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A Reporter Based Cellular Assay for Monitoring Splicing Efficiency
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Competition between the Rex1 exonuclease and the La protein affects both Trf4p-mediated RNA quality control and

Laura A Copela1, Cesar F Fernandez, R Lynn Sherrer

  • 1Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06519-1418, USA.

RNA (New York, N.Y.)
|May 6, 2008
PubMed

Insights

Competition between the La protein and Rex1 exonuclease determines the fate of nascent noncoding RNAs. La protein binding protects RNAs from degradation, while Rex1p mediates decay by the TRAMP pathway.

Area of Science:

  • Molecular Biology
  • RNA Biology
  • Gene Regulation

Background:

  • Nascent noncoding RNAs face a critical choice: maturation into functional molecules or degradation via quality control pathways.
  • The precise molecular events governing this choice remain largely unelucidated.
  • Understanding these pathways is crucial for comprehending cellular RNA homeostasis.

Purpose of the Study:

  • To investigate the factors influencing the degradation versus maturation of nascent noncoding RNAs.
  • To identify the specific proteins and pathways involved in the quality control of pre-tRNAs and other noncoding RNAs.
  • To elucidate the mechanism by which the TRAMP pathway targets noncoding RNAs for decay.

Main Methods:

  • Comparative analysis of RNA extracted from wild-type and mutant yeast strains (trf4Δ).
  • Investigated the role of the La protein (Lhp1p) and Rex1 exonuclease in RNA processing and decay.
  • Utilized overexpression studies of the La protein to assess its impact on RNA trimming and accumulation.

Main Results:

  • The La protein protects nascent noncoding RNAs from exonucleolytic degradation by binding to their 3' ends.
  • Rex1p was identified as the major exonuclease responsible for pre-tRNA trailer trimming and potentially nuclear CCA turnover.
  • Defective noncoding RNAs, including pre-tRNAs, 5S rRNA, and SRP RNA, accumulate in trf4Δ cells and require Rex1p for their formation, indicating TRAMP pathway involvement in their decay.
  • Overexpression of Lhp1p suppressed both exonucleolytic trimming and the accumulation of defective RNAs in trf4Δ cells.

Conclusions:

  • The competition between the La protein and Rex1 exonuclease at the 3' end of nascent noncoding RNAs dictates their fate.
  • Rex1p-dependent 3' trimming generates aberrant RNAs that are subsequently targeted for decay by the TRAMP pathway.
  • This study reveals a key regulatory mechanism in noncoding RNA quality control, highlighting the interplay between protective factors and degradation machinery.

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