DNaseI has long been used to map general chromatin accessibility and the DNaseI "hyperaccessibility" or "hypersensitivity" that is a universal feature of active cis-regulatory sequences. The Regulome tracks annotate continuous DNaseI sensitivity measurements and DNaseI hypersensitive sites (HSs) over ENCODE regions. The data were produced using quantitative chromatin profiling (QCP) (Dorschner et al., 2004).
In QCP, ~250 bp PCR amplicons are tiled end-to-end across study regions. High-throughput real-time PCR is used to quantify DNaseI at each amplicon by measuring copies remaining in DNaseI-treated vs. untreated samples. The results are then analyzed with a statistical algorithm to compute the moving baseline of mean DNaseI sensitivity and to identify outliers that correspond with DNaseI hypersensitive sites.
DNaseI-treated and untreated chromatin samples from the following cell lines/phenotypes were studied:
This track shows the moving baseline of mean DNaseI sensitivity, computed over each amplicon using a locally-weighted least squares (LOWESS)-based algorithm described in Dorschner et al. The displayed values are calculated as 1/(copies in DNaseI treated / copies in DNaseI untreated). Thus, increasing values represent increasing sensitivity.
QCP was performed as described in Dorschner et al. An amplicon tiling path has been computed over all regions and is available through UniSTS. Chromatin preparation and DNaseI treatment were performed on the aforementioned cell types as described in Dorschner et al.
QCP measurements were performed in replicate (6X) on pooled biological replicate samples. Validation of the results was carried out by conventional DNaseI hypersensitivity assays using end-labeling/Southern blotting. A total of 1.17 Mb have been evaluated by conventional assay.
The specificity was defined as the number of true negative evaluable QCP amplicons divided by the sum of the true negatives plus false positives. Using 246.2 Kb from ENm002, the specificity was calculated to be 0.997. The sensitivity of the QCP assay was calculated as the true positives divided by the sum of the true positives plus false negatives. The sensitivity measured for ENm002 was 0.9487.
Data generation, analysis, and validation were performed jointly by groups at Regulome Corporation and the University of Washington (UW) in Seattle.
Regulome Corp.: Michael O. Dorschner, Richard Humbert, Peter J. Sabo, Anthony Shafer, Jeff Goldy, Molly Weaver, Kristin Lee, Fidencio Neri, Brendan Henry, Mike Hawrylycz, Paul Tittel, Jim Wallace, Josh Mack, Janelle Kawamoto, John A. Stamatoyannopoulos.
UW Medical Genetics: Patrick Navas, Man Yu, Hua Cao, Brent Johnson, Ericka Johnson, George Stamatoyannopoulos.
UW Genome Sciences: Scott Kuehn, Robert Thurman, William S. Noble.
Dorschner, M.O., Hawrylycz, M., Humbert, R., Wallace, J.C., Shafer, A., Kawamoto, J., Mack, J., Hall, R., Goldy, J., Sabo, P.J. et al. High-throughput localization of functional elements by quantitative chromatin profiling. Nat Methods 1(3), 219-25 (2004).