Abstract
Development, tissue renewal and long term survival of multi-cellular organisms is dependent upon the persistence of stem cells that are quiescent, but retain the capacity to re-enter the cell cycle to self-renew, or to produce progeny that can differentiate and re-populate the tissue. Deregulated release of these cells from the quiescent state, or preventing them from entering quiescence, results in uncontrolled proliferation and cancer. Conversely, loss of quiescent cells, or their failure to re-enter cell division, disrupts organ development and prevents tissue regeneration and repair. Understanding the quiescent state and how cells control the transitions in and out of this state is of fundamental importance. Investigations into the mechanics of G1 arrest during the transition to quiescence continue to identify striking parallels between the strategies used by yeast and mammals to regulate this transition. When cells commit to a stable but reversible arrest, the G1/S genes responsible for promoting S phase must be inhibited. This process, from yeast to humans, involves the formation of quiescence-specific complexes on their promoters. In higher cells, these so-called DREAM complexes of E2F4/DP/RBL/MuvB recruit the highly conserved histone deacetylase HDAC1, which leads to local histone deacetylation and repression of S phase-promoting transcripts. Quiescent yeast cells also show pervasive histone deacetylation by the HDAC1 counterpart Rpd3. In addition, these cells contain quiescence-specific regulators of G1/S genes: Msa1 and Msa2, which can be considered components of the yeast equivalent of the DREAM complex. Despite a lack of physical similarities, the goals and the strategies used to achieve a reversible transition to quiescence are highly conserved. This motivates a detailed study of this process in the simple model organism: budding yeast.
Similar content being viewed by others
References
Alland L, David G, Shen-Li H, Potes J, Muhle R, Lee HC, Hou H Jr, Chen K, DePinho RA (2002) Identification of mammalian Sds3 as an integral component of the Sin3/histone deacetylase corepressor complex. Mol Cell Biol 22:2743–2750
Allen JB, Zhou Z, Siede W, Friedberg EC, Elledge SJ (1994) The SAD1/RAD53 protein kinase controls multiple checkpoints and DNA damage-induced transcription in yeast. Genes Dev 8:2401–2415
Allen C, Buttner S, Aragon AD, Thomas JA, Meirelles O, Jaetao JE, Benn D, Ruby SW, Veenhuis M, Madeo F, Werner-Washburne M (2006) Isolation of quiescent and nonquiescent cells from yeast stationary-phase cultures. J Cell Biol 174:89–100
Ashe M, de Bruin RA, Kalashnikova T, McDonald WH, Yates JR 3rd, Wittenberg C (2008) The SBF- and MBF-associated protein Msa1 is required for proper timing of G1-specific transcription in Saccharomyces cerevisiae. J Biol Chem 283:6040–6049
Barbet NC, Schneider U, Helliwell SB, Stansfield I, Tuite MF, Hall MN (1996) TOR controls translation initiation and early G1 progression in yeast. Mol Biol Cell 7:25–42
Bertoli C, Klier S, McGowan C, Wittenberg C, de Bruin RA (2013) Chk1 inhibits E2F6 repressor function in response to replication stress to maintain cell-cycle transcription. Curr Biol 23:1629–1637. doi:10.1016/j.cub.2013.06.063
Brehm A, Miska EA, McCance DJ, Reid JL, Bannister AJ, Kouzarides T (1998) Retinoblastoma protein recruits histone deacetylase to repress transcription. Nature 391:597–601. doi:10.1038/35404
Ceol CJ, Horvitz HR (2001) dpl-1 DP and efl-1 E2F act with lin-35 Rb to antagonize Ras signaling in C. elegans vulval development. Mol Cell 7:461–473
Chen YC, Kenworthy J, Gabrielse C, Hanni C, Zegerman P, Weinreich M (2013) DNA replication checkpoint signaling depends on a Rad53-Dbf4N-terminal interaction in Saccharomyces cerevisiae. Genetics 194:389–401. doi:10.1534/genetics.113.149740
