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Absence of a simple code: how transcription factors read the genome
Open accessAbstract
Transcription factors (TFs) influence cell fate by interpreting the regulatory DNA within a genome. TFs recognize DNA in a specific manner; the mechanisms underlying this specificity have been identified for many TFs based on 3D structures of protein-DNA complexes. More recently, structural views have been complemented with data from high-throughput in vitro and in vivo explorations of the DNA-binding preferences of many TFs. Together, these approaches have greatly expanded our understanding of TF-DNA interactions. However, the mechanisms by which TFs select in vivo binding sites and alter gene expression remain unclear. Recent work has highlighted the many variables that influence TF-DNA binding, while demonstrating that a biophysical understanding of these many factors will be central to understanding TF function.
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“However, these interactions do not have any base specificity 26 .”
From Mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator (2015) · cites this paper as [26]
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Additional file 3 of Systematic identification of non-canonical transcription factor motifs
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Metadata
- Authors
- Slattery, M., Zhou, T., Yang, L., Dantas Machado, A. C., Gordân, R., & Rohs, R.
- Affiliations
- University of Minnesota (US)
- University of Southern California (US)
- Duke University (US)
- Corresponding author
- Slattery, Matthew
- Gordân, Raluca
- Rohs, Remo
- Venue
- Trends in Biochemical Sciences
- Publisher
- Elsevier BV
- Published
- 2014-09
- Volume
- 39
- Issue
- 9
- Pages
- 381-399
- ISSN
- 0968-0004 (ISSN-L)
- PMC
- PMC4149858
- OpenAlex
- W2022736304
- Cited by
- 537
- References
- 254
- Citations by year
- 2026: 22 · 2025: 43 · 2024: 39 · 2023: 42 · 2022: 38 · 2021: 67 · 2020: 43 · 2019: 55 · 2018: 42 · 2017: 47 · 2016: 47 · 2015: 45 · 2014: 7
- FWCI
- 4.58
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Trends in Biochemical Sciences (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Science Foundation
- National Institutes of Health
- National Human Genome Research Institute (R01HG003008)
- National Institute of General Medical Sciences (U01GM103804, R01GM106056)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Diffusion and Search Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- transcription factors, DNA binding specificity, protein-DNA complex, binding site selection, gene expression regulation, cell fate
- MeSH terms
- Animals, Binding Sites, DNA, Humans, Protein Binding, Transcription Factors, Genome, Computational Biology, Biophysical Phenomena
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