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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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Oberbeckmann, E., Krietenstein, N., Niebauer, V., Wang, Y., Schall, K., Moldt, M., Straub, T., Rohs, R., Hopfner, K., Korber, P., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-23016-z · Cited by 60
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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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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