ArticleAnalytical chemistry2014
Measuring the formaldehyde Protein-DNA cross-link reversal rate.
Article in Analytical chemistry, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 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.
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Who cites it
31 citing papers in PubMed, 60 citations in OpenAlex.
- ChIP happens: from biochemical origins to the modern omics toolbox for understanding steroid hormone receptors.The Biochemical journal · 2026Review
- Mass spectrometry-based proteomics of FFPE tissues: progress, limitations, and clinical translation barriers.Clinical proteomics · 2025Review
- Cell type-specific 3D-genome organization and transcription regulation in the brain.Science advances · 2025Article
- Extraction, Purification, and Next-Generation Sequencing (NGS) Analysis of DNA and RNA from Formalin-Fixed and Paraffin-Embedded (FFPE) Tissue.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Be bold, start cold! cold formalin fixation of colorectal cancer specimens granted superior DNA and RNA quality for downstream molecular analysis.Histochemistry and cell biology · 2024Article
- Chromatin Immunoprecipitation Using Imbibed Seeds of Arabidopsis thaliana.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Chromatin and non-chromatin immunoprecipitations to capture protein-protein and protein-nucleic acid interactions in living cells.Methods (San Diego, Calif.) · 2023Article
- Epigenomic analysis of formalin-fixed paraffin-embedded samples by CUT&Tag.Nature communications · 2023Article
- Quantitative whole-tissue 3D imaging reveals bacteria in close association with mouse jejunum mucosa.NPJ biofilms and microbiomes · 2023Article
- Occurrence, Histopathological Findings, and Molecular Identification of Pathogenic Eimeria Infections in Rabbits (Mammalia: Lagomorpha) in Japan.Acta parasitologica · 2023Article
- The mutational signatures of formalin fixation on the human genome.Nature communications · 2022Article
- FFPE-ATAC: A Highly Sensitive Method for Profiling Chromatin Accessibility in Formalin-Fixed Paraffin-Embedded Samples.Current protocols · 2022Article
- Biomimetic mimicry of formaldehyde-induced DNA-protein crosslinks in the confined space of a metal-organic framework.Chemical science · 2022Article
- Identifying Protein Interactomes of Target RNAs Using HyPR-MS.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Genome-wide spatial expression profiling in formalin-fixed tissues.Cell genomics · 2021Article
- Formation and repair of unavoidable, endogenous interstrand cross-links in cellular DNA.DNA repair · 2021Review
- DNA adducts: Formation, biological effects, and new biospecimens for mass spectrometric measurements in humans.Mass spectrometry reviews · 2020Review
- Article
- Characterization of FFPE-induced bacterial DNA damage and development of a repair method.Biology methods & protocols · 2020Article
- Single-cell stabilization method identifies gonadotrope transcriptional dynamics and pituitary cell type heterogeneity.Nucleic acids research · 2018Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Protein-DNA binding interactions play critical roles in important cellular processes such as gene expression, cell division, and chromosomal organization. Techniques to identify and characterize these interactions often utilize formaldehyde cross-linking for stabilization of the complexes. Advantages of formaldehyde as a cross-linking reagent include cell permeability, relatively fast cross-linking kinetics, and short cross-linker length. In addition, formaldehyde cross-links are reversible, which has the advantage of allowing complexes to be dissociated if desired but may also present a problem if undesired dissociation occurs in the course of an experiment. While the kinetics of formaldehyde cross-link formation have been well-established in numerous studies, there have been no reports of the rate of cross-link dissociation, even though it is clearly a critical variable when developing a biochemical protocol involving formaldehyde cross-linking. We present here a method for measurement of the rate of formaldehyde cross-link reversal based upon the Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) procedure and use it to determine the rate of cross-link reversal for cross-linked protein-DNA complexes from yeast cell lysate. The half-life of the protein-DNA cross-links varies from 179 h at 4 °C to 11.3 h at 47 °C, with a rate that increases exponentially with temperature and is independent of salt concentration.
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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.