1
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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: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [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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2
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Touceda-Suárez M, Kita EM, Acemel RD, Firbas PN, Magri MS, Naranjo S, Tena JJ, Gómez-Skarmeta JL, Maeso I, Irimia M. Ancient Genomic Regulatory Blocks Are a Source for Regulatory Gene Deserts in Vertebrates after Whole-Genome Duplications. Mol Biol Evol 2020; 37:2857-2864. [PMID: 32421818 PMCID: PMC7530604 DOI: 10.1093/molbev/msaa123] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
We investigated how the two rounds of whole-genome duplication that occurred at the base of the vertebrate lineage have impacted ancient microsyntenic associations involving developmental regulators (known as genomic regulatory blocks, GRBs). We showed that the majority of GRBs identified in the last common ancestor of chordates have been maintained as a single copy in humans. We found evidence that dismantling of the duplicated GRB copies occurred early in vertebrate evolution often through the differential retention of the regulatory gene but loss of the bystander gene’s exonic sequences. Despite the large evolutionary scale, the presence of duplicated highly conserved noncoding regions provided unambiguous proof for this scenario for multiple ancient GRBs. Remarkably, the dismantling of ancient GRB duplicates has contributed to the creation of large gene deserts associated with regulatory genes in vertebrates, providing a potentially widespread mechanism for the origin of these enigmatic genomic traits.
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Affiliation(s)
- María Touceda-Suárez
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, pain
| | - Elizabeth M Kita
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, pain
| | - Rafael D Acemel
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Panos N Firbas
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Marta S Magri
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Silvia Naranjo
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Juan J Tena
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Jose Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Ignacio Maeso
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, pain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,ICREA, Barcelona, Spain
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3
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Hedgehog-FGF signaling axis patterns anterior mesoderm during gastrulation. Proc Natl Acad Sci U S A 2020; 117:15712-15723. [PMID: 32561646 DOI: 10.1073/pnas.1914167117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The mechanisms used by embryos to pattern tissues across their axes has fascinated developmental biologists since the founding of embryology. Here, using single-cell technology, we interrogate complex patterning defects and define a Hedgehog (Hh)-fibroblast growth factor (FGF) signaling axis required for anterior mesoderm lineage development during gastrulation. Single-cell transcriptome analysis of Hh-deficient mesoderm revealed selective deficits in anterior mesoderm populations, culminating in defects to anterior embryonic structures, including the pharyngeal arches, heart, and anterior somites. Transcriptional profiling of Hh-deficient mesoderm during gastrulation revealed disruptions to both transcriptional patterning of the mesoderm and FGF signaling for mesoderm migration. Mesoderm-specific Fgf4/Fgf8 double-mutants recapitulated anterior mesoderm defects and Hh-dependent GLI transcription factors modulated enhancers at FGF gene loci. Cellular migration defects during gastrulation induced by Hh pathway antagonism were mitigated by the addition of FGF4 protein. These findings implicate a multicomponent signaling hierarchy activated by Hh ligands from the embryonic node and executed by FGF signals in nascent mesoderm to control anterior mesoderm patterning.
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4
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Yasuoka Y. Enhancer evolution in chordates: Lessons from functional analyses of cephalochordate cis‐regulatory modules. Dev Growth Differ 2020; 62:279-300. [DOI: 10.1111/dgd.12684] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/25/2020] [Accepted: 05/27/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Yuuri Yasuoka
- Laboratory for Comprehensive Genomic Analysis RIKEN Center for Integrative Medical Sciences Tsurumi‐ku Japan
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5
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Amano T. Gene regulatory landscape of the sonic hedgehog locus in embryonic development. Dev Growth Differ 2020; 62:334-342. [PMID: 32343848 DOI: 10.1111/dgd.12668] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/31/2020] [Accepted: 04/15/2020] [Indexed: 12/22/2022]
Abstract
The organs of vertebrate species display a wide variety of morphology. A remaining challenge in evolutionary developmental biology is to elucidate how vertebrate lineages acquire distinct morphological features. Developmental programs are driven by spatiotemporal regulation of gene expression controlled by hundreds of thousands of cis-regulatory elements. Changes in the regulatory elements caused by the introduction of genetic variants can confer regulatory innovation that may underlie morphological novelties. Recent advances in sequencing technology have revealed a number of potential regulatory variants that can alter gene expression patterns. However, a limited number of studies demonstrate causal dependence between genetic and morphological changes. Regulation of Shh expression is a good model to understand how multiple regulatory elements organize tissue-specific gene expression patterns. This model also provides insights into how evolution of molecular traits, such as gene regulatory networks, lead to phenotypic novelty.
