Post-transcriptional 3´-UTR cleavage of mRNA transcripts generates thousands of stable uncapped autonomous RNA fragments

Abstract

The majority of mammalian genes contain one or more alternative polyadenylation sites. Choice of polyadenylation sites was suggested as one of the underlying mechanisms for generating longer/shorter transcript isoforms. Here, we demonstrate that mature mRNA transcripts can undergo additional cleavage and polyadenylation at a proximal internal site in the 3′-UTR, resulting in two stable, autonomous, RNA fragments: a coding sequence with a shorter 3′-UTR (body) and an uncapped 3′-UTR sequence downstream of the cleavage point (tail). Analyses of the human transcriptome has revealed thousands of such cleavage positions, suggesting a widespread post-transcriptional phenomenon producing thousands of stable 3′-UTR RNA tails that exist alongside their transcripts of origin. By analyzing the impact of microRNAs, we observed a significantly stronger effect for microRNA regulation at the body compared to the tail fragments. Our findings open a variety of future research prospects and call for a new perspective on 3′-UTR-dependent gene regulation.

Widespread Accumulation of Ribosome-Associated Isolated 3′ UTRs in Neuronal Cell Populations of the Aging Brain

“…Analyzing total RNA sequencing data from several mouse tissues and the mouse NIH 3T3 cell line, we identified several genes, including Frat2 , Hnrnpa0 , and Sox12 , that had read densities at least several-fold higher in the 3′ UTR than in the coding region in most or all of these samples (Figures S1G and S1H). Thus, the phenomenon of 3′ UTR-enriched genes observed so widely in aged D1 SPNs extends to some genes in other mouse cells and tissues, as observed previously (Kocabas et al, 2015; Malka et al, 2017). …”

“…We confirmed a several-fold increased abundance of 3′ UTRs relative to coding regions in aged D1 SPNs for several of these genes by qPCR analysis (Figure S1D), suggesting that full-length (or ORF-only) mRNAs are reduced but not absent for this set of genes. The signatures associated with isolated 3′ UTRs observed here in aged D1 SPNs are of much greater magnitude and extend across far more genes than has been previously reported (Kocabas et al, 2015; Malka et al, 2017). …”

“…Although the presence of 3′ UTR RNAs lacking the coding region has been observed previously in some instances (Carninci et al, 2006; Kocabas et al, 2015; Malka et al, 2017; Mercer et al, 2011), the mechanism of their biogenesis remains elusive. Analyzing total RNA sequencing data from several mouse tissues and the mouse NIH 3T3 cell line, we identified several genes, including Frat2 , Hnrnpa0 , and Sox12 , that had read densities at least several-fold higher in the 3′ UTR than in the coding region in most or all of these samples (Figures S1G and S1H).…”

“…CAGE-detected cleavage products originating in 3′ UTRs also showed substantial overlap (40%) with Ago2- and Drosha-independent cleavage products identified from transcriptome-wide profiling of endonucleolytic cleavage products that retain a 5′ phosphate (Karginov et al, 2010). Isolated 3′ UTRs have also been described in murine immune cells and human cell lines (Malka et al, 2017). However, the biogenesis and potential functions of isolated 3′ UTRs, and whether they are of particular importance in the brain are not well understood.…”

Two separation-of-function isoforms of human TPP1 and a novel intragenic noncoding RNA dictate telomerase regulation in somatic and germ cells

“…4A). Such processing has been observed for thousands of human transcripts, although the full functional implications of this phenomenon remain uncovered (Malka et al, 2017). However the sunRNA was identified from CAGE analysis of the polyA-enriched nuclear fraction, suggesting that it somehow undergoes maturation following its genesis from TPP1 mRNA in the nucleus.…”