The effects of exposure to low doses of ionizing radiation on humans results largely from changes in gene expression mediated by the activation of sequence-specific DNA binding proteins (transcription factors) and perhaps changes to other chromosomal proteins. To develop a molecular understanding of the consequences of exposures to low doses of ionizing radiation, it will be necessary to understanding where radiation-activated transcription factors bind in whole genomes and how radiation induces changes in factor binding and chromosome structure. We have developed a method, SACO¹ (Serial Analysis of Chromatin Occupancy), for profiling the functional chromatin binding sites of proteins in cells across whole genomes. SACO combines chromatin immunoprecipitation with Genome Signature Tags, a technique developed at BNL that associates 20/21 bp DNA sequences (tags) with molecular events, to identify and quantify functional protein binding sites in the chromatin of whole genomes. For example, p53 is a transcription factor that is activated in response to DNA double-strand breaks. p53 regulates ~1500 genes, directly or indirectly, but only a few of its response elements have been identified and characterized. Furthermore, p53-mediated activation or repression of transcription depends interactions with other factors including histone acetyltransferases (HATs) and deacetylases (HDACs). Radiation-induced epigenetic changes (e.g. changes in DNA methylation) and changes in the state of histone modifications also affect cellular responses. We will describe improvements to the SACO technology and show how it may be used to address issues relevant to cellular responses to low dose radiation.

¹Impey, S., S.R. McCorkle, H. Cha-Molstad, J.M. Dwyer, G.S. Yochum, J.M. Boss, S.McWeeney, J.J. Dunn, G. Mandel, and R.H. Goodman. 2004.

Defining the CREB regulon; a genome-wide analysis of transcription factor regulatory regions. Cell 119:1041-54.