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Affiliation(s)
- Takanori Amano
- Next Generation Human Disease Model Team, RIKEN BioResource Research Center, Tsukuba, Japan
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6
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Okuhara S, Birjandi AA, Adel Al-Lami H, Sagai T, Amano T, Shiroishi T, Xavier GM, Liu KJ, Cobourne MT, Iseki S. Temporospatial sonic hedgehog signalling is essential for neural crest-dependent patterning of the intrinsic tongue musculature. Development 2019; 146:146/21/dev180075. [PMID: 31719045 DOI: 10.1242/dev.180075] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 08/17/2019] [Indexed: 01/20/2023]
Abstract
The tongue is a highly specialised muscular organ with a complex anatomy required for normal function. We have utilised multiple genetic approaches to investigate local temporospatial requirements for sonic hedgehog (SHH) signalling during tongue development. Mice lacking a Shh cis-enhancer, MFCS4 (ShhMFCS4/-), with reduced SHH in dorsal tongue epithelium have perturbed lingual septum tendon formation and disrupted intrinsic muscle patterning, with these defects reproduced following global Shh deletion from E10.5 in pCag-CreERTM; Shhflox/flox embryos. SHH responsiveness was diminished in local cranial neural crest cell (CNCC) populations in both mutants, with SHH targeting these cells through the primary cilium. CNCC-specific deletion of orofaciodigital syndrome 1 (Ofd1), which encodes a ciliary protein, in Wnt1-Cre; Ofdfl/Y mice led to a complete loss of normal myotube arrangement and hypoglossia. In contrast, mesoderm-specific deletion of Ofd1 in Mesp1-Cre; Ofdfl/Y embryos resulted in normal intrinsic muscle arrangement. Collectively, these findings suggest key temporospatial requirements for local SHH signalling in tongue development (specifically, lingual tendon differentiation and intrinsic muscle patterning through signalling to CNCCs) and provide further mechanistic insight into the tongue anomalies seen in patients with disrupted hedgehog signalling.
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Affiliation(s)
- Shigeru Okuhara
- Section of Molecular Craniofacial Embryology, Graduate School of Dental and Medical Sciences, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
| | - Anahid A Birjandi
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London SE1 9RT, UK
| | - Hadeel Adel Al-Lami
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London SE1 9RT, UK
| | - Tomoko Sagai
- Mammalian Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan
| | - Takanori Amano
- Mammalian Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan
| | - Toshihiko Shiroishi
- Mammalian Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan
| | - Guilherme M Xavier
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London SE1 9RT, UK
| | - Karen J Liu
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London SE1 9RT, UK
| | - Martyn T Cobourne
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London SE1 9RT, UK
| | - Sachiko Iseki
- Section of Molecular Craniofacial Embryology, Graduate School of Dental and Medical Sciences, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
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7
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Mikhaleva Y, Skinnes R, Sumic S, Thompson EM, Chourrout D. Development of the house secreting epithelium, a major innovation of tunicate larvaceans, involves multiple homeodomain transcription factors. Dev Biol 2018; 443:117-126. [DOI: 10.1016/j.ydbio.2018.09.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 07/27/2018] [Accepted: 09/05/2018] [Indexed: 01/24/2023]
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8
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Prevalence of Mutation-Prone Microhomology-Mediated End Joining in a Chordate Lacking the c-NHEJ DNA Repair Pathway. Curr Biol 2018; 28:3337-3341.e4. [PMID: 30293719 DOI: 10.1016/j.cub.2018.08.048] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 07/18/2018] [Accepted: 08/21/2018] [Indexed: 12/20/2022]
Abstract
Classical non-homologous end joining (c-NHEJ), a fundamental pathway that repairs double-strand breaks in DNA, is almost universal in eukaryotes and involves multiple proteins highly conserved from yeast to human [1]. The genes encoding these proteins were not detected in the genome of Oikopleura dioica, a new model system of tunicate larvaceans known for its very compact and highly rearranged genome [2-4]. After showing their absence in the genomes of six other larvacean species, the present study examined how O. dioica oocytes and embryos repair double-strand DNA breaks (DSBs), using two approaches: the injection of linearized plasmids, which resulted in their rapid end joining, and a newly established CRISPR Cas9 technique. In both cases, end joining merged short microhomologous sequences surrounding the break (mainly 4 bp long), thus inducing deletions larger than for the tunicate ascidian Ciona intestinalis and human cells. A relatively high frequency of nucleotide insertions was also observed. Finally, a survey of genomic indels supports the involvement of microhomology-mediated repair in natural conditions. Overall, O. dioica repairs DSBs as other organisms do when their c-NHEJ pathway is experimentally rendered deficient, using another mode of end joining with the same effect as alternative NHEJ (a-NHEJ) or microhomology-mediated end joining (MMEJ) [5-7]. We discuss how the exceptional loss of c-NHEJ and its replacement by a more mutation-prone mechanism may have contributed to reshaping this genome and even been advantageous under pressure for genome compaction.
