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Research Article

Existence, Transition, and Propagation of Intermediate Silencing States in Ribosomal DNA

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Article: e00146-19 | Received 28 Mar 2019, Accepted 10 Sep 2019, Published online: 03 Mar 2023

REFERENCES

  • Sanchez A, Choubey S, Kondev J. 2013. Regulation of noise in gene expression. Annu Rev Biophys 42:469–491. https://doi.org/10.1146/annurev-biophys-083012-130401.
  • Munsky B, Neuert G, van Oudenaarden A. 2012. Using gene expression noise to understand gene regulation. Science 336:183–187. https://doi.org/10.1126/science.1216379.
  • Raser JM, O’Shea EK. 2005. Noise in gene expression: origins, consequences, and control. Science 309:2010–2013. https://doi.org/10.1126/science.1105891.
  • Rusche LN, Kirchmaier AL, Rine J. 2003. The establishment, inheritance, and function of silenced chromatin in Saccharomyces cerevisiae. Annu Rev Biochem 72:481–516. https://doi.org/10.1146/annurev.biochem.72.121801.161547.
  • Srivastava R, Srivastava R, Ahn SH. 2016. The epigenetic pathways to ribosomal DNA silencing. Microbiol Mol Biol Rev 80:545–563. https://doi.org/10.1128/MMBR.00005-16.
  • Chen L, Widom J. 2005. Mechanism of transcriptional silencing in yeast. Cell 120:37–48. https://doi.org/10.1016/j.cell.2004.11.030.
  • Sekinger EA, Gross DS. 2001. Silenced chromatin is permissive to activator binding and PIC recruitment. Cell 105:403–414. https://doi.org/10.1016/s0092-8674(01)00329-4.
  • Gottschling DE, Aparicio OM, Billington BL, Zakian VA. 1990. Position effect at S. cerevisiae telomeres: reversible repression of Pol II transcription. Cell 63:751–762. https://doi.org/10.1016/0092-8674(90)90141-z.
  • Anderson MZ, Gerstein AC, Wigen L, Baller JA, Berman J. 2014. Silencing is noisy: population and cell level noise in telomere-adjacent genes is dependent on telomere position and sir2. PLoS Genet 10:e1004436. https://doi.org/10.1371/journal.pgen.1004436.
  • Ottaviani A, Gilson E, Magdinier F. 2008. Telomeric position effect: from the yeast paradigm to human pathologies? Biochimie 90:93–107. https://doi.org/10.1016/j.biochi.2007.07.022.
  • Kitada T, Kuryan BG, Tran NN, Song C, Xue Y, Carey M, Grunstein M. 2012. Mechanism for epigenetic variegation of gene expression at yeast telomeric heterochromatin. Genes Dev 26:2443–2455. https://doi.org/10.1101/gad.201095.112.
  • Xu EY, Zawadzki KA, Broach JR. 2006. Single-cell observations reveal intermediate transcriptional silencing states. Mol Cell 23:219–229. https://doi.org/10.1016/j.molcel.2006.05.035.
  • Du M, Zhang Q, Bai L. 2017. Three distinct mechanisms of long-distance modulation of gene expression in yeast. PLoS Genet 13:e1006736. https://doi.org/10.1371/journal.pgen.1006736.
  • Aparicio OM, Gottschling DE. 1994. Overcoming telomeric silencing: a trans-activator competes to establish gene expression in a cell cycle-dependent way. Genes Dev 8:1133–1146. https://doi.org/10.1101/gad.8.10.1133.
  • Zou F, Bai L. 2018. Using time-lapse fluorescence microscopy to study gene regulation. Methods https://doi.org/10.1016/j.ymeth.2018.12.010.
  • Swain PS, Elowitz MB, Siggia ED. 2002. Intrinsic and extrinsic contributions to stochasticity in gene expression. Proc Natl Acad Sci U S A 99:12795–12800. https://doi.org/10.1073/pnas.162041399.
