Genome-wide Analysis Reveals Extensive Functional Interaction between DNA Replication Initiation and Transcription in the Genome of Trypanosoma brucei

SummaryIdentification of replication initiation sites, termed origins, is a crucial step in understanding genome transmission in any organism. Transcription of the Trypanosoma brucei genome is highly unusual, with each chromosome comprising a few discrete transcription units. To understand how DNA replication occurs in the context of such organization, we have performed genome-wide mapping of the binding sites of the replication initiator ORC1/CDC6 and have identified replication origins, revealing that both localize to the boundaries of the transcription units. A remarkably small number of active origins is seen, whose spacing is greater than in any other eukaryote. We show that replication and transcription in T. brucei have a profound functional overlap, as reducing ORC1/CDC6 levels leads to genome-wide increases in mRNA levels arising from the boundaries of the transcription units. In addition, ORC1/CDC6 loss causes derepression of silent Variant Surface Glycoprotein genes, which are critical for host immune evasion.

Graphical AbstractFigure optionsDownload as PowerPoint slideHighlights
► DNA replication origins are widely dispersed in T. brucei chromosome cores
► Origins and ORC1/CDC6 localize at the boundaries of multigene transcription units
► Localization of T. brucei ORC1/CDC6 is distinct in chromosome cores and subtelomeres
► ORC1/CDC6 acts in transcription regulation, including of some VSGs, in T. brucei