1
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Hintermann A, Bolt CC, Hawkins MB, Valentin G, Lopez-Delisle L, Gitto S, Gómez PB, Mascrez B, Mansour TA, Nakamura T, Harris MP, Shubin NH, Duboule D. EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE DURING THE EMERGENCE OF DIGITS AND GENITALS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.24.586442. [PMID: 38585989 PMCID: PMC10996561 DOI: 10.1101/2024.03.24.586442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The transition from fins to limbs has been a rich source of discussion for more than a century. One open and important issue is understanding how the mechanisms that pattern digits arose during vertebrate evolution. In this context, the analysis of Hox gene expression and functions to infer evolutionary scenarios has been a productive approach to explain the changes in organ formation, particularly in limbs. In tetrapods, the transcription of Hoxd genes in developing digits depends on a well-characterized set of enhancers forming a large regulatory landscape1,2. This control system has a syntenic counterpart in zebrafish, even though they lack bona fide digits, suggestive of deep homology3 between distal fin and limb developmental mechanisms. We tested the global function of this landscape to assess ancestry and source of limb and fin variation. In contrast to results in mice, we show here that the deletion of the homologous control region in zebrafish has a limited effect on the transcription of hoxd genes during fin development. However, it fully abrogates hoxd expression within the developing cloaca, an ancestral structure related to the mammalian urogenital sinus. We show that similar to the limb, Hoxd gene function in the urogenital sinus of the mouse also depends on enhancers located in this same genomic domain. Thus, we conclude that the current regulation underlying Hoxd gene expression in distal limbs was co-opted in tetrapods from a preexisting cloacal program. The orthologous chromatin domain in fishes may illustrate a rudimentary or partial step in this evolutionary co-option.
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Affiliation(s)
- Aurélie Hintermann
- Department of Genetics and Evolution, University of Geneva, 30 quai Ernest Ansermet, 1211, Geneva, Switzerland
| | - Christopher Chase Bolt
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne EPFL, 1015 Lausanne, Switzerland
| | - M. Brent Hawkins
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA, Department of Orthopedic Research, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Guillaume Valentin
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne EPFL, 1015 Lausanne, Switzerland
| | - Lucille Lopez-Delisle
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne EPFL, 1015 Lausanne, Switzerland
| | - Sandra Gitto
- Department of Genetics and Evolution, University of Geneva, 30 quai Ernest Ansermet, 1211, Geneva, Switzerland
| | - Paula Barrera Gómez
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne EPFL, 1015 Lausanne, Switzerland
| | - Bénédicte Mascrez
- Department of Genetics and Evolution, University of Geneva, 30 quai Ernest Ansermet, 1211, Geneva, Switzerland
| | | | - Tetsuya Nakamura
- Department of Genetics, Rutgers University, New Brunswick, NJ, USA
| | - Matthew P. Harris
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA, Department of Orthopedic Research, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Neil H. Shubin
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, IL, USA
| | - Denis Duboule
- Department of Genetics and Evolution, University of Geneva, 30 quai Ernest Ansermet, 1211, Geneva, Switzerland
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne EPFL, 1015 Lausanne, Switzerland
- Center for Interdisciplinary Research in Biology CIRB, Collège de France, CNRS, INSERM, Université PSL, Paris, France
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2
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Thorburn DMJ, Sagonas K, Binzer-Panchal M, Chain FJJ, Feulner PGD, Bornberg-Bauer E, Reusch TBH, Samonte-Padilla IE, Milinski M, Lenz TL, Eizaguirre C. Origin matters: Using a local reference genome improves measures in population genomics. Mol Ecol Resour 2023; 23:1706-1723. [PMID: 37489282 DOI: 10.1111/1755-0998.13838] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/10/2023] [Accepted: 06/02/2023] [Indexed: 07/26/2023]
Abstract
Genome sequencing enables answering fundamental questions about the genetic basis of adaptation, population structure and epigenetic mechanisms. Yet, we usually need a suitable reference genome for mapping population-level resequencing data. In some model systems, multiple reference genomes are available, giving the challenging task of determining which reference genome best suits the data. Here, we compared the use of two different reference genomes for the three-spined stickleback (Gasterosteus aculeatus), one novel genome derived from a European gynogenetic individual and the published reference genome of a North American individual. Specifically, we investigated the impact of using a local reference versus one generated from a distinct lineage on several common population genomics analyses. Through mapping genome resequencing data of 60 sticklebacks from across Europe and North America, we demonstrate that genetic distance among samples and the reference genomes impacts downstream analyses. Using a local reference genome increased mapping efficiency and genotyping accuracy, effectively retaining more and better data. Despite comparable distributions of the metrics generated across the genome using SNP data (i.e. π, Tajima's D and FST ), window-based statistics using different references resulted in different outlier genes and enriched gene functions. A marker-based analysis of DNA methylation distributions had a comparably high overlap in outlier genes and functions, yet with distinct differences depending on the reference genome. Overall, our results highlight how using a local reference genome decreases reference bias to increase confidence in downstream analyses of the data. Such results have significant implications in all reference-genome-based population genomic analyses.
