ArticleNucleic acids research2014
Multiple LacI-mediated loops revealed by Bayesian statistics and tethered particle motion.
Article in Nucleic acids research, 2014. 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, 30 citations in OpenAlex.
- Detecting DNA Loops Using Tethered Particle Motion.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Bayesian Inference: The Comprehensive Approach to Analyzing Single-Molecule Experiments.Annual review of biophysics · 2021Review
- LPS-binding IgG arrests actively motile Salmonella Typhimurium in gastrointestinal mucus.Mucosal immunology · 2020Article
- Sequence-dependent dynamics of synthetic and endogenous RSSs in V(D)J recombination.Nucleic acids research · 2020Article
- An automated Bayesian pipeline for rapid analysis of single-molecule binding data.Nature communications · 2019Article
- Tethered multifluorophore motion reveals equilibrium transition kinetics of single DNA double helices.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Variational Algorithms for Analyzing Noisy Multistate Diffusion Trajectories.Biophysical journal · 2018Article
- Protein-mediated loops in supercoiled DNA create large topological domains.Nucleic acids research · 2018Article
- Single-Molecule Tethered Particle Motion: Stepwise Analyses of Site-Specific DNA Recombination.Micromachines · 2018Review
- Protein-mediated looping of DNA under tension requires supercoiling.Nucleic acids research · 2018Article
- Tethered Particle Motion: An Easy Technique for Probing DNA Topology and Interactions with Transcription Factors.Methods in molecular biology (Clifton, N.J.) · 2018Article
- Proteins mediating DNA loops effectively block transcription.Protein science : a publication of the Protein Society · 2017Article
- Multiplexed, Tethered Particle Microscopy for Studies of DNA-Enzyme Dynamics.Methods in enzymology · 2017Article
- Decoding Single Molecule Time Traces with Dynamic Disorder.PLoS computational biology · 2016Article
- An information-based approach to change-point analysis with applications to biophysics and cell biology.Biophysical journal · 2015Article
- Empirical Bayes methods enable advanced population-level analyses of single-molecule FRET experiments.Biophysical journal · 2014Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
The bacterial transcription factor LacI loops DNA by binding to two separate locations on the DNA simultaneously. Despite being one of the best-studied model systems for transcriptional regulation, the number and conformations of loop structures accessible to LacI remain unclear, though the importance of multiple coexisting loops has been implicated in interactions between LacI and other cellular regulators of gene expression. To probe this issue, we have developed a new analysis method for tethered particle motion, a versatile and commonly used in vitro single-molecule technique. Our method, vbTPM, performs variational Bayesian inference in hidden Markov models. It learns the number of distinct states (i.e. DNA-protein conformations) directly from tethered particle motion data with better resolution than existing methods, while easily correcting for common experimental artifacts. Studying short (roughly 100 bp) LacI-mediated loops, we provide evidence for three distinct loop structures, more than previously reported in single-molecule studies. Moreover, our results confirm that changes in LacI conformation and DNA-binding topology both contribute to the repertoire of LacI-mediated loops formed in vitro, and provide qualitatively new input for models of looping and transcriptional regulation. We expect vbTPM to be broadly useful for probing complex protein-nucleic acid interactions.
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Registered trials
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.