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Prediction and Validation of Gene Regulatory Elements Activated During Retinoic Acid Induced Embryonic Stem Cell Differentiation
Published on: June 21, 2016
An evolutionarily conserved three-dimensional structure in the vertebrate Irx clusters facilitates enhancer sharing
Juan J Tena1, M Eva Alonso, Elisa de la Calle-Mustienes
1Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas and Universidad Pablo de Olavide, Carretera de Utrera Km1, 41013 Sevilla, Spain.
Nature Communications
|May 11, 2011
Summary
Vertebrate Irx gene clusters show widespread enhancer sharing and a conserved 3D genomic architecture. This structure is crucial for coregulating the first two genes while allowing the third gene independent regulation.
Area of Science:
- Genomics
- Developmental Biology
- Gene Regulation
Background:
- Developmental gene clusters are key models for gene regulation.
- Mechanisms like coregulation and enhancer sharing are not fully understood.
Purpose of the Study:
- To investigate the mechanisms of coregulation and enhancer sharing in vertebrate Irx gene clusters.
- To analyze the genomic architecture and its role in gene regulation within Irx clusters.
Main Methods:
- Deep enhancer screening of the IrxA cluster.
- Chromosome conformation capture (3C) to analyze 3D genome organization.
- Comparative analysis across mouse, Xenopus, and zebrafish.
Main Results:
- Widespread enhancer sharing identified within the Irx cluster, explaining conserved organization.
- A conserved three-dimensional genomic architecture involving CCCTC-binding factor (CTCF) was found in mouse, Xenopus, and zebrafish Irx clusters.
- This architecture physically juxtaposes the promoters of the first two Irx genes.
Conclusions:
- The conserved 3D genomic architecture of vertebrate Irx clusters facilitates coregulation of the first two genes.
- This architecture allows for partially independent regulation of the third gene.
- Enhancer sharing and 3D organization are critical for the conserved structure and function of developmental gene clusters.
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