In vivo validation of a computationally predicted conserved Ath5 target gene set.
So far, the computational identification of transcription factor binding sites is hampered by the complexity of vertebrate genomes. Here we present an in silico procedure to predict target sites of a transcription factor in complex genomes using its binding site. In a first step sequence, comparison of closely related genomes identifies the binding sites in conserved cis-regulatory regions (phylogenetic footprinting). Subsequently, more remote genomes are introduced into the comparison to identify highly conserved and therefore putatively functional binding sites (phylogenetic filtering). When applied to the binding site of atonal homolog 5 (Ath5 or ATOH7), this procedure efficiently filters evolutionarily conserved binding sites out of more than 300,000 instances in a vertebrate genome. We validate a selection of the linked target genes by showing coexpression with and transcriptional regulation by Ath5. Finally, chromatin immunoprecipitation demonstrates the occupancy of the target gene promoters by Ath5. Thus, our procedure, applied to whole genomes, is a fast and predictive tool to in silico filter the target genes of a given transcription factor with defined binding site.
Del Bene
Filippo
F
Developmental Biology Programme, European Molecular Biology Laboratory, Heidelberg, Heidelberg, Germany.
Ettwiller
Laurence
L
Skowronska-Krawczyk
Dorota
D
Baier
Herwig
H
Matter
Jean-Marc
JM
Birney
Ewan
E
Wittbrodt
Joachim
J
D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D004247:DNA; D004268:DNA-Binding Proteins / Q000235:genetics*; D005786:Gene Expression Regulation; D016678:Genome; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D012689:Sequence Homology, Nucleic Acid; D014157:Transcription Factors / Q000378:metabolism
D004268:DNA-Binding Proteins; D014157:Transcription Factors; D004247:DNA