PUBLICATION

An evolutionarily conserved three-dimensional structure in the vertebrate Irx clusters facilitates enhancer sharing and coregulation

Authors
Tena, J.J., Alonso, M.E., de la Calle-Mustienes, E., Splinter, E., de Laat, W., Manzanares, M., and Gómez-Skarmeta, J.L.
ID
ZDB-PUB-110523-27
Date
2011
Source
Nature communications   2: 310 (Journal)
Registered Authors
de la Calle-Mustienes, Elisa, Gómez-Skarmeta, José Luis, Tena, Juan
Keywords
none
MeSH Terms
  • Animals
  • Conserved Sequence/genetics
  • Evolution, Molecular*
  • Gene Expression Regulation, Developmental*
  • Homeodomain Proteins/genetics*
  • Mice
  • Multigene Family*
  • Promoter Regions, Genetic*
  • Repressor Proteins/genetics
  • Transcription Factors/genetics
  • Xenopus/embryology
  • Xenopus/genetics*
  • Xenopus Proteins/genetics
  • Zebrafish/embryology
  • Zebrafish/genetics*
  • Zebrafish Proteins/genetics
(all 16)
PubMed
21556064 Full text @ Nat. Commun.
Abstract
Developmental gene clusters are paradigms for the study of gene regulation; however, the mechanisms that mediate phenomena such as coregulation and enhancer sharing remain largely elusive. Here we address this issue by analysing the vertebrate Irx clusters. We first present a deep enhancer screen of a 2-Mbp span covering the IrxA cluster. Using chromosome conformation capture, we show that enhancer sharing is widespread within the cluster, explaining its evolutionarily conserved organization. We also identify a three-dimensional architecture, probably formed through interactions with CCCTC-binding factor, which is present within both Irx clusters of mouse, Xenopus and zebrafish. This architecture brings the promoters of the first two genes together in the same chromatin landscape. We propose that this unique and evolutionarily conserved genomic architecture of the vertebrate Irx clusters is essential for the coregulation of the first two genes and simultaneously maintains the third gene in a partially independent regulatory landscape.
Genes / Markers
Marker Marker Type Name
ctcfGENECCCTC-binding factor (zinc finger protein)
gata2aGENEGATA binding protein 2a
irx1aGENEiroquois homeobox 1a
irx2aGENEiroquois homeobox 2a
irx3aGENEiroquois homeobox 3a
irx4aGENEiroquois homeobox 4a
irx5aGENEiroquois homeobox 5a
irx6aGENEiroquois homeobox 6a
1 - 8 of 8
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Figures
No images available
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Expression
Phenotype
Fish Conditions Stage Phenotype Figure
WT + MO5-ctcfstandard conditionsPrim-5 to Long-pec
1 - 1 of 1
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Mutations / Transgenics
Allele Construct Type Affected Genomic Region
upo75TgTransgenic Insertion
    upo76TgTransgenic Insertion
      upo77TgTransgenic Insertion
        upo78TgTransgenic Insertion
          upo79TgTransgenic Insertion
            upo80TgTransgenic Insertion
              upo81TgTransgenic Insertion
                upo82TgTransgenic Insertion
                  upo83TgTransgenic Insertion
                    upo84TgTransgenic Insertion
                      1 - 10 of 12
                      Show
                      Human Disease / Model
                      No data available
                      Sequence Targeting Reagents
                      Target Reagent Reagent Type
                      ctcfMO3-ctcfMRPHLNO
                      ctcfMO5-ctcfMRPHLNO
                      1 - 2 of 2
                      Show
                      Fish
                      Antibodies
                      No data available
                      Orthology
                      Engineered Foreign Genes
                      Marker Marker Type Name
                      DsRedEFGDsRed
                      EGFPEFGEGFP
                      1 - 2 of 2
                      Show
                      Mapping
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                      Citation
                      Tena, J.J., Alonso, M.E., de la Calle-Mustienes, E., Splinter, E., de Laat, W., Manzanares, M., and Gómez-Skarmeta, J.L. (2011) An evolutionarily conserved three-dimensional structure in the vertebrate Irx clusters facilitates enhancer sharing and coregulation. Nature communications. 2:310.