Feed-forward loop circuits as a side effect of genome evolution

Molecular Biology and Evolution

Volumn 23, Issue 10, 2006, Pages 1931-1936

  Cordero, Otto X ^a   Hogeweg, Paulien ^a  

^a UTRECHT UNIVERSITY   (Netherlands)

Author keywords

Feed forward loop; Genome evolution; Mutational dynamics; Network motifs; Regulatory networks; Yeast

Indexed keywords

ARTICLE; BINDING SITE; COMPUTER AIDED DESIGN; EVOLUTIONARY DEVELOPMENTAL BIOLOGY; FEED FORWARD LOOP SYSTEM; GENE CLUSTER; GENE DELETION; GENE DUPLICATION; GENE EXPRESSION REGULATION; GENE MUTATION; MOLECULAR EVOLUTION; NONHUMAN; STATISTICAL MODEL; STOCHASTIC MODEL; TRANSCRIPTION REGULATION;

EVOLUTION, MOLECULAR; GENE DELETION; GENE DUPLICATION; GENE EXPRESSION REGULATION, FUNGAL; GENOME; GENOME, FUNGAL; MODELS, GENETIC; MUTATION; SACCHAROMYCES CEREVISIAE; STOCHASTIC PROCESSES; TRANSCRIPTION, GENETIC;

EID: 33748773071     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msl060     Document Type: Article

References (25)

1. Artzy-Randrup Y, Fleishman SJ, BenTal N, Stone L. 2004. Comment on "network motifs: simple building blocks of complex networks" and "superfamilies of evolved and designed networks". Science 305:1107.
2. Babu MM, Luscombe NM, Aravind L, Gerstein M, Teichmann SA. 2004. Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol 14:283-91.
3. Barabaśi AL, Albert R. 1999. Emergence of scaling in random networks. Science 286:509-12.
4. Berg J, Willmann S, Lassig M. 2004. Adaptive evolution of transcription factor binding sites. BMC Evol Biol 4:42.
5. Conant GC, Wagner A. 2003. Convergent evolution of gene circuits. Nat Genet 34:264-6.
6. Dobrin R, Beg QK, Barabasi AL, Oltvai ZN. 2004. Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network. BMC Bioinformatics 5:10.
7. Evangelisti AM, Wagner A. 2004. Molecular evolution in the yeast transcriptional regulation network. J Exp Zool B Mol Dev Evol 302:392-411.
8. Guelzim N, Bottani S, Bourgine P, Kepes F. 2002. Topological and causal structure of the yeast transcriptional regulatory network. Nat Genet 31:60-3.
9. Horak CE, Luscombe NM, Qian J, Bertone P, Piccirrillo S, Gerstein M, Snyder M. 2002. Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes Dev 16:3017-33.
10. Itzkovitz S, Milo R, Kashtan N, Ziv G, Alon U. 2003. Subgraphs in random networks. Phys Rev E Stat Nonlin Soft Matter Phys 68:026127.
11. Kashtan N, Itzkovitz S, Milo R, Alon U. 2004. Topological generalizations of network motifs. Phys Rev E 70:031909.
12. Kellis M, Birren BW, Lander ES. 2004. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428:617-24.
13. Kumar R, Reynolds DM, Shevchenko A, Goldstone SD, Dalton S. 2000. Forkhead transcription factors, Fkh1p and Fkh2p, collaborate with Mcm1p to control transcription required for M-phase. Curr Biol 10:896-906.
14. Lee TI, Rinaldi NJ, Robert F, et al. (21 co-authors). 2002. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298:799-804.
15. Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, Gerstein M. 2004. Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431:308-12.
16. Mangan S, Alon U. 2003. Structure and function of the feedforward loop network motif. Proc Natl Acad Sci USA 100:11980-5.
17. Mangan S, Zaslaver A, Alon U. 2003. The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks. J Mol Biol 334:197-204.
18. Maslov S, Sneppen K, Eriksen KA, Yan KK. 2004. Upstream plasticity and downstream robustness in evolution of molecular networks. BMC Evol Biol 4:9.
19. Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U. 2002. Network motifs: simple building blocks of complex networks. Science 298:824-7.
20. Milo R, Itzkovtiz S, Kashtan N, Levitt R, Shen-Orr S, Ayzenshtat I, Sheffer M, Alon U. 2004. Superfamilies of evolved and designed networks. Science 303:1538-42.
21. Simon I, Barnett J, Hannett NA, et al. (11 co-authors). 2001. Serial regulation of transcriptional regulators in the yeast cell cycle. Cell 106:697-708.
22. Stone JR, Wray GA. 2001. Rapid evolution of cis-regulatory sequences via local point mutations. Mol Biol Evol 18:1764-70.
23. Tanay A, Regev A, Shamir R. 2005. Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast. Proc Natl Acad Sci USA 102:7203-8.
24. Teichmann SA, Babu MM. 2004. Gene regulatory network growth by duplication. Nat Genet 36:492-6.
25. Van Noort V, Snel B, Huynen MA. 2004. The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model. EMBO Rep 5:280-4.