Costanzo M, Nishikawa JL, Tang X, Millman JS, Schub O, Breitkreuz K, Dewar D, Rupes I, Andrews B, Tyers M (2004) CDK activity antagonizes Whi5, an inhibitor of G1/S transcription in yeast. Cell 117:899–913
Cross FR (1988) DAF1, a mutant gene affecting size control, pheromone arrest, and cell cycle kinetics of Saccharomyces cerevisiae. Mol Cell Biol 8:4675–4684
David G, Grandinetti KB, Finnerty PM, Simpson N, Chu GC, Depinho RA (2008) Specific requirement of the chromatin modifier mSin3B in cell cycle exit and cellular differentiation. Proc Natl Acad Sci USA 105:4168–4172. doi:10.1073/pnas.0710285105
de Bruin RA, McDonald WH, Kalashnikova TI, Yates J 3rd, Wittenberg C (2004) Cln3 activates G1-specific transcription via phosphorylation of the SBF bound repressor Whi5. Cell 117:887–898
de Bruin RA, Kalashnikova TI, Aslanian A, Wohlschlegel J, Chahwan C, Yates JR 3rd, Russell P, Wittenberg C (2008) DNA replication checkpoint promotes G1-S transcription by inactivating the MBF repressor Nrm1. Proc Natl Acad Sci USA 105:11230–11235
DeRisi JL, Iyer VR, Brown PO (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278:680–686
Dovey OM, Foster CT, Cowley SM (2010) Histone deacetylase 1 (HDAC1), but not HDAC2, controls embryonic stem cell differentiation. Proc Natl Acad Sci USA 107:8242–8247. doi:10.1073/pnas.1000478107
Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11:4241–4257
Gonzalez-Novo A, Jimenez J, Clotet J, Nadal-Ribelles M, Cavero S, de Nadal E, Posas F (2015) Hog1 targets Whi5 and Msa1 transcription factors to downregulate cyclin expression upon stress. Mol Cell Biol 35:1606–1618. doi:10.1128/MCB.01279-14
Heideman MR, Wilting RH, Yanover E, Velds A, de Jong J, Kerkhoven RM, Jacobs H, Wessels LF, Dannenberg JH (2013) Dosage-dependent tumor suppression by histone deacetylases 1 and 2 through regulation of c-Myc collaborating genes and p53 function. Blood 121:2038–2050. doi:10.1182/blood-2012-08-450916
Huang D, Kaluarachchi S, van Dyk D, Friesen H, Sopko R, Ye W, Bastajian N, Moffat J, Sassi H, Costanzo M, Andrews BJ (2009) Dual regulation by pairs of cyclin-dependent protein kinases and histone deacetylases controls G1 transcription in budding yeast. PLoS Biol 7:e1000188. doi:10.1371/journal.pbio.1000188
Jiang JC, Wawryn J, Shantha Kumara HM, Jazwinski SM (2002) Distinct roles of processes modulated by histone deacetylases Rpd3p, Hda1p, and Sir2p in life extension by caloric restriction in yeast. Exp Gerontol 37:1023–1030
Koc A, Wheeler LJ, Mathews CK, Merrill GF (2004) Hydroxyurea arrests DNA replication by a mechanism that preserves basal dNTP pools. J Biol Chem 279:223–230. doi:10.1074/jbc.M303952200
Koch C, Moll T, Neuberg M, Ahorn H, Nasmyth K (1993) A role for the transcription factors Mbp1 and Swi4 in progression from G1 to S phase. Science 261:1551–1557
Korenjak M, Taylor-Harding B, Binne UK, Satterlee JS, Stevaux O, Aasland R, White-Cooper H, Dyson N, Brehm A (2004) Native E2F/RBF complexes contain Myb-interacting proteins and repress transcription of developmentally controlled E2F target genes. Cell 119:181–193. doi:10.1016/j.cell.2004.09.034
Lee SE, Pellicioli A, Demeter J, Vaze MP, Gasch AP, Malkova A, Brown PO, Botstein D, Stearns T, Foiani M, Haber JE (2000) Arrest, adaptation, and recovery following a chromosome double-strand break in Saccharomyces cerevisiae. Cold Spring Harb Symp Quant Biol 65:303–314
Li JM, Tetzlaff MT, Elledge SJ (2008) Identification of MSA1, a cell cycle-regulated, dosage suppressor of drc1/sld2 and dpb11 mutants. Cell Cycle 7:3388–3398
Li L, Lu Y, Qin LX, Bar-Joseph Z, Werner-Washburne M, Breeden LL (2009) Budding yeast SSD1-V regulates transcript levels of many longevity genes and extends chronological life span in purified quiescent cells. Mol Biol Cell 20:3851–3864. doi:10.1091/mbc.E09-04-0347
