Petra De Graaf

Dr. Petra De Graaf

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Research Focus & Metrics

Academic Career Length

32Years (1995-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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1 July 2004 in Molecular and Cellular Biology
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DDDavide Danovi
Davide Danovi
EMErik Meulmeester
Erik Meulmeester
DPDiego Pasini
Diego Pasini
DMDomenico Migliorini
Domenico Migliorini
MCMaria Capra
Maria Capra
JMJean-Christophe Marine
Jean-Christophe Marine
Human tumors are believed to harbor a disabled p53 tumor suppressor pathway, either through direct mutation of the p53 gene or through aberrant expression of proteins acting in the p53 pathway, such as p14ARF or Mdm2. A role for Mdmx (or Mdm4) as a key negative regulator of p53 function in vivo has been established. However, a direct contribution of Mdmx to tumor formation remains to be demonstrated. Here we show that retrovirus-mediated Mdmx overexpression allows primary mouse embryonic fibroblast immortalization and leads to neoplastic transformation in combination with HRasV12. Furthermore, the human Mdmx ortholog, Hdmx, was found to be overexpressed in a significant percentage of various human tumors and amplified in 5% of primary breast tumors, all of which retained wild-type p53. Hdmx was also amplified and highly expressed in MCF-7, a breast cancer cell line harboring wild-type p53, and interfering RNA-mediated reduction of Hdmx markedly inhibited the growth potential of these cells in a p53-dependent manner. Together, these results make Hdmx a new putative drug target for cancer therapy.

23 March 2005 in Proceedings of the National Academy of Sciences
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YPYaron Pereg
Yaron Pereg
DSDganit Shkedy
Dganit Shkedy
PGPetra De Graaf
Petra De Graaf
EMErik Meulmeester
Erik Meulmeester
MEMarina Edelson-Averbukh
Marina Edelson-Averbukh
YSYosef Shiloh
Yosef Shiloh
Maintenance of genomic stability depends on the DNA damage response, an extensive signaling network that is activated by DNA lesions such as double-strand breaks (DSBs). The primary activator of the mammalian DSB response is the nuclear protein kinase ataxia–telangiectasia, mutated (ATM), which phosphorylates key players in various arms of this network. The activation and stabilization of the p53 protein play a major role in the DNA damage response and are mediated by ATM-dependent posttranslational modifications of p53 and Mdm2, a ubiquitin ligase of p53. p53's response to DNA damage also depends on Mdm2-dependent proteolysis of Mdmx, a homologue of Mdm2 that represses p53's transactivation function. Here we show that efficient damage-induced degradation of human Hdmx depends on functional ATM and at least three sites on the Hdmx that are phosphorylated in response to DSBs. One of these sites, S403, is a direct ATM target. Accordingly, each of these sites is important for Hdm2-mediated ubiquitination of Hdmx after DSB induction. These results demonstrate a sophisticated mechanism whereby ATM fine-tunes the optimal activation of p53 by simultaneously modifying each player in the process.

1 October 2003 in Journal of Biological Chemistry
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PGPetra De Graaf
Petra De Graaf
NLNatalie A. Little
Natalie A. Little
YRYolande F. M. Ramos
Yolande F. M. Ramos
EMErik Meulmeester
Erik Meulmeester
SLStef J. F. Letteboer
Stef J. F. Letteboer
AJAart G. Jochemsen
Aart G. Jochemsen
The stability of the p53 tumor suppressor protein is critically regulated by the Hdm2 and Hdmx proteins. Hdm2 protein levels are auto-regulated by the self-ubiquitination activity of Hdm2 and on the transcriptional level by p53-activated transcription of the hdm2 gene. Little is known about the regulation of Hdmx expression levels, apart from the observation that the Mdmx protein can be cleaved by caspase-3 in a p53-inducible manner. In the functional analysis of two mutant Hdmx proteins, products of two alternatively spliced mRNAs, it was found that Hdmx proteins are targets for ubiquitination by Mdm2. The stability of the Hdmx protein is partly dependent on the presence of its internal acidic domain. Mdm2 appears only to require an intact RING domain to be able to ubiquitinate Hdmx and target it for proteasomal degradation. These findings highlight the intricate functional relationships between p53, Mdm2, and Hdmx.

