ArticleNature2012
Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function.
Article in Nature, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 161 papers.
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Who cites it
161 citing papers in PubMed.
- The future of Forkhead box O transcription factors.The Biochemical journal · 2026Review
- MITF, TFEB, and TFE3 drive distinct adaptive gene expression programs and immune infiltration in melanoma.Cell reports · 2025Article
- Variations in flanking or less conserved positions of Reb1 and Abf1 consensus binding sites lead to major changes in their ability to modulate nucleosome sliding activity.Biological research · 2025Article
- Rap1 overexpression boosts triterpenoid saponin production in yeast by enhancing precursor supply and heterologous gene expression.Microbial cell factories · 2025Article
- Co-profiling of single-cell gene expression and chromatin landscapes in stickleback pituitary.Scientific data · 2025Article
- Transcriptional silencing in Saccharomyces cerevisiae: known unknowns.Epigenetics & chromatin · 2024Review
- The next-generation sequencing-chess problem.NAR genomics and bioinformatics · 2024Article
- A continuum of zinc finger transcription factor retention on native chromatin underlies dynamic genome organization.Molecular systems biology · 2024Article
- Genome-scale chromatin binding dynamics of RNA Polymerase II general transcription machinery components.The EMBO journal · 2024Article
- PML::RARA and GATA2 proteins interact via DNA templates to induce aberrant self-renewal in mouse and human hematopoietic cells.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Yeast heterochromatin stably silences only weak regulatory elements by altering burst duration.Cell reports · 2024Article
- Transcription factor exchange enables prolonged transcriptional bursts.Molecular cell · 2024Article
- Active compensation for changes in TDH3 expression mediated by direct regulators of TDH3 in Saccharomyces cerevisiae.PLoS genetics · 2023Article
- Yeast Heterochromatin Only Stably Silences Weak Regulatory Elements by Altering Burst Duration.bioRxiv : the preprint server for biology · 2023Article
- Context-dependent function of the transcriptional regulator Rap1 in gene silencing and activation inProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Acetylation reprograms MITF target selectivity and residence time.Nature communications · 2023Article
- A spatio-temporally constrained gene regulatory network directed by PBX1/2 acquires limb patterning specificity via HAND2.Nature communications · 2023Article
- Transcription factor localization dynamics and DNA binding drive distinct promoter interpretations.Cell reports · 2023Article
- Context dependent function of the transcriptional regulator Rap1 in gene silencing and activation inbioRxiv : the preprint server for biology · 2023Article
- Dynamics of nuclear architecture during early embryonic development and lessons from liveimaging.Developmental cell · 2023Review
101 more citing papers are in PubMed but not listed here.
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5 authors.
Funding
Abstract
Dynamic access to genetic information is central to organismal development and environmental response. Consequently, genomic processes must be regulated by mechanisms that alter genome function relatively rapidly. Conventional chromatin immunoprecipitation (ChIP) experiments measure transcription factor occupancy, but give no indication of kinetics and are poor predictors of transcription factor function at a given locus. To measure transcription-factor-binding dynamics across the genome, we performed competition ChIP (refs 6, 7) with a sequence-specific Saccharomyces cerevisiae transcription factor, Rap1 (ref. 8). Rap1-binding dynamics and Rap1 occupancy were only weakly correlated (R(2) = 0.14), but binding dynamics were more strongly linked to function than occupancy. Long Rap1 residence was coupled to transcriptional activation, whereas fast binding turnover, which we refer to as 'treadmilling', was linked to low transcriptional output. Thus, DNA-binding events that seem identical by conventional ChIP may have different underlying modes of interaction that lead to opposing functional outcomes. We propose that transcription factor binding turnover is a major point of regulation in determining the functional consequences of transcription factor binding, and is mediated mainly by control of competition between transcription factors and nucleosomes. Our model predicts a clutch-like mechanism that rapidly engages a treadmilling transcription factor into a stable binding state, or vice versa, to modulate transcription factor function.
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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.