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9
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Roessler E, Hu P, Marino J, Hong S, Hart R, Berger S, Martinez A, Abe Y, Kruszka P, Thomas JW, Mullikin JC, Wang Y, Wong WSW, Niederhuber JE, Solomon BD, Richieri-Costa A, Ribeiro-Bicudo LA, Muenke M. Common genetic causes of holoprosencephaly are limited to a small set of evolutionarily conserved driver genes of midline development coordinated by TGF-β, hedgehog, and FGF signaling. Hum Mutat 2018; 39:1416-1427. [PMID: 29992659 DOI: 10.1002/humu.23590] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 06/05/2018] [Accepted: 07/05/2018] [Indexed: 01/01/2023]
Abstract
Here, we applied targeted capture to examine 153 genes representative of all the major vertebrate developmental pathways among 333 probands to rank their relative significance as causes for holoprosencephaly (HPE). We now show that comparisons of variant transmission versus nontransmission among 136 HPE Trios indicates some reported genes now lack confirmation, while novel genes are implicated. Furthermore, we demonstrate that variation of modest intrinsic effect can synergize with these driver mutations as gene modifiers.
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Affiliation(s)
- Erich Roessler
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Ping Hu
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | | | - Sungkook Hong
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Rachel Hart
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Seth Berger
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Ariel Martinez
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Yu Abe
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Paul Kruszka
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - James W Thomas
- NIH Intramural Sequencing Center, NISC, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - James C Mullikin
- NIH Intramural Sequencing Center, NISC, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
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- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Yupeng Wang
- Inova Translational Medicine Institute, Virginia Commonwealth University School of Medicine, Falls Church, Virginia
| | - Wendy S W Wong
- Inova Translational Medicine Institute, Virginia Commonwealth University School of Medicine, Falls Church, Virginia
| | - John E Niederhuber
- Inova Translational Medicine Institute, Virginia Commonwealth University School of Medicine, Falls Church, Virginia
| | - Benjamin D Solomon
- Inova Translational Medicine Institute, Virginia Commonwealth University School of Medicine, Falls Church, Virginia.,Presently the Managing Director, GeneDx, Gaithersburg, Maryland
| | - Antônio Richieri-Costa
- Hospital for the Rehabilitation of Craniofacial Anomalies, São Paulo University, São Paulo, Brazil
| | - L A Ribeiro-Bicudo
- Institute of Bioscience, Department of Genetics, Federal University of Goias, Goias, Brazil
| | - Maximilian Muenke
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
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10
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Franke M, Gómez-Skarmeta JL. An evolutionary perspective of regulatory landscape dynamics in development and disease. Curr Opin Cell Biol 2018; 55:24-29. [PMID: 30006052 DOI: 10.1016/j.ceb.2018.06.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 06/11/2018] [Accepted: 06/13/2018] [Indexed: 01/01/2023]
Abstract
The organization of animal genomes into topologically associating domains (TADs) provides a structural scaffold in which cis-regulatory elements (CREs) operate on their target genes. Determining the position of CREs and genes relative to TADs has become instrumental to trace gene expression changes during evolution and in diseases. Here we will review recent studies and discuss TADs as structural units with respect to their conservation and stability during genome reorganization. Furthermore, we describe how TAD restructuring contributed to morphological novelties during evolution but also their deleterious effects associated with disease. Despite considering TADs as structural units, the nested and dynamic scaffold within TADs contributes to tissue-specific gene expression, implying that such changes can also account for gene expression differences during evolution.
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Affiliation(s)
- Martin Franke
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Sevilla, Spain.
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Sevilla, Spain.
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11
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Kaucka M, Petersen J, Tesarova M, Szarowska B, Kastriti ME, Xie M, Kicheva A, Annusver K, Kasper M, Symmons O, Pan L, Spitz F, Kaiser J, Hovorakova M, Zikmund T, Sunadome K, Matise MP, Wang H, Marklund U, Abdo H, Ernfors P, Maire P, Wurmser M, Chagin AS, Fried K, Adameyko I. Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. eLife 2018; 7:34465. [PMID: 29897331 PMCID: PMC6019068 DOI: 10.7554/elife.34465] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 06/12/2018] [Indexed: 12/14/2022] Open
Abstract
Facial shape is the basis for facial recognition and categorization. Facial features reflect the underlying geometry of the skeletal structures. Here, we reveal that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped by signals generated by neural structures: brain and olfactory epithelium. Brain-derived Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal capsule, whereas the formation of a capsule roof is controlled by signals from the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule turned out to be important for shaping membranous facial bones during development. This suggests that conserved neurosensory structures could benefit from protection and have evolved signals inducing cranial cartilages encasing them. Experiments with mutant mice revealed that the genomic regulatory regions controlling production of SHH in the nervous system contribute to facial cartilage morphogenesis, which might be a mechanism responsible for the adaptive evolution of animal faces and snouts.