  • Lau A, Blitzblau H, Bell SP. 2002. Cell-cycle control of the establishment of mating-type silencing in S. cerevisiae. Genes Dev 16:2935–2945. https://doi.org/10.1101/gad.764102.
  • Bai L, Charvin G, Siggia ED, Cross FR. 2010. Nucleosome-depleted regions in cell-cycle-regulated promoters ensure reliable gene expression in every cell cycle. Dev Cell 18:544–555. https://doi.org/10.1016/j.devcel.2010.02.007.
  • Shou W, Sakamoto KM, Keener J, Morimoto KW, Traverso EE, Azzam R, Hoppe GJ, Feldman RM, DeModena J, Moazed D, Charbonneau H, Nomura M, Deshaies RJ. 2001. Net1 stimulates RNA polymerase I transcription and regulates nucleolar structure independently of controlling mitotic exit. Mol Cell 8:45–55. https://doi.org/10.1016/S1097-2765(01)00291-X.
  • Buck SW, Maqani N, Matecic M, Hontz RD, Fine RD, Li M, Smith JS. 2016. RNA Polymerase I and Fob1 contributions to transcriptional silencing at the yeast rDNA locus. Nucleic Acids Res 44:6173–6184. https://doi.org/10.1093/nar/gkw212.
  • Walker N, Nghe P, Tans SJ. 2016. Generation and filtering of gene expression noise by the bacterial cell cycle. BMC Biol 14:11. https://doi.org/10.1186/s12915-016-0231-z.
  • Voichek Y, Bar-Ziv R, Barkai N. 2016. Expression homeostasis during DNA replication. Science 351:1087–1090. https://doi.org/10.1126/science.aad1162.
  • Zopf CJ, Quinn K, Zeidman J, Maheshri N. 2013. Cell-cycle dependence of transcription dominates noise in gene expression. PLoS Comput Biol 9:e1003161. https://doi.org/10.1371/journal.pcbi.1003161.
  • Uhlmann F, Wernic D, Poupart MA, Koonin EV, Nasmyth K. 2000. Cleavage of cohesin by the CD clan protease separin triggers anaphase in yeast. Cell 103:375–386. https://doi.org/10.1016/s0092-8674(00)00130-6.
  • Charvin G, Cross FR, Siggia ED. 2008. A microfluidic device for temporally controlled gene expression and long-term fluorescent imaging in unperturbed dividing yeast cells. PLoS One 3:e1468. https://doi.org/10.1371/journal.pone.0001468.
  • Budhavarapu VN, Chavez M, Tyler JK. 2013. How is epigenetic information maintained through DNA replication? Epigenetics Chromatin 6:32. https://doi.org/10.1186/1756-8935-6-32.
  • Osborne EA, Hiraoka Y, Rine J. 2011. Symmetry, asymmetry, and kinetics of silencing establishment in Saccharomyces cerevisiae revealed by single-cell optical assays. Proc Natl Acad Sci U S A 108:1209–1216. https://doi.org/10.1073/pnas.1018742108.
  • Shou W, Seol JH, Shevchenko A, Baskerville C, Moazed D, Chen ZW, Jang J, Shevchenko A, Charbonneau H, Deshaies RJ. 1999. Exit from mitosis is triggered by Tem1-dependent release of the protein phosphatase Cdc14 from nucleolar RENT complex. Cell 97:233–244. https://doi.org/10.1016/s0092-8674(00)80733-3.
  • Yan C, Wu S, Pocetti C, Bai L. 2016. Regulation of cell-to-cell variability in divergent gene expression. Nat Commun 7:11099. https://doi.org/10.1038/ncomms11099.
  • Zhang Q, Yoon Y, Yu Y, Parnell EJ, Garay JA, Mwangi MM, Cross FR, Stillman DJ, Bai L. 2013. Stochastic expression and epigenetic memory at the yeast HO promoter. Proc Natl Acad Sci U S A 110:14012–14017. https://doi.org/10.1073/pnas.1306113110.
  • Brewer BJ, Chlebowicz-Sledziewska E, Fangman WL. 1984. Cell cycle phases in the unequal mother/daughter cell cycles of Saccharomyces cerevisiae. Mol Cell Biol 4:2529–2531. https://doi.org/10.1128/mcb.4.11.2529.

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