title: Transcriptional autoregulatory loops are highly conserved in vertebrate evolution.
abstract: BACKGROUND
  Feedback loops are the simplest building blocks of transcriptional regulatory networks and therefore their behavior in the course of evolution is of prime interest.
  
  
  METHODS
  We address the question of enrichment of the number of autoregulatory feedback loops in higher organisms. First, based on predicted autoregulatory binding sites we count the number of autoregulatory loops. We compare it to estimates obtained either by assuming that each (conserved) gene has the same chance to be a target of a given factor or by assuming that each conserved sequence position has an equal chance to be a binding site of the factor.
  
  
  CONCLUSIONS
  We demonstrate that the numbers of putative autoregulatory loops conserved between human and fugu, danio or chicken are significantly higher than expected. Moreover we show, that conserved autoregulatory binding sites cluster close to the factors' starts of transcription. We conclude, that transcriptional autoregulatory feedback loops constitute a core transcriptional network motif and their conservation has been maintained in higher vertebrate organism evolution.
authors.affiliation: Max Planck Institute for Molecular Genetics, Berlin, Germany. szymon.kielbasa@molgen.mpg.de
authors.forename: Szymon M
authors.initials: SM
authors.lastname: Kiełbasa
authors.forename: Martin
authors.initials: M
authors.lastname: Vingron
mesh_terms: D000818:Animals; D001665:Binding Sites; D002645:Chickens; D017124:Conserved Sequence; D030541:Databases, Genetic; D019143:Evolution, Molecular; D005786:Gene Expression Regulation; D006801:Humans; D015233:Models, Statistical; D008969:Molecular Sequence Data; D011336:Probability; D023741:Takifugu; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic; D014714:Vertebrates / Q000235:genetics*; D015027:Zebrafish
chemical_list: D014157:Transcription Factors
references.citation: BMC Bioinformatics. 2004 May 18;5:62
references.pmid: 15149555
references.citation: Genome Res. 2004 Jun;14(6):1107-18
references.pmid: 15173116
references.citation: Dev Cell. 2007 Aug;13(2):283-97
references.pmid: 17681138
references.citation: Oncogene. 1990 Dec;5(12):1761-7
references.pmid: 2284095
references.citation: Curr Biol. 2007 Apr 17;17(8):668-77
references.pmid: 17398098
references.citation: Nucleic Acids Res. 2003 Jan 1;31(1):374-8
references.pmid: 12520026
references.citation: Stat Appl Genet Mol Biol. 2003;2:Article7
references.pmid: 16646785
references.citation: Nature. 2000 Jun 1;405(6786):590-3
references.pmid: 10850721
references.citation: J Biol Chem. 2000 Nov 24;275(47):36910-9
references.pmid: 10967107
references.citation: Mol Syst Biol. 2006;2:41
references.pmid: 16883354
references.citation: Nat Rev Microbiol. 2006 Apr;4(4):259-71
references.pmid: 16541134
references.citation: J Mol Biol. 2002 Nov 8;323(5):785-93
references.pmid: 12417193
references.citation: J Theor Biol. 2004 Jul 21;229(2):147-56
references.pmid: 15207470
references.citation: Nat Rev Genet. 2007 Jun;8(6):450-61
references.pmid: 17510665
references.citation: J Mol Biol. 2006 Jun 30;360(1):213-27
references.pmid: 16762362
references.citation: Dev Biol. 2003 May 1;257(1):1-13
references.pmid: 12710953
references.citation: EMBO J. 2001 May 15;20(10):2528-35
references.pmid: 11350942
references.citation: Genes Dev. 1994 Jul 1;8(13):1514-25
references.pmid: 7958836
references.citation: Nat Genet. 2004 May;36(5):492-6
references.pmid: 15107850
references.citation: Genome Res. 2003 Jan;13(1):103-7
references.pmid: 12529312
references.citation: J Biol Chem. 1997 Jul 18;272(29):18222-31
references.pmid: 9218459
references.citation: Development. 1998 Jun;125(11):1991-8
references.pmid: 9570764
references.citation: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D468-70
references.pmid: 14681459