Click
here to close Hello! We notice that
you are using Internet Explorer, which is not supported by Echinobase
and may cause the site to display incorrectly. We suggest using a
current version of Chrome,
FireFox,
or Safari.
Proc Natl Acad Sci U S A
2015 Jun 16;11224:7542-7. doi: 10.1073/pnas.1505463112.
Show Gene links
Show Anatomy links
Evolutionary comparison reveals that diverging CTCF sites are signatures of ancestral topological associating domains borders.
Gómez-Marín C
,
Tena JJ
,
Acemel RD
,
López-Mayorga M
,
Naranjo S
,
de la Calle-Mustienes E
,
Maeso I
,
Beccari L
,
Aneas I
,
Vielmas E
,
Bovolenta P
,
Nobrega MA
,
Carvajal J
,
Gómez-Skarmeta JL
.
???displayArticle.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.
Andrey,
A switch between topological domains underlies HoxD genes collinearity in mouse limbs.
2013, Pubmed
Andrey,
A switch between topological domains underlies HoxD genes collinearity in mouse limbs.
2013,
Pubmed
Angerer,
The evolution of nervous system patterning: insights from sea urchin development.
2011,
Pubmed
,
Echinobase
Buenrostro,
Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes.
2014,
Pubmed
Bussmann,
Rapid BAC selection for tol2-mediated transgenesis in zebrafish.
2011,
Pubmed
Calo,
Modification of enhancer chromatin: what, how, and why?
2013,
Pubmed
Dekker,
Capturing chromosome conformation.
2002,
Pubmed
Dixon,
Topological domains in mammalian genomes identified by analysis of chromatin interactions.
2012,
Pubmed
ENCODE Project Consortium,
An integrated encyclopedia of DNA elements in the human genome.
2012,
Pubmed
Frith,
Detection of functional DNA motifs via statistical over-representation.
2004,
Pubmed
Gallardo,
Genomic cloning and characterization of the human homeobox gene SIX6 reveals a cluster of SIX genes in chromosome 14 and associates SIX6 hemizygosity with bilateral anophthalmia and pituitary anomalies.
1999,
Pubmed
Gehrke,
Deep conservation of wrist and digit enhancers in fish.
2015,
Pubmed
Ghavi-Helm,
Enhancer loops appear stable during development and are associated with paused polymerase.
2014,
Pubmed
Hagège,
Quantitative analysis of chromosome conformation capture assays (3C-qPCR).
2007,
Pubmed
Hughes,
Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment.
2014,
Pubmed
Irimia,
Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints.
2012,
Pubmed
Jin,
A high-resolution map of the three-dimensional chromatin interactome in human cells.
2013,
Pubmed
Jowett,
Whole-mount in situ hybridizations on zebrafish embryos using a mixture of digoxigenin- and fluorescein-labelled probes.
1994,
Pubmed
Li,
Characterization of constitutive CTCF/cohesin loci: a possible role in establishing topological domains in mammalian genomes.
2013,
Pubmed
Lieberman-Aiden,
Comprehensive mapping of long-range interactions reveals folding principles of the human genome.
2009,
Pubmed
Materna,
Diversification of oral and aboral mesodermal regulatory states in pregastrular sea urchin embryos.
2013,
Pubmed
,
Echinobase
Montavon,
Landscapes and archipelagos: spatial organization of gene regulation in vertebrates.
2012,
Pubmed
Nagano,
Single-cell Hi-C reveals cell-to-cell variability in chromosome structure.
2013,
Pubmed
Noordermeer,
Temporal dynamics and developmental memory of 3D chromatin architecture at Hox gene loci.
2014,
Pubmed
Noordermeer,
The dynamic architecture of Hox gene clusters.
2011,
Pubmed
Nora,
Spatial partitioning of the regulatory landscape of the X-inactivation centre.
2012,
Pubmed
Ong,
CTCF: an architectural protein bridging genome topology and function.
2014,
Pubmed
Phillips-Cremins,
Unraveling architecture of the pluripotent genome.
2014,
Pubmed
Ransick,
Whole mount in situ hybridization shows Endo 16 to be a marker for the vegetal plate territory in sea urchin embryos.
1993,
Pubmed
,
Echinobase
Rao,
A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.
2014,
Pubmed
Sexton,
Three-dimensional folding and functional organization principles of the Drosophila genome.
2012,
Pubmed
Smemo,
Obesity-associated variants within FTO form long-range functional connections with IRX3.
2014,
Pubmed
Splinter,
Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: from fixation to computation.
2012,
Pubmed
Stadhouders,
Multiplexed chromosome conformation capture sequencing for rapid genome-scale high-resolution detection of long-range chromatin interactions.
2013,
Pubmed
Steinmetz,
Six3 demarcates the anterior-most developing brain region in bilaterian animals.
2010,
Pubmed
Summerbell,
The expression of Myf5 in the developing mouse embryo is controlled by discrete and dispersed enhancers specific for particular populations of skeletal muscle precursors.
2000,
Pubmed
Suster,
Transposon-mediated BAC transgenesis in zebrafish.
2011,
Pubmed
Taylor,
Comparative genomics provides evidence for an ancient genome duplication event in fish.
2001,
Pubmed
Tena,
Odd-skipped genes encode repressors that control kidney development.
2007,
Pubmed
Wei,
The sea urchin animal pole domain is a Six3-dependent neurogenic patterning center.
2009,
Pubmed
,
Echinobase
de Laat,
Topology of mammalian developmental enhancers and their regulatory landscapes.
2013,
Pubmed