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Affiliation(s)
- Doko-Miles J Thorburn
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- Department of Life Sciences, Imperial College London, London, UK
| | - Kostas Sagonas
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Mahesh Binzer-Panchal
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden (NBIS), Uppsala University, Uppsala, Sweden
| | - Frederic J J Chain
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Philine G D Feulner
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Erich Bornberg-Bauer
- Evolutionary Bioinformatics, Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Thorsten B H Reusch
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Irene E Samonte-Padilla
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Manfred Milinski
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
| | - Christophe Eizaguirre
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
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3
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Kozol RA, Conith AJ, Yuiska A, Cree-Newman A, Tolentino B, Benesh K, Paz A, Lloyd E, Kowalko JE, Keene AC, Albertson C, Duboue ER. A brain-wide analysis maps structural evolution to distinct anatomical module. eLife 2023; 12:e80777. [PMID: 37498318 PMCID: PMC10435234 DOI: 10.7554/elife.80777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 07/26/2023] [Indexed: 07/28/2023] Open
Abstract
The vertebrate brain is highly conserved topologically, but less is known about neuroanatomical variation between individual brain regions. Neuroanatomical variation at the regional level is hypothesized to provide functional expansion, building upon ancestral anatomy needed for basic functions. Classically, animal models used to study evolution have lacked tools for detailed anatomical analysis that are widely used in zebrafish and mice, presenting a barrier to studying brain evolution at fine scales. In this study, we sought to investigate the evolution of brain anatomy using a single species of fish consisting of divergent surface and cave morphs, that permits functional genetic testing of regional volume and shape across the entire brain. We generated a high-resolution brain atlas for the blind Mexican cavefish Astyanax mexicanus and coupled the atlas with automated computational tools to directly assess variability in brain region shape and volume across all populations. We measured the volume and shape of every grossly defined neuroanatomical region of the brain and assessed correlations between anatomical regions in surface fish, cavefish, and surface × cave F2 hybrids, whose phenotypes span the range of surface to cave. We find that dorsal regions of the brain are contracted, while ventral regions have expanded, with F2 hybrid data providing support for developmental constraint along the dorsal-ventral axis. Furthermore, these dorsal-ventral relationships in anatomical variation show similar patterns for both volume and shape, suggesting that the anatomical evolution captured by these two parameters could be driven by similar developmental mechanisms. Together, these data demonstrate that A. mexicanus is a powerful system for functionally determining basic principles of brain evolution and will permit testing how genes influence early patterning events to drive brain-wide anatomical evolution.
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Affiliation(s)
- Robert A Kozol
- Jupiter Life Science Initiative, Florida Atlantic UniversityJupiterUnited States
| | - Andrew J Conith
- Department of Biology, University of Massachusetts AmherstAmherstUnited States
| | - Anders Yuiska
- Jupiter Life Science Initiative, Florida Atlantic UniversityJupiterUnited States
| | - Alexia Cree-Newman
- Jupiter Life Science Initiative, Florida Atlantic UniversityJupiterUnited States
| | - Bernadeth Tolentino
- Jupiter Life Science Initiative, Florida Atlantic UniversityJupiterUnited States
| | - Kasey Benesh
- Jupiter Life Science Initiative, Florida Atlantic UniversityJupiterUnited States
| | - Alexandra Paz
- Jupiter Life Science Initiative, Florida Atlantic UniversityJupiterUnited States
| | - Evan Lloyd
- Department of Biology, Texas A&M UniversityCollege StationUnited States
| | - Johanna E Kowalko
- Department of Biological Sciences, Lehigh UniversityBethlehemUnited States
| | - Alex C Keene
- Department of Biology, Texas A&M UniversityCollege StationUnited States
| | - Craig Albertson
- Department of Biology, University of Massachusetts AmherstAmherstUnited States
| | - Erik R Duboue
- Jupiter Life Science Initiative, Florida Atlantic UniversityJupiterUnited States
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4
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Pinglay S, Bulajić M, Rahe DP, Huang E, Brosh R, Mamrak NE, King BR, German S, Cadley JA, Rieber L, Easo N, Lionnet T, Mahony S, Maurano MT, Holt LJ, Mazzoni EO, Boeke JD. Synthetic regulatory reconstitution reveals principles of mammalian Hox cluster regulation. Science 2022; 377:eabk2820. [PMID: 35771912 PMCID: PMC9648154 DOI: 10.1126/science.abk2820] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Precise Hox gene expression is crucial for embryonic patterning. Intra-Hox transcription factor binding and distal enhancer elements have emerged as the major regulatory modules controlling Hox gene expression. However, quantifying their relative contributions has remained elusive. Here, we introduce "synthetic regulatory reconstitution," a conceptual framework for studying gene regulation, and apply it to the HoxA cluster. We synthesized and delivered variant rat HoxA clusters (130 to 170 kilobases) to an ectopic location in the mouse genome. We found that a minimal HoxA cluster recapitulated correct patterns of chromatin remodeling and transcription in response to patterning signals, whereas the addition of distal enhancers was needed for full transcriptional output. Synthetic regulatory reconstitution could provide a generalizable strategy for deciphering the regulatory logic of gene expression in complex genomes.
