ZFIN ID: ZDB-PUB-150603-3
Evolutionary comparison reveals that diverging CTCF sites are signatures of ancestral topological associating domains borders
Gómez-Marín, C., Tena, J.J., Acemel, R.D., López-Mayorga, M., Naranjo, S., de la Calle-Mustienes, E., Maeso, I., Beccari, L., Aneas, I., Vielmas, E., Bovolenta, P., Nobrega, M.A., Carvajal, J., Gómez-Skarmeta, J.L.
Date: 2015
Source: Proceedings of the National Academy of Sciences of the United States of America   112(24): 7542-7 (Journal)
Registered Authors: Bovolenta, Paola, de la Calle-Mustienes, Elisa, Gómez-Skarmeta, José Luis, Maeso, Ignacio, Naranjo, Silvia, Tena, Juan
Keywords: CTCF, Six cluster, TAD, evolution, regulatory landscapes
Microarrays: GEO:GSE66900
MeSH Terms:
  • Animals
  • Animals, Genetically Modified
  • Base Sequence
  • Binding Sites/genetics
  • Chromatin/chemistry
  • Chromatin/genetics
  • Chromatin/metabolism
  • Conserved Sequence
  • DNA/genetics
  • Enhancer Elements, Genetic
  • Evolution, Molecular*
  • Genes, Homeobox
  • Homeodomain Proteins/chemistry
  • Homeodomain Proteins/genetics
  • Homeodomain Proteins/metabolism
  • Humans
  • Mice
  • Models, Genetic
  • Multigene Family
  • Promoter Regions, Genetic
  • Protein Interaction Domains and Motifs
  • Repressor Proteins/chemistry*
  • Repressor Proteins/genetics*
  • Repressor Proteins/metabolism
  • Strongylocentrotus purpuratus/genetics
  • Zebrafish/genetics
PubMed: 26034287 Full text @ Proc. Natl. Acad. Sci. USA
Increasing evidence in the last years indicates that the vast amount of regulatory information contained in mammalian genomes is organized in precise 3D chromatin structures. However, the impact of this spatial chromatin organization on gene expression and its degree of evolutionary conservation is still poorly understood. The Six homeobox genes are essential developmental regulators organized in gene clusters conserved during evolution. Here, we reveal that the Six clusters share a deeply evolutionarily conserved 3D chromatin organization that predates the Cambrian explosion. This chromatin architecture generates two largely independent regulatory landscapes (RLs) contained in two adjacent topological associating domains (TADs). By disrupting the conserved TAD border in one of the zebrafish Six clusters, we demonstrate that this border is critical for preventing competition between promoters and enhancers located in separated RLs, thereby generating different expression patterns in genes located in close genomic proximity. Moreover, evolutionary comparison of Six-associated TAD borders reveals the presence of CCCTC-binding factor (CTCF) sites with diverging orientations in all studied deuterostomes. Genome-wide examination of mammalian HiC data reveals that this conserved CTCF configuration is a general signature of TAD borders, underscoring that common organizational principles underlie TAD compartmentalization in deuterostome evolution.