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Tena JJ, Santos-Pereira JM. Topologically Associating Domains and Regulatory Landscapes in Development, Evolution and Disease. Front Cell Dev Biol 2021; 9:702787. [PMID: 34295901 PMCID: PMC8290416 DOI: 10.3389/fcell.2021.702787] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/17/2021] [Indexed: 01/02/2023] Open
Abstract
Animal genomes are folded in topologically associating domains (TADs) that have been linked to the regulation of the genes they contain by constraining regulatory interactions between cis-regulatory elements and promoters. Therefore, TADs are proposed as structural scaffolds for the establishment of regulatory landscapes (RLs). In this review, we discuss recent advances in the connection between TADs and gene regulation, their relationship with gene RLs and their dynamics during development and differentiation. Moreover, we describe how restructuring TADs may lead to pathological conditions, which explains their high evolutionary conservation, but at the same time it provides a substrate for the emergence of evolutionary innovations that lay at the origin of vertebrates and other phylogenetic clades.
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Affiliation(s)
- Juan J. Tena
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain
| | - José M. Santos-Pereira
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain
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Abstract
Ros discusses the report by Beccari et al. on the mechanism of HOX13 regulation of HoxD gene expression in the developing tetrapod limb to create a region of low Hox expression that ultimately gives rise to the wrist as well as the evolutionary implications of this finding. The striking correlation between the genomic arrangement of Hox genes and their temporal and spatial pattern of expression during embryonic development has been a source of fascination since its discovery. This correspondence has been used as a privileged example in the investigation of the connection between genomic architecture and function. In this issue of Genes & Development, Beccari and colleagues (pp. 1172–1186) make a big step forward in understanding Hox gene regulation during limb development by showing the pivotal role of HOXA13 and HOXD13 proteins in the transition from a proximal to a distal type of Hoxd transcriptional regulation.
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Affiliation(s)
- Marian A Ros
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas-Universidad de Cantabria, 39011 Santander, Spain
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Neijts R, Amin S, van Rooijen C, Tan S, Creyghton MP, de Laat W, Deschamps J. Polarized regulatory landscape and Wnt responsiveness underlie Hox activation in embryos. Genes Dev 2016; 30:1937-42. [PMID: 27633012 PMCID: PMC5066237 DOI: 10.1101/gad.285767.116] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 08/26/2016] [Indexed: 01/14/2023]
Abstract
Neijts et al. show that a series of enhancers, some of which are Wnt-dependent, is located within a HoxA 3′ subTAD. This subTAD forms the structural basis for multiple layers of 3′-polarized features, including DNA accessibility and enhancer activation. Sequential 3′-to-5′ activation of the Hox gene clusters in early embryos is a most fascinating issue in developmental biology. Neither the trigger nor the regulatory elements involved in the transcriptional initiation of the 3′-most Hox genes have been unraveled in any organism. We demonstrate that a series of enhancers, some of which are Wnt-dependent, is located within a HoxA 3′ subtopologically associated domain (subTAD). This subTAD forms the structural basis for multiple layers of 3′-polarized features, including DNA accessibility and enhancer activation. Deletion of the cassette of Wnt-dependent enhancers proves its crucial role in initial transcription of HoxA at the 3′ side of the cluster.
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Affiliation(s)
- Roel Neijts
- Hubrecht Institute, University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Shilu Amin
- Hubrecht Institute, University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Carina van Rooijen
- Hubrecht Institute, University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Sander Tan
- Hubrecht Institute, University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Menno P Creyghton
- Hubrecht Institute, University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Wouter de Laat
- Hubrecht Institute, University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Jacqueline Deschamps
- Hubrecht Institute, University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
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Beccari L, Yakushiji-Kaminatsui N, Woltering JM, Necsulea A, Lonfat N, Rodríguez-Carballo E, Mascrez B, Yamamoto S, Kuroiwa A, Duboule D. A role for HOX13 proteins in the regulatory switch between TADs at the HoxD locus. Genes Dev 2016; 30:1172-86. [PMID: 27198226 PMCID: PMC4888838 DOI: 10.1101/gad.281055.116] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 04/22/2016] [Indexed: 11/24/2022]
Abstract
During vertebrate limb development, Hoxd genes are regulated following a bimodal strategy involving two topologically associating domains (TADs) located on either side of the gene cluster. These regulatory landscapes alternatively control different subsets of Hoxd targets, first into the arm and subsequently into the digits. We studied the transition between these two global regulations, a switch that correlates with the positioning of the wrist, which articulates these two main limb segments. We show that the HOX13 proteins themselves help switch off the telomeric TAD, likely through a global repressive mechanism. At the same time, they directly interact with distal enhancers to sustain the activity of the centromeric TAD, thus explaining both the sequential and exclusive operating processes of these two regulatory domains. We propose a model in which the activation of Hox13 gene expression in distal limb cells both interrupts the proximal Hox gene regulation and re-enforces the distal regulation. In the absence of HOX13 proteins, a proximal limb structure grows without any sign of wrist articulation, likely related to an ancestral fish-like condition.
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Affiliation(s)
- Leonardo Beccari
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva 4, Switzerland
| | | | - Joost M Woltering
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva 4, Switzerland
| | - Anamaria Necsulea
- School of Life Sciences, Federal Institute of Technology, Lausanne, 1015 Lausanne, Switzerland
| | - Nicolas Lonfat
- School of Life Sciences, Federal Institute of Technology, Lausanne, 1015 Lausanne, Switzerland
| | | | - Benedicte Mascrez
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva 4, Switzerland
| | - Shiori Yamamoto
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
| | - Atsushi Kuroiwa
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
| | - Denis Duboule
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva 4, Switzerland; School of Life Sciences, Federal Institute of Technology, Lausanne, 1015 Lausanne, Switzerland
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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. Evolutionary comparison reveals that diverging CTCF sites are signatures of ancestral topological associating domains borders. Proc Natl Acad Sci U S A 2015; 112:7542-7. [PMID: 26034287 DOI: 10.1073/pnas.1505463112] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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.
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Abstract
We discuss here a series of testable hypotheses concerning the role of chromosome folding into topologically associating domains (TADs). Several lines of evidence suggest that segmental packaging of chromosomal neighborhoods may underlie features of chromatin that span large domains, such as heterochromatin blocks, association with the nuclear lamina and replication timing. By defining which DNA elements preferentially contact each other, the segmentation of chromosomes into TADs may also underlie many properties of long-range transcriptional regulation. Several observations suggest that TADs can indeed provide a structural basis to regulatory landscapes, by controlling enhancer sharing and allocation. We also discuss how TADs may shape the evolution of chromosomes, by causing maintenance of synteny over large chromosomal segments. Finally we suggest a series of experiments to challenge these ideas and provide concrete examples illustrating how they could be practically applied.
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