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Affiliation(s)
- Sudarshan Pinglay
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Milica Bulajić
- Department of Biology, New York University, New York, NY 10003, USA
| | - Dylan P. Rahe
- Department of Biology, New York University, New York, NY 10003, USA
| | - Emily Huang
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Ran Brosh
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Nicholas E. Mamrak
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Benjamin R. King
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Sergei German
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - John A. Cadley
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Lila Rieber
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Nicole Easo
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Timothée Lionnet
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
- Department of Cell Biology, NYU Langone Health, New York, NY 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
| | - Shaun Mahony
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Matthew T. Maurano
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
- Department of Pathology, NYU Langone Health, New York, NY 10016, USA
| | - Liam J. Holt
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | | | - Jef D. Boeke
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
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5
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Hintermann A, Guerreiro I, Lopez-Delisle L, Bolt CC, Gitto S, Duboule D, Beccari L. Developmental and evolutionary comparative analysis of a regulatory landscape in mouse and chicken. Development 2022; 149:275867. [PMID: 35770682 PMCID: PMC9307994 DOI: 10.1242/dev.200594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 05/23/2022] [Indexed: 12/12/2022]
Abstract
Modifications in gene regulation are driving forces in the evolution of organisms. Part of these changes involve cis-regulatory elements (CREs), which contact their target genes through higher-order chromatin structures. However, how such architectures and variations in CREs contribute to transcriptional evolvability remains elusive. We use Hoxd genes as a paradigm for the emergence of regulatory innovations, as many relevant enhancers are located in a regulatory landscape highly conserved in amniotes. Here, we analysed their regulation in murine vibrissae and chicken feather primordia, two skin appendages expressing different Hoxd gene subsets, and compared the regulation of these genes in these appendages with that in the elongation of the posterior trunk. In the two former structures, distinct subsets of Hoxd genes are contacted by different lineage-specific enhancers, probably as a result of using an ancestral chromatin topology as an evolutionary playground, whereas the gene regulation that occurs in the mouse and chicken embryonic trunk partially relies on conserved CREs. A high proportion of these non-coding sequences active in the trunk have functionally diverged between species, suggesting that transcriptional robustness is maintained, despite considerable divergence in enhancer sequences. Summary: Analyses of the relationships between chromatin architecture and regulatory activities at the HoxD locus show that ancestral transcription patterns can be maintained while new regulations evolve.
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Affiliation(s)
- Aurélie Hintermann
- University of Geneva 1 Department of Genetics and Evolution , , 30 quai Ernest-Ansermet, 1211 Geneva , Switzerland
| | - Isabel Guerreiro
- University of Geneva 1 Department of Genetics and Evolution , , 30 quai Ernest-Ansermet, 1211 Geneva , Switzerland
| | - Lucille Lopez-Delisle
- Swiss Institute for Experimental Cancer Research (EPFL ISREC), School of Life Sciences, Federal School of Technology (EPFL) 2 , 1015 Lausanne , Switzerland
| | - Christopher Chase Bolt
- Swiss Institute for Experimental Cancer Research (EPFL ISREC), School of Life Sciences, Federal School of Technology (EPFL) 2 , 1015 Lausanne , Switzerland
| | - Sandra Gitto
- University of Geneva 1 Department of Genetics and Evolution , , 30 quai Ernest-Ansermet, 1211 Geneva , Switzerland
| | - Denis Duboule
- University of Geneva 1 Department of Genetics and Evolution , , 30 quai Ernest-Ansermet, 1211 Geneva , Switzerland
- Swiss Institute for Experimental Cancer Research (EPFL ISREC), School of Life Sciences, Federal School of Technology (EPFL) 2 , 1015 Lausanne , Switzerland
- Collège de France 3 , 11 Place Marcelin Berthelot, 75005 Paris , France
| | - Leonardo Beccari
- University of Geneva 1 Department of Genetics and Evolution , , 30 quai Ernest-Ansermet, 1211 Geneva , Switzerland
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6
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Singh NP, Krumlauf R. Diversification and Functional Evolution of HOX Proteins. Front Cell Dev Biol 2022; 10:798812. [PMID: 35646905 PMCID: PMC9136108 DOI: 10.3389/fcell.2022.798812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 04/08/2022] [Indexed: 01/07/2023] Open
Abstract
Gene duplication and divergence is a major contributor to the generation of morphological diversity and the emergence of novel features in vertebrates during evolution. The availability of sequenced genomes has facilitated our understanding of the evolution of genes and regulatory elements. However, progress in understanding conservation and divergence in the function of proteins has been slow and mainly assessed by comparing protein sequences in combination with in vitro analyses. These approaches help to classify proteins into different families and sub-families, such as distinct types of transcription factors, but how protein function varies within a gene family is less well understood. Some studies have explored the functional evolution of closely related proteins and important insights have begun to emerge. In this review, we will provide a general overview of gene duplication and functional divergence and then focus on the functional evolution of HOX proteins to illustrate evolutionary changes underlying diversification and their role in animal evolution.
