Nuclear stability and transcriptional directionality separate functionally distinct RNA species

Abstract

Mammalian genomes are pervasively transcribed, yielding a complex transcriptome with high variability in composition and cellular abundance. While recent efforts have identified thousands of new long non-coding (lnc) RNAs and demonstrated a complex transcriptional repertoire produced by protein-coding (pc) genes, limited progress has been made in distinguishing functional RNA from spurious transcription events. This is partly due to present RNA classification, which is typically based on technical rather than biochemical criteria. Here we devise a strategy to systematically categorize human RNAs by their sensitivity to the ribonucleolytic RNA exosome complex and by the nature of their transcription initiation. These measures are surprisingly effective at correctly classifying annotated transcripts, including lncRNAs of known function. The approach also identifies uncharacterized stable lncRNAs, hidden among a vast majority of unstable transcripts. The predictive power of the approach promises to streamline the functional analysis of known and novel RNAs.

The identification and functional annotation of RNA structures conserved in vertebrates

“…Expressed regions were defined by empirical P-value < 0.01 and CPM/RLE ≥ 1. (D,H) Transcript stability at ENCODE HeLa DHSs, as described in Andersson et al (2014b), and GC content of structured (CRS) and unstructured regions (no CRS). Odds ratios quantify how strongly stability is associated with CRS overlap.…”

“…To disambiguate these alternatives, we examined CAGE data for transcription initiation at DHSs in control versus exosome-depleted HeLa cells (Andersson et al 2014b). Defining "stability" based on the change of expression level after exosome depletion (Methods), we find that stable eRNAs of preferentially unidirectional transcription were enriched for transcripts containing CRS regions (P = 0.002, FET, BH-corrected) (Fig.…”

“…To test for stability of transcripts, we analyzed triplicate published CAGE libraries from hRRP40 (exosome) depleted and EGFP depleted (control) HeLa cells (Andersson et al 2014b). We got premapped 5…”

“…Exosome sensitivity was calculated as described previously (Andersson et al 2014b) for both strands by max[(E exo − E ctr )/E exo , 0], with E exo and E ctr denoting the expression level after exosome depletion and in control HeLa cells, respectively. We used thresholds of ≤0.25 and ≥0.75 to identify highly stable and highly unstable RNAs emanating from transcribed DHSs.…”

Epigenomic Promoter Alterations Amplify Gene Isoform and Immunogenic Diversity in Gastric Adenocarcinoma

“…Second, particularly for clinical samples, epigenome-guided promoter identification is less prone to transcript degradation artifacts caused by 5′ RNA exonucleases (32). Epigenome-marked promoters may also highlight transcript classes not easily detectible by other means, such as promoters originating via recapping events, short-lived RNAs (27), or unstable RNAs with greater sensitivity to exosome-mediated decay, such as promoter upstream transcripts (33) and/or enhancer RNAs (34)(35)(36).…”