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Absence of a simple code: how transcription factors read the genome

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Slattery, Matthew, Zhou, Tianyin, Yang, Lin, Dantas Machado, Ana Carolina, Gordân, Raluca, Rohs, Remo·2014·Trends in Biochemical Sciences

DOI 10.1016/j.tibs.2014.07.002PMC PMC4149858

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Abstract

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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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
ORCID: Slattery, Matthew
Yang, Lin
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)
DOI: 10.1016/j.tibs.2014.07.002
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: cc-by-nc-nd
www.elsevier.com/tdm/userlicense/1.0/ (tdm)
creativecommons.org/licenses/by-nc-nd/3.0/ (vor)
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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Absence of a simple code: how transcription factors read the genome

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