ArticleNature communications2020
Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 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
30 citing papers in PubMed, 43 citations in OpenAlex.
- NuXLApp: Interactive data analysis and visualization for protein-nucleic acid crosslinking mass spectrometry.Protein science : a publication of the Protein Society · 2026Article
- Direct and high-yield chromatin isolation by SBCP unlocks superior plant proteomics and epigenomic profiling.Plant cell reports · 2026Article
- Rapid photo-crosslinking in living cells reveals protein-nucleic acid dynamics on a timescale of minutes.Nucleic acids research · 2026Article
- Tuning nuclear rheology through transient chromatin cross-links.Physical review. E · 2025Article
- Chemotherapy-induced CA-repeat DNA fragments in breast cancer trigger antitumor immune responses.Nature immunology · 2025Article
- Nucleosome interaction of the CPC secures centromeric chromatin integrity and chromosome segregation fidelity.The EMBO journal · 2025Article
- Chemical crosslinking extends and complements UV crosslinking in analysis of RNA/DNA nucleic acid-protein interaction sites by mass spectrometry.Nucleic acids research · 2025Article
- Molecular Determinants of the Human Retinal Pigment Epithelium Cell Fate and Potential Pharmacogenomic Targets for Precision Medicine.International journal of molecular sciences · 2025Article
- UV-C and hydration state drive pulsed light-induced proteome damage inFrontiers in microbiology · 2025Article
- Endogenous Cellular Metabolite Methylglyoxal Induces DNA-Protein Cross-Links in Living Cells.ACS chemical biology · 2024Article
- Denaturing mass photometry for rapid optimization of chemical protein-protein cross-linking reactions.Nature communications · 2024Article
- Galectin-3 does not interact with RNA directly.Glycobiology · 2024Article
- Enzymatic Processing of DNA-Protein Crosslinks.Genes · 2024Review
- CHHM: a Manually Curated Catalogue of Human Histone Modifications Revealing Hotspot Regions and Unique Distribution Patterns.International journal of biological sciences · 2024Article
- DNA-Histone Cross-Link Formation via Hole Trapping in Nucleosome Core Particles.Journal of the American Chemical Society · 2023Article
- Advantages and limitations of UV cross-linking analysis of protein-RNA interactomes in microbes.Molecular microbiology · 2023Review
- Spatiotemporal and global profiling of DNA-protein interactions enables discovery of low-affinity transcription factors.Nature chemistry · 2023Article
- RNA interactome capture in Escherichia coli globally identifies RNA-binding proteins.Nucleic acids research · 2023Article
- A widely applicable and cost-effective method for specific RNA-protein complex isolation.Scientific reports · 2023Article
- Characterizing crosstalk in epigenetic signaling to understand disease physiology.The Biochemical journal · 2023Article
Corrections and comments
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Authors and funding
14 authors at 6 institutions in 3 countries.
Funding
Abstract
Protein-DNA interactions are key to the functionality and stability of the genome. Identification and mapping of protein-DNA interaction interfaces and sites is crucial for understanding DNA-dependent processes. Here, we present a workflow that allows mass spectrometric (MS) identification of proteins in direct contact with DNA in reconstituted and native chromatin after cross-linking by ultraviolet (UV) light. Our approach enables the determination of contact interfaces at amino-acid level. With the example of chromatin-associated protein SCML2 we show that our technique allows differentiation of nucleosome-binding interfaces in distinct states. By UV cross-linking of isolated nuclei we determined the cross-linking sites of several factors including chromatin-modifying enzymes, demonstrating that our workflow is not restricted to reconstituted materials. As our approach can distinguish between protein-RNA and DNA interactions in one single experiment, we project that it will be possible to obtain insights into chromatin and its regulation in the future.
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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.