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Affiliation(s)
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO, United States
- Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, KS, United States
- *Correspondence: Robb Krumlauf,
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7
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Sengupta A, Hileman LC. A CYC-RAD-DIV-DRIF interaction likely pre-dates the origin of floral monosymmetry in Lamiales. EvoDevo 2022; 13:3. [PMID: 35093179 PMCID: PMC8801154 DOI: 10.1186/s13227-021-00187-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 12/18/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND An outstanding question in evolutionary biology is how genetic interactions defining novel traits evolve. They may evolve either by de novo assembly of previously non-interacting genes or by en bloc co-option of interactions from other functions. We tested these hypotheses in the context of a novel phenotype-Lamiales flower monosymmetry-defined by a developmental program that relies on regulatory interaction among CYCLOIDEA, RADIALIS, DIVARICATA, and DRIF gene products. In Antirrhinum majus (snapdragon), representing Lamiales, we tested whether components of this program likely function beyond their previously known role in petal and stamen development. In Solanum lycopersicum (tomato), representing Solanales which diverged from Lamiales before the origin of Lamiales floral monosymmetry, we additionally tested for regulatory interactions in this program. RESULTS We found that RADIALIS, DIVARICATA, and DRIF are expressed in snapdragon ovaries and developing fruit, similar to their homologs during tomato fruit development. In addition, we found that a tomato CYCLOIDEA ortholog positively regulates a tomato RADIALIS ortholog. CONCLUSION Our results provide preliminary support to the hypothesis that the developmental program defining floral monosymmetry in Lamiales was co-opted en bloc from a function in carpel development. This expands our understanding of novel trait evolution facilitated by co-option of existing regulatory interactions.
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Affiliation(s)
- Aniket Sengupta
- Department of Ecology and Evolutionary Biology, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA.
- St. Albert Hall, 8000 Utopia Pkwy, Room 257, Queens, NY, 11439, USA.
| | - Lena C Hileman
- Department of Ecology and Evolutionary Biology, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA
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8
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Hajirnis N, Mishra RK. Homeotic Genes: Clustering, Modularity, and Diversity. Front Cell Dev Biol 2021; 9:718308. [PMID: 34458272 PMCID: PMC8386295 DOI: 10.3389/fcell.2021.718308] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/22/2021] [Indexed: 11/13/2022] Open
Abstract
Hox genes code for transcription factors and are evolutionarily conserved. They regulate a plethora of downstream targets to define the anterior-posterior (AP) body axis of a developing bilaterian embryo. Early work suggested a possible role of clustering and ordering of Hox to regulate their expression in a spatially restricted manner along the AP axis. However, the recent availability of many genome assemblies for different organisms uncovered several examples that defy this constraint. With recent advancements in genomics, the current review discusses the arrangement of Hox in various organisms. Further, we revisit their discovery and regulation in Drosophila melanogaster. We also review their regulation in different arthropods and vertebrates, with a significant focus on Hox expression in the crustacean Parahyale hawaiensis. It is noteworthy that subtle changes in the levels of Hox gene expression can contribute to the development of novel features in an organism. We, therefore, delve into the distinct regulation of these genes during primary axis formation, segment identity, and extra-embryonic roles such as in the formation of hair follicles or misregulation leading to cancer. Toward the end of each section, we emphasize the possibilities of several experiments involving various organisms, owing to the advancements in the field of genomics and CRISPR-based genome engineering. Overall, we present a holistic view of the functioning of Hox in the animal world.
