Abstract
DNA lesions interfere with DNA and RNA polymerase activity. Cyclobutane pyrimidine dimers and photoproducts generated by ultraviolet irradiation cause stalling of RNA polymerase II, activation of transcription-coupled repair enzymes, and inhibition of RNA synthesis1,2. During the S phase of the cell cycle, collision of replication forks with damaged DNA blocks ongoing DNA replication while also triggering a biochemical signal that suppresses the firing of distant origins of replication3,4. Whether the transcription machinery is affected by the presence of DNA double-strand breaks remains a long-standing question. Here we monitor RNA polymerase I (Pol I) activity in mouse cells exposed to genotoxic stress and show that induction of DNA breaks leads to a transient repression in Pol I transcription. Surprisingly, we find Pol I inhibition is not itself the direct result of DNA damage but is mediated by ATM kinase activity and the repair factor proteins NBS1 (also known as NLRP2) and MDC1. Using live-cell imaging, laser micro-irradiation, and photobleaching technology we demonstrate that DNA lesions interfere with Pol I initiation complex assembly and lead to a premature displacement of elongating holoenzymes from ribosomal DNA. Our data reveal a novel ATM/NBS1/MDC1-dependent pathway that shuts down ribosomal gene transcription in response to chromosome breaks.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 51 print issues and online access
$199.00 per year
only $3.90 per issue
Rent or buy this article
Prices vary by article type
from$1.95
to$39.95
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Mayne, L. V. & Lehmann, A. R. Failure of RNA synthesis to recover after UV irradiation: an early defect in cells from individuals with Cockayne's syndrome and xeroderma pigmentosum. Cancer Res. 42, 1473–1478 (1982)
Hanawalt, P. C. Subpathways of nucleotide excision repair and their regulation. Oncogene 21, 8949–8956 (2002)
Nyberg, K. A., Michelson, R. J., Putnam, C. W. & Weinert, T. A. Toward maintaining the genome: DNA damage and replication checkpoints. Annu. Rev. Genet. 36, 617–656 (2002)
Bartek, J., Lukas, C. & Lukas, J. Checking on DNA damage in S phase. Nature Rev. Mol. Cell Biol. 5, 792–804 (2004)
Dundr, M. et al. A kinetic framework for a mammalian RNA polymerase in vivo. Science 298, 1623–1626 (2002)
Shav-Tal, Y. et al. Dynamic sorting of nuclear components into distinct nucleolar caps during transcriptional inhibition. Mol. Biol. Cell 16, 2395–2413 (2005)
Mone, M. J. et al. Local UV-induced DNA damage in cell nuclei results in local transcription inhibition. EMBO Rep. 2, 1013–1017 (2001)
Kruhlak, M. J. et al. Changes in chromatin structure and mobility in living cells at sites of DNA double-strand breaks. J. Cell Biol. 172, 823–834 (2006)
Michaelidis, T. M. & Grummt, I. Mechanism of inhibition of RNA polymerase I transcription by DNA-dependent protein kinase. Biol. Chem. 383, 1683–1690 (2002)
Mayer, C. & Grummt, I. Cellular stress and nucleolar function. Cell Cycle 4, 1036–1038 (2005)
Kleiman, F. E. et al. BRCA1/BARD1 inhibition of mRNA 3′ processing involves targeted degradation of RNA polymerase II. Genes Dev. 19, 1227–1237 (2005)
Kastan, M. B. & Lim, D. S. The many substrates and functions of ATM. Nature Rev. Mol. Cell Biol. 1, 179–186 (2000)
Shiloh, Y. ATM and related protein kinases: safeguarding genome integrity. Nature Rev. Cancer 3, 155–168 (2003)
Rogakou, E. P., Boon, C., Redon, C. & Bonner, W. M. Megabase chromatin domains involved in DNA double-strand breaks in vivo. J. Cell Biol. 146, 905–916 (1999)
Difilippantonio, S. et al. Role of Nbs1 in the activation of the Atm kinase revealed in humanized mouse models. Nature Cell Biol. 7, 675–685 (2005)
