title: Ancestral and conserved cis-regulatory architectures in developmental control genes.
abstract: Among developmental control genes, transcription factor-target gene "linkages"--the direct connections between target genes and the factors that control their patterns of expression--can show remarkable evolutionary stability. However, the specific binding sites that mediate and define these regulatory connections are themselves often subject to rapid turnover. Here we describe several instances in which particular transcription factor binding motif combinations have evidently been conserved upstream of orthologous target genes for extraordinarily long evolutionary periods. This occurs against a backdrop in which other binding sites for the same factors are coming and going rapidly. Our examples include a particular Dpp Silencer Element upstream of insect brinker genes, in combination with a novel motif we refer to as the Downstream Element; combinations of a Suppressor of Hairless Paired Site (SPS) and a specific proneural protein binding site associated with arthropod Notch pathway target genes; and a three-motif combination, also including an SPS, upstream of deuterostome Hes repressor genes, which are also Notch targets. We propose that these stable motif architectures have been conserved intact from a deep ancestor, in part because they mediate a special mode of regulation that cannot be supplied by the other, unstable motif instances.
authors.affiliation: Division of Biological Sciences/CDB, University of California San Diego, La Jolla, CA 92093, USA.
authors.forename: Mark
authors.initials: M
authors.lastname: Rebeiz
authors.forename: Brian
authors.initials: B
authors.lastname: Castro
authors.forename: Feng
authors.initials: F
authors.lastname: Liu
authors.forename: Feng
authors.initials: F
authors.lastname: Yue
authors.forename: James W
authors.initials: JW
authors.lastname: Posakony
mesh_terms: D000818:Animals; D001483:Base Sequence; D016000:Cluster Analysis; D017124:Conserved Sequence / Q000235:genetics; D017931:DNA Primers / Q000235:genetics; D004330:Drosophila; D019143:Evolution, Molecular; D050437:Genes, Developmental / Q000235:genetics*; D018613:Microscopy, Confocal; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D054730:Protein Interaction Domains and Motifs / Q000235:genetics*; D037941:Silencer Elements, Transcriptional / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism; D019076:Transgenes / Q000235:genetics
chemical_list: D017931:DNA Primers; D014157:Transcription Factors