Artículo

Lengyel, I.M.; Morelli, L.G."Multiple binding sites for transcriptional repressors can produce regular bursting and enhance noise suppression" (2017) Physical Review E. 95(4)
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Abstract:

Cells may control fluctuations in protein levels by means of negative autoregulation, where transcription factors bind DNA sites to repress their own production. Theoretical studies have assumed a single binding site for the repressor, while in most species it is found that multiple binding sites are arranged in clusters. We study a stochastic description of negative autoregulation with multiple binding sites for the repressor. We find that increasing the number of binding sites induces regular bursting of gene products. By tuning the threshold for repression, we show that multiple binding sites can also suppress fluctuations. Our results highlight possible roles for the presence of multiple binding sites of negative autoregulators. © 2017 American Physical Society.

Registro:

Documento: Artículo
Título:Multiple binding sites for transcriptional repressors can produce regular bursting and enhance noise suppression
Autor:Lengyel, I.M.; Morelli, L.G.
Filiación:Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET-Partner Institute of the Max Planck Society, Polo Científico Tecnológico, Godoy Cruz 2390, Buenos Aires, C1425FQD, Argentina
Departamento de Física, FCEyN UBA, Ciudad Universitaria, Buenos Aires, 1428, Argentina
Max Planck Institute for Molecular Physiology, Department of Systemic Cell Biology, Otto-Hahn-Strasse 1DUMMY, Dortmund, D-44227, Germany
Palabras clave:Bins; Stochastic systems; Transcription; Gene products; Multiple binding sites; Negative autoregulation; Noise suppression; Protein level; Single binding sites; Theoretical study; Transcriptional repressors; Binding sites; DNA; transcription factor; binding site; biological model; gene expression regulation; kinetics; Markov chain; metabolism; physiology; protein degradation; Binding Sites; DNA; Gene Expression Regulation; Kinetics; Models, Genetic; Proteolysis; Stochastic Processes; Transcription Factors
Año:2017
Volumen:95
Número:4
DOI: http://dx.doi.org/10.1103/PhysRevE.95.042412
Handle:http://hdl.handle.net/20.500.12110/paper_24700045_v95_n4_p_Lengyel
Título revista:Physical Review E
Título revista abreviado:Phys. Rev. E
ISSN:24700045
CAS:DNA, 9007-49-2; DNA; Transcription Factors
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_24700045_v95_n4_p_Lengyel

Referencias:

