ReviewCritical reviews in biochemistry and molecular biology2015
Protein-DNA binding in high-resolution.
Review in Critical reviews in biochemistry and molecular biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 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
26 citing papers in PubMed, 49 citations in OpenAlex.
- A rapid test for protein-DNA interactions.Nucleic acids research · 2026Article
- Article
- Review and Evaluate the Bioinformatics Analysis Strategies of ATAC-seq and CUT&Tag Data.Genomics, proteomics & bioinformatics · 2024Review
- Global chromatin landscapes identify candidate noncoding modifiers of cardiac rhythm.The Journal of clinical investigation · 2023Article
- Higher-order G-quadruplexes in promoters are untapped drug targets.Frontiers in chemistry · 2023Review
- Bibliometric review of ATAC-Seq and its application in gene expression.Briefings in bioinformatics · 2022Review
- Effects of size, cooperativity, and competitive binding on protein positioning on DNA.Biophysical journal · 2021Article
- Functional genomic approaches to elucidate the role of enhancers during development.Wiley interdisciplinary reviews. Systems biology and medicine · 2020Review
- Comparative analysis of ChIP-exo peak-callers: impact of data quality, read duplication and binding subtypes.BMC bioinformatics · 2020Article
- A single ChIP-seq dataset is sufficient for comprehensive analysis of motifs co-occurrence with MCOT package.Nucleic acids research · 2019Article
- Redefining the IBDs using genome-scale molecular phenotyping.Nature reviews. Gastroenterology & hepatology · 2019Review
- Intrinsic DNA Shape Accounts for Affinity Differences between Hox-Cofactor Binding Sites.Cell reports · 2018Article
- Insights from resolving protein-DNA interactions at near base-pair resolution.Briefings in functional genomics · 2018Review
- Genome-Wide Identification of Transcription Factor-Binding Sites in Quiescent Adult Neural Stem Cells.Methods in molecular biology (Clifton, N.J.) · 2018Article
- Genetic and epigenetic determinants of inter-individual variability in responses to toxicants.Current opinion in toxicology · 2017Article
- Data exploration, quality control and statistical analysis of ChIP-exo/nexus experiments.Nucleic acids research · 2017Article
- Emerging Chemistry Strategies for Engineering Native Chromatin.Journal of the American Chemical Society · 2017Article
- Mocap: large-scale inference of transcription factor binding sites from chromatin accessibility.Nucleic acids research · 2017Article
- Paf1 Has Distinct Roles in Transcription Elongation and Differential Transcript Fate.Molecular cell · 2017Article
- Deciphering the regulon of a GntR family regulator via transcriptome and ChIP-exo analyses and its contribution to virulence in Xanthomonas citri.Molecular plant pathology · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Recent advances in experimental and computational methodologies are enabling ultra-high resolution genome-wide profiles of protein-DNA binding events. For example, the ChIP-exo protocol precisely characterizes protein-DNA cross-linking patterns by combining chromatin immunoprecipitation (ChIP) with 5' → 3' exonuclease digestion. Similarly, deeply sequenced chromatin accessibility assays (e.g. DNase-seq and ATAC-seq) enable the detection of protected footprints at protein-DNA binding sites. With these techniques and others, we have the potential to characterize the individual nucleotides that interact with transcription factors, nucleosomes, RNA polymerases and other regulatory proteins in a particular cellular context. In this review, we explain the experimental assays and computational analysis methods that enable high-resolution profiling of protein-DNA binding events. We discuss the challenges and opportunities associated with such approaches.
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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.