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Article Dans Une Revue Genome Research Année : 2007

Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates.

Hiroshi Kikuta
  • Fonction : Auteur
Mary Laplante
  • Fonction : Auteur
Pavla Navratilova
  • Fonction : Auteur
Anna Z Komisarczuk
  • Fonction : Auteur
Pär G Engström
  • Fonction : Auteur
David Fredman
  • Fonction : Auteur
Altuna Akalin
  • Fonction : Auteur
Mario Caccamo
  • Fonction : Auteur
Ian Sealy
  • Fonction : Auteur
Kerstin Howe
  • Fonction : Auteur
Julien Ghislain
  • Fonction : Auteur
Guillaume Pezeron
Philippe Mourrain
  • Fonction : Auteur
Staale Ellingsen
  • Fonction : Auteur
Andrew C Oates
  • Fonction : Auteur
Isabelle Foucher
  • Fonction : Auteur
Birgit Adolf
  • Fonction : Auteur
Andrea Geling
  • Fonction : Auteur
Boris Lenhard
  • Fonction : Auteur
Thomas S Becker
  • Fonction : Auteur

Résumé

We report evidence for a mechanism for the maintenance of long-range conserved synteny across vertebrate genomes. We found the largest mammal-teleost conserved chromosomal segments to be spanned by highly conserved noncoding elements (HCNEs), their developmental regulatory target genes, and phylogenetically and functionally unrelated "bystander" genes. Bystander genes are not specifically under the control of the regulatory elements that drive the target genes and are expressed in patterns that are different from those of the target genes. Reporter insertions distal to zebrafish developmental regulatory genes pax6.1/2, rx3, id1, and fgf8 and miRNA genes mirn9-1 and mirn9-5 recapitulate the expression patterns of these genes even if located inside or beyond bystander genes, suggesting that the regulatory domain of a developmental regulatory gene can extend into and beyond adjacent transcriptional units. We termed these chromosomal segments genomic regulatory blocks (GRBs). After whole genome duplication in teleosts, GRBs, including HCNEs and target genes, were often maintained in both copies, while bystander genes were typically lost from one GRB, strongly suggesting that evolutionary pressure acts to keep the single-copy GRBs of higher vertebrates intact. We show that loss of bystander genes and other mutational events suffered by duplicated GRBs in teleost genomes permits target gene identification and HCNE/target gene assignment. These findings explain the absence of evolutionary breakpoints from large vertebrate chromosomal segments and will aid in the recognition of position effect mutations within human GRBs.

Dates et versions

hal-00189979 , version 1 (22-11-2007)

Identifiants

Citer

Hiroshi Kikuta, Mary Laplante, Pavla Navratilova, Anna Z Komisarczuk, Pär G Engström, et al.. Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates.. Genome Research, 2007, 17 (5), pp.545-55. ⟨10.1101/gr.6086307⟩. ⟨hal-00189979⟩
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