PROMoter uPstream Transcripts share characteristics with mRNAs and are produced upstream of all three major types of mammalian promoters

Nucleic Acids Res. 2011 Sep 1;39(16):7179-93. doi: 10.1093/nar/gkr370. Epub 2011 May 19.


PROMoter uPstream Transcripts (PROMPTs) were identified as a new class of human RNAs, which are heterologous in length and produced only upstream of the promoters of active protein-coding genes. Here, we show that PROMPTs carry 3'-adenosine tails and 5'-cap structures. However, unlike mRNAs, PROMPTs are largely nuclear and rapidly turned over by the RNA exosome. PROMPT-transcribing DNA is occupied by RNA polymerase II (RNAPII) complexes with serine 2 phosphorylated C-terminal domains (CTDs), mimicking that of the associated genic region. Thus, the inefficient elongation capacity of PROMPT transcription cannot solely be assigned to poor CTD phosphorylation. Conditions that reduce gene transcription increase RNAPII occupancy of the upstream PROMPT region, suggesting that they reside in a common transcription compartment. Surprisingly, gene promoters that are actively transcribed by RNAPI or RNAPIII also produce PROMPTs that are targeted by the exosome. RNAPIII PROMPTs bear hallmarks of RNAPII promoter-associated RNAs, explaining the physical presence of RNAPII upstream of many RNAPIII-transcribed genes. We propose that RNAPII activity upstream gene promoters are wide-spread and integral to the act of gene transcription.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cyclin D1 / genetics
  • Genes, myc
  • HEK293 Cells
  • HeLa Cells
  • Humans
  • Polyadenylation
  • Promoter Regions, Genetic*
  • RNA Nucleotidyltransferases / metabolism
  • RNA Polymerase I / metabolism
  • RNA Polymerase II / chemistry
  • RNA Polymerase II / metabolism
  • RNA Polymerase III / metabolism
  • RNA, Messenger / chemistry
  • RNA, Nuclear / chemistry*
  • RNA, Nuclear / metabolism
  • Serine / metabolism


  • RNA, Messenger
  • RNA, Nuclear
  • Cyclin D1
  • Serine
  • RNA Nucleotidyltransferases
  • RNA Polymerase II
  • TENT4B protein, human
  • RNA Polymerase I
  • RNA Polymerase III