ArticleNucleic acids research2016
Single molecule tracking of Ace1p in Saccharomyces cerevisiae defines a characteristic residence time for non-specific interactions of transcription factors with chromatin.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed, 70 citations in OpenAlex.
- Heparan Sulfate Controls Nanoscale Assembly of GPC3-Wnt Receptor Complexes.bioRxiv : the preprint server for biology · 2026Article
- Live-cell single-molecule dynamics of eukaryotic RNA polymerase machineries.Science (New York, N.Y.) · 2026Article
- Single-molecule tracking reveals the dynamic turnover of Ipl1 at the kinetochores inLife science alliance · 2025Article
- Mechanisms for DNA Interplay in Eukaryotic Transcription Factors.Annual review of biophysics · 2025Review
- Autophagy-related protein Atg11 is essential for microtubule-mediated chromosome segregation.PLoS biology · 2025Article
- The yeast genome is globally accessible in living cells.Nature structural & molecular biology · 2025Article
- Halofilins as emerging bactofilin families of archaeal cell shape plasticity orchestrators.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- The relationship between nanoscale genome organization and gene expression in mouse embryonic stem cells during pluripotency transition.Nucleic acids research · 2024Article
- Real-time single-molecule imaging of transcriptional regulatory networks in living cells.Nature reviews. Genetics · 2024Review
- Transcription factor exchange enables prolonged transcriptional bursts.Molecular cell · 2024Article
- Interplay between stochastic enzyme activity and microtubule stability drives detyrosination enrichment on microtubule subsets.Current biology : CB · 2023Article
- Single-molecule tracking dataset of histone H3 (Hht1) inData in brief · 2023Article
- Single-molecule tracking for studying protein dynamics and target-search mechanism in live cells of S. cerevisiae.STAR protocols · 2022Article
- Impact ofInternational journal of molecular sciences · 2022Review
- Following the tracks: How transcription factor binding dynamics control transcription.Biophysical journal · 2022Review
- MYC amplifies gene expression through global changes in transcription factor dynamics.Cell reports · 2022Article
- Spatiotemporal coordination of transcription preinitiation complex assembly in live cells.Molecular cell · 2021Article
- Bound2Learn: a machine learning approach for classification of DNA-bound proteins from single-molecule tracking experiments.Nucleic acids research · 2021Article
- Transcription-mediated supercoiling regulates genome folding and loop formation.Molecular cell · 2021Article
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Authors and funding
8 authors at 5 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In vivo single molecule tracking has recently developed into a powerful technique for measuring and understanding the transient interactions of transcription factors (TF) with their chromatin response elements. However, this method still lacks a solid foundation for distinguishing between specific and non-specific interactions. To address this issue, we took advantage of the power of molecular genetics of yeast. Yeast TF Ace1p has only five specific sites in the genome and thus serves as a benchmark to distinguish specific from non-specific binding. Here, we show that the estimated residence time of the short-residence molecules is essentially the same for Hht1p, Ace1p and Hsf1p, equaling 0.12-0.32 s. These three DNA-binding proteins are very different in their structure, function and intracellular concentration. This suggests that (i) short-residence molecules are bound to DNA non-specifically, and (ii) that non-specific binding shares common characteristics between vastly different DNA-bound proteins and thus may have a common underlying mechanism. We develop new and robust procedure for evaluation of adverse effects of labeling, and new quantitative analysis procedures that significantly improve residence time measurements by accounting for fluorophore blinking. Our results provide a framework for the reliable performance and analysis of single molecule TF experiments in yeast.
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