The Use of Oscillatory Signals in the Study of Genetic Networks

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 2005 May 11

PMID 15883385

Citations 25

Authors

Ovidiu Lipan

Wing H Wong

Affiliations

Soon will be listed here.

Abstract

The structure of a genetic network is uncovered by studying its response to external stimuli (input signals). We present a theory of propagation of an input signal through a linear stochastic genetic network. We found that there are important advantages in using oscillatory signals over step or impulse signals and that the system may enter into a pure fluctuation resonance for a specific input frequency.

Citing Articles

Oscillations of Delta-like1 regulate the balance between differentiation and maintenance of muscle stem cells.

Zhang Y, Lahmann I, Baum K, Shimojo H, Mourikis P, Wolf J Nat Commun. 2021; 12(1):1318.

PMID: 33637744 PMC: 7910593. DOI: 10.1038/s41467-021-21631-4.

Biological signal generators: integrating synthetic biology tools and control.

Scott T, Sweeney K, McClean M Curr Opin Syst Biol. 2019; 14:58-65.

PMID: 31673669 PMC: 6822565. DOI: 10.1016/j.coisb.2019.02.007.

Oscillations of MyoD and Hes1 proteins regulate the maintenance of activated muscle stem cells.

Lahmann I, Brohl D, Zyrianova T, Isomura A, Czajkowski M, Kapoor V Genes Dev. 2019; 33(9-10):524-535.

PMID: 30862660 PMC: 6499323. DOI: 10.1101/gad.322818.118.

Adaptive Benefits of Storage Strategy and Dual AMPK/TOR Signaling in Metabolic Stress Response.

Pfeuty B, Thommen Q PLoS One. 2016; 11(8):e0160247.

PMID: 27505075 PMC: 4978418. DOI: 10.1371/journal.pone.0160247.

Integrative systems and synthetic biology of cell-matrix adhesion sites.

Zamir E Cell Adh Migr. 2016; 10(5):451-460.

PMID: 26853318 PMC: 5079407. DOI: 10.1080/19336918.2016.1148865.

References

Storch K, Lipan O, Leykin I, Viswanathan N, Davis F, Wong W . Extensive and divergent circadian gene expression in liver and heart. Nature. 2002; 417(6884):78-83. DOI: 10.1038/nature744. View

Vance W, Arkin A, Ross J . Determination of causal connectivities of species in reaction networks. Proc Natl Acad Sci U S A. 2002; 99(9):5816-21. PMC: 122859. DOI: 10.1073/pnas.022049699. View

Reppert S, Weaver D . Coordination of circadian timing in mammals. Nature. 2002; 418(6901):935-41. DOI: 10.1038/nature00965. View

Shimizu-Sato S, Huq E, Tepperman J, Quail P . A light-switchable gene promoter system. Nat Biotechnol. 2002; 20(10):1041-4. DOI: 10.1038/nbt734. View

Swain P, Elowitz M, Siggia E . Intrinsic and extrinsic contributions to stochasticity in gene expression. Proc Natl Acad Sci U S A. 2002; 99(20):12795-800. PMC: 130539. DOI: 10.1073/pnas.162041399. View

Lee T, Rinaldi N, Robert F, Odom D, Bar-Joseph Z, Gerber G . Transcriptional regulatory networks in Saccharomyces cerevisiae. Science. 2002; 298(5594):799-804. DOI: 10.1126/science.1075090. View

Rosenfeld N, Elowitz M, Alon U . Negative autoregulation speeds the response times of transcription networks. J Mol Biol. 2002; 323(5):785-93. DOI: 10.1016/s0022-2836(02)00994-4. View

Simpson M, Cox C, Sayler G . Frequency domain analysis of noise in autoregulated gene circuits. Proc Natl Acad Sci U S A. 2003; 100(8):4551-6. PMC: 404696. DOI: 10.1073/pnas.0736140100. View

Isaacs F, Hasty J, Cantor C, Collins J . Prediction and measurement of an autoregulatory genetic module. Proc Natl Acad Sci U S A. 2003; 100(13):7714-9. PMC: 164653. DOI: 10.1073/pnas.1332628100. View

10.

Gardner T, di Bernardo D, Lorenz D, Collins J . Inferring genetic networks and identifying compound mode of action via expression profiling. Science. 2003; 301(5629):102-5. DOI: 10.1126/science.1081900. View

11.

Izumo M, Johnson C, Yamazaki S . Circadian gene expression in mammalian fibroblasts revealed by real-time luminescence reporting: temperature compensation and damping. Proc Natl Acad Sci U S A. 2003; 100(26):16089-94. PMC: 307697. DOI: 10.1073/pnas.2536313100. View

12.

Kennell D, Riezman H . Transcription and translation initiation frequencies of the Escherichia coli lac operon. J Mol Biol. 1977; 114(1):1-21. DOI: 10.1016/0022-2836(77)90279-0. View

13.

Sheng H, Fields R, Nelson P . Specific regulation of immediate early genes by patterned neuronal activity. J Neurosci Res. 1993; 35(5):459-67. DOI: 10.1002/jnr.490350502. View

14.

Itoh K, Stevens B, Schachner M, Fields R . Regulated expression of the neural cell adhesion molecule L1 by specific patterns of neural impulses. Science. 1995; 270(5240):1369-72. DOI: 10.1126/science.270.5240.1369. View

15.

Smolen P, Baxter D, Byrne J . Frequency selectivity, multistability, and oscillations emerge from models of genetic regulatory systems. Am J Physiol. 1998; 274(2):C531-42. DOI: 10.1152/ajpcell.1998.274.2.C531. View

16.

van der Horst G, Muijtjens M, Kobayashi K, Takano R, Kanno S, Takao M . Mammalian Cry1 and Cry2 are essential for maintenance of circadian rhythms. Nature. 1999; 398(6728):627-30. DOI: 10.1038/19323. View

17.

Gadgil C, Lee C, Othmer H . A stochastic analysis of first-order reaction networks. Bull Math Biol. 2005; 67(5):901-46. PMC: 6388624. DOI: 10.1016/j.bulm.2004.09.009. View

18.

Becskei A, Serrano L . Engineering stability in gene networks by autoregulation. Nature. 2000; 405(6786):590-3. DOI: 10.1038/35014651. View

19.

Thattai M, van Oudenaarden A . Intrinsic noise in gene regulatory networks. Proc Natl Acad Sci U S A. 2001; 98(15):8614-9. PMC: 37484. DOI: 10.1073/pnas.151588598. View

20.

Hasty J, Dolnik M, Rottschafer V, Collins J . Synthetic gene network for entraining and amplifying cellular oscillations. Phys Rev Lett. 2002; 88(14):148101. DOI: 10.1103/PhysRevLett.88.148101. View