A Proteomic Characterization of Factors Enriched at Nascent DNA Molecules

• Published in: Cell reports (Cambridge) 2013-04, Vol.3 (4), p.1105-1116
• Main Authors: Lopez-Contreras, Andres J., Ruppen, Isabel, Nieto-Soler, Maria, Murga, Matilde, Rodriguez-Acebes, Sara, Remeseiro, Silvia, Rodrigo-Perez, Sara, Rojas, Ana M., Mendez, Juan, Muñoz, Javier, Fernandez-Capetillo, Oscar
• Format: Article
• Language: English
• Subjects: Cell Line; DNA - metabolism; DNA biosynthesis; DNA Replication; Gene Regulatory Networks; HEK293 Cells; Humans; Kruppel-Like Transcription Factors - genetics; Kruppel-Like Transcription Factors - metabolism; Mass Spectrometry; Proteomics; Small Ubiquitin-Related Modifier Proteins - metabolism; Ubiquitination; Williams Syndrome - genetics; Williams Syndrome - metabolism
• ISSN: 2211-1247; 2211-1247
• DOI: 10.1016/j.celrep.2013.03.009

DNA replication is facilitated by multiple factors that concentrate in the vicinity of replication forks. Here, we developed an approach that combines the isolation of proteins on nascent DNA chains with mass spectrometry (iPOND-MS), allowing a comprehensive proteomic characterization of the human replisome and replisome-associated factors. In addition to known replisome components, we provide a broad list of proteins that reside in the vicinity of the replisome, some of which were not previously associated with replication. For instance, our data support a link between DNA replication and the Williams-Beuren syndrome and identify ZNF24 as a replication factor. In addition, we reveal that SUMOylation is widespread for factors that concentrate near replisomes, which contrasts with lower UQylation levels at these sites. This resource provides a panoramic view of the proteins that concentrate in the surroundings of the replisome, which should facilitate future investigations on DNA replication and genome maintenance. [Display omitted] ► A comprehensive resource of replisome and replisome-associated factors ► A putative link between Williams-Beuren syndrome and DNA replication ► SUMO and UQ show opposite concentrations around replisomes ► ZNF24 is a newly identified DNA-replication factor In this study, Fernandez-Capetillo and colleagues combine molecular isolation and analysis techniques to uncover proteins that are either part of or associated with the human DNA replisome. Analysis of the resultant dataset indicates a possible link between DNA replication and Williams-Beuren syndrome and identifies ZNF24 as a DNA replication factor. Moreover, the authors find widespread SUMOylation on proteins that concentrate at the vicinity of replication forks, which contrasts with decreased levels of ubiquitinylation at these sites. The full proteomic dataset is provided for further analyses.