Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.

Originally published in Science Express on 4 December 2008
Science 19 December 2008:
Vol. 322. no. 5909, pp. 1851 - 1854
DOI: 10.1126/science.1164096
Prev | Table of Contents | Next

Reports

RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters

Pascal Preker,1 Jesper Nielsen,2 Susanne Kammler,1* Søren Lykke-Andersen,1 Marianne S. Christensen,1 Christophe K. Mapendano,1 Mikkel H. Schierup,2 Torben Heick Jensen1{dagger}

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.

1 Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology, C. F. Møllers Alle, Building 1130, Aarhus University, Denmark.
2 Bioinformatics Research Center, C. F. Møllers Alle, Building 1110, Aarhus University, Denmark.

* Present address: Exiqon A/S, Bygstubben 9, 2850 Vedbæk, Denmark.

{dagger} To whom correspondence should be addressed. E-mail: thj{at}mb.au.dk

Read the Full Text


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Transcriptional Analysis of the Adeno-Associated Virus Integration Site.
N. Dutheil, E. Henckaerts, E. Kohlbrenner, and R. M. Linden (2009)
J. Virol. 83, 12512-12525
   Abstract »    Full Text »    PDF »
Pervasive transcription of the eukaryotic genome: functional indices and conceptual implications.
M. E. Dinger, P. P. Amaral, T. R. Mercer, and J. S. Mattick (2009)
Brief Funct Genomic Proteomic 8, 407-423
   Abstract »    Full Text »    PDF »
Establishing legitimacy and function in the new transcriptome.
H. van Bakel and T. R. Hughes (2009)
Brief Funct Genomic Proteomic 8, 424-436
   Abstract »    Full Text »    PDF »
Annotating non-coding transcription using functional genomics strategies.
A. R. R. Forrest, R. F. Abdelhamid, and P. Carninci (2009)
Brief Funct Genomic Proteomic 8, 437-443
   Abstract »    Full Text »    PDF »
Human mitochondrial RNA turnover caught in flagranti: involvement of hSuv3p helicase in RNA surveillance.
R. J. Szczesny, L. S. Borowski, L. K. Brzezniak, A. Dmochowska, K. Gewartowski, E. Bartnik, and P. P. Stepien (2009)
Nucleic Acids Res.
   Abstract »    Full Text »    PDF »
The Adenovirus E1B 55-Kilodalton and E4 Open Reading Frame 6 Proteins Limit Phosphorylation of eIF2{alpha} during the Late Phase of Infection.
M. E. Spurgeon and D. A. Ornelles (2009)
J. Virol. 83, 9970-9982
   Abstract »    Full Text »    PDF »
Transcriptome analysis by strand-specific sequencing of complementary DNA.
D. Parkhomchuk, T. Borodina, V. Amstislavskiy, M. Banaru, L. Hallen, S. Krobitsch, H. Lehrach, and A. Soldatov (2009)
Nucleic Acids Res. 37, e123
   Abstract »    Full Text »    PDF »
Microarray analysis of cytoplasmic versus whole cell RNA reveals a considerable number of missed and false positive mRNAs.
H. W. Trask, R. Cowper-Sal-lari, M. A. Sartor, J. Gui, C. V. Heath, J. Renuka, A.-J. Higgins, P. Andrews, M. Korc, J. H. Moore, et al. (2009)
RNA 15, 1917-1928
   Abstract »    Full Text »    PDF »
Long noncoding RNAs: functional surprises from the RNA world.
J. E. Wilusz, H. Sunwoo, and D. L. Spector (2009)
Genes & Dev. 23, 1494-1504
   Abstract »    Full Text »    PDF »
DBH2H: vertebrate head-to-head gene pairs annotated at genomic and post-genomic levels.
H. Yu, F.-D. Yu, G.-Q. Zhang, X. Shen, Y.-Q. Chen, Y.-Y. Li, and Y.-X. Li (2009)
Database 2009, bap006
   Abstract »    Full Text »    PDF »
Origins and activities of the eukaryotic exosome.
S. Lykke-Andersen, D. E. Brodersen, and T. H. Jensen (2009)
J. Cell Sci. 122, 1487-1494
   Abstract »    Full Text »    PDF »
Promoter targeted small RNAs induce long-term transcriptional gene silencing in human cells.
P. G. Hawkins, S. Santoso, C. Adams, V. Anest, and K. V. Morris (2009)
Nucleic Acids Res. 37, 2984-2995
   Abstract »    Full Text »    PDF »


To Advertise     Find Products

Science. ISSN 0036-8075 (print), 1095-9203 (online)