title: Evolutionary comparison reveals that diverging CTCF sites are signatures of ancestral topological associating domains borders.
abstract: 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.
authors.affiliation: Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville 41013, Spain;
authors.forename: Carlos
authors.initials: C
authors.lastname: Gómez-Marín
authors.affiliation: Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville 41013, Spain;
authors.forename: Juan J
authors.initials: JJ
authors.lastname: Tena
authors.affiliation: Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville 41013, Spain;
authors.forename: Rafael D
authors.initials: RD
authors.lastname: Acemel
authors.affiliation: Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville 41013, Spain;
authors.forename: Macarena
authors.initials: M
authors.lastname: López-Mayorga
authors.affiliation: Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville 41013, Spain;
authors.forename: Silvia
authors.initials: S
authors.lastname: Naranjo
authors.affiliation: Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville 41013, Spain;
authors.forename: Elisa
authors.initials: E
authors.lastname: de la Calle-Mustienes
authors.affiliation: Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville 41013, Spain;
authors.forename: Ignacio
authors.initials: I
authors.lastname: Maeso
authors.affiliation: Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid, Madrid 28049, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, 28049 Madrid, Spain;
authors.forename: Leonardo
authors.initials: L
authors.lastname: Beccari
authors.affiliation: Department of Human Genetics, University of Chicago, IL 60637;
authors.forename: Ivy
authors.initials: I
authors.lastname: Aneas
authors.affiliation: Division of Biology, California Institute of Technology, Pasadena, CA 91125.
authors.forename: Erika
authors.initials: E
authors.lastname: Vielmas
authors.affiliation: Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid, Madrid 28049, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, 28049 Madrid, Spain;
authors.forename: Paola
authors.initials: P
authors.lastname: Bovolenta
authors.affiliation: Department of Human Genetics, University of Chicago, IL 60637;
authors.forename: Marcelo A
authors.initials: MA
authors.lastname: Nobrega
authors.affiliation: Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville 41013, Spain;
authors.forename: Jaime
authors.initials: J
authors.lastname: Carvajal
authors.affiliation: Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville 41013, Spain; jlgomska@upo.es.
authors.forename: José Luis
authors.initials: JL
authors.lastname: Gómez-Skarmeta
mesh_terms: D000818:Animals; D030801:Animals, Genetically Modified; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D000076246:CCCTC-Binding Factor; D002843:Chromatin / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D017124:Conserved Sequence; D004247:DNA / Q000235:genetics; D004742:Enhancer Elements, Genetic; D019143:Evolution, Molecular; D005801:Genes, Homeobox; D018398:Homeodomain Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D006801:Humans; D051379:Mice; D008957:Models, Genetic; D005810:Multigene Family; D011401:Promoter Regions, Genetic; D054730:Protein Interaction Domains and Motifs; D012097:Repressor Proteins / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D047270:Strongylocentrotus purpuratus / Q000235:genetics; D015027:Zebrafish / Q000235:genetics
chemical_list: D000076246:CCCTC-Binding Factor; C000619697:CTCF protein, human; D002843:Chromatin; C000619698:Ctcf protein, mouse; D018398:Homeodomain Proteins; D012097:Repressor Proteins; D004247:DNA
keywords: CTCF; Six cluster; TAD; evolution; regulatory landscapes