title: Small interfering RNA-producing loci in the ancient parasitic eukaryote Trypanosoma brucei.
abstract: BACKGROUND
  At the core of the RNA interference (RNAi) pathway in Trypanosoma brucei is a single Argonaute protein, TbAGO1, with an established role in controlling retroposon and repeat transcripts. Recent evidence from higher eukaryotes suggests that a variety of genomic sequences with the potential to produce double-stranded RNA are sources for small interfering RNAs (siRNAs).
  
  
  RESULTS
  To test whether such endogenous siRNAs are present in T. brucei and to probe the individual role of the two Dicer-like enzymes, we affinity purified TbAGO1 from wild-type procyclic trypanosomes, as well as from cells deficient in the cytoplasmic (TbDCL1) or nuclear (TbDCL2) Dicer, and subjected the bound RNAs to Illumina high-throughput sequencing. In wild-type cells the majority of reads originated from two classes of retroposons. We also considerably expanded the repertoire of trypanosome siRNAs to encompass a family of 147-bp satellite-like repeats, many of the regions where RNA polymerase II transcription converges, large inverted repeats and two pseudogenes. Production of these newly described siRNAs is strictly dependent on the nuclear DCL2. Notably, our data indicate that putative centromeric regions, excluding the CIR147 repeats, are not a significant source for endogenous siRNAs.
  
  
  CONCLUSIONS
  Our data suggest that endogenous RNAi targets may be as evolutionarily old as the mechanism itself.
authors.affiliation: Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT 06536, USA.
authors.forename: Christian
authors.initials: C
authors.lastname: Tschudi
authors.forename: Huafang
authors.initials: H
authors.lastname: Shi
authors.forename: Joseph B
authors.initials: JB
authors.lastname: Franklin
authors.forename: Elisabetta
authors.initials: E
authors.lastname: Ullu
mesh_terms: D060565:Argonaute Proteins / Q000235:genetics / Q000378:metabolism; D056426:Genetic Loci; D055029:Inverted Repeat Sequences; D015800:Protozoan Proteins / Q000235:genetics / Q000378:metabolism; D034622:RNA Interference; D034741:RNA, Small Interfering / Q000378:metabolism*; D018626:Retroelements; D043244:Ribonuclease III / Q000235:genetics / Q000378:metabolism; D014346:Trypanosoma brucei brucei / Q000235:genetics*
chemical_list: D060565:Argonaute Proteins; D015800:Protozoan Proteins; D034741:RNA, Small Interfering; D018626:Retroelements; D043244:Ribonuclease III