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Affiliation(s)
- Nikhil Hajirnis
- CSIR – Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
| | - Rakesh K. Mishra
- CSIR – Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
- AcSIR – Academy of Scientific and Innovative Research, Ghaziabad, India
- Tata Institute for Genetics and Society (TIGS), Bangalore, India
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9
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Yamada K, Maeno A, Araki S, Kikuchi M, Suzuki M, Ishizaka M, Satoh K, Akama K, Kawabe Y, Suzuki K, Kobayashi D, Hamano N, Kawamura A. An atlas of seven zebrafish hox cluster mutants provides insights into sub/neofunctionalization of vertebrate Hox clusters. Development 2021; 148:269044. [PMID: 34096572 DOI: 10.1242/dev.198325] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 04/30/2021] [Indexed: 12/20/2022]
Abstract
Vertebrate Hox clusters are comprised of multiple Hox genes that control morphology and developmental timing along multiple body axes. Although results of genetic analyses using Hox-knockout mice have been accumulating, genetic studies in other vertebrates have not been sufficient for functional comparisons of vertebrate Hox genes. In this study, we isolated all of the seven hox cluster loss-of-function alleles in zebrafish using the CRISPR-Cas9 system. Comprehensive analysis of the embryonic phenotype and X-ray micro-computed tomography scan analysis of adult fish revealed several species-specific functional contributions of homologous Hox clusters along the appendicular axis, whereas important shared general principles were also confirmed, as exemplified by serial anterior vertebral transformations along the main body axis, observed in fish for the first time. Our results provide insights into discrete sub/neofunctionalization of vertebrate Hox clusters after quadruplication of the ancient Hox cluster. This set of seven complete hox cluster loss-of-function alleles provide a formidable resource for future developmental genetic analysis of the Hox patterning system in zebrafish.
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Affiliation(s)
- Kazuya Yamada
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Akiteru Maeno
- Plant Resource Development, Division of Genetic Resource Center, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Soh Araki
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Morimichi Kikuchi
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Masato Suzuki
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Mizuki Ishizaka
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Koumi Satoh
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Kagari Akama
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Yuki Kawabe
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Kenya Suzuki
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Daiki Kobayashi
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Nanami Hamano
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Akinori Kawamura
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
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10
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Beccari L, Jaquier G, Lopez-Delisle L, Rodriguez-Carballo E, Mascrez B, Gitto S, Woltering J, Duboule D. Dbx2 regulation in limbs suggests interTAD sharing of enhancers. Dev Dyn 2021; 250:1280-1299. [PMID: 33497014 PMCID: PMC8451760 DOI: 10.1002/dvdy.303] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/17/2021] [Accepted: 01/17/2021] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND During tetrapod limb development, the HOXA13 and HOXD13 transcription factors are critical for the emergence and organization of the autopod, the most distal aspect where digits will develop. Since previous work had suggested that the Dbx2 gene is a target of these factors, we set up to analyze in detail this potential regulatory interaction. RESULTS We show that HOX13 proteins bind to mammalian-specific sequences at the vicinity of the Dbx2 locus that have enhancer activity in developing digits. However, the functional inactivation of the DBX2 protein did not elicit any particular phenotype related to Hox genes inactivation in digits, suggesting either redundant or compensatory mechanisms. We report that the neighboring Nell2 and Ano6 genes are also expressed in distal limb buds and are in part controlled by the same Dbx2 enhancers despite being localized into two different topologically associating domains (TADs) flanking the Dbx2 locus. CONCLUSIONS We conclude that Hoxa13 and Hoxd genes cooperatively activate Dbx2 expression in developing digits through binding to mammalian specific regulatory sequences in the Dbx2 neighborhood. Furthermore, these enhancers can overcome TAD boundaries in either direction to co-regulate a set of genes located in distinct chromatin domains.
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Affiliation(s)
- Leonardo Beccari
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,Institut NeuroMyoGène, CNRS UMR 5310, INSERM U1217, University Claude Bernard Lyon1, Lyon, France
| | - Gabriel Jaquier
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | | | - Eddie Rodriguez-Carballo
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,Department of Molecular Biology, University of Geneva, Geneva, Switzerland
| | - Bénédicte Mascrez
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Sandra Gitto
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Joost Woltering
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Denis Duboule
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,School of Life Sciences, Federal School of Technology (EPFL), Lausanne, Switzerland.,Collège de France, Paris, France
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11
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Gonçalves CS, Le Boiteux E, Arnaud P, Costa BM. HOX gene cluster (de)regulation in brain: from neurodevelopment to malignant glial tumours. Cell Mol Life Sci 2020; 77:3797-3821. [PMID: 32239260 PMCID: PMC11105007 DOI: 10.1007/s00018-020-03508-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 03/10/2020] [Accepted: 03/17/2020] [Indexed: 12/19/2022]
Abstract
HOX genes encode a family of evolutionarily conserved homeodomain transcription factors that are crucial both during development and adult life. In humans, 39 HOX genes are arranged in four clusters (HOXA, B, C, and D) in chromosomes 7, 17, 12, and 2, respectively. During embryonic development, particular epigenetic states accompany their expression along the anterior-posterior body axis. This tightly regulated temporal-spatial expression pattern reflects their relative chromosomal localization, and is critical for normal embryonic brain development when HOX genes are mainly expressed in the hindbrain and mostly absent in the forebrain region. Epigenetic marks, mostly polycomb-associated, are dynamically regulated at HOX loci and regulatory regions to ensure the finely tuned HOX activation and repression, highlighting a crucial epigenetic plasticity necessary for homeostatic development. HOX genes are essentially absent in healthy adult brain, whereas they are detected in malignant brain tumours, namely gliomas, where HOX genes display critical roles by regulating several hallmarks of cancer. Here, we review the major mechanisms involved in HOX genes (de)regulation in the brain, from embryonic to adult stages, in physiological and oncologic conditions. We focus particularly on the emerging causes of HOX gene deregulation in glioma, as well as on their functional and clinical implications.