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Affiliation(s)
- Marketa Kaucka
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.,Department of Molecular Neurosciences, Medical University Vienna, Vienna, Austria
| | - Julian Petersen
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.,Department of Molecular Neurosciences, Medical University Vienna, Vienna, Austria
| | - Marketa Tesarova
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Bara Szarowska
- Department of Molecular Neurosciences, Medical University Vienna, Vienna, Austria
| | - Maria Eleni Kastriti
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.,Department of Molecular Neurosciences, Medical University Vienna, Vienna, Austria
| | - Meng Xie
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Anna Kicheva
- Institute of Science and Technology IST Austria, Klosterneuburg, Austria
| | - Karl Annusver
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.,Center for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Maria Kasper
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.,Center for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Orsolya Symmons
- Department of Bioengineering, University of Pennsylvania, Philadelphia, United States
| | - Leslie Pan
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Francois Spitz
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Genomics of Animal Development Unit, Institut Pasteur, Paris, France
| | - Jozef Kaiser
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Maria Hovorakova
- Department of Developmental Biology, Institute of Experimental Medicine, The Czech Academy of Sciences, Prague, Czech Republic
| | - Tomas Zikmund
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Kazunori Sunadome
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Michael P Matise
- Department of Neuroscience & Cell Biology, Rutgers-Robert Wood Johnson Medical School, Piscataway, United States
| | - Hui Wang
- Department of Neuroscience & Cell Biology, Rutgers-Robert Wood Johnson Medical School, Piscataway, United States
| | - Ulrika Marklund
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Hind Abdo
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Patrik Ernfors
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Pascal Maire
- Department of Development, Reproduction and Cancer, Institute Cochin, Paris, France
| | - Maud Wurmser
- Department of Development, Reproduction and Cancer, Institute Cochin, Paris, France
| | - Andrei S Chagin
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.,Institute for Regenerative Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Kaj Fried
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Igor Adameyko
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.,Department of Molecular Neurosciences, Medical University Vienna, Vienna, Austria
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12
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Roessler E, Hu P, Muenke M. Holoprosencephaly in the genomics era. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2018; 178:165-174. [PMID: 29770992 DOI: 10.1002/ajmg.c.31615] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 04/06/2018] [Accepted: 04/11/2018] [Indexed: 01/08/2023]
Abstract
Holoprosencephaly (HPE) is the direct consequence of specific genetic and/or environmental insults interrupting the midline specification of the nascent forebrain. Such disturbances can lead to a broad range of phenotypic consequences for the brain and face in humans. This malformation sequence is remarkably common in utero (1 in 250 human fetuses), but 97% typically do not survive to birth. The precise molecular pathogenesis of HPE in these early human embryos remains largely unknown. Here, we outline our current understanding of the principal driving factors leading to HPE pathologies and elaborate our multifactorial integrated genomics approach. Overall, our understanding of the pathogenesis continues to become simpler, rather than more complicated. Genomic technologies now provide unprecedented insight into disease-associated variation, including the overall extent of genetic interactions (coding and noncoding) predicted to explain divergent phenotypes.
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Affiliation(s)
- Erich Roessler
- Medical Genetics Branch, National Human, Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Ping Hu
- Medical Genetics Branch, National Human, Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Maximilian Muenke
- Medical Genetics Branch, National Human, Genome Research Institute, National Institutes of Health, Bethesda, Maryland
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13
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A conserved Shh cis-regulatory module highlights a common developmental origin of unpaired and paired fins. Nat Genet 2018; 50:504-509. [PMID: 29556077 PMCID: PMC5896732 DOI: 10.1038/s41588-018-0080-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 02/02/2018] [Indexed: 12/23/2022]
Abstract
Despite their evolutionary, developmental, and functional importance the origin of vertebrate paired appendages remains uncertain. In mice, a single enhancer termed ZRS is solely responsible for Shh expression in limbs. Here, zebrafish and mouse transgenic assays trace the functional equivalence of ZRS across the gnathostome phylogeny. CRISPR/Cas9-mediated deletion of the medaka-ZRS and enhancer assays reveal the existence of ZRS shadow enhancers in both teleost and human genomes. Deletion of both ZRS and shadow ZRS abolish shh expression and completely truncate pectoral fin formation. Strikingly, deletion of ZRS results in an almost complete ablation of the dorsal fin. This finding indicates that a ZRS-Shh regulatory module is shared by paired and median fins, and that paired fins likely emerged by the co‐option of developmental programs established in the median fins of stem gnathostomes. Shh function was later reinforced in pectoral fin development with the recruitment of shadow enhancers, conferring additional robustness.
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14
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Harmston N, Ing-Simmons E, Tan G, Perry M, Merkenschlager M, Lenhard B. Topologically associating domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation. Nat Commun 2017; 8:441. [PMID: 28874668 PMCID: PMC5585340 DOI: 10.1038/s41467-017-00524-5] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Accepted: 07/05/2017] [Indexed: 02/08/2023] Open
Abstract
Developmental genes in metazoan genomes are surrounded by dense clusters of conserved noncoding elements (CNEs). CNEs exhibit unexplained extreme levels of sequence conservation, with many acting as developmental long-range enhancers. Clusters of CNEs define the span of regulatory inputs for many important developmental regulators and have been described previously as genomic regulatory blocks (GRBs). Their function and distribution around important regulatory genes raises the question of how they relate to 3D conformation of these loci. Here, we show that clusters of CNEs strongly coincide with topological organisation, predicting the boundaries of hundreds of topologically associating domains (TADs) in human and Drosophila. The set of TADs that are associated with high levels of noncoding conservation exhibit distinct properties compared to TADs devoid of extreme noncoding conservation. The close correspondence between extreme noncoding conservation and TADs suggests that these TADs are ancient, revealing a regulatory architecture conserved over hundreds of millions of years. Metazoan genomes contain many clusters of conserved noncoding elements. Here, the authors provide evidence that these clusters coincide with distinct topologically associating domains in humans and Drosophila, revealing a conserved regulatory genomic architecture.
