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. Although 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.

Perspectives on Unidirectional versus Divergent Transcription

“…Third, the chromatin signature, as seen in Promoter State 2, is different in unidirectional versus divergent promoter regions (Figure S1C). This latter point was the fourth major conclusion of our previous study (Duttke et al, 2015) and was not described by Andersson et al (2014, 2015) or Core et al (2014). These analyses show many significant differences between unidirectional and divergent promoter regions and thus provide some validation of the methods that we used to classify them.…”

“…In their Letter to the Editor, Andersson et al (2015) examined divergent and unidirectional human promoter regions reported in our February 2015 Molecular Cell paper (Duttke et al, 2015) and compared our results with data from their concurrent studies (Andersson et al, 2014; Core et al, 2014). They concluded that the nature of our transcription start site (TSS) data generated by the 5′-GRO-seq method (Lam et al, 2013) led to an inflation of the percentage of unidirectional promoter regions, and further suggested that unidirectional promoter regions may not exist.…”

“…For their negative reference regions, the authors chose inactive chromatin by excluding any genic regions as well as any annotated DHSs or enhancer regions. This strategy yields a positive reverse-direction signal in their new hRRP40 knockdown CAGE data (Andersson et al, 2014) with three reads across all three pooled replicates totaling ~45 million mapped reads. With these criteria, about 18% of promoters are found to be unidirectional.…”

“…We felt that it would be useful to address the concerns of Andersson et al (2015) by analyzing their data (Andersson et al, 2014; with results from the same cell type) and by using their approach, with two differences. First, we calculated TSS activity by the maximal read count in a 10-nt window from −100 to +1 relative to the DHS edge.…”

Structure of the RBM7–ZCCHC8 core of the NEXT complex reveals connections to splicing factors

“…In turn, SAP145 Pro binds the RRM region of the splicing factor SAP49 (ref. 44), linking RBM7 to RNA splicing factors, in addition to its connection to exosome-mediated RNA degradation273046. The mutually exclusive binding of ZCCHC8 and SAP145 to RBM7 could reflect independent functions of RBM7 in exosome-mediated degradation and splicing.…”