title: Long noncoding RNAs promote transcriptional poising of inducible genes.
abstract: Long noncoding RNAs (lncRNAs) are a class of molecules that impinge on the expression of protein-coding genes. Previous studies have suggested that the GAL cluster-associated lncRNAs of Saccharomyces cerevisiae repress expression of the protein-coding GAL genes. Herein, we demonstrate a previously unrecognized role for the GAL lncRNAs in activating gene expression. In yeast strains lacking the RNA helicase, DBP2, or the RNA decay enzyme, XRN1, we find that the GAL lncRNAs specifically accelerate gene expression from a prior repressive state. Furthermore, we provide evidence that the previously suggested repressive role is a result of specific mutant phenotypes, rather than a reflection of the normal, wild-type function of these noncoding RNAs. To shed light on the mechanism for lncRNA-dependent gene activation, we show that rapid induction of the protein-coding GAL genes is associated with faster recruitment of RNA polymerase II and reduced association of transcriptional repressors with GAL gene promoters. This suggests that the GAL lncRNAs enhance expression by derepressing the GAL genes. Consistently, the GAL lncRNAs enhance the kinetics of transcriptional induction, promoting faster expression of the protein-coding GAL genes upon the switch in carbon source. We suggest that the GAL lncRNAs poise inducible genes for rapid activation, enabling cells to more effectively trigger new transcriptional programs in response to cellular cues.
authors.affiliation: Department of Biochemistry, Purdue University, West Lafayette, Indiana, United States of America.
authors.forename: Sara C
authors.initials: SC
authors.lastname: Cloutier
authors.forename: Siwen
authors.initials: S
authors.lastname: Wang
authors.forename: Wai Kit
authors.initials: WK
authors.lastname: Ma
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Petell
authors.forename: Elizabeth J
authors.initials: EJ
authors.lastname: Tran
mesh_terms: D053487:DEAD-box RNA Helicases / Q000235:genetics; D004722:Endoribonucleases / Q000235:genetics; D005686:Galactokinase / Q000235:genetics; D015966:Gene Expression Regulation, Fungal; D005800:Genes, Fungal; D007700:Kinetics; D005810:Multigene Family; D009713:Nucleotidyltransferases / Q000235:genetics; D011485:Protein Binding; D012331:RNA, Fungal / Q000502:physiology*; D062085:RNA, Long Noncoding / Q000502:physiology*; D012097:Repressor Proteins / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic; D015533:Transcriptional Activation
chemical_list: C065455:CYC8 protein, S cerevisiae; D012331:RNA, Fungal; D062085:RNA, Long Noncoding; D012097:Repressor Proteins; D029701:Saccharomyces cerevisiae Proteins; D005686:Galactokinase; D009713:Nucleotidyltransferases; C400572:DCP2 protein, S cerevisiae; D004722:Endoribonucleases; C438898:Dbp2 protein, S cerevisiae; D053487:DEAD-box RNA Helicases