Whole Genome Analysis of Functional Protein Binding Sites and DNA Methylation: Potential Application to p53 and Low Dose Ionizing Radiation

Carl W. Anderson
cwa@bnl.gov
Biology Department, Brookhaven National Laboratory

Why this Project?

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.

Project Goals

To develop a molecular understanding of the consequences of exposures to low doses of ionizing radiation:

1. By characterizing radiation-activated transcription factors
2. By determining where these factors bind in whole genomes
3. By studying how radiation induces changes in binding of transcriptions factors and chromosome structure

Experimental Approach

A method for profiling the functional chromatin binding sites of proteins in cells across whole genomes has been developed. It is called SACO (Serial Analysis of Chromatin Occupancy). SACO combines chromatin immunoprecipitation with Genome Signature Tags, a technique developed at Brookhaven National Lab 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.

Expected Outcomes

Improvements to the SACO technology will make it possible to use this technique to address issues relevant to cellular responses to low dose radiation.