Discussion

Genome-wide transcription studies are revealing ever more �dispersed promoters� that unlike �focused promoters�, lack well-conserved sequence motifs and tight regulation. Dispersed promoters are nevertheless marked by well-defined chromatin structures, suggesting that specific sequence elements must exist in these unregulated promoters. Here, we have analyzed regions of transcription initiation in the eukaryotic parasite Trypanosoma brucei, in which RNA polymerase II transcription initiation lacks regulation and occurs over broad (~10kb) regions without distinct promoter motifs. Using a combination of site-specific and genome-wide assays, we identified GT-rich promoters that can drive unidirectional transcription and promote the targeted deposition of the histone variant H2A.Z. In addition, mapping nucleosome occupancy at high resolution, we find that nucleosome positioning may affect RNA maturation, pointing to a previously unrecognized layer of gene regulation in trypanosomes.  Our findings show that even highly dispersed, unregulated promoters contain specific DNA elements able to induce transcription and changes in chromatin structure.