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Affiliation(s)
- Nathan Harmston
- Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London, W12 0NN, UK. .,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK. .,Program in Cardiovascular and Metabolic Disease, Duke-NUS Graduate Medical School, 8 College Road, Singapore, 169857, Singapore.
| | - Elizabeth Ing-Simmons
- Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London, W12 0NN, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK.,Lymphocyte Development, MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - Ge Tan
- Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London, W12 0NN, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Malcolm Perry
- Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London, W12 0NN, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Matthias Merkenschlager
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK.,Lymphocyte Development, MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - Boris Lenhard
- Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London, W12 0NN, UK. .,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK. .,Sars International Centre for Marine Molecular Biology, University of Bergen, N-5008, Bergen, Norway.
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15
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Maeso I, Acemel RD, Gómez-Skarmeta JL. Cis-regulatory landscapes in development and evolution. Curr Opin Genet Dev 2016; 43:17-22. [PMID: 27842294 DOI: 10.1016/j.gde.2016.10.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 10/17/2016] [Indexed: 10/20/2022]
Abstract
The recent advances in our understanding of the 3D organization of the chromatin together with an almost unlimited ability to detect cis-regulatory elements genome-wide using different biochemical signatures has provided us with an unprecedented power to study gene regulation. It is now possible to profile the complete regulatory apparatus controlling the spatio-temporal expression of any given gene, the so-called gene Regulatory Landscapes (RLs). Here we review several studies over the last two years demonstrating the functional consequences of altering RL structure in development, disease and evolution. These works clearly show that a deep understanding of transcriptional regulation is no longer conceivable without considering the 3D modular organization of animal genomes.
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Affiliation(s)
- Ignacio Maeso
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Carretera de Utrera Km1, Seville, Spain.
| | - Rafael D Acemel
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Carretera de Utrera Km1, Seville, Spain
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Carretera de Utrera Km1, Seville, Spain.
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16
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Yue JX, Kozmikova I, Ono H, Nossa CW, Kozmik Z, Putnam NH, Yu JK, Holland LZ. Conserved Noncoding Elements in the Most Distant Genera of Cephalochordates: The Goldilocks Principle. Genome Biol Evol 2016; 8:2387-405. [PMID: 27412606 PMCID: PMC5010895 DOI: 10.1093/gbe/evw158] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Cephalochordates, the sister group of vertebrates + tunicates, are evolving particularly slowly. Therefore, genome comparisons between two congeners of Branchiostoma revealed so many conserved noncoding elements (CNEs), that it was not clear how many are functional regulatory elements. To more effectively identify CNEs with potential regulatory functions, we compared noncoding sequences of genomes of the most phylogenetically distant cephalochordate genera, Asymmetron and Branchiostoma, which diverged approximately 120-160 million years ago. We found 113,070 noncoding elements conserved between the two species, amounting to 3.3% of the genome. The genomic distribution, target gene ontology, and enriched motifs of these CNEs all suggest that many of them are probably cis-regulatory elements. More than 90% of previously verified amphioxus regulatory elements were re-captured in this study. A search of the cephalochordate CNEs around 50 developmental genes in several vertebrate genomes revealed eight CNEs conserved between cephalochordates and vertebrates, indicating sequence conservation over >500 million years of divergence. The function of five CNEs was tested in reporter assays in zebrafish, and one was also tested in amphioxus. All five CNEs proved to be tissue-specific enhancers. Taken together, these findings indicate that even though Branchiostoma and Asymmetron are distantly related, as they are evolving slowly, comparisons between them are likely optimal for identifying most of their tissue-specific cis-regulatory elements laying the foundation for functional characterizations and a better understanding of the evolution of developmental regulation in cephalochordates.