1 April 2004 in Molecular Biology of the Cell
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PGPetra De Graaf
Petra De Graaf
WZWilbert Zwart
Wilbert Zwart
RDRemco A.J. van Dijken
Remco A.J. van Dijken
MDMagdalena Deneka
Magdalena Deneka
TSThomas K.F. Schulz
Thomas K.F. Schulz
PHPaul M.P. van Bergen En Henegouwen
Paul M.P. van Bergen En Henegouwen
Phosphatidylinositol 4-kinaseβ (PI4Kβ) plays an essential role in maintaining the structural integrity of the Golgi complex. In a search for PI4Kβ-interacting proteins, we found that PI4Kβ specifically interacts with the GTP-bound form of the small GTPase rab11. The PI4Kβ-rab11 interaction is of functional significance because inhibition of rab11 binding to PI4Kβ abolished the localization of rab11 to the Golgi complex and significantly inhibited transport of vesicular stomatitis virus G protein from the Golgi complex to the plasma membrane. We propose that a novel function of PI4Kβ is to act as a docking protein for rab11 in the Golgi complex, which is important for biosynthetic membrane transport from the Golgi complex to the plasma membrane.

1 April 2013 in Cell Reports
Verified
Journal Article
Open access
NONikolay S. Outchkourov
Nikolay S. Outchkourov
JMJose M. Muiño
Jose M. Muiño
KKKerstin Kaufmann
Kerstin Kaufmann
WIWilfred van IJcken
Wilfred van IJcken
MKMarian J. Groot Koerkamp
Marian J. Groot Koerkamp
HTH.T. Marc Timmers
H.T. Marc Timmers
The functional organization of eukaryotic genomes correlates with specific patterns of histone methylations. Regulatory regions in genomes such as enhancers and promoters differ in their extent of methylation of histone H3 at lysine-4 (H3K4), but it is largely unknown how the different methylation states are specified and controlled. Here, we show that the Kdm5c/Jarid1c/SMCX member of the Kdm5 family of H3K4 demethylases can be recruited to both enhancer and promoter elements in mouse embryonic stem cells and in neuronal progenitor cells. Knockdown of Kdm5c deregulates transcription via local increases in H3K4me3. Our data indicate that by restricting H3K4me3 modification at core promoters, Kdm5c dampens transcription, but at enhancers Kdm5c stimulates their activity. Remarkably, an impaired enhancer function activates the intrinsic promoter activity of Kdm5c-bound distal elements. Our results demonstrate that the Kdm5c demethylase plays a crucial and dynamic role in the functional discrimination between enhancers and core promoters.

1 July 2010 in Molecular and Cellular Biology
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Journal Article
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KFKlaus Fortschegger
Klaus Fortschegger
PGPetra De Graaf
Petra De Graaf
NONikolay S. Outchkourov
Nikolay S. Outchkourov
FSFrederik M. A. van Schaik
Frederik M. A. van Schaik
HTH. T. Marc Timmers
H. T. Marc Timmers
RSRamin Shiekhattar
Ramin Shiekhattar
Mutations in PHF8 are associated with X-linked mental retardation and cleft lip/cleft palate. PHF8 contains a plant homeodomain (PHD) in its N terminus and is a member of a family of JmjC domain-containing proteins. While PHDs can act as methyl lysine recognition motifs, JmjC domains can catalyze lysine demethylation. Here, we show that PHF8 is a histone demethylase that removes repressive histone H3 dimethyl lysine 9 marks. Our biochemical analysis revealed specific association of the PHF8 PHD with histone H3 trimethylated at lysine 4 (H3K4me3). Chromatin immunoprecipitation followed by high-throughput sequencing indicated that PHF8 is enriched at the transcription start sites of many active or poised genes, mirroring the presence of RNA polymerase II (RNAPII) and of H3K4me3-bearing nucleosomes. We show that PHF8 can act as a transcriptional coactivator and that its activation function largely depends on binding of the PHD to H3K4me3. Furthermore, we present evidence for direct interaction of PHF8 with the C-terminal domain of RNAPII. Importantly, a PHF8 disease mutant was defective in demethylation and in coactivation. This is the first demonstration of a chromatin-modifying enzyme that is globally recruited to promoters through its association with H3K4me3 and RNAPII.