Meiosis pp 325-334 | Cite as

A Computational Approach to Study Gene Expression Networks

  • Amir Rubinstein
  • Yona KassirEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1471)


We describe a simple computational approach that can be used for the study and simulation of regulatory networks. The advantage of this approach is that it requires neither computational background nor exact quantitative data about the biological system under study. Moreover, it is suitable for examining alternative hypotheses about the structure of a biological network. We used a tool called BioNSi (Biological Network Simulator) that is based on a simple computational model, which can be easily integrated as part of the lab routine, in parallel to experimental work. One benefit of this approach is that it enables the identification of regulatory proteins, which are missing from the experimental work. We describe the general methodology for modeling a network’s dynamics in the tool, and then give a point by point example for a specific known network, entry into meiosis in budding yeast.

Key words

Regulatory network Computational model Simulation Gene expression Meiosis Yeast 


  1. 1.
    Schaub MA, Henzinger TA, Fisher J (2007) Qualitative networks: a symbolic approach to analyze biological signaling networks. BMC Syst Biol 1:4CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Rubinstein A et al (2007) Faithful modeling of transient expression and its application to elucidating negative feedback regulation. Proc Natl Acad Sci U S A 104(15):6241–6246CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Akman OE et al (2012) Digital clocks: simple Boolean models can quantitatively describe circadian systems. J R Soc Interface 9(74):2365–2382CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Yeheskely-Hayon D et al (2013) The roles of the catalytic and noncatalytic activities of Rpd3L and Rpd3S in the regulation of gene transcription in yeast. PLoS One 8(12):e85088CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Shannon P et al (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13(11):2498–2504CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Kassir Y et al (2003) Transcriptional regulation of meiosis in budding yeast. Int Rev Cytol 224:111–171CrossRefPubMedGoogle Scholar
  7. 7.
    Kassir Y, Granot D, Simchen G (1988) IME1, a positive regulator gene of meiosis in S. cerevisiae. Cell 52(6):853–862CrossRefPubMedGoogle Scholar
  8. 8.
    Shefer-Vaida M, Sherman A, Ashkenazi T, Robzyk K, Kassir Y (1995) Positive and negative feedback loops affect the transcription of IME1, a positive regulator of meiosis in Saccharomyces cerevisiae. Dev Genet 16(3):219–228CrossRefPubMedGoogle Scholar
  9. 9.
    Kadosh D, Struhl K (1997) Repression by Ume6 involves recruitment of a complex containing Sin3 corepressor and Rpd3 histone deacetylase to target promoters. Cell 89(3):365–371CrossRefPubMedGoogle Scholar
  10. 10.
    Pnueli L, Edry I, Cohen M, Kassir Y (2004) Glucose and nitrogen regulate the switch from histone deacetylation to acetylation for expression of early meiosis-specific genes in budding yeast. Mol Cell Biol 24(12):5197–5208CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Sherman A, Shefer M, Sagee S, Kassir Y (1993) Post-transcriptional regulation of IME1 determines initiation of meiosis in Saccharomyces cerevisiae. Mol Gen Genet 237(3):375–384PubMedGoogle Scholar
  12. 12.
    Colomina N, Gari E, Gallego C, Herrero E, Aldea M (1999) G1 cyclins block the Ime1 pathway to make mitosis and meiosis incompatible in budding yeast. EMBO J 18(2):320–329CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Guttmann-Raviv N, Kassir Y (2002) Ime2, a meiosis-specific kinase in yeast, is required for destabilization of its transcriptional activator, Ime1. Mol Cell Biol 22(7):2047–2056CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  1. 1.School of Computer ScienceTel Aviv UniversityTel AvivIsrael
  2. 2.Department of BiologyTechnion-Israel Institute of TechnologyHaifaIsrael

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