Thus, it remains possible that it is the location of the sites, rather than their particular binding preferences, that determines the activity of an enhancer.
In other words, the binding preferences that are revealed from the in vitro DNA curtain measurements would be otherwise obscured in an in vivo scenario due to the presence of other proteins.
Taken together, our TAP, ERAP, and CTL-recognition data suggest that proteasomal digestion preferences often produce fragments that accommodate TAP binding preferences, that most epitope precursors are transported well into the ER, that a fraction is trimmed to shorter epitope precursors and optimal epitopes and that patients can recognize a variety of epitope-peptide forms.
Alternatively, since Otx2 has a nearly identical binding preference to that of Crx, some of these sites may actually be bound by Otx2 in vivo.
Finally, we asked whether KLF4 binding preferences to both methylated and unmethylated motifs that we identified in vitro reflect sequences preferred in vivo.
Functional predictions based on zinc finger transcription factor (ZNF) DNA binding preferences also suggested that many common substitutions could potentially alter binding specificity.
Since CBMs have different binding preferences [ 13, 14, 39, 40], we conclude that this CBM2a is more specific for cellulose sites accessible within the less crystalline substrate IL-MCC [ 37] than for sites within MCC.
The first class of methods (also termed enumerating or dictionary-based methods; e.g., [34], [35], [36], [37]) is better suited for representation of the binding preferences of those transcription factors that have a restricted set of DNA targets.
Furthermore, the sequence-based results were obtained using prediction models that were trained on binding data for MHC types whose peptide binding preferences are similar enough that even a prediction model trained only on data for the single closest allotype attains relatively high accuracy [29], [30].
