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

Summary

Identification 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.

Abstract

Graphical Abstract

Highlights

► 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

Abstract

Designation of DNA replication origins, the sites where DNA synthesis initiates, remains poorly understood in most eukaryotic genomes, including the relationship of this reaction with transcription. McCulloch, Bell, and colleagues now map origins and the binding sites of a key replication initiator, termed ORC1/CDC6, in the African trypanosome genome, which is highly unusual among eukaryotes in that each chromosome comprises a few discrete multigene transcription units. These data, coupled with global transcript mapping, reveal extensive functional overlap between DNA replication and transcription.