A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts.
Recent studies of the genome architecture of vertebrates have uncovered two unforeseen aspects of its organization. First, large regions of the genome, called gene deserts, are devoid of protein-coding sequences and have no obvious biological role. Second, comparative genomics has highlighted the existence of an array of highly conserved non-coding regions (HCNRs) in all vertebrates. Most surprisingly, these structural features are strongly associated with genes that have essential functions during development. Among these, the vertebrate Iroquois (Irx) genes stand out on both fronts. Mammalian Irx genes are organized in two clusters (IrxA and IrxB) that span >1 Mb each with no other genes interspersed. Additionally, a large number of HCNRs exist within Irx clusters. We have systematically examined the enhancer activity of HCNRs from the IrxB cluster using transgenic Xenopus and zebrafish embryos. Most of these HCNRs are active in subdomains of endogenous Irx expression, and some are candidates to contain shared enhancers of neighboring genes, which could explain the evolutionary conservation of Irx clusters. Furthermore, HCNRs present in tetrapod IrxB but not in fish may be responsible for novel Irx expression domains that appeared after their divergence. Finally, we have performed a more detailed analysis on two IrxB ultraconserved non-coding regions (UCRs) duplicated in IrxA clusters in similar relative positions. These four regions share a core region highly conserved among all of them and drive expression in similar domains. However, inter-species conserved sequences surrounding the core, specific for each of these UCRs, are able to modulate their expression.
de la Calle-Mustienes
Elisa
E
Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas and Universidad Pablo de Olavide, 41013 Sevilla, Spain.
Feijóo
Cármen Gloria
CG
Manzanares
Miguel
M
Tena
Juan J
JJ
Rodríguez-Seguel
Elisa
E
Letizia
Annalisa
A
Allende
Miguel L
ML
Gómez-Skarmeta
José Luis
JL
D000818:Animals; D030801:Animals, Genetically Modified; D001483:Base Sequence; D017124:Conserved Sequence; D021901:DNA, Intergenic; D004625:Embryo, Nonmammalian; D004742:Enhancer Elements, Genetic; D018507:Gene Expression Regulation, Developmental; D018398:Homeodomain Proteins / Q000235:genetics*; D008969:Molecular Sequence Data; D005810:Multigene Family; D014157:Transcription Factors / Q000235:genetics*; D014714:Vertebrates / Q000235:genetics*; D014981:Xenopus / Q000196:embryology / Q000235:genetics; D015027:Zebrafish / Q000196:embryology / Q000235:genetics; D029961:Zebrafish Proteins
D021901:DNA, Intergenic; D018398:Homeodomain Proteins; D014157:Transcription Factors; D029961:Zebrafish Proteins; C501593:irx1a protein, zebrafish