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Sci. Signal., 7 December 2010
Vol. 3, Issue 151, p. rs3
[DOI: 10.1126/scisignal.2001034]

RESEARCH RESOURCES

ATM-Dependent and -Independent Dynamics of the Nuclear Phosphoproteome After DNA Damage

Ariel Bensimon1*{dagger}, Alexander Schmidt2,3*, Yael Ziv1, Ran Elkon4, Shih-Ya Wang5, David J. Chen5, Ruedi Aebersold2,6,7{ddagger}, and Yosef Shiloh1{ddagger}

1 David and Inez Myers Laboratory for Cancer Genetics, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
2 Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zurich, Zurich 8093, Switzerland.
3 Biozentrum, University of Basel, Basel 4056, Switzerland.
4 Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands.
5 Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390–9187, USA.
6 Competence Center for Systems Physiology and Metabolic Diseases, Eidgenössische Technische Hochschule Zurich, Zurich 8093, Switzerland.
7 Faculty of Science, University of Zurich, Zurich 8057, Switzerland.

* These authors contributed equally to this work.

{dagger} Present address: Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zurich, Zurich 8093, Switzerland.

Abstract: The double-strand break (DSB) is a cytotoxic DNA lesion caused by oxygen radicals, ionizing radiation, and radiomimetic chemicals. Cells cope with DNA damage by activating the DNA damage response (DDR), which leads either to damage repair and cellular survival or to programmed cell death. The main transducer of the DSB response is the nuclear protein kinase ataxia telangiectasia mutated (ATM). We applied label-free quantitative mass spectrometry to follow the dynamics of DSB-induced phosphoproteome in nuclear fractions of the human melanoma G361 cells after radiomimetic treatment. We found that these dynamics are complex, including both phosphorylation and dephosphorylation events. In addition to identifying previously unknown ATM-dependent phosphorylation and dephosphorylation events, we found that about 40% of DSB-induced phosphorylations were ATM-independent and that several other kinases are potentially involved. Sustained activity of ATM was required to maintain many ATM-dependent phosphorylations. We identified an ATM-dependent phosphorylation site on ATM itself that played a role in its retention on damaged chromatin. By connecting many of the phosphorylated and dephosphorylated proteins into functional networks, we highlight putative crosstalks between proteins pertaining to several cellular biological processes. Our study expands the DDR phosphorylation landscape and identifies previously unknown ATM-dependent and -independent branches. It reveals insights into the breadth and complexity of the cellular responses involved in the coordination of many DDR pathways, which is in line with the critical importance of genomic stability in maintenance of cellular homeostasis.

{ddagger} To whom correspondence should be addressed. E-mail: yossih{at}post.tau.ac.il (Y.S.); rudolf.aebersold{at}imsb.biol.ethz.ch (R.A.)

Citation: A. Bensimon, A. Schmidt, Y. Ziv, R. Elkon, S.-Y. Wang, D. J. Chen, R. Aebersold, Y. Shiloh, ATM-Dependent and -Independent Dynamics of the Nuclear Phosphoproteome After DNA Damage. Sci. Signal. 3, rs3 (2010).

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