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Affiliation(s)
- Céline S Gonçalves
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Elisa Le Boiteux
- Université Clermont Auvergne, CNRS, INSERM-iGReD, Clermont-Ferrand, France
| | - Philippe Arnaud
- Université Clermont Auvergne, CNRS, INSERM-iGReD, Clermont-Ferrand, France
| | - Bruno M Costa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal.
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12
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Sheth R, Barozzi I, Langlais D, Osterwalder M, Nemec S, Carlson HL, Stadler HS, Visel A, Drouin J, Kmita M. Distal Limb Patterning Requires Modulation of cis-Regulatory Activities by HOX13. Cell Rep 2017; 17:2913-2926. [PMID: 27974206 PMCID: PMC5697718 DOI: 10.1016/j.celrep.2016.11.039] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 11/08/2016] [Accepted: 11/11/2016] [Indexed: 01/12/2023] Open
Abstract
The combinatorial expression of Hox genes along the body axes is a major determinant of cell fate and plays a pivotal role in generating the animal body plan. Loss of HOXA13 and HOXD13 transcription factors (HOX13) leads to digit agenesis in mice, but how HOX13 proteins regulate transcriptional outcomes and confer identity to the distal-most limb cells has remained elusive. Here, we report on the genome-wide profiling of HOXA13 and HOXD13 in vivo binding and changes of the transcriptome and chromatin state in the transition from the early to the late-distal limb developmental program, as well as in Hoxa13−/−; Hoxd13−/−limbs. Our results show that proper termination of the early limb transcriptional program and activation of the late-distal limb program are coordinated by the dual action of HOX13 on cis-regulatory modules.
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Affiliation(s)
- Rushikesh Sheth
- Laboratory of Genetics and Development, Institut de Recherches Cliniques de Montréal (IRCM), 110 avenue des Pins Ouest, Montréal, QC H2W1R7, Canada.
| | - Iros Barozzi
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - David Langlais
- Department of Biochemistry, McGill University, 3649 Promenade Sir-William-Osler, Montréal, H3G0B1 QC, Canada
| | | | - Stephen Nemec
- Laboratory of Molecular Genetics, Institut de Recherches Cliniques de Montréal (IRCM), 110 avenue des Pins Ouest, Montréal, H2W1R7 QC, Canada
| | - Hanqian L Carlson
- Department of Skeletal Biology, Shriners Hospital for Children, 3101 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - H Scott Stadler
- Department of Skeletal Biology, Shriners Hospital for Children, 3101 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Axel Visel
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA; School of Natural Sciences, University of California, Merced, CA 95340, USA
| | - Jacques Drouin
- Laboratory of Molecular Genetics, Institut de Recherches Cliniques de Montréal (IRCM), 110 avenue des Pins Ouest, Montréal, H2W1R7 QC, Canada; Department of Medicine, Université de Montréal, Montréal, H3T1J4 QC, Canada
| | - Marie Kmita
- Laboratory of Genetics and Development, Institut de Recherches Cliniques de Montréal (IRCM), 110 avenue des Pins Ouest, Montréal, QC H2W1R7, Canada; Department of Medicine, Université de Montréal, Montréal, H3T1J4 QC, Canada.
