ArticleiScience2020
Transcription Factor Binding Affinities and DNA Shape Readout.
Article in iScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
15 citing papers in PubMed, 22 citations in OpenAlex.
- Motif-based models accurately predict cell type-specific distal regulatory elements.Nature communications · 2025Article
- Site-specific DNA insertion into the human genome with engineered recombinases.Nature biotechnology · 2025Article
- Article
- Mechanisms driving functional divergence of transcription factor paralogs.The New phytologist · 2025Review
- Experimental approaches to investigate biophysical interactions between homeodomain transcription factors and DNA.Biochimica et biophysica acta. Gene regulatory mechanisms · 2025Review
- Skipping events impose repeated binding attempts: profound kinetic implications of protein-DNA conformational changes.Nucleic acids research · 2024Article
- Harnessing regulatory networks in Actinobacteria for natural product discovery.Journal of industrial microbiology & biotechnology · 2024Review
- Position Weight Matrix or Acyclic Probabilistic Finite Automaton: Which model to use? A decision rule inferred for the prediction of transcription factor binding sites.Genetics and molecular biology · 2024Article
- The presence of a G-quadruplex prone sequence upstream of a minimal promoter increases transcriptional activity in the yeast Saccharomyces cerevisiae.Bioscience reports · 2023Article
- Substrate DNA Promoting Binding ofMicroorganisms · 2023Article
- Decoding enhancer complexity with machine learning and high-throughput discovery.Genome biology · 2023Review
- Structural predictions of protein-DNA binding: MELD-DNA.Nucleic acids research · 2023Article
- Structure-Guided Design of a Potent and Specific Inhibitor against the Genomic Mutator APOBEC3A.ACS chemical biology · 2022Article
- Elucidating the biology of transcription factor-DNA interaction for accurate identification of cis-regulatory elements.Current opinion in plant biology · 2022Review
- Technologies for profiling the impact of genomic variants on transcription factor binding.Medizinische Genetik : Mitteilungsblatt des Berufsverbandes Medizinische Genetik e.V · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
An essential event in gene regulation is the binding of a transcription factor (TF) to its target DNA. Models considering the interactions between the TF and the DNA geometry proved to be successful approaches to describe this binding event, while conserving data interpretability. However, a direct characterization of the DNA shape contribution to binding is still missing due to the lack of accurate and large-scale binding affinity data. Here, we use a binding assay we recently established to measure with high sensitivity the binding specificities of 13
Indexed as
Identifiers
What OpenQuestion holds
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.