RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters

Pascal Preker; Jesper Nielsen; Susanne Kammler; Søren Lykke-Andersen; Marianne S Christensen; Christophe K Mapendano; Mikkel Heide Schierup; Torben Heick Jensen

doi:10.1126/science.1164096

RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters

Pascal Preker, Jesper Nielsen, Susanne Kammler, Søren Lykke-Andersen, Marianne S Christensen, Christophe K Mapendano, Mikkel Heide Schierup, Torben Heick Jensen

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Abstract

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.

Original language	English
Journal	Science
Volume	322
Issue	5909
Pages (from-to)	1851-1854
Number of pages	4
ISSN	0036-8075
DOIs	https://doi.org/10.1126/science.1164096
Publication status	Published - 19 Dec 2008

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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 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.",

author = "Pascal Preker and Jesper Nielsen and Susanne Kammler and S{\o}ren Lykke-Andersen and Christensen, {Marianne S} and Mapendano, {Christophe K} and Schierup, {Mikkel Heide} and Jensen, {Torben Heick}",

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T1 - RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters

AU - Preker, Pascal

AU - Nielsen, Jesper

AU - Kammler, Susanne

AU - Lykke-Andersen, Søren

AU - Christensen, Marianne S

AU - Mapendano, Christophe K

AU - Schierup, Mikkel Heide

AU - Jensen, Torben Heick

PY - 2008/12/19

Y1 - 2008/12/19

N2 - 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.

AB - 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.

U2 - 10.1126/science.1164096

DO - 10.1126/science.1164096

M3 - Journal article

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VL - 322

SP - 1851

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JO - Science

JF - Science

IS - 5909

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RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters

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