RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription

TLDR

Large portions of eukaryotic genomes produce RNA that is largely unannotated and lacks protein‑coding potential. The study investigates the genomic origins and associations of human nuclear and cytosolic polyadenylated RNAs longer than 200 nt and whole‑cell RNAs shorter than 200 nt in a genome‑wide analysis. The authors mapped subcellular locations of detected RNAs, assigning addresses to nucleotides and examining their potential processing into short RNAs. The data indicate that some unannotated RNAs act as primary transcripts for short RNAs, identify three potentially functional RNA classes—two syntenically conserved and correlated with protein‑coding gene expression—and reveal a highly interleaved organization of the human transcriptome.

Abstract

Significant fractions of eukaryotic genomes give rise to RNA, much of which is unannotated and has reduced protein-coding potential. The genomic origins and the associations of human nuclear and cytosolic polyadenylated RNAs longer than 200 nucleotides (nt) and whole-cell RNAs less than 200 nt were investigated in this genome-wide study. Subcellular addresses for nucleotides present in detected RNAs were assigned, and their potential processing into short RNAs was investigated. Taken together, these observations suggest a novel role for some unannotated RNAs as primary transcripts for the production of short RNAs. Three potentially functional classes of RNAs have been identified, two of which are syntenically conserved and correlate with the expression state of protein-coding genes. These data support a highly interleaved organization of the human transcriptome.