ArticleScientific reports2020
Inferring quantity and qualities of superimposed reaction rates from single molecule survival time distributions.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Single-molecule imaging reveals RNA polymerase II dynamics and TAF1-dependent promoter-proximal pause release.Nature communications · 2026Article
- Discovery of an Endonuclease G-inhibitory Ku80-peptide protecting against leukemogenic rearrangements at the MLL breakpoint cluster.Nature communications · 2026Article
- Mechanisms of gene regulation by SRCAP and H2A.Z.Nature communications · 2026Article
- Article
- Electrostatic properties of disordered regions control transcription factor search and pioneer activity.Nature communications · 2026Article
- Histone acetylation readers Bdf1 and Yaf9 direct SWR1 remodeler to +1 nucleosome.Science advances · 2025Article
- Increasingly efficient chromatin binding of cohesin and CTCF supports chromatin architecture formation during zebrafish embryogenesis.Nature communications · 2025Article
- Effective in vivo binding energy landscape illustrates kinetic stability of RBPJ-DNA binding.Nature communications · 2025Article
- Transcription dynamics and genome organization in the mammalian nucleus: Recent advances.Molecular cell · 2025Review
- A high-throughput platform for single-molecule tracking identifies drug interaction and cellular mechanisms.eLife · 2025Article
- Single-molecule imaging of SWI/SNF chromatin remodelers reveals bromodomain-mediated and cancer-mutants-specific landscape of multi-modal DNA-binding dynamics.Nature communications · 2024Article
- Real-time single-molecule imaging of transcriptional regulatory networks in living cells.Nature reviews. Genetics · 2024Review
- Single-molecule tracking (SMT): a window into live-cell transcription biochemistry.Biochemical Society transactions · 2023Article
- Impact ofInternational journal of molecular sciences · 2022Review
- Span of regularization for solution of inverse problems with application to magnetic resonance relaxometry of the brain.Scientific reports · 2022Article
- Single-molecule tracking of Nodal and Lefty in live zebrafish embryos supports hindered diffusion model.Nature communications · 2022Article
- Article
- Bromodomains regulate dynamic targeting of the PBAF chromatin-remodeling complex to chromatin hubs.Biophysical journal · 2022Article
- Following the tracks: How transcription factor binding dynamics control transcription.Biophysical journal · 2022Review
- Single-molecule tracking (SMT) and localization of SRF and MRTF transcription factors during neuronal stimulation and differentiation.Open biology · 2022Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Actions of molecular species, for example binding of transcription factors to chromatin, may comprise several superimposed reaction pathways. The number and the rate constants of such superimposed reactions can in principle be resolved by inverse Laplace transformation of the corresponding distribution of reaction lifetimes. However, current approaches to solve this transformation are challenged by photobleaching-prone fluorescence measurements of lifetime distributions. Here, we present a genuine rate identification method (GRID), which infers the quantity, rates and amplitudes of dissociation processes from fluorescence lifetime distributions using a dense grid of possible decay rates. In contrast to common multi-exponential analysis of lifetime distributions, GRID is able to distinguish between broad and narrow clusters of decay rates. We validate GRID by simulations and apply it to CDX2-chromatin interactions measured by live cell single molecule fluorescence microscopy. GRID reveals well-separated narrow decay rate clusters of CDX2, in part overlooked by multi-exponential analysis. We discuss the amplitudes of the decay rate spectrum in terms of frequency of observed events and occupation probability of reaction states. We further demonstrate that a narrow decay rate cluster is compatible with a common model of TF sliding on DNA.
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