A proteomic characterization of factors enriched at nascent DNA molecules

Andres J Lopez-Contreras; Isabel Ruppen; Maria Nieto-Soler; Matilde Murga; Sara Rodriguez-Acebes; Silvia Remeseiro; Sara Rodrigo-Perez; Ana M Rojas; Juan Mendez; Javier Muñoz; Oscar Fernandez-Capetillo

doi:10.1016/j.celrep.2013.03.009

A proteomic characterization of factors enriched at nascent DNA molecules

Andres J Lopez-Contreras, Isabel Ruppen, Maria Nieto-Soler, Matilde Murga, Sara Rodriguez-Acebes, Silvia Remeseiro, Sara Rodrigo-Perez, Ana M Rojas, Juan Mendez, Javier Muñoz, Oscar Fernandez-Capetillo

72 Citations (Scopus)

Abstract

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.

Original language	English
Journal	Cell Reports
Volume	3
Issue number	4
Pages (from-to)	1105-16
Number of pages	12
ISSN	2211-1247
DOIs	https://doi.org/10.1016/j.celrep.2013.03.009
Publication status	Published - 25 Apr 2013
Externally published	Yes

Keywords

Cell Line
DNA
DNA Replication
Gene Regulatory Networks
HEK293 Cells
Humans
Kruppel-Like Transcription Factors
Mass Spectrometry
Proteomics
Small Ubiquitin-Related Modifier Proteins
Ubiquitination
Williams Syndrome

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10.1016/j.celrep.2013.03.009

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title = "A proteomic characterization of factors enriched at nascent DNA molecules",

abstract = "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.",

keywords = "Cell Line, DNA, DNA Replication, Gene Regulatory Networks, HEK293 Cells, Humans, Kruppel-Like Transcription Factors, Mass Spectrometry, Proteomics, Small Ubiquitin-Related Modifier Proteins, Ubiquitination, Williams Syndrome",

author = "Lopez-Contreras, {Andres J} and Isabel Ruppen and Maria Nieto-Soler and Matilde Murga and Sara Rodriguez-Acebes and Silvia Remeseiro and Sara Rodrigo-Perez and Rojas, {Ana M} and Juan Mendez and Javier Mu{\~n}oz and Oscar Fernandez-Capetillo",

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AU - Lopez-Contreras, Andres J

AU - Ruppen, Isabel

AU - Nieto-Soler, Maria

AU - Murga, Matilde

AU - Rodriguez-Acebes, Sara

AU - Remeseiro, Silvia

AU - Rodrigo-Perez, Sara

AU - Rojas, Ana M

AU - Mendez, Juan

AU - Muñoz, Javier

AU - Fernandez-Capetillo, Oscar

PY - 2013/4/25

Y1 - 2013/4/25

N2 - 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.

AB - 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.

KW - Cell Line

KW - DNA

KW - DNA Replication

KW - Gene Regulatory Networks

KW - HEK293 Cells

KW - Humans

KW - Kruppel-Like Transcription Factors

KW - Mass Spectrometry

KW - Proteomics

KW - Small Ubiquitin-Related Modifier Proteins

KW - Ubiquitination

KW - Williams Syndrome

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DO - 10.1016/j.celrep.2013.03.009

M3 - Journal article

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SN - 2639-1856

VL - 3

SP - 1105

EP - 1116

JO - Cell Reports

JF - Cell Reports

IS - 4

ER -

A proteomic characterization of factors enriched at nascent DNA molecules

Abstract

Keywords

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