Li L, Miles S, Melville Z, Prasad A, Bradley G, Breeden LL (2013) Key events during the transition from rapid growth to quiescence in budding yeast require posttranscriptional regulators. Mol Biol Cell 24:3697–3709. doi:10.1091/mbc.E13-05-0241
Lillie SH, Pringle JR (1980) Reserve carbohydrate metabolism in Saccharomyces cerevisiae: responses to nutrient limitation. J Bacteriol 143:1384–1394
Litovchick L, Sadasivam S, Florens L, Zhu X, Swanson SK, Velmurugan S, Chen R, Washburn MP, Liu XS, DeCaprio JA (2007) Evolutionarily conserved multisubunit RBL2/p130 and E2F4 protein complex represses human cell cycle-dependent genes in quiescence. Mol Cell 26:539–551. doi:10.1016/j.molcel.2007.04.015
Luo RX, Postigo AA, Dean DC (1998) Rb interacts with histone deacetylase to repress transcription. Cell 92:463–473
Mai B, Breeden L (1997) Xbp1, a stress-induced transcriptional repressor of the Saccharomyces cerevisiae Swi4/Mbp1 family. Mol Cell Biol 17:6491–6501
Margolis DM (2011) Histone deacetylase inhibitors and HIV latency. Curr Opin HIV AIDS 6:25–29. doi:10.1097/COH.0b013e328341242d
McKnight JN, Boerma JW, Breeden LL, Tsukiyama T (2015) Global promoter targeting of a conserved lysine deacetylase for transcriptional shutoff during quiescence entry. Mol Cell 59:732–743. doi:10.1016/j.molcel.2015.07.014
Miles S, Li L, Davison J, Breeden LL (2013) Xbp1 directs global repression of budding yeast transcription during the transition to quiescence and is important for the longevity and reversibility of the quiescent state. PLoS Genet 9:e1003854. doi:10.1371/journal.pgen.1003854
Miles S, Croxford MW, Abeysinghe AP, Breeden LL (2016) Msa1 and Msa2 modulate G1-specific transcription to promote G1 arrest and the transition to quiescence in budding yeast. PLoS Genet 12:e1006088. doi:10.1371/journal.pgen.1006088
Nevins JR (1992) E2F: a link between the Rb tumor suppressor protein and viral oncoproteins. Science 258:424–429
Ouspenski II, Elledge SJ, Brinkley BR (1999) New yeast genes important for chromosome integrity and segregation identified by dosage effects on genome stability. Nucleic Acids Res 27:3001–3008
Ragni E, Piberger H, Neupert C, Garcia-Cantalejo J, Popolo L, Arroyo J, Aebi M, Strahl S (2011) The genetic interaction network of CCW12, a Saccharomyces cerevisiae gene required for cell wall integrity during budding and formation of mating projections. BMC Genom 12:107. doi:10.1186/1471-2164-12-107
Rayman JB, Takahashi Y, Indjeian VB, Dannenberg JH, Catchpole S, Watson RJ, te Riele H, Dynlacht BD (2002) E2F mediates cell cycle-dependent transcriptional repression in vivo by recruitment of an HDAC1/mSin3B corepressor complex. Genes Dev 16:933–947. doi:10.1101/gad.969202
Sadasivam S, DeCaprio JA (2013) The DREAM complex: master coordinator of cell cycle-dependent gene expression. Nat Rev Cancer 13:585–595. doi:10.1038/nrc3556
Santoro F, Botrugno OA, Dal Zuffo R, Pallavicini I, Matthews GM, Cluse L, Barozzi I, Senese S, Fornasari L, Moretti S, Altucci L, Pelicci PG, Chiocca S, Johnstone RW, Minucci S (2013) A dual role for Hdac1: oncosuppressor in tumorigenesis, oncogene in tumor maintenance. Blood 121:3459–3468. doi:10.1182/blood-2012-10-461988
Savarino A, Mai A, Norelli S, El Daker S, Valente S, Rotili D, Altucci L, Palamara AT, Garaci E (2009) “Shock and kill” effects of class I-selective histone deacetylase inhibitors in combination with the glutathione synthesis inhibitor buthionine sulfoximine in cell line models for HIV-1 quiescence. Retrovirology 6:52. doi:10.1186/1742-4690-6-52
Shimoi H, Kitagaki H, Ohmori H, Iimura Y, Ito K (1998) Sed1p is a major cell wall protein of Saccharomyces cerevisiae in the stationary phase and is involved in lytic enzyme resistance. J Bacteriol 180:3381–3387
