Stability of RNA in developing Xenopus embryos and identification of a destabilizing sequence in TFIIIA messenger RNA

Abstract

Synthetic capped RNA transcripts injected into fertilized eggs of Xenopus laevis have a half-life of 3–4 h. Addition of a long (approximately 200 nucleotide) poly(A) tail increases the half-life to 6–8 h which approaches the half-life of natural polyadenylated globin RNA injected into embryos. Since exonucleolytic action alone could account for the degradation of RNA, we tested whether circular RNA is stable after injection and find that circles are exceptionally stable (half-life greater than 40 h). After the midblastula transition, polyadenylated chloramphenicol transferase (CAT) mRNAs transcribed from injected plasmids have a half-life of 2.5 h. Insertion of a 1000 nucleotide 3′ untranslated region from the Xhox-36 gene into the transcripts does not affect the half-life. In contrast to the finding that internal sequences do not affect stability, we find that sequences from the TFIIIA message reduce the half-life of CAT mRNA from 2.5 h to less than 30 min. We conclude that most RNAs are degraded exonucleolytically from the 3′ end, but specialized internal sequences can greatly destabilize the RNA, possibly by acting as a site for an endonuclease.