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Affiliation(s)
- Jia-Xing Yue
- Biosciences at Rice, Rice University, Houston, Texas Present address: Institute for Research on Cancer and Aging, Nice (IRCAN), CNRS UMR 7284, INSERM U1081, Nice 06107 France
| | - Iryna Kozmikova
- Department of Transcriptional Regulation, Institute of Molecular Genetics, Prague 14220, Czech Republic
| | - Hiroki Ono
- Marine Biology Research Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, California
| | - Carlos W Nossa
- Biosciences at Rice, Rice University, Houston, Texas Present address: Gene by Gene Ltd., Houston, TX 77008
| | - Zbynek Kozmik
- Department of Transcriptional Regulation, Institute of Molecular Genetics, Prague 14220, Czech Republic
| | - Nicholas H Putnam
- Biosciences at Rice, Rice University, Houston, Texas Present address: Dovetail Genomics, Santa Cruz, CA 95060
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Linda Z Holland
- Marine Biology Research Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, California
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17
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Yao Y, Minor PJ, Zhao YT, Jeong Y, Pani AM, King AN, Symmons O, Gan L, Cardoso WV, Spitz F, Lowe CJ, Epstein DJ. Cis-regulatory architecture of a brain signaling center predates the origin of chordates. Nat Genet 2016; 48:575-80. [PMID: 27064252 PMCID: PMC4848136 DOI: 10.1038/ng.3542] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 03/11/2016] [Indexed: 12/13/2022]
Abstract
Genomic approaches have predicted hundreds of thousands of tissue-specific cis-regulatory sequences, but the determinants critical to their function and evolutionary history are mostly unknown. Here we systematically decode a set of brain enhancers active in the zona limitans intrathalamica (zli), a signaling center essential for vertebrate forebrain development via the secreted morphogen Sonic hedgehog (Shh). We apply a de novo motif analysis tool to identify six position-independent sequence motifs together with their cognate transcription factors that are essential for zli enhancer activity and Shh expression in the mouse embryo. Using knowledge of this regulatory lexicon, we discover new Shh zli enhancers in mice and a functionally equivalent element in hemichordates, indicating an ancient origin of the Shh zli regulatory network that predates the chordate phylum. These findings support a strategy for delineating functionally conserved enhancers in the absence of overt sequence homologies and over extensive evolutionary distances.
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Affiliation(s)
- Yao Yao
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, 415 Curie Blvd, Clinical Research Building 470, Philadelphia, PA 19104, USA
| | - Paul J. Minor
- Hopkins Marine Station, Department of Biology, Stanford University, 120 Oceanview Blvd. Pacific Grove, CA 93950, USA
| | - Ying-Tao Zhao
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, 415 Curie Blvd, Clinical Research Building 470, Philadelphia, PA 19104, USA
| | - Yongsu Jeong
- Department of Genetic Engineering, College of Life Sciences and Graduate School of Biotechnology, Kyung Hee University, Yongin-si 446-701, Republic of Korea
| | - Ariel M. Pani
- Hopkins Marine Station, Department of Biology, Stanford University, 120 Oceanview Blvd. Pacific Grove, CA 93950, USA
| | - Anna N. King
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, 415 Curie Blvd, Clinical Research Building 470, Philadelphia, PA 19104, USA
| | - Orsolya Symmons
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Lin Gan
- Department of Ophthalmology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Wellington V. Cardoso
- Columbia Center for Human Development, Department of Medicine, Pulmonary Allergy Critical Care, Columbia University Medical Center, New York, NY 10032, USA
| | - François Spitz
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Christopher J. Lowe
- Hopkins Marine Station, Department of Biology, Stanford University, 120 Oceanview Blvd. Pacific Grove, CA 93950, USA
| | - Douglas J. Epstein
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, 415 Curie Blvd, Clinical Research Building 470, Philadelphia, PA 19104, USA
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18
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Maeso I, Tena JJ. Favorable genomic environments for cis-regulatory evolution: A novel theoretical framework. Semin Cell Dev Biol 2015; 57:2-10. [PMID: 26673387 DOI: 10.1016/j.semcdb.2015.12.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 12/02/2015] [Accepted: 12/05/2015] [Indexed: 12/22/2022]
Abstract
Cis-regulatory changes are arguably the primary evolutionary source of animal morphological diversity. With the recent explosion of genome-wide comparisons of the cis-regulatory content in different animal species is now possible to infer general principles underlying enhancer evolution. However, these studies have also revealed numerous discrepancies and paradoxes, suggesting that the mechanistic causes and modes of cis-regulatory evolution are still not well understood and are probably much more complex than generally appreciated. Here, we argue that the mutational mechanisms and genomic regions generating new regulatory activities must comply with the constraints imposed by the molecular properties of cis-regulatory elements (CREs) and the organizational features of long-range chromatin interactions. Accordingly, we propose a new integrative evolutionary framework for cis-regulatory evolution based on two major premises for the origin of novel enhancer activity: (i) an accessible chromatin environment and (ii) compatibility with the 3D structure and interactions of pre-existing CREs. Mechanisms and DNA sequences not fulfilling these premises, will be less likely to have a measurable impact on gene expression and as such, will have a minor contribution to the evolution of gene regulation. Finally, we discuss current comparative cis-regulatory data under the light of this new evolutionary model, and propose that the two most prominent mechanisms for the evolution of cis-regulatory changes are the overprinting of ancestral CREs and the exaptation of transposable elements.
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Affiliation(s)
- Ignacio Maeso
- Centro Andaluz de Biología del Desarrollo (CSIC/UPO/JA), Universidad Pablo de Olavide, 41013 Seville, Spain.
| | - Juan J Tena
- Centro Andaluz de Biología del Desarrollo (CSIC/UPO/JA), Universidad Pablo de Olavide, 41013 Seville, Spain.
