Description

This track displays DNaseI sensitivity/hypersensitivity mapped over ENCODE regions in lymphoblastoid cells (ENCODE common cell line GM06990) using the DNase-array methodology described in Sabo et al. (2006). DNaseI hypersensitivity signifies chromatin accessibility following binding of trans-acting factors in place of a canonical nucleosome, and is a universal feature of active cis-regulatory sequences in vivo. Peaks in DNaseI sensitivity signal measured using DNase/Array represent DNaseI hypersensitive sites.

Methods

DNase-array comprises the following steps: (1) treatment of nuclear chromatin with DNaseI; (2) isolation of short (avg. length ~450 bp) DNA segments released by two DNaseI “hits” occurring in close proximity on the same nuclear chromatin template; (3) differential labeling of fragments and a control (DNaseI-treated naked DNA); (4) hybridization to a tiling DNA microarray (Nimblegen ENCODE array), without amplification. Signal peaks correspond to DNaseI hypersensitive sites.

Validation

The data have been extensively validated by conventional DNaseI hypersensitivity assays (indirect end-label + Southern blotting method). The data have an overall sensitivity of 91.7%, and specificity of >99.5% for DNaseI hypersensitive sites. Note that the tiling array covers only non-repetitive regions.

Credits

These data were generated by the UW ENCODE group.

References

Sabo PJ, Kuehn MS, Thurman R, Johnson BE, Johnson EM, Cao H, Yu M, Rosenzweig E, Goldy J, Haydock A, Weaver M, Shafer A, Lee K, Neri F, Humbert R, Singer MA, Richmond TA, Dorschner MO, McArthur M, Hawrylycz M, Green RD, Navas PA, Noble WS, Stamatoyannopoulos JA. Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nature Methods 3:511-18 (2006)