mRNA 5′ ends targeted by cytoplasmic recapping cluster at CAGE tags and select transcripts are alternatively spliced

Abstract

Until cytoplasmic recapping was discovered, decapping was thought to irreversibly destine an mRNA to degradation. Contradicting this idea, we readily observe mRNAs targeted by cytoplasmic capping in uncapped, yet stable forms. 5′ rapid amplification of cDNA ends (RACE) shows that nearly all uncapped ends correspond to capped analysis of gene expression tags and that the recapping of ZNF207 mRNA may be restricted to a single splice isoform. Here, a modified RACE approach detected uncapped 5′ RNA ends mapping to 46 mRNAs in cells expressing a dominant negative cytoplasmic capping enzyme and in normal cells. Eleven of 46 cloned mRNAs also contained splice isoform‐limiting sequences. Collectively, these data reinforce earlier work and suggest that alternative splicing may play a role in targeting transcripts for – and/or determining the position of – cytoplasmic capping.

Enzymatic characterization of mRNA cap adenosine-N6 methyltransferase PCIF1 activity on uncapped RNAs

“…In this study, we first ask whether human PCIF1 is active in vitro on RNA substrates lacking a cap, since uncapped mRNA molecules do appear and can be recapped by cytoplasmic enzymes (13,14). At least in 12 yeast species, only a fraction of RNAs were capped with m 7 G: ~75% of those having a purine (A or G) at the 5′ end, and ~50% of those starting with a pyrimidine (15).…”

Global analysis of transcription start sites in the new ovine reference genome (Oar rambouillet v1.0)

“…mammary gland, pituitary gland and urinary bladder had more uni-directional TSS mapping to intergenic regions, which might indicate evidence of alternative splicing or differential TSS usage across tissues (Figure 5). Alternative splicing events and differential TSS usage, captured by CAGE, are often not included in the reference gene prediction models (Berger et al, 2019).…”

Global Analysis of Transcription Start Sites in the New Ovine Reference Genome (Oar rambouillet v1.0)

“…Some tissues, e.g., mammary gland, pituitary gland, and urinary bladder, had more uni-directional TSS mapping to intergenic regions, which might indicate evidence of alternative splicing or differential TSS usage across tissues (Figure 5). Alternative splicing events and differential TSS usage, captured by CAGE, are often not included in reference gene prediction models (Berger et al, 2019).…”