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Published Online December 4, 2008
Science DOI: 10.1126/science.1164096

Reports

Submitted on August 1, 2008
Accepted on November 12, 2008

RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters

Pascal Preker 1, Jesper Nielsen 2, Susanne Kammler 3, Søren Lykke-Andersen 1, Marianne S. Christensen 1, Christophe K. Mapendano 1, Mikkel H. Schierup 2, Torben Heick Jensen 1*

1 Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology, C.F. Møllers Alle, Bldg. 1130, Aarhus University, Denmark.
2 Bioinformatics Research Center, C.F. Møllers Alle, Bldg. 1110, Aarhus University, Denmark.
3 Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology, C.F. Møllers Alle, Bldg. 1130, Aarhus University, Denmark.; Present address: Exiqon A/S, Bygstubben 9, 2850 Vedbæk, Denmark.

* To whom correspondence should be addressed.
Torben Heick Jensen , E-mail: thj{at}mb.au.dk

Studies have shown that the bulk of eukaryotic genomes is transcribed. Transcriptome maps are frequently updated, but low-abundant transcripts have likely 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 about 0.5 to 2.5 kb upstream of active transcription start sites (TSSs). 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.


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