  • Alberts, B., Bray, D., Lewis, J., Raff, M., Roberts, K., Watson, J.D., (2002) Molecular Biology of the Cell, p. 1408. , 4th ed. (Garland Science, New York)
  • Alon, U., (2006) An Introduction to Systems Biology: Design Principles of Biological Circuits, , (CRC Press, Boca Raton, FL)
  • Thieffry, D., Huerta, A.M., Pérez-Rueda, E., Collado-Vides, J., (1998) BioEssays, 20, p. 433
  • Rosenfeld, N., Elowitz, M.B., Alon, U., (2002) J. Mol. Biol., 323, p. 785
  • Raser, J.M., O'Shea, E.K., (2005) Science, 309, p. 2010
  • Kaern, M., Elston, T.C., Blake, W.J., Collins, J.J., (2005) Nat. Rev. Genet., 6, p. 451
  • Sanchez, A., Choubey, S., Kondev, J., (2013) Annu. Rev. Biophys., 42, p. 469
  • Tsimring, L.S., (2014) Rep. Prog. Phys., 77, p. 026601
  • Norman, T.M., Lord, N.D., Paulsson, J., Losick, R., (2015) Annu. Rev. Microbiol., 69, p. 381
  • Becskei, A., Serrano, L., (2000) Nature (London), 405, p. 590
  • Dublanche, Y., Michalodimitrakis, K., Kümmerer, N., Foglierini, M., Serrano, L., (2006) Mol. Syst. Biol., 2, p. 41
  • Stekel, D.J., Jenkins, D.J., (2008) BMC Syst. Biol., 2, p. 6
  • Singh, A., Hespanha, J.P., (2009) Biophys. J., 96, p. 4013
  • Grönlund, A., Lötstedt, P., Elf, J., (2013) Nat. Commun., 4, p. 1864
  • Lestas, I., Vinnicombe, G., Paulsson, J., (2010) Nature (London), 467, p. 174
  • Morelli, L.G., Jülicher, F., (2007) Phys. Rev. Lett., 98, p. 228101
  • Morant, P.E., Thommen, Q., Lemaire, F., Vandermoëre, C., Parent, B., Lefranc, M., (2009) Phys. Rev. Lett., 102, p. 068104
  • Wang, J., Lefranc, M., Thommen, Q., (2014) Biophys. J., 107, p. 2403
  • Takebayashi, K., Sasai, Y., Sakai, Y., Watanabe, T., Nakanishi, S., Kageyama, R., (1994) J. Biol. Chem., 269, p. 5150
  • Kazemian, M., Pham, H., Wolfe, S.A., Brodsky, M.H., Sinha, S., (2013) Nucl. Acids Res., 41, p. 8237
  • Rydenfelt, M., Garcia, H.G., Cox, R.S., Phillips, R., (2014) PLoS ONE, 9, p. e114347
  • Bothma, J.P., Garcia, H.G., Ng, S., Perry, M.W., Gregor, T., Levine, M., (2015) ELife, 4, p. e07956
  • Wagner, A., (1997) Nucl. Acids Res., 25, p. 3594
  • Wagner, A., (1999) Bioinformatics, 15, p. 776
  • Lifanov, A.P., Makeev, V.J., Nazina, A.G., Papatsenko, D.A., (2003) Genome Res., 13, p. 579
  • Berman, B.P., Nibu, Y., Pfeiffer, B.D., Tomancak, P., Celniker, S.E., Levine, M., Rubin, G.M., Eisen, M.B., (2002) Proc. Natl. Acad. Sci. USA, 99, p. 757
  • Gotea, V., Visel, A., Westlund, J.M., Nobrega, M.A., Pennacchio, L.A., Ovcharenko, I., (2010) Genome Res., 20, p. 565
  • Thomas, E.E., (2005) Curr. Opin. Genet. Dev., 15, p. 640
  • To, T.-L., Maheshri, N., (2010) Science, 327, p. 1142
  • Suter, D.M., Molina, N., Gatfield, D., Schneider, K., Schibler, U., Naef, F., (2011) Science, 332, p. 472
  • Van Kampen, N.G., (1992) Stochastic Processes in Physics and Chemistry, 11, p. 465. , (North-Holland, Amsterdam)
  • Xu, H., Sepúlveda, L.A., Figard, L., Sokac, A.M., Golding, I., (2015) Nat. Meth., 12, p. 739
  • Lengyel, I.M., Soroldoni, D., Oates, A.C., Morelli, L.G., (2014) Papers Phys., 6, p. 060012
  • Sharon, E., Van Dijk, D., Kalma, Y., Keren, L., Manor, O., Yakhini, Z., Segal, E., (2014) Genome Res., 24, p. 1698
  • Grima, R., Schmidt, D.R., Newman, T.J., (2012) J. Chem. Phys., 137, p. 035104
  • Gillespie, D.T., (1976) J. Comput. Phys., 22, p. 403
  • Gillespie, D.T., (2007) Annu. Rev. Phys. Chem., 58, p. 35
  • Huang, L., Yuan, Z., Liu, P., Zhou, T., (2014) Phys. Rev. E, 90, p. 052702
  • Novák, B., Tyson, J.J., (2008) Nat. Rev. Mol. Cell Biol., 9, p. 981
  • Ferrell, J.E., Tsai, T.Y., Yang, Q., (2011) Cell, 144, p. 874
  • Guisoni, N., Monteoliva, D., Diambra, L., (2016) PLoS ONE, 11, p. e0151086
  • Oates, A.C., Morelli, L.G., Ares, S., (2012) Development, 139, p. 625
  • Schröter, C., Ares, S., Morelli, L.G., Isakova, A., Hens, K., Soroldoni, D., Gajewski, M., Oates, A.C., (2012) PLoS Biol., 10, p. e1001364
  • Webb, A.B., Lengyel, I.M., Jörg, D.J., Valentin, G., Jülicher, F., Morelli, L.G., Oates, A.C., (2016) ELife, 5, p. e08438
  • Lewis, J., (2003) Curr. Biol., 13, p. 1398
  • Masamizu, Y., Ohtsuka, T., Takashima, Y., Nagahara, H., Takenaka, Y., Yoshikawa, K., Okamura, H., Kageyama, R., (2006) Proc. Natl. Acad. Sci. USA, 103, p. 1313
  • Sternberg, S.H., Doudna, J.A., (2015) Mol. Cell, 58, p. 568
  • Elowitz, M.B., Leibler, S., (2000) Nature (London), 403, p. 335
  • Stricker, J., Cookson, S., Bennett, M.R., Mather, W.H., Tsimring, L., Hasty, J., (2008) Nature (London), 456, p. 516
  • Ferrell, J.E., Jr., (2009) J. Biol., 8, p. 53
  • Gutierrez, P.S., Monteoliva, D., Diambra, L., (2009) Phys. Rev. E, 80, p. 011914
  • Gutierrez, P.S., Monteoliva, D., Diambra, L., (2012) PLoS ONE, 7, p. e44812
  • Li, Y.-C., Korol, A.B., Fahima, T., Nevo, E., (2004) Mol. Biol. Evol., 21, p. 991
  • Iglesias, A.R., Kindlund, E., Tammi, M., Wadelius, C., (2004) Gene, 341, p. 149
  • Sinha, S., Siggia, E.D., (2005) Mol. Biol. Evol., 22, p. 874
  • Pikovsky, A.S., Rosenblum, M.G., Kurths, J., (2001) Synchronization: A Universal Concept in Nonlinear Sciences, , (Cambridge University Press, Cambridge)
  • Stein, J.Y., (2000) Digital Signal Processing: A Computer Science Perspective, , (Wiley, New York)

Citas:

---------- APA ----------
Lengyel, I.M. & Morelli, L.G. (2017) . Multiple binding sites for transcriptional repressors can produce regular bursting and enhance noise suppression. Physical Review E, 95(4).
http://dx.doi.org/10.1103/PhysRevE.95.042412
---------- CHICAGO ----------
Lengyel, I.M., Morelli, L.G. "Multiple binding sites for transcriptional repressors can produce regular bursting and enhance noise suppression" . Physical Review E 95, no. 4 (2017).
http://dx.doi.org/10.1103/PhysRevE.95.042412
---------- MLA ----------
Lengyel, I.M., Morelli, L.G. "Multiple binding sites for transcriptional repressors can produce regular bursting and enhance noise suppression" . Physical Review E, vol. 95, no. 4, 2017.
http://dx.doi.org/10.1103/PhysRevE.95.042412
---------- VANCOUVER ----------
Lengyel, I.M., Morelli, L.G. Multiple binding sites for transcriptional repressors can produce regular bursting and enhance noise suppression. Phys. Rev. E. 2017;95(4).
http://dx.doi.org/10.1103/PhysRevE.95.042412