title: Regulation of ribosomal DNA amplification by the TOR pathway.
abstract: Repeated regions are widespread in eukaryotic genomes, and key functional elements such as the ribosomal DNA tend to be formed of high copy repeated sequences organized in tandem arrays. In general, high copy repeats are remarkably stable, but a number of organisms display rapid ribosomal DNA amplification at specific times or under specific conditions. Here we demonstrate that target of rapamycin (TOR) signaling stimulates ribosomal DNA amplification in budding yeast, linking external nutrient availability to ribosomal DNA copy number. We show that ribosomal DNA amplification is regulated by three histone deacetylases: Sir2, Hst3, and Hst4. These enzymes control homologous recombination-dependent and nonhomologous recombination-dependent amplification pathways that act in concert to mediate rapid, directional ribosomal DNA copy number change. Amplification is completely repressed by rapamycin, an inhibitor of the nutrient-responsive TOR pathway; this effect is separable from growth rate and is mediated directly through Sir2, Hst3, and Hst4. Caloric restriction is known to up-regulate expression of nicotinamidase Pnc1, an enzyme that enhances Sir2, Hst3, and Hst4 activity. In contrast, normal glucose concentrations stretch the ribosome synthesis capacity of cells with low ribosomal DNA copy number, and we find that these cells show a previously unrecognized transcriptional response to caloric excess by reducing PNC1 expression. PNC1 down-regulation forms a key element in the control of ribosomal DNA amplification as overexpression of PNC1 substantially reduces ribosomal DNA amplification rate. Our results reveal how a signaling pathway can orchestrate specific genome changes and demonstrate that the copy number of repetitive DNA can be altered to suit environmental conditions.
authors.affiliation: Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom;
authors.forename: Carmen V
authors.initials: CV
authors.lastname: Jack
authors.affiliation: Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom;
authors.forename: Cristina
authors.initials: C
authors.lastname: Cruz
authors.affiliation: Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom;
authors.forename: Ryan M
authors.initials: RM
authors.lastname: Hull
authors.affiliation: Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom;
authors.forename: Markus A
authors.initials: MA
authors.lastname: Keller
authors.affiliation: Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom; Division of Physiology and Metabolism, Medical Research Council National Institute for Medical Research, London NW7 1AA, United Kingdom.
authors.forename: Markus
authors.initials: M
authors.lastname: Ralser
authors.affiliation: Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom; jon.houseley@babraham.ac.uk.
authors.forename: Jonathan
authors.identifier: http://orcid.org/0000-0001-8509-1500
authors.initials: J
authors.lastname: Houseley
mesh_terms: D000107:Acetylation / Q000187:drug effects; D004275:DNA, Ribosomal / Q000235:genetics*; D004777:Environment; D005784:Gene Amplification / Q000187:drug effects; D006655:Histone Deacetylases / Q000378:metabolism; D006657:Histones / Q000378:metabolism; D059765:Homologous Recombination / Q000187:drug effects / Q000235:genetics; D008239:Lysine / Q000378:metabolism; D008954:Models, Biological; D009243:NAD / Q000378:metabolism; D017346:Protein Serine-Threonine Kinases / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000187:drug effects / Q000201:enzymology / Q000235:genetics* / Q000254:growth & development; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*; D015398:Signal Transduction / Q000187:drug effects; D020123:Sirolimus / Q000494:pharmacology
chemical_list: D004275:DNA, Ribosomal; D006657:Histones; D029701:Saccharomyces cerevisiae Proteins; D009243:NAD; D017346:Protein Serine-Threonine Kinases; C500749:target of rapamycin protein, S cerevisiae; D006655:Histone Deacetylases; D008239:Lysine; D020123:Sirolimus
keywords: Sir2; TOR; copy number variation; homologous recombination; ribosomal DNA