ReviewBriefings in functional genomics2015
Spec-seq: determining protein-DNA-binding specificity by sequencing.
Review in Briefings in functional genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 28 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
28 citing papers in PubMed.
- The evolutionary foundations of transcriptional regulation in animals.Nature reviews. Genetics · 2025Review
- Unzipping the defense: a comprehensive review on bZIP transcription factors inFrontiers in cellular and infection microbiology · 2025Review
- The emergence of Sox and POU transcription factors predates the origins of animal stem cells.Nature communications · 2024Article
- bcRflow: a Nextflow pipeline for characterizing B cell receptor repertoires from non-targeted transcriptomic data.NAR genomics and bioinformatics · 2024Article
- High-throughput data and modeling reveal insights into the mechanisms of cooperative DNA-binding by transcription factor proteins.Nucleic acids research · 2023Article
- Missense mutations in CRX homeodomain cause dominant retinopathies through two distinct mechanisms.eLife · 2023Article
- KaScape: a sequencing-based method for global characterization of protein‒DNA binding affinity.Scientific reports · 2023Article
- Directed Evolution of an Enhanced POU Reprogramming Factor for Cell Fate Engineering.Molecular biology and evolution · 2021Article
- Integrating genome sequence and structural data for statistical learning to predict transcription factor binding sites.Nucleic acids research · 2020Article
- How affinity of the ELT-2 GATA factor binding toDevelopment (Cambridge, England) · 2020Article
- Quantitative analysis of transcription factor binding and expression using calling cards reporter arrays.Nucleic acids research · 2020Article
- Systematic in vitro profiling of off-target affinity, cleavage and efficiency for CRISPR enzymes.Nucleic acids research · 2020Article
- Low-Affinity Binding Sites and the Transcription Factor Specificity Paradox in Eukaryotes.Annual review of cell and developmental biology · 2019Review
- Specificity landscapes unmask submaximal binding site preferences of transcription factors.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- High-throughput characterization of genetic effects on DNA-protein binding and gene transcription.Genome research · 2018Article
- A High-Throughput Mutational Scan of an Intrinsically Disordered Acidic Transcriptional Activation Domain.Cell systems · 2018Article
- Quantitative profiling of BATF family proteins/JUNB/IRF hetero-trimers using Spec-seq.BMC molecular biology · 2018Article
- Deciphering the protein-DNA code of bacterial winged helix-turn-helix transcription factors.Quantitative biology (Beijing, China) · 2018Article
- The Human Transcription Factors.Cell · 2018Review
- Measuring quantitative effects of methylation on transcription factor-DNA binding affinity.Science advances · 2017Article
Corrections and comments
- Erratum issued
Authors and funding
3 authors.
Funding
Abstract
The specificity of protein-DNA interactions can be determined directly by sequencing the bound and unbound fractions in a standard binding reaction. The procedure is easy and inexpensive, and the accuracy can be high for thousands of sequences assayed in parallel. From the measurements, simple models of specificity, such as position weight matrices, can be assessed for their accuracy and more complex models developed if useful. Those may provide more accurate predictions of in vivo binding sites and can help us to understand the details of recognition. As an example, we demonstrate new information gained about the binding of lac repressor. One can apply the same method to combinations of factors that bind simultaneously to a single DNA and determine both the specificity of the individual factors and the cooperativity between them.
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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.