Seither, P., Coy, J. F., Pouska, A. & Grummt, I. Molecular cloning and characterization of the cDNA encoding the largest subunit of mouse RNA polymerase I. Mol. Gen. Genet. 255, 180–186 (1997)
Chen, D. & Huang, S. Nucleolar components involved in ribosome biogenesis cycle between the nucleolus and nucleoplasm in interphase cells. J. Cell Biol. 153, 169–176 (2001)
Mari, P. O. et al. Dynamic assembly of end-joining complexes requires interaction between Ku70/80 and XRCC4. Proc. Natl Acad. Sci. USA 103, 18597–18602 (2006)
Stefanovsky, V., Langlois, F., Gagnon-Kugler, T., Rothblum, L. I. & Moss, T. Growth factor signaling regulates elongation of RNA polymerase I transcription in mammals via UBF Phosphorylation and r-chromatin remodeling. Mol. Cell 21, 629–639 (2006)
Olson, M. O. Sensing cellular stress: another new function for the nucleolus? Sci. STKE 2004, pe10 (2004)
Mayer, C., Bierhoff, H. & Grummt, I. The nucleolus as a stress sensor: JNK2 inactivates the transcription factor TIF-IA and down-regulates rRNA synthesis. Genes Dev. 19, 933–941 (2005)
Banin, S. et al. Enhanced phosphorylation of p53 by ATM in response to DNA damage. Science 281, 1674–1677 (1998)
Acknowledgements
We thank Y. Shiloh for reagents and comments. We are grateful to Z. Lou, J. Chen and C. Deng for cell lines, J. Ionita, K. Zaal and S. Twitty for technical assistance, and I. Grummt for antibodies and protocols. We also thank S. Wincovitch for access to the multi-photon microscope. This research was supported (in part) by the Intramural Research Program of the National Institute of Arthritis and Musculoskeletal and Skin Diseases and the Center for Cancer Research of the National Cancer Institute, National Institutes of Health.
Author Contributions M.K. and R.C. planned the project and did experimental work, data analysis, and wrote the manuscript. E.E.C., M.O., C.M. and R.D.P. did experimental work, data analysis, and provided assistance in writing the manuscript. S.A.G. shared unpublished data and provided advice during experimental design. A.N. and T.M. provided advice and expertise and proof-read the manuscript.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Competing interests
Reprints and permissions information is available at www.nature.com/reprints. The authors declare no competing financial interests.
Supplementary information
Supplementary Information
This file contains Supplementary Figures S1-S10 with Legends, Supplementary Methods 1-2 and Supplementary Table 1. The Supplementary Figures provide data that corroborate the main findings of the text. The Supplementary Methods include a detailed description of Pol I kinetic studies and statistical analysis applied during FRAP analysis. The Supplementary Table 1 provides the kinetic constant values described in the assembly/displacement model. (PDF 6341 kb)
Rights and permissions
About this article
Cite this article
Kruhlak, M., Crouch, E., Orlov, M. et al. The ATM repair pathway inhibits RNA polymerase I transcription in response to chromosome breaks. Nature 447, 730–734 (2007). https://doi.org/10.1038/nature05842
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1038/nature05842
This article is cited by
-
CX-5461 causes nucleolar compaction, alteration of peri- and intranucleolar chromatin arrangement, an increase in both heterochromatin and DNA damage response
Scientific Reports (2022)
-
Speckles and paraspeckles coordinate to regulate HSV-1 genes transcription
Communications Biology (2021)
-
Treacle controls the nucleolar response to rDNA breaks via TOPBP1 recruitment and ATR activation
Nature Communications (2020)
-
RNA: a double-edged sword in genome maintenance
Nature Reviews Genetics (2020)
-
Early neuronal accumulation of DNA double strand breaks in Alzheimer’s disease
Acta Neuropathologica Communications (2019)
Comments
By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.