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1.  3′-End Polishing of the Kinetoplastid Spliced Leader RNA Is Performed by SNIP, a 3′→5′ Exonuclease with a Motley Assortment of Small RNA Substrates†  
Molecular and Cellular Biology  2004;24(23):10390-10396.
In all trypanosomatids, trans splicing of the spliced leader (SL) RNA is a required step in the maturation of all nucleus-derived mRNAs. The SL RNA is transcribed with an oligo-U 3′ extension that is removed prior to trans splicing. Here we report the identification and characterization of a nonexosomal, 3′→5′ exonuclease required for SL RNA 3′-end formation in Trypanosoma brucei. We named this enzyme SNIP (for snRNA incomplete 3′ processing). The central 158-amino-acid domain of SNIP is related to the exonuclease III (ExoIII) domain of the 3′→5′ proofreading ɛ subunit of Escherichia coli DNA polymerase III holoenzyme. SNIP had a preference for oligo(U) 3′ extensions in vitro. RNA interference-mediated knockdown of SNIP resulted in a growth defect and correlated with the accumulation of one- to two- nucleotide 3′ extensions of SL RNA, U2 and U4 snRNAs, a five-nucleotide extension of 5S rRNA, and the destabilization of U3 snoRNA and U2 snRNA. SNIP-green fluorescent protein localized to the nucleoplasm, and substrate SL RNA derived from SNIP knockdown cells showed wild-type cap 4 modification, indicating that SNIP acts on SL RNA after cytosolic trafficking. Since the primary SL RNA transcript was not the accumulating species in SNIP knockdown cells, SL RNA 3′-end formation is a multistep process in which SNIP provides the ultimate 3′-end polishing. We speculate that SNIP is part of an organized nucleoplasmic machinery responsible for processing of SL RNA.
PMCID: PMC529039  PMID: 15542846
2.  SmD1 Is Required for Spliced Leader RNA Biogenesis 
Eukaryotic Cell  2004;3(1):241-244.
The Sm-binding site of the kinetoplastid spliced leader RNA has been implicated in accurate spliced leader RNA maturation and trans-splicing competence. In Trypanosoma brucei, RNA interference-mediated knockdown of SmD1 caused defects in spliced leader RNA maturation, displaying aberrant 3′-end formation, partial formation of cap 4, and overaccumulation in the cytoplasm; U28 pseudouridylation was unaffected.
PMCID: PMC329508  PMID: 14871954

Results 1-2 (2)