Shirakawa K, Chavez L, Hakre S, Calvanese V, Verdin E (2013) Reactivation of latent HIV by histone deacetylase inhibitors. Trends Microbiol 21:277–285. doi:10.1016/j.tim.2013.02.005
Sidorova J, Breeden LL (2002) Precocious S-phase entry in budding yeast prolongs replicative state and increases dependence upon Rad53 for viability. Genetics 160:123–136
Takahata S, Yu Y, Stillman DJ (2009) The E2F functional analogue SBF recruits the Rpd3(L) HDAC, via Whi5 and Stb1, and the FACT chromatin reorganizer, to yeast G1 cyclin promoters. EMBO J 28:3378–3389. doi:10.1038/emboj.2009.270
Tang Z (2016) Model organisms for studying the cell cycle. Methods Mol Biol 1342:21–57. doi:10.1007/978-1-4939-2957-3_2
Tao R, Chen H, Gao C, Xue P, Yang F, Han JD, Zhou B, Chen YG (2011) Xbp1-mediated histone H4 deacetylation contributes to DNA double-strand break repair in yeast. Cell Res. doi:10.1038/cr.2011.58
Taunton J, Hassig CA, Schreiber SL (1996) A mammalian histone deacetylase related to the yeast transcriptional regulator Rpd3p. Science 272:408–411
Travesa A, Kalashnikova T, de Bruin R, Cass SR, Chahwan C, Lee DE, Lowndes N, Wittenberg C (2013) Repression of G1/S transcription is mediated via interaction of the GTB motif of Nrm1 and Whi5 with Swi6. Mol Cell Biol. doi:10.1128/MCB.01333-12
Trimarchi JM, Lees JA (2002) Sibling rivalry in the E2F family. Nat Rev Mol Cell Biol 3:11–20
Valcourt JR, Lemons JM, Haley EM, Kojima M, Demuren OO, Coller HA (2012) Staying alive: metabolic adaptations to quiescence. Cell Cycle 11:1680–1696. doi:10.4161/cc.19879
Vallen EA, Cross FR (1999) Interaction between the MEC1-dependent DNA synthesis checkpoint and G1 cyclin function in Saccaromyces cerevisiae. Genetics 151:459–471
van der Felden J, Weisser S, Bruckner S, Lenz P, Mosch HU (2014) The transcription factors Tec1 and Ste12 interact with coregulators Msa1 and Msa2 to activate adhesion and multicellular development. Mol Cell Biol 34:2283–2293. doi:10.1128/MCB.01599-13
Wang H, Carey LB, Cai Y, Wijnen H, Futcher B (2009) Recruitment of Cln3 cyclin to promoters controls cell cycle entry via histone deacetylase and other targets. PLoS Biol 7:e1000189. doi:10.1371/journal.pbio.1000189
Winter M, Moser MA, Meunier D, Fischer C, Machat G, Mattes K, Lichtenberger BM, Brunmeir R, Weissmann S, Murko C, Humer C, Meischel T, Brosch G, Matthias P, Sibilia M, Seiser C (2013) Divergent roles of HDAC1 and HDAC2 in the regulation of epidermal development and tumorigenesis. EMBO J 32:3176–3191. doi:10.1038/emboj.2013.243
Yahya G, Parisi E, Flores A, Gallego C, Aldea M (2014) A Whi7-anchored loop controls the G1 Cdk-cyclin complex at start. Mol Cell 53:115–126. doi:10.1016/j.molcel.2013.11.015
Yang XJ, Seto E (2008) The Rpd3/Hda1 family of lysine deacetylases: from bacteria and yeast to mice and men. Nat Rev Mol Cell Biol 9:206–218. doi:10.1038/nrm2346
Zhang B, Strauss AC, Chu S, Li M, Ho Y, Shiang KD, Snyder DS, Huettner CS, Shultz L, Holyoake T, Bhatia R (2010) Effective targeting of quiescent chronic myelogenous leukemia stem cells by histone deacetylase inhibitors in combination with imatinib mesylate. Cancer Cell 17:427–442. doi:10.1016/j.ccr.2010.03.011
Acknowledgments
We thank members of the Breeden lab for helpful comments on the manuscript. This work was supported by the National Institutes of Health, National Institute on Aging Grant R21-AG048595 to L. L. B.
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by M. Kupiec.
Rights and permissions
About this article
Cite this article
Miles, S., Breeden, L. A common strategy for initiating the transition from proliferation to quiescence. Curr Genet 63, 179–186 (2017). https://doi.org/10.1007/s00294-016-0640-0
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00294-016-0640-0