hox specificities group into three main classes that obey Hox gene collinearity rules and DNA structure predictions suggest that anterior and posterior Hox proteins prefer DNA sequences with distinct minor groove topographies. Together, these data suggest that emergent DNA recognition properties revealed by interactions with cofactors contribute to transcription factor specificities in vivo.
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Self-citationOrigins of Specificity in Protein-DNA Recognition
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Self-citationModulating Hox gene functions during animal body patterning
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Cited by
The Human Transcription Factors
Lambert, S. A., Jolma, A., Campitelli, L. F., Das, P. K., Yin, Y., Albu, M., Chen, X., Taipale, J., Hughes, T. R., & Weirauch, M. T. (2018) · Cell · doi:10.1016/j.cell.2018.01.029 · Cited by 3,399
Transcription factors: from enhancer binding to developmental control
Spitz, F., & Furlong, E. E. M. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3207 · Cited by 2,227
Transcriptional enhancers: from properties to genome-wide predictions
Shlyueva, D., Stampfel, G., & Stark, A. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3682 · Cited by 1,356
DNA-dependent formation of transcription factor pairs alters their binding specificity
Jolma, A., Yin, Y., Nitta, K. R., Dave, K., Popov, A., Taipale, M., Enge, M., Kivioja, T., Morgunova, E., & Taipale, J. (2015) · Nature · doi:10.1038/nature15518 · Cited by 559
Absence of a simple code: how transcription factors read the genome
Slattery, M., Zhou, T., Yang, L., Dantas Machado, A. C., Gordân, R., & Rohs, R. (2014) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2014.07.002 · Cited by 537
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Metadata
- Authors
- Slattery, M., Riley, T., Liu, P., Abe, N., Gomez-Alcala, P., Dror, I., Zhou, T., Rohs, R., Honig, B., Bussemaker, H. J., & Mann, R. S.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2011-12
- Volume
- 147
- Issue
- 6
- Pages
- 1270-1282
- ISSN
- 0092-8674 (ISSN-L)
- OpenAlex
- W2159942968
- Cited by
- 507
- References
- 65
- FWCI
- 12.93
- Type
- journal article
- Language
- en
- Open access
- bronze
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