title: Exploring DNA-binding proteins with in vivo chemical cross-linking and mass spectrometry.
abstract: DNA-binding proteins are very important constituents of proteomes of all species and play crucial roles in transcription, DNA replication, recombination, repair, and other activities associated with DNA. Although a number of DNA-binding proteins have been identified, many proteins involved in gene regulation and DNA repair are likely still unknown because of their dynamic and/or weak interactions with DNA. In this report, we described an approach for the comprehensive identification of DNA-binding proteins with in vivo formaldehyde cross-linking and LC-MS/MS. DNA-binding proteins could be purified via the isolation of DNA-protein complexes and released from the complexes by reversing the cross-linking. By using this method, we were able to identify more than one hundred DNA-binding proteins, such as proteins involved in transcription, gene regulation, DNA replication and repair, and a large number of proteins that are potentially associated with DNA and DNA-binding proteins. This method should be generally applicable to the investigation of other nucleic acid-binding proteins, and hold great potential in the comprehensive study of gene regulation, DNA damage response and repair, as well as many other critical biological processes at proteomic level.
authors.affiliation: Department of Chemistry, University of California, Riverside, California 92521-0403, USA.
authors.forename: Haibo
authors.initials: H
authors.lastname: Qin
authors.forename: Yinsheng
authors.initials: Y
authors.lastname: Wang
mesh_terms: D045744:Cell Line, Tumor; D002853:Chromatography, Liquid; D003432:Cross-Linking Reagents / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000378:metabolism*; D005557:Formaldehyde / Q000737:chemistry; D006801:Humans; D020543:Proteome / Q000378:metabolism*; D053719:Tandem Mass Spectrometry
chemical_list: D003432:Cross-Linking Reagents; D004268:DNA-Binding Proteins; D020543:Proteome; D005557:Formaldehyde