Unexpected diversity in eukaryotic transcription revealed by the retrotransposon hotspot family of Trypanosoma brucei

Abstract

The path from DNA to RNA to protein in eukaryotes is guided by a series of factors linking transcription, mRNA export and translation. Many of these are conserved from yeast to humans. Trypanosomatids, which diverged early in the eukaryotic lineage, exhibit unusual features such as polycistronic transcription and trans-splicing of all messenger RNAs. They possess basal transcription factors, but lack recognisable orthologues of many factors required for transcription elongation and mRNA export. We show that retrotransposon hotspot (RHS) proteins fulfil some of these functions and that their depletion globally impairs nascent RNA synthesis by RNA polymerase II. Three sub-families are part of a coordinated process in which RHS6 is most closely associated with chromatin, RHS4 is part of the Pol II complex and RHS2 connects transcription with the translation machinery. In summary, our results show that the components of eukaryotic transcription are far from being universal, and reveal unsuspected plasticity in the course of evolution.

Regulation of gene expression in trypanosomatids: living with polycistronic transcription

“…[37]), as well as results from modelling [38], indicate that transcription elongation (figure 2(2)) is usually constitutive. New results from the sequencing of 5-ethynyl uridine-labelled RNA should provide much more detail about transcription initiation and elongation [39].…”

“…The ‘retroposon hotspot’ (RHS) proteins of T. brucei [40] fall into six groups, of which all but RHS6 can be cross-linked to mRNA [41]. By ChIP-Seq, RHS2, RHS4 and RHS6 all colocalize with RNA polymerase II, and RHS6 proteins are directly associated with chromatin [39]. RHS4 and RHS6 proteins are also associated with several other proteins implicated in transcription, whereas RHS2 associates with ribosomes and mRNA-binding proteins [39].…”

Genomic Organization and Generation of Genetic Variability in the RHS (Retrotransposon Hot Spot) Protein Multigene Family in Trypanosoma cruzi

“…Finally, we showed the nuclear location of RHS in the replicative forms of T. cruzi. Although evidence for the functions of RHS in T. cruzi has been elusive, we suggest that these proteins could play a role in modulating the chromatin structure at the transcriptional and posttranscriptional levels, as has been suggested in T. brucei [10,11].…”

“…TbRRM, a modulator of the chromatin structure in T. brucei, interacts with RHS transcripts, proteins and histones, suggesting that the RHS family could be involved in chromatin modeling [10]. Recently, it has been reported that several RHS proteins (RHS2, RHS4, and RHS6) may act as factors involved in the transcription elongation and mRNA export in T. brucei [11].…”

“…High throughput analysis of small non-coding RNAs showed that a large number of pseudogene-derived siRNAs originated from pseudogene-pseudogene pairs, in which the major components were RHS pseudogenes [9], and it has been hypothesized that RHS pseudogenes in T. brucei are a source of antisense siRNAs, which regulate the expression of the RHS family. More recent studies proposed that the RHS family could be involved in the chromatin modeling [10], transcription elongation, and mRNA export in T. brucei [11].…”