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13
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Rodríguez-Carballo E, Lopez-Delisle L, Zhan Y, Fabre PJ, Beccari L, El-Idrissi I, Huynh THN, Ozadam H, Dekker J, Duboule D. The HoxD cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes. Genes Dev 2017; 31:2264-2281. [PMID: 29273679 PMCID: PMC5769770 DOI: 10.1101/gad.307769.117] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 11/21/2017] [Indexed: 12/11/2022]
Abstract
The mammalian HoxD cluster lies between two topologically associating domains (TADs) matching distinct enhancer-rich regulatory landscapes. During limb development, the telomeric TAD controls the early transcription of Hoxd genes in forearm cells, whereas the centromeric TAD subsequently regulates more posterior Hoxd genes in digit cells. Therefore, the TAD boundary prevents the terminal Hoxd13 gene from responding to forearm enhancers, thereby allowing proper limb patterning. To assess the nature and function of this CTCF-rich DNA region in embryos, we compared chromatin interaction profiles between proximal and distal limb bud cells isolated from mutant stocks where various parts of this boundary region were removed. The resulting progressive release in boundary effect triggered inter-TAD contacts, favored by the activity of the newly accessed enhancers. However, the boundary was highly resilient, and only a 400-kb deletion, including the whole-gene cluster, was eventually able to merge the neighboring TADs into a single structure. In this unified TAD, both proximal and distal limb enhancers nevertheless continued to work independently over a targeted transgenic reporter construct. We propose that the whole HoxD cluster is a dynamic TAD border and that the exact boundary position varies depending on both the transcriptional status and the developmental context.
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Affiliation(s)
| | - Lucille Lopez-Delisle
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Ye Zhan
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Pierre J Fabre
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Leonardo Beccari
- Department of Genetics and Evolution, University of Geneva, 1205 Geneva, Switzerland
| | - Imane El-Idrissi
- Department of Genetics and Evolution, University of Geneva, 1205 Geneva, Switzerland
| | - Thi Hanh Nguyen Huynh
- Department of Genetics and Evolution, University of Geneva, 1205 Geneva, Switzerland
| | - Hakan Ozadam
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Denis Duboule
- Department of Genetics and Evolution, University of Geneva, 1205 Geneva, Switzerland
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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14
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Abstract
During embryonic development, Hox genes participate in the building of a functional digestive system in metazoans, and genetic conditions involving these genes lead to important, sometimes lethal, growth retardation. Recently, this phenotype was obtained after deletion of Haglr, the Hoxd antisense growth-associated long noncoding RNA (lncRNA) located between Hoxd1 and Hoxd3 In this study, we have analyzed the function of Hoxd genes in delayed growth trajectories by looking at several nested targeted deficiencies of the mouse HoxD cluster. Mutant pups were severely stunted during the suckling period, but many recovered after weaning. After comparing seven distinct HoxD alleles, including CRISPR/Cas9 deletions involving Haglr, we identified Hoxd3 as the critical component for the gut to maintain milk-digestive competence. This essential function could be abrogated by the dominant-negative effect of HOXD10 as shown by a genetic rescue approach, thus further illustrating the importance of posterior prevalence in Hox gene function. A role for the lncRNA Haglr in the control of postnatal growth could not be corroborated.
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15
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Amaral T, Sinnberg T, Meier F, Krepler C, Levesque M, Niessner H, Garbe C. The mitogen-activated protein kinase pathway in melanoma part I - Activation and primary resistance mechanisms to BRAF inhibition. Eur J Cancer 2017; 73:85-92. [PMID: 28169047 DOI: 10.1016/j.ejca.2016.12.010] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 12/05/2016] [Indexed: 02/07/2023]
Abstract
Mitogen-activated protein kinase (MAPK) pathway has an important role in normal cells and can be activated under physiological conditions. MAPK pathway activation is a fundamental step in several intracellular processes requiring a sequential phosphorylation of the different pathway components. In normal cells, when MAPK pathway activation occurs, it leads to cell growth and differentiation. In order to prevent persistent MAPK pathway activation, physiological upstream negative feedback also takes place. In cells harbouring BRAFV600 mutations, the process leading to MAPK pathway activation is different, and the negative physiological feedback does not exist thus leading to permanent MAPK pathway activation, which ultimately can lead to uncontrolled proliferation. Targeted therapy with rapidly accelerated fibrosarcoma - B (BRAF) and/or mitogen-activated extracellular signal-regulated kinase kinase (MEK) inhibitors is indicated in patients with metastatic melanoma harboring BRAFV600 mutations. However, several different resistance mechanisms to this therapy were identified. In this review, we focus on primary or intrinsic resistance mechanisms to BRAF and MEK inhibition. In this setting, although a BRAF mutation is identified, there is no response to treatment with either BRAF or MEK inhibitor.
