ReviewNature protocols2021
Genome-wide quantification of transcription factor binding at single-DNA-molecule resolution using methyl-transferase footprinting.
Review in Nature protocols, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
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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
12 citing papers in PubMed.
- A practical guide to studying genome function using single-molecule genomics.Nature reviews. Molecular cell biology · 2026Review
- Cumulative transcription factor binding and p300-mediated histone acetylation drive enhancer activation frequency.Nature genetics · 2026Article
- LEMONmethyl-seq: Targeted long-read DNA methylation profiling reveals dynamics of CRISPR epigenome editing and endogenous DNA methylation patterns.bioRxiv : the preprint server for biology · 2026Article
- SMTrackR: an R/Bioconductor package for mapping protein binding at individual DNA molecules.Bioinformatics advances · 2026Article
- FootprintCharter: unsupervised detection and quantification of footprints in single molecule footprinting data.Bioinformatics (Oxford, England) · 2025Article
- Mouse promoters are characterised by low occupancy and high turnover of RNA polymerase II.Molecular systems biology · 2025Article
- Basic Epigenetic Mechanisms.Sub-cellular biochemistry · 2025Review
- cBAF generates subnucleosomes that expand OCT4 binding and function beyond DNA motifs at enhancers.Nature structural & molecular biology · 2024Article
- Identification of transcription factor co-binding patterns with non-negative matrix factorization.Nucleic acids research · 2024Article
- Beyond assembly: the increasing flexibility of single-molecule sequencing technology.Nature reviews. Genetics · 2023Review
- Up-regulation of PRKDC was associated with poor renal dysfunction after renal transplantation: A multi-centre analysis.Journal of cellular and molecular medicine · 2023Article
- Decreased complement 4d increases poor prognosis in patients with non-small cell lung cancer combined with gastrointestinal lymph node metastasis.Experimental and therapeutic medicine · 2022Article
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.
Funding
Abstract
Precise control of gene expression requires the coordinated action of multiple factors at cis-regulatory elements. We recently developed single-molecule footprinting to simultaneously resolve the occupancy of multiple proteins including transcription factors, RNA polymerase II and nucleosomes on single DNA molecules genome-wide. The technique combines the use of cytosine methyltransferases to footprint the genome with bisulfite sequencing to resolve transcription factor binding patterns at cis-regulatory elements. DNA footprinting is performed by incubating permeabilized nuclei with recombinant methyltransferases. Upon DNA extraction, whole-genome or targeted bisulfite libraries are prepared and loaded on Illumina sequencers. The protocol can be completed in 4-5 d in any laboratory with access to high-throughput sequencing. Analysis can be performed in 2 d using a dedicated R package and requires access to a high-performance computing system. Our method can be used to analyze how transcription factors cooperate and antagonize to regulate transcription.
Indexed as
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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.