ArticleMolecular systems biology2020
Genome-wide off-rates reveal how DNA binding dynamics shape transcription factor function.
Article in Molecular systems biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Sequence and chemical specificity define the functional landscape of intrinsically disordered regions.Nature cell biology · 2026Article
- Synthetic promoter design in plants: integration of computational and experimental approaches.Frontiers in plant science · 2026Review
- 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
- Protein target search diffusion-association/dissociation free energy landscape around DNA binding site with flanking sequences.Biophysical journal · 2025Article
- RNA fine-tunes estrogen receptor-alpha binding on low-affinity DNA motifs for transcriptional regulation.The EMBO journal · 2024Article
- Article
- 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
- Context dependent function of the transcriptional regulator Rap1 in gene silencing and activation inbioRxiv : the preprint server for biology · 2023Article
- Transcription factor binding process is the primary driver of noise in gene expression.PLoS genetics · 2022Article
- Reading oscillatory instructions: How cells achieve time-dependent responses to oscillating transcription factors.Current opinion in cell biology · 2022Review
- Following the tracks: How transcription factor binding dynamics control transcription.Biophysical journal · 2022Review
- Facilitated dissociation of nucleoid-associated proteins from DNA in the bacterial confinement.Biophysical journal · 2022Article
- Transcription Factor Dynamics.Cold Spring Harbor perspectives in biology · 2021Review
- Genome-wide off-rates reveal how DNA binding dynamics shape transcription factor function.Molecular systems biology · 2020Article
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Authors and funding
5 authors.
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Abstract
Protein-DNA interactions are dynamic, and these dynamics are an important aspect of chromatin-associated processes such as transcription or replication. Due to a lack of methods to study on- and off-rates across entire genomes, protein-DNA interaction dynamics have not been studied extensively. Here, we determine in vivo off-rates for the Saccharomyces cerevisiae chromatin organizing factor Abf1, at 191 sites simultaneously across the yeast genome. Average Abf1 residence times span a wide range, varying between 4.2 and 33 min. Sites with different off-rates are associated with different functional characteristics. This includes their transcriptional dependency on Abf1, nucleosome positioning and the size of the nucleosome-free region, as well as the ability to roadblock RNA polymerase II for termination. The results show how off-rates contribute to transcription factor function and that DIVORSEQ (Determining In Vivo Off-Rates by SEQuencing) is a meaningful way of investigating protein-DNA binding dynamics genome-wide.
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