Genomic instability and changes in gene expression are conserved hallmarks of eukaryotic aging. Recent data suggest that DNA damage may promote wide-ranging, age-related changes in chromatin that can result in the abnormal silencing or expression of genes and may, thereby, explain the deterioration of cell function associated with aging, degenerative diseases and cancer. We have previously shown that DNA damage can cause the redistribution of the histone deacetylase SIRT1 on chromatin, resulting in its recruitment to DNA breaks and concomitant deregulation of otherwise SIRT1 regulated genomic loci. These data demonstrated (1) the direct involvement of SIRT1 in DNA break repair and (2) a molecular mechanism that may link DNA damage to large-scale epigenetic deregulation, even of undamaged loci. However, SIRT1-regulated genomic loci account for only a fraction of age-associated transcriptional deregulation. To test if DNA damage can indeed result in a genome-wide remodeling of chromatin, we used an RNA interference based screening approach to identify additional DNA-repair linked chromatin modifiers from a comprehensive list of NCBI annotated chromatin remodelers. Our preliminary results suggest that a large number of chromatin-modifying enzymes are involved in DNA break repair. Interestingly, many of the recruited proteins are transcriptional repressors and associated with the formation of silent chromatin. While it has been postulated that chromatin surrounding DNA breaks is made accessible for efficient repair factor access, our data suggest large-scale chromatin compaction at sites of DNA damage, possibly a mechanism to help confine the site of damage and to aid the repair process. In cases of continuous damage, the resulting chronic changes in chromatin structure, both at DSBs and at distant sites deregulated due to chromatin-modifier redistribution, may have a detrimental effect on cell function. We are currently investigating our hypothesis of DNA break-associated chromatin compaction using a range of molecular biology and cell-based imaging techniques. Initial fluorescence-based in situ hybridization analyses support our model and provide the basis for an in depth analysis of the role of DNA-repair related chromatin modifiers during this process. We have further established several independent cell-based systems to induce defined DNA breaks in mammalian cells, thereby enabling us to investigate direct association of said chromatin modifiers with DNA breaks. Future work will determine the extend to which these chromatin modifiers are directly linked with DNA break repair and how DNA damage affects their distribution across the genome. Consequently, we will investigate how the involvement of repressor complexes in DNA repair will affect gene silencing across the genome, focusing on known, critical functions of these repressors. Taken together, this project is expected to shed light on the molecular basis for major age- and DNA damage related epigenomic disturbance, which is thought to be directly associated with aging and disease.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Investigator-Initiated Intramural Research Projects (ZIA)
Project #
1ZIABC011282-01
Application #
8175352
Study Section
Project Start
Project End
Budget Start
Budget End
Support Year
1
Fiscal Year
2010
Total Cost
$334,566
Indirect Cost
Name
National Cancer Institute Division of Basic Sciences
Department
Type
DUNS #
City
State
Country
Zip Code
Shi, Lei; Oberdoerffer, Philipp (2012) Chromatin dynamics in DNA double-strand break repair. Biochim Biophys Acta 1819:811-9