ArticlePloS one2011
Sequence-specific capture of protein-DNA complexes for mass spectrometric protein identification.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 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
21 citing papers in PubMed, 29 citations in OpenAlex.
- Review
- Zinc homeostasis in Schizosaccharomyces pombe.Archives of microbiology · 2023Review
- Biomimetic mimicry of formaldehyde-induced DNA-protein crosslinks in the confined space of a metal-organic framework.Chemical science · 2022Article
- Understanding the chemistry of the artificial electron acceptors PES, PMS, DCPIP and Wurster's Blue in methanol dehydrogenase assays.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2020Article
- Article
- Second-generation method for analysis of chromatin binding with formaldehyde-cross-linking kinetics.The Journal of biological chemistry · 2017Article
- Elucidating Protein-DNA Interactions in Human Alphoid Chromatin via Hybridization Capture and Mass Spectrometry.Journal of proteome research · 2017Article
- Synthesis of Oligodeoxynucleotides Containing Electrophilic Groups.Organic letters · 2016Article
- Streamlined discovery of cross-linked chromatin complexes and associated histone modifications by mass spectrometry.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Glycome characterization of immunoglobulin G from buffalo (Bubalus bubalis) colostrum.Glycoconjugate journal · 2015Article
- Formaldehyde crosslinking: a tool for the study of chromatin complexes.The Journal of biological chemistry · 2015Review
- Prostate cancer risk locus at 8q24 as a regulatory hub by physical interactions with multiple genomic loci across the genome.Human molecular genetics · 2015Article
- Analysis of chromatin binding dynamics using the crosslinking kinetics (CLK) method.Methods (San Diego, Calif.) · 2014Article
- Enzymatic fabrication of high-density RNA arrays.Angewandte Chemie (International ed. in English) · 2014Article
- Multiplexed programmable release of captured DNA.Chembiochem : a European journal of chemical biology · 2014Article
- How the proteome packages the genome for cardiovascular development.Proteomics · 2014Review
- Discovery of Chromatin-Associated Proteins via Sequence-Specific Capture and Mass Spectrometric Protein Identification in Saccharomyces cerevisiae.Journal of proteome research · 2014Article
- Advanced methods for the analysis of chromatin-associated proteins.Physiological genomics · 2014Review
- Article
- Combining genomic and proteomic approaches for epigenetics research.Epigenomics · 2013Review
Corrections and comments
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Authors and funding
11 authors at 2 institutions in 1 country.
Funding
Abstract
The regulation of gene transcription is fundamental to the existence of complex multicellular organisms such as humans. Although it is widely recognized that much of gene regulation is controlled by gene-specific protein-DNA interactions, there presently exists little in the way of tools to identify proteins that interact with the genome at locations of interest. We have developed a novel strategy to address this problem, which we refer to as GENECAPP, for Global ExoNuclease-based Enrichment of Chromatin-Associated Proteins for Proteomics. In this approach, formaldehyde cross-linking is employed to covalently link DNA to its associated proteins; subsequent fragmentation of the DNA, followed by exonuclease digestion, produces a single-stranded region of the DNA that enables sequence-specific hybridization capture of the protein-DNA complex on a solid support. Mass spectrometric (MS) analysis of the captured proteins is then used for their identification and/or quantification. We show here the development and optimization of GENECAPP for an in vitro model system, comprised of the murine insulin-like growth factor-binding protein 1 (IGFBP1) promoter region and FoxO1, a member of the forkhead rhabdomyosarcoma (FoxO) subfamily of transcription factors, which binds specifically to the IGFBP1 promoter. This novel strategy provides a powerful tool for studies of protein-DNA and protein-protein interactions.
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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.