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Updated: Nov 15, 2025

Analysis of RNA Processing Reactions Using Cell Free Systems: 3' End Cleavage of Pre-mRNA Substrates in vitro
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Analysis of RNA Processing Reactions Using Cell Free Systems: 3' End Cleavage of Pre-mRNA Substrates in vitro

Published on: May 3, 2014

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Comparative parallel analysis of RNA ends identifies mRNA substrates of a tRNA splicing endonuclease-initiated mRNA

Jennifer E Hurtig1, Michelle A Steiger1,2, Vinay K Nagarajan3

  • 1Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, TX 77030.

Proceedings of the National Academy of Sciences of the United States of America
|March 2, 2021
PubMed

Insights

Yeast transfer RNA (tRNA) splicing endonuclease (TSEN) cleaves specific messenger RNAs (mRNAs) encoding mitochondrial proteins. This discovery explains TSEN

Area of Science:

  • Molecular Biology
  • Biochemistry
  • Genetics

Background:

  • Eukaryotes utilize conserved mRNA decay pathways involving exoribonucleases and specialized endonucleolytic cleavage.
  • The transfer RNA (tRNA) splicing endonuclease (TSEN) is known for pre-tRNA intron removal and its link to pontocerebellar hypoplasia.
  • Previous research indicated TSEN possesses other functions, but their nature remained unclear.

Purpose of the Study:

  • To investigate the previously obscure functions of the transfer RNA (tRNA) splicing endonuclease (TSEN) in eukaryotes.
  • To identify specific messenger RNA (mRNA) targets cleaved by yeast TSEN.
  • To elucidate the mechanism and implications of TSEN-mediated mRNA cleavage.

Main Methods:

  • Experimental cleavage assays using yeast TSEN.
  • Development and application of the "comPARE" (comparative parallel analysis of RNA ends) bioinformatic approach.
  • Sequence analysis to determine mRNA cleavage site determinants.

Main Results:

  • Yeast TSEN specifically cleaves a subset of messenger RNAs (mRNAs) encoding mitochondrial proteins.
  • Cleavage sites on these mRNAs are partially determined by their nucleotide sequence.
  • This finding explains the previously counterintuitive mitochondrial localization of yeast TSEN.

Conclusions:

  • The transfer RNA (tRNA) splicing endonuclease (TSEN) plays a direct role in the decay of specific mitochondrial protein-encoding mRNAs.
  • The "comPARE" bioinformatic tool offers a broadly applicable method for studying endoribonuclease targets.
  • mRNA specificity through colocalization, similar to tRNA endonuclease-initiated decay, may be crucial for localized mRNA degradation in eukaryotes.
Keywords:
endonucleasemRNA degradationtRNA splicing

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