RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters

TLDR

Eukaryotic genomes are largely transcribed, yet low‑abundant transcripts have likely been overlooked by current transcriptome maps. The study proposes that promoter‑upstream transcripts (PROMPTs) are a common feature of RNA polymerase II‑transcribed genes and may have regulatory potential. To reveal these transcripts, the authors depleted the exonucleolytic RNA exosome from human cells and performed tiling microarray analysis on the remaining RNA. The analysis uncovered short, polyadenylated, highly unstable PROMPTs located 0.5–2.5 kb upstream of active transcription start sites, produced in both sense and antisense directions, requiring promoter presence and correlating positively with gene activity.

Abstract

Studies have shown that the bulk of eukaryotic genomes is transcribed. Transcriptome maps are frequently updated, but low-abundant transcripts have probably gone unnoticed. To eliminate RNA degradation, we depleted the exonucleolytic RNA exosome from human cells and then subjected the RNA to tiling microarray analysis. This revealed a class of short, polyadenylated and highly unstable RNAs. These promoter upstream transcripts (PROMPTs) are produced ∼0.5 to 2.5 kilobases upstream of active transcription start sites. PROMPT transcription occurs in both sense and antisense directions with respect to the downstream gene. In addition, it requires the presence of the gene promoter and is positively correlated with gene activity. We propose that PROMPT transcription is a common characteristic of RNA polymerase II (RNAPII) transcribed genes with a possible regulatory potential.