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19
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Kozmikova I, Kozmik Z. Gene regulation in amphioxus: An insight from transgenic studies in amphioxus and vertebrates. Mar Genomics 2015; 24 Pt 2:159-66. [PMID: 26094865 DOI: 10.1016/j.margen.2015.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 06/10/2015] [Accepted: 06/10/2015] [Indexed: 01/07/2023]
Abstract
Cephalochordates, commonly known as amphioxus or lancelets, are the most basal subphylum of chordates. Cephalochordates are thus key to understanding the origin of vertebrates and molecular mechanisms underlying vertebrate evolution. The evolution of developmental control mechanisms during invertebrate-to-vertebrate transition involved not only gene duplication events, but also specific changes in spatial and temporal expression of many genes. To get insight into the spatiotemporal regulation of gene expression during invertebrate-to-vertebrate transition, functional studies of amphioxus gene regulatory elements are highly warranted. Here, we review transgenic studies performed in amphioxus and vertebrates using promoters and enhancers derived from the genome of Branchiostoma floridae. We describe the current methods of transgenesis in amphioxus, provide evidence of Tol2 transposon-generated transgenic embryos of Branchiostoma lanceolatum and discuss possible future directions. We envision that comparative transgenic analysis of gene regulatory sequences in the context of amphioxus and vertebrate embryos will likely provide an important mechanistic insight into the evolution of vertebrate body plan.
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Affiliation(s)
- Iryna Kozmikova
- Institute of Molecular Genetics of the Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Zbynek Kozmik
- Institute of Molecular Genetics of the Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic.
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20
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Pereira J, Johnson WE, O’Brien SJ, Jarvis ED, Zhang G, Gilbert MTP, Vasconcelos V, Antunes A. Evolutionary genomics and adaptive evolution of the Hedgehog gene family (Shh, Ihh and Dhh) in vertebrates. PLoS One 2014; 9:e74132. [PMID: 25549322 PMCID: PMC4280113 DOI: 10.1371/journal.pone.0074132] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 07/29/2013] [Indexed: 12/21/2022] Open
Abstract
The Hedgehog (Hh) gene family codes for a class of secreted proteins composed of two active domains that act as signalling molecules during embryo development, namely for the development of the nervous and skeletal systems and the formation of the testis cord. While only one Hh gene is found typically in invertebrate genomes, most vertebrates species have three (Sonic hedgehog – Shh; Indian hedgehog – Ihh; and Desert hedgehog – Dhh), each with different expression patterns and functions, which likely helped promote the increasing complexity of vertebrates and their successful diversification. In this study, we used comparative genomic and adaptive evolutionary analyses to characterize the evolution of the Hh genes in vertebrates following the two major whole genome duplication (WGD) events. To overcome the lack of Hh-coding sequences on avian publicly available databases, we used an extensive dataset of 45 avian and three non-avian reptilian genomes to show that birds have all three Hh paralogs. We find suggestions that following the WGD events, vertebrate Hh paralogous genes evolved independently within similar linkage groups and under different evolutionary rates, especially within the catalytic domain. The structural regions around the ion-binding site were identified to be under positive selection in the signaling domain. These findings contrast with those observed in invertebrates, where different lineages that experienced gene duplication retained similar selective constraints in the Hh orthologs. Our results provide new insights on the evolutionary history of the Hh gene family, the functional roles of these paralogs in vertebrate species, and on the location of mutational hotspots.
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Affiliation(s)
- Joana Pereira
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - Warren E. Johnson
- Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, Virginia, United States of America
| | - Stephen J. O’Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
- Oceanographic Center, N. Ocean Drive, Nova Southeastern University, Ft. Lauderdale, Florida, United States of America
| | - Erich D. Jarvis
- Howard Hughes Medical Institute, Department of Neurobiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Guojie Zhang
- BGI-Shenzhen, Beishan Industrial Zoon, Yantian District, Shenzhen, China
| | - M. Thomas P. Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Vitor Vasconcelos
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- * E-mail:
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21
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Genome-wide analysis of functional and evolutionary features of tele-enhancers. G3-GENES GENOMES GENETICS 2014; 4:579-93. [PMID: 24496725 PMCID: PMC4059231 DOI: 10.1534/g3.114.010447] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We investigated sequence features of enhancers separated from their target gene by at least one intermediate gene/exon (named tele-enhancers in this study) and enhancers residing inside their target gene locus. In this study, we used whole genome enhancer maps and gene expression profiles to establish a large panel of tele-enhancers. By contrasting tele-enhancers to proximal enhancers targeting heart genes, we observed that heart tele-enhancers use unique regulatory mechanisms based on the cardiac transcription factors SRF, TEAD, and NKX-2.5, whereas proximal heart enhancers rely on GATA4 instead. A functional analysis showed that tele-enhancers preferentially regulate house-keeping genes and genes with a metabolic role during heart development. In addition, tele-enhancers are significantly more conserved than their proximal counterparts. Similar trends have been observed for non-heart tissues and cell types, suggesting that our findings represent general characteristics of tele-enhancers.
