Book of Abstracts: Albany 2005
The Genome in Three Dimensions: Structural Maps of Genomic DNA at Single-Nucleotide Resolution
As part of the ENCODE Program that is sponsored by the National Human Genome Research Institute (http://www.genome.gov/ENCODE), my laboratory is developing a combined experimental and computational approach for extracting structural information that is embodied in genomic DNA. The method that we use to produce maps of genomic DNA structure makes use of the hydroxyl radical, a high-resolution chemical probe of DNA structure. Previous work in my lab used deuterium kinetic isotope effect experiments to show that the hydroxyl radical cleavage pattern represents an experimental map of the solvent-accessible surface area of a DNA duplex.
We have now implemented the hydroxyl radical cleavage experiment on an automated fluorescence-based sequencer, and we are engaged in constructing a library of hydroxyl radical cleavage patterns obtained from a wide variety of DNA sequences. The hydroxyl radical cleavage pattern database will be used to construct a model for how the structure of DNA depends on the sequence of nucleotides. This model will be used to predict the hydroxyl radical cleavage patterns of regions in genomic DNA. We have developed an initial prediction algorithm, based on a trinucleotide model for the sequence-dependence of DNA structure, which is moderately successful in predicting the hydroxyl radical cleavage pattern of a DNA sequence. We expect eventually to be able to compute the hydroxyl radical cleavage pattern of any DNA sequence to high accuracy.
Computational tools, including hidden Markov models, are being trained on the database of hydroxyl radical cleavage patterns in order to recognize structural patterns in genomic DNA sequences. Currently we are focusing our attention on developing a ?consensus? hydroxyl cleavage pattern for strong nucleosome-forming sequences, in order to map regions of the genome involved in chromatin architecture.
This research was supported by the ENCODE Project of the National Human Genome Research Institute of the National Institutes of Health (R01 HG003541).
Department of Chemistry