Procyclic Trypanosoma brucei rhodesiense transcriptome

The genome of Trypanosoma brucei, the causative agent of African trypanosomiasis, was published five years ago, yet identification of all genes and their transcripts remains to be accomplished. Annotation is challenged by the organization of genes transcribed by RNA polymerase II (Pol II) into long unidirectional gene clusters with no knowledge how transcription is initiated. Here we report a single-nucleotide resolution genomic map of the T. brucei transcriptome, confirming and correcting many of the annotated features, adding 1,114 new genes, including 103 non-coding transcripts, and revealing an extensive heterogeneity of 5' and 3'ends. High-throughput RNA sequencing (RNA-Seq) was sensitive enough to detect transcripts at putative Pol II transcription initiation sites. Our results, as well as recent data from the literature, indicate that transcription initiation is not solely restricted to regions at the beginning of gene clusters, but may occur at internal sites. We also provide evidence that transcription at all putative initiation sites in T. brucei is bidirectional, a recently recognized fundamental property of eukaryotic promoters.