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22
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Irimia M, Maeso I, Roy SW, Fraser HB. Ancient cis-regulatory constraints and the evolution of genome architecture. Trends Genet 2013; 29:521-8. [PMID: 23791467 DOI: 10.1016/j.tig.2013.05.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 05/02/2013] [Accepted: 05/15/2013] [Indexed: 01/18/2023]
Abstract
The order of genes along metazoan chromosomes has generally been thought to be largely random, with few implications for organismal function. However, two recent studies, reporting hundreds of pairs of genes that have remained linked in diverse metazoan species over hundreds of millions of years of evolution, suggest widespread functional implications for gene order. These associations appear to largely reflect cis-regulatory constraints, with either (i) multiple genes sharing transcriptional regulatory elements, or (ii) regulatory elements for a developmental gene being found within a neighboring 'bystander' gene (known as a genomic regulatory block). We discuss implications, questions raised, and new research directions arising from these studies, as well as evidence for similar phenomena in other eukaryotic groups.
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Affiliation(s)
- Manuel Irimia
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.
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23
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Cañestro C, Albalat R, Irimia M, Garcia-Fernàndez J. Impact of gene gains, losses and duplication modes on the origin and diversification of vertebrates. Semin Cell Dev Biol 2013; 24:83-94. [DOI: 10.1016/j.semcdb.2012.12.008] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 12/25/2012] [Indexed: 02/06/2023]
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24
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Ariza-Cosano A, Visel A, Pennacchio LA, Fraser HB, Gómez-Skarmeta JL, Irimia M, Bessa J. Differences in enhancer activity in mouse and zebrafish reporter assays are often associated with changes in gene expression. BMC Genomics 2012; 13:713. [PMID: 23253453 PMCID: PMC3541358 DOI: 10.1186/1471-2164-13-713] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 12/14/2012] [Indexed: 01/18/2023] Open
Abstract
Background Phenotypic evolution in animals is thought to be driven in large part by differences in gene expression patterns, which can result from sequence changes in cis-regulatory elements (cis-changes) or from changes in the expression pattern or function of transcription factors (trans-changes). While isolated examples of trans-changes have been identified, the scale of their overall contribution to regulatory and phenotypic evolution remains unclear. Results Here, we attempt to examine the prevalence of trans-effects and their potential impact on gene expression patterns in vertebrate evolution by comparing the function of identical human tissue-specific enhancer sequences in two highly divergent vertebrate model systems, mouse and zebrafish. Among 47 human conserved non-coding elements (CNEs) tested in transgenic mouse embryos and in stable zebrafish lines, at least one species-specific expression domain was observed in the majority (83%) of cases, and 36% presented dramatically different expression patterns between the two species. Although some of these discrepancies may be due to the use of different transgenesis systems in mouse and zebrafish, in some instances we found an association between differences in enhancer activity and changes in the endogenous gene expression patterns between mouse and zebrafish, suggesting a potential role for trans-changes in the evolution of gene expression. Conclusions In total, our results: (i) serve as a cautionary tale for studies investigating the role of human enhancers in different model organisms, and (ii) suggest that changes in the trans environment may play a significant role in the evolution of gene expression in vertebrates.
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Affiliation(s)
- Ana Ariza-Cosano
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Ctra. Utrera Km 1, Seville 41013, Spain
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25
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Irimia M, Tena JJ, Alexis MS, Fernandez-Miñan A, Maeso I, Bogdanovic O, de la Calle-Mustienes E, Roy SW, Gómez-Skarmeta JL, Fraser HB. Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints. Genome Res 2012; 22:2356-67. [PMID: 22722344 PMCID: PMC3514665 DOI: 10.1101/gr.139725.112] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The order of genes in eukaryotic genomes has generally been assumed to be neutral, since gene order is largely scrambled over evolutionary time. Only a handful of exceptional examples are known, typically involving deeply conserved clusters of tandemly duplicated genes (e.g., Hox genes and histones). Here we report the first systematic survey of microsynteny conservation across metazoans, utilizing 17 genome sequences. We identified nearly 600 pairs of unrelated genes that have remained tightly physically linked in diverse lineages across over 600 million years of evolution. Integrating sequence conservation, gene expression data, gene function, epigenetic marks, and other genomic features, we provide extensive evidence that many conserved ancient linkages involve (1) the coordinated transcription of neighboring genes, or (2) genomic regulatory blocks (GRBs) in which transcriptional enhancers controlling developmental genes are contained within nearby bystander genes. In addition, we generated ChIP-seq data for key histone modifications in zebrafish embryos, which provided further evidence of putative GRBs in embryonic development. Finally, using chromosome conformation capture (3C) assays and stable transgenic experiments, we demonstrate that enhancers within bystander genes drive the expression of genes such as Otx and Islet, critical regulators of central nervous system development across bilaterians. These results suggest that ancient genomic functional associations are far more common than previously thought—involving ∼12% of the ancestral bilaterian genome—and that cis-regulatory constraints are crucial in determining metazoan genome architecture.
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Affiliation(s)
- Manuel Irimia
- Department of Biology, Stanford University, Stanford, California 94305, USA
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