title: Widespread changes in mRNA stability contribute to quiescence-specific gene expression patterns in a fibroblast model of quiescence.
abstract: Quiescence, reversible exit from the cell division cycle, is characterized by large-scale changes in steady-state gene expression, yet mechanisms controlling these changes are in need of further elucidation. In order to characterize the effects of post-transcriptional control on the quiescent transcriptome in human fibroblasts, we determined mRNA decay rates for over 10,000 genes using a transcription shut-off time-course.
  
  
  
  We found that ~500 of the genes monitored exhibited significant changes in decay rate upon quiescence induction. Genes involved in RNA processing and ribosome biogenesis were destabilized with quiescence, while genes involved in the developmental process were stabilized with quiescence. Moreover, extracellular matrix genes demonstrated an upregulation of gene expression that corresponded with a stabilization of these transcripts. Additionally, targets of a quiescence-associated microRNA (miR-29) were significantly enriched in the fraction of transcripts that were stabilized during quiescence.
  
  
  
  Coordinated stability changes in clusters of genes with important functions in fibroblast quiescence maintenance are highly correlated with quiescence gene expression patterns. Analysis of miR-29 target decay rates suggests that microRNA-induced changes in RNA stability are important contributors to the quiescence gene expression program in fibroblasts. The identification of multiple stability-related gene clusters suggests that other posttranscriptional regulators of transcript stability may contribute to the coordination of quiescence gene expression. Such regulators may ultimately prove to be valuable targets for therapeutics that target proliferative cells, for instance, in cancer or fibrosis.
authors.affiliation: Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.
authors.forename: Elizabeth L
authors.initials: EL
authors.lastname: Johnson
authors.affiliation: Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA.
authors.forename: David G
authors.initials: DG
authors.lastname: Robinson
authors.affiliation: Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, 90095, USA. hcoller@ucla.edu.|Department of Biological Chemistry, David Geffen School of Medicine, Los Angeles, CA, 90095, USA. hcoller@ucla.edu.
authors.forename: Hilary A
authors.initials: HA
authors.lastname: Coller
mesh_terms: D016000:Cluster Analysis; D005347:Fibroblasts / Q000378:metabolism*; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D015894:Genome, Human; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods; D006801:Humans; D034622:RNA Interference; D020871:RNA Stability; D012333:RNA, Messenger / Q000235:genetics*; D016192:Resting Phase, Cell Cycle / Q000235:genetics*; D059467:Transcriptome
chemical_list: D012333:RNA, Messenger
keywords: Cell-cycle; Gene expression; Post-transcriptional regulation; Quiescence; mRNA stability; miR-29