title: High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay.
abstract: RNA levels in a cell are determined by the relative rates of RNA synthesis and decay. State-of-the-art transcriptional analyses only employ total cellular RNA. Therefore, changes in RNA levels cannot be attributed to RNA synthesis or decay, and temporal resolution is poor. Recently, it was reported that newly transcribed RNA can be biosynthetically labeled for 1-2 h using thiolated nucleosides, purified from total cellular RNA and subjected to microarray analysis. However, in order to study signaling events at molecular level, analysis of changes occurring within minutes is required. We developed an improved approach to separate total cellular RNA into newly transcribed and preexisting RNA following 10-15 min of metabolic labeling. Employing new computational tools for array normalization and half-life determination we simultaneously study short-term RNA synthesis and decay as well as their impact on cellular transcript levels. As an example we studied the response of fibroblasts to type I and II interferons (IFN). Analysis of RNA transcribed within 15-30 min at different times during the first three hours of interferon-receptor activation resulted in a >10-fold increase in microarray sensitivity and provided a comprehensive profile of the kinetics of IFN-mediated changes in gene expression. We identify a previously undisclosed highly connected network of short-lived transcripts selectively down-regulated by IFNgamma in between 30 and 60 min after IFN treatment showing strong associations with cell cycle and apoptosis, indicating novel mechanisms by which IFNgamma affects these pathways.
authors.affiliation: Max von Pettenkofer-Institute, Ludwig Maximilians-University Munich, Munich 80337, Germany. doelken@mvp.uni-muenchen.de
authors.forename: Lars
authors.initials: L
authors.lastname: Dölken
authors.forename: Zsolt
authors.initials: Z
authors.lastname: Ruzsics
authors.forename: Bernd
authors.initials: B
authors.lastname: Rädle
authors.forename: Caroline C
authors.initials: CC
authors.lastname: Friedel
authors.forename: Ralf
authors.initials: R
authors.lastname: Zimmer
authors.forename: Jörg
authors.initials: J
authors.lastname: Mages
authors.forename: Reinhard
authors.initials: R
authors.lastname: Hoffmann
authors.forename: Paul
authors.initials: P
authors.lastname: Dickinson
authors.forename: Thorsten
authors.initials: T
authors.lastname: Forster
authors.forename: Peter
authors.initials: P
authors.lastname: Ghazal
authors.forename: Ulrich H
authors.initials: UH
authors.lastname: Koszinowski
mesh_terms: D000818:Animals; D005347:Fibroblasts / Q000187:drug effects / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation; D007370:Interferon Type I / Q000494:pharmacology; D007371:Interferon-gamma / Q000494:pharmacology; D051379:Mice; D041681:NIH 3T3 Cells; D020871:RNA Stability / Q000235:genetics*; D012333:RNA, Messenger / Q000032:analysis / Q000096:biosynthesis*; D014158:Transcription, Genetic
chemical_list: D007370:Interferon Type I; D012333:RNA, Messenger; D007371:Interferon-gamma