Description

This track displays the predicted hydroxyl radical cleavage intensity on naked DNA for each nucleotide in the ENCODE regions. Because the hydroxyl radical cleavage intensity is proportional to the solvent accessible surface area of the deoxyribose hydrogen atoms (Balasubramanian et al., 1998), this track represents a structural profile of the DNA in the ENCODE regions.

Please visit the ORChID web site maintained by the Tullius group for access to experimental hydroxyl radical cleavage data, and to a server which can be used to predict the cleavage pattern for any input sequence.

Display Conventions and Configuration

This track may be configured in a variety of ways to highlight different aspects of the displayed data. The graphical configuration options are shown at the top of the track description page. For more information, click the Graph configuration help link.

Methods

Hydroxyl radical cleavage intensity predictions were performed using an in-house sliding tetramer window (STW) algorithm. This algorithm draws data from the ·OH Radical Cleavage Intensity Database (ORChID), which contains more than 150 experimentally determined cleavage patterns. These predictions are fairly accurate, with a Pearson coefficient of 0.88 between the predicted and experimentally determined cleavage intensities. For more details on the hydroxyl radical cleavage method, see below for reference (Greenbaum et al. 2007).

Verification

The STW algorithm has been cross-validated by removing each test sequence from the training set and performing a prediction. The mean correlation coefficient (between predicted and experimental cleavage patterns) from this study was 0.88.

Credits

These data were generated through the combined effort of Bo Pang at MIT, Jason Greenbaum at The La Jolla Institute for Allergy and Immunology and Steve Parker, Eric Bishop and Tom Tullius of Boston University.

References

Balasubramanian B, Pogozelski WK, and Tullius TD DNA strand breaking by the hydroxyl radical is governed by the accessible surface areas of the hydrogen atoms of the DNA backbone. Proc. Natl. Acad. Sci. USA 95(17), 9738-9743 (1998).

Price MA, and Tullius TD Using the Hydroxyl Radical to Probe DNA Structure. Meth. Enzymol. 212, 194-219 (1992).

Tullius TD. Probing DNA Structure with Hydroxyl Radicals. In Current Protocols in Nucleic Acid Chemistry, (eds. Beaucage, S.L., Bergstrom, D.E., Glick, G.D. and Jones, R.A.) (Wiley, 2001), pp. 6.7.1-6.7.8.

Greenbaum JA, Pang B, and Tullius TD Construction of a genome-scale structural map at single-nucleotide resolution. Genome Res. 17(6), 947-953 (2007).