Identification of the Elusive Core Promoters Driving Polycistronic Transcription by RNA Polymerase II in Trypanosomes

Protein-coding genes in the trypanosome genome are organized in polycistronic transcription units (PTUs). How RNA Polymerase II (Pol II) initiates PTU transcription has not been resolved and the current model favors initiation driven by chromatin epigenetic marks, rather than core-promoters. Here, we identify sequence-specific promoters by functional characterization of Pol II accumulation peaks identified by ChIP-Seq. Sequences located between oppositely orientated PTUs contained two independent and distinct promoters, each driving unidirectional transcription. Detailed analysis identified a 75-bp promoter necessary and sufficient to drive full reporter expression and containing functional motifs. Analysis of further promoters suggested activity and initiation is regulated and transcription-pattern is either focused or dispersed. In contrast to previous model of unregulated and promoter-independent transcription initiation, sequence-specific promoters determine the initiation of Pol II transcription of protein-coding genes in trypanosomes. These findings resolve the discrepancy between trypanosomes and other eukaryotes in how Pol II initiates protein-coding gene transcription and provide a new framework to events underlying eukaryotic transcription evolution.