title: CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting.
abstract: Prediction of transcription-factor target sites in promoters remains difficult due to the short length and degeneracy of the target sequences. Although the use of orthologous sequences and phylogenetic footprinting approaches may help in the recognition of conserved and potentially functional sequences, correct alignment of the short transcription-factor binding sites can be problematic for established algorithms, especially when aligning more divergent species. Here, we report a novel phylogenetic footprinting approach, CONREAL, that uses biologically relevant information, that is, potential transcription-factor binding sites as represented by positional weight matrices, to establish anchors between orthologous sequences and to guide promoter sequence alignment. Comparison of the performance of CONREAL with the global alignment programs LAGAN and AVID using a reference data set, shows that CONREAL performs equally well for closely related species like rodents and human, and has a clear added value for aligning promoter elements of more divergent species like human and fish, as it identifies conserved transcription-factor binding sites that are not found by other methods. CONREAL is accessible via a Web interface at http://conreal.niob.knaw.nl/.
authors.affiliation: Hubrecht Laboratory, Netherlands Institute for Developmental Biology, 3584 CT, Utrecht, The Netherlands. berezikov@niob.knaw.nl
authors.forename: Eugene
authors.initials: E
authors.lastname: Berezikov
authors.forename: Victor
authors.initials: V
authors.lastname: Guryev
authors.forename: Ronald H A
authors.initials: RH
authors.lastname: Plasterk
authors.forename: Edwin
authors.initials: E
authors.lastname: Cuppen
mesh_terms: D000465:Algorithms; D000818:Animals; D001665:Binding Sites / Q000235:genetics; D017124:Conserved Sequence / Q000235:genetics*; D018983:DNA Footprinting / Q000379:methods* / Q000706:statistics & numerical data; D004268:DNA-Binding Proteins / Q000235:genetics; D051542:Hepatocyte Nuclear Factor 3-beta; D006801:Humans; D020407:Internet; D051379:Mice; D009687:Nuclear Proteins / Q000235:genetics; D010802:Phylogeny; D011401:Promoter Regions, Genetic / Q000235:genetics; D051381:Rats; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods / Q000706:statistics & numerical data; D012689:Sequence Homology, Nucleic Acid; D023741:Takifugu / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism*; D015027:Zebrafish / Q000235:genetics
chemical_list: D004268:DNA-Binding Proteins; C496502:FOXA2 protein, human; C496503:Foxa2 protein, mouse; C496504:Foxa2 protein, rat; D009687:Nuclear Proteins; D014157:Transcription Factors; D051542:Hepatocyte Nuclear Factor 3-beta