ArticlePhysical biology2013
DNA sequence-dependent mechanics and protein-assisted bending in repressor-mediated loop formation.
Article in Physical biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 24 citations in OpenAlex.
- Article
- Multiplexed characterization of rationally designed promoter architectures deconstructs combinatorial logic for IPTG-inducible systems.Nature communications · 2021Article
- How the avidity of polymerase binding to the -35/-10 promoter sites affects gene expression.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Selection of DNA Cleavage Sites by Topoisomerase II Results from Enzyme-Induced Flexibility of DNA.Cell chemical biology · 2019Article
- Mapping DNA sequence to transcription factor binding energy in vivo.PLoS computational biology · 2019Article
- Tuning Transcriptional Regulation through Signaling: A Predictive Theory of Allosteric Induction.Cell systems · 2018Article
- Protein-mediated looping of DNA under tension requires supercoiling.Nucleic acids research · 2018Article
- Towards quantitative analysis of gene regulation by enhancers.Epigenomics · 2017Review
- Genetic cargo and bacterial species set the rate of vesicle-mediated horizontal gene transfer.Scientific reports · 2017Article
- Nucleosome-free DNA regions differentially affect distant communication in chromatin.Nucleic acids research · 2017Article
- Supercoiling biases the formation of loops involved in gene regulation.Biophysical reviews · 2016Review
- Predicting the impact of promoter variability on regulatory outputs.Scientific reports · 2015Article
- High-resolution mapping of architectural DNA binding protein facilitation of a DNA repression loop in Escherichia coli.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- DNA topology confers sequence specificity to nonspecific architectural proteins.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- What controls DNA looping?International journal of molecular sciences · 2014Article
- Bacterial promoter repression by DNA looping without protein-protein binding competition.Nucleic acids research · 2014Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
As the chief informational molecule of life, DNA is subject to extensive physical manipulations. The energy required to deform double-helical DNA depends on sequence, and this mechanical code of DNA influences gene regulation, such as through nucleosome positioning. Here we examine the sequence-dependent flexibility of DNA in bacterial transcription factor-mediated looping, a context for which the role of sequence remains poorly understood. Using a suite of synthetic constructs repressed by the Lac repressor and two well-known sequences that show large flexibility differences in vitro, we make precise statistical mechanical predictions as to how DNA sequence influences loop formation and test these predictions using in vivo transcription and in vitro single-molecule assays. Surprisingly, sequence-dependent flexibility does not affect in vivo gene regulation. By theoretically and experimentally quantifying the relative contributions of sequence and the DNA-bending protein HU to DNA mechanical properties, we reveal that bending by HU dominates DNA mechanics and masks intrinsic sequence-dependent flexibility. Such a quantitative understanding of how mechanical regulatory information is encoded in the genome will be a key step towards a predictive understanding of gene regulation at single-base pair resolution.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.