Genome-wide PRO-seq Analysis of Transcription in Leishmania major

Using precision run-on sequence analysis, we performed a genome-wide mapping and density analysis of RNA polymerases in isolated nuclei of the protozoan parasite Leishmania major. We map transcription initiation sites within the chromosomes and correlate them with known sites of chromatin modifications. We confirm continuous, polycistronic RNA synthesis in all RNA polymerase II-dependent gene arrays and find comparable RNA polymerase occupancies for all transcription units and chromosomes, thus excluding gene-specific transcription regulation. Lastly, we find evidence for transcriptional pausing in RNA polymerase I- and III-dependent genes, but also at the transcription start sites in diverging strand switch regions and 5'-telomeric transcription starts, hinting at a possible mechanism of gene expression control.