title: RNA exosome depletion reveals transcription upstream of active human promoters.
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 approximately 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.
authors.affiliation: Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology, C. F. Møllers Alle, Building 1130, Aarhus University, Denmark.
authors.forename: Pascal
authors.initials: P
authors.lastname: Preker
authors.forename: Jesper
authors.initials: J
authors.lastname: Nielsen
authors.forename: Susanne
authors.initials: S
authors.lastname: Kammler
authors.forename: Søren
authors.initials: S
authors.lastname: Lykke-Andersen
authors.forename: Marianne S
authors.initials: MS
authors.lastname: Christensen
authors.forename: Christophe K
authors.initials: CK
authors.lastname: Mapendano
authors.forename: Mikkel H
authors.initials: MH
authors.lastname: Schierup
authors.forename: Torben Heick
authors.initials: TH
authors.lastname: Jensen
mesh_terms: D019175:DNA Methylation; D055354:Exosomes / Q000378:metabolism*; D006367:HeLa Cells; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic; D012319:RNA Polymerase II / Q000378:metabolism; D020871:RNA Stability; D016372:RNA, Antisense / Q000235:genetics* / Q000378:metabolism*; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism*; D014157:Transcription Factors / Q000378:metabolism; D024363:Transcription Initiation Site; D014158:Transcription, Genetic; D014162:Transfection
chemical_list: D016372:RNA, Antisense; D012333:RNA, Messenger; D014157:Transcription Factors; D012319:RNA Polymerase II