ENCODE soon provides DNase I hypersensitivity data for the whole genome in a multitude of different tissues. DNase I hypersensitivity marks genomic positions that are exposed and can hence be used to pinpoint active promoters or enhancers in the studied tissue. DNase I resistant regions, in contrast, mark genomic areas that are protected, e.g. because a transcription factor (TF) is bound. Since the data provides a base-pair resolution, it is possible to "zoom" in on the protected areas (== transcription factor binding sites) of the otherwise exposed regions (== enhancers). One can hence identify the shadow-prints on the genome left by the regulatory TFs in a given tissue. To identify which TFs are casting the shadows one could use ChIP-seq (rough binding regions) or Protein Binding Arrays (binding motif).
The question is: has the in-silico prediction of enhancers, binding sites or partners still merit or will we be soon able to look-up the binding events of TFs in the different tissues?