This set of tracks displays the predicted hydroxyl radical cleavage
intensity on naked DNA for each nucleotide in the genome.
Because the hydroxyl radical cleavage intensity is proportional to the solvent
accessible surface area of the deoxyribose hydrogen atoms
(Balasubramanian et al., 1998), these tracks represent a structural
profile of the DNA in the genome.
For additional details, please visit the Tullius lab website.
Display Conventions and Configuration
These tracks 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,
configuration help link.
In the full and pack display modes, positive intensity values are shown in
red and negative intensity values are shown in tan.
In the squish and dense display modes, intensity is represented in grayscale (the darker
the shading, the higher the intensity).
To show only selected subtracks, uncheck the boxes next to the tracks that
you wish to hide.
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. The ORChID Version 1 predictions are performed on the + strand of the DNA sequence.
These predictions are fairly accurate, with a Pearson
coefficient of 0.88 between the predicted and experimentally
determined cleavage intensities.
For ORChID Version 2, two predictions are performed, one on the + strand and the other on
the - strand, and then the average of the predicted cleavage intensity for nucleotides in close proximity across the minor groove is presented.
For more details on the hydroxyl
radical cleavage method, see below for reference (Greenbaum et al. 2007).
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.
These data were generated at Boston University
These data are the result of the combined efforts of Bo Pang
(now at MIT),
Jason Greenbaum (now at The La Jolla Institute for Allergy and Immunology),
Steve Parker and Elliott Margulies
at The National Human Genome Research Institute,
National Institutes of Health,
and Eric Bishop and Tom Tullius at Boston University.
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. 1998 Aug 18;95(17):9738-43.
Price MA, and Tullius TD.
Using the Hydroxyl Radical to Probe DNA Structure.
Meth. Enzymol. 1992;212:194-219.
Probing DNA Structure with Hydroxyl Radicals.
Curr Protoc Nucleic Acid Chem. 2002 Feb;Chapter 6:Unit 6.7. Review.
Greenbaum JA, Pang B, and Tullius TD.
Construction of a genome-scale structural map at single-nucleotide resolution.
Genome Res. 2007 Jun;17(6):947-53.
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