Basal splicing factors regulate the stability of mature mRNAs in trypanosomes

J Biol Chem. 2013 Feb 15;288(7):4991-5006. doi: 10.1074/jbc.M112.416578. Epub 2013 Jan 2.


Gene expression in trypanosomes is mainly regulated post-transcriptionally. Genes are transcribed as polycistronic mRNAs that are dissected by the concerted action of trans-splicing and polyadenylation. In trans-splicing, a common exon, the spliced leader, is added to all mRNAs from a small RNA. In this study, we examined by microarray analysis the transcriptome following RNAi silencing of the basal splicing factors U2AF65, SF1, and U2AF35. The transcriptome data revealed correlations between the affected genes and their splicing and polyadenylation signaling properties, suggesting that differential binding of these factors to pre-mRNA regulates trans-splicing and hence expression of specific genes. Surprisingly, all these factors were shown to affect not only splicing but also mRNA stability. Affinity purification of SF1 and U2AF35 complexes supported their role in mRNA stability. U2AF35 but not SF1 was shown to bind to ribosomes. To examine the role of splicing factors in mRNA stability, mutations were introduced into the polypyrimidine tract located in the 3' UTR of a mini-gene, and the results demonstrate that U2AF65 binds to such a site and controls the mRNA stability. We propose that transcripts carrying splicing signals in their 3' UTR bind the splicing factors and control their stability.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • DNA-Binding Proteins / chemistry
  • DNA-Binding Proteins / physiology*
  • Gene Expression
  • Leishmania / metabolism
  • Models, Genetic
  • Nuclear Proteins / chemistry
  • Nuclear Proteins / physiology*
  • Oligonucleotide Array Sequence Analysis
  • Poly A / metabolism
  • RNA Interference
  • RNA Splicing Factors
  • RNA Splicing*
  • RNA, Messenger / metabolism
  • RNA-Binding Proteins / chemistry*
  • Ribonucleoproteins / chemistry
  • Ribonucleoproteins / physiology*
  • Splicing Factor U2AF
  • Tetrazolium Salts / pharmacology
  • Thiazoles / pharmacology
  • Trans-Splicing*
  • Transcription Factors / chemistry
  • Transcription Factors / physiology*
  • Transcription, Genetic
  • Trypanosoma brucei brucei / metabolism


  • DNA-Binding Proteins
  • Nuclear Proteins
  • RNA Splicing Factors
  • RNA, Messenger
  • RNA-Binding Proteins
  • Ribonucleoproteins
  • SF1 protein, human
  • Splicing Factor U2AF
  • Tetrazolium Salts
  • Thiazoles
  • Transcription Factors
  • U2AF1 protein, human
  • U2AF2 protein, human
  • Poly A
  • thiazolyl blue