  Transcription factors (TF) play an essential role in the cell as locus- and
condition-specific recruiters of transcriptional machinery or
chromatin-modifying complexes. However, predicting the in vivo profile of TF
occupancy along the genome, which depends on complex interactions with other
chromatin-associated proteins, from the DNA sequence remains a major challenge.
Through careful reanalysis of ChIP-chip data for 138 TFs obtained in rich
media, we were able to classify the upstream promoter regions of S. cerevisiae
into 15 distinct chromatin types. One of these encompasses 5% of all promoters
and is unique in that it is highly occupied by (essentially) all TFs expressed
in rich media. These "hotspots" of TF occupancy are strongly
nucleosome-depleted and preferentially targeted by chromatin-remodeling
complexes and the origin-of-replication complex (ORC). They are also the only
chromatin type enriched for predicted Rap1p and Pdr1p binding sites, which we
found to work cooperatively with AAA/TTT motifs, known to affect local DNA
structure, to reduce nucleosome occupancy. Taken together, our results reveal
and characterize a new type of local chromatin structure in yeast.