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Affiliation(s)
- Teresa Amaral
- Center for Dermatooncology, Department of Dermatology, University Hospital Tübingen, Liebermeisterstr. 25, 72076 Tübingen, Germany; Portuguese Air Force Health Direction, Paço do Lumiar, 1649-020 Lisbon, Portugal.
| | - Tobias Sinnberg
- Center for Dermatooncology, Department of Dermatology, University Hospital Tübingen, Liebermeisterstr. 25, 72076 Tübingen, Germany
| | - Friedegund Meier
- Department of Dermatology, University Hospital Carl Gustav Carus, Technical University Dresden, Fetscherstr. 74D, 01307 Dresden, Germany
| | - Clemens Krepler
- Molecular and Cellular Oncogenesis Program and Melanoma Research Center, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Mitchell Levesque
- University of Zürich Hospital, Department of Dermatology, Wagistrasse 14, CH-8952 Schlieren, Zürich, Switzerland
| | - Heike Niessner
- Center for Dermatooncology, Department of Dermatology, University Hospital Tübingen, Liebermeisterstr. 25, 72076 Tübingen, Germany
| | - Claus Garbe
- Center for Dermatooncology, Department of Dermatology, University Hospital Tübingen, Liebermeisterstr. 25, 72076 Tübingen, Germany
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16
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Li L, Helms JA, Chang HY. Comment on "Hotair Is Dispensable for Mouse Development". PLoS Genet 2016; 12:e1006406. [PMID: 27977686 PMCID: PMC5157954 DOI: 10.1371/journal.pgen.1006406] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 09/27/2016] [Indexed: 11/22/2022] Open
Affiliation(s)
- Lingjie Li
- Program in Epithelial Biology Stanford University School of Medicine, Stanford, California, United States of America
| | - Jill A. Helms
- Department of Surgery, Stanford University School of Medicine, Stanford, California, United States of America
| | - Howard Y. Chang
- Program in Epithelial Biology Stanford University School of Medicine, Stanford, California, United States of America
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17
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Guerreiro I, Gitto S, Novoa A, Codourey J, Nguyen Huynh TH, Gonzalez F, Milinkovitch MC, Mallo M, Duboule D. Reorganisation of Hoxd regulatory landscapes during the evolution of a snake-like body plan. eLife 2016; 5. [PMID: 27476854 PMCID: PMC4969037 DOI: 10.7554/elife.16087] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 07/10/2016] [Indexed: 12/15/2022] Open
Abstract
Within land vertebrate species, snakes display extreme variations in their body plan, characterized by the absence of limbs and an elongated morphology. Such a particular interpretation of the basic vertebrate body architecture has often been associated with changes in the function or regulation of Hox genes. Here, we use an interspecies comparative approach to investigate different regulatory aspects at the snake HoxD locus. We report that, unlike in other vertebrates, snake mesoderm-specific enhancers are mostly located within the HoxD cluster itself rather than outside. In addition, despite both the absence of limbs and an altered Hoxd gene regulation in external genitalia, the limb-associated bimodal HoxD chromatin structure is maintained at the snake locus. Finally, we show that snake and mouse orthologous enhancer sequences can display distinct expression specificities. These results show that vertebrate morphological evolution likely involved extensive reorganisation at Hox loci, yet within a generally conserved regulatory framework.
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Affiliation(s)
- Isabel Guerreiro
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Sandra Gitto
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Ana Novoa
- Instituto Gulbenkian de Ciência, Lisbon, Portugal
| | - Julien Codourey
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | | | - Federico Gonzalez
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | | | - Moises Mallo
- Instituto Gulbenkian de Ciência, Lisbon, Portugal
| | - Denis Duboule
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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18
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Spitz F. Gene regulation at a distance: From remote enhancers to 3D regulatory ensembles. Semin Cell Dev Biol 2016; 57:57-67. [PMID: 27364700 DOI: 10.1016/j.semcdb.2016.06.017] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 06/24/2016] [Indexed: 10/21/2022]
Abstract
Large-scale identification of elements associated with gene expression revealed that many of them are located extremely far from gene transcriptional start sites. We review here the growing evidence that show that distal cis-acting elements provide key instructions to genes, as genetic variation affecting them is growingly identified as an importance source of phenotypic diversity and disease. We discuss the different mechanisms that allow these elements to exert their regulatory functions, in a robust and specific manner, despite the large genomic distances separating them from their target genes. We particularly focus on the role of the structural organization of the genome in guiding such regulatory interactions.
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Affiliation(s)
- François Spitz
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany; Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany; Department of Developmental Biology and Stem Cells, Institut Pasteur, Paris, France.
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19
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Machnicki AL, Lovejoy CO, Reno PL. Developmental identity versus typology: Lucy has only four sacral segments. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 160:729-39. [DOI: 10.1002/ajpa.22997] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 02/25/2016] [Accepted: 03/31/2016] [Indexed: 12/28/2022]
Affiliation(s)
| | - C. Owen Lovejoy
- Department of Anthropology and School of Biomedical SciencesKent State UniversityKent OH
| | - Philip L. Reno
- Department of AnthropologyPennsylvania State UniversityUniversity Park PA
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20
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Ren X, Yang GL, Peng WF, Zhao YX, Zhang M, Chen ZH, Wu FA, Kantanen J, Shen M, Li MH. A genome-wide association study identifies a genomic region for the polycerate phenotype in sheep (Ovis aries). Sci Rep 2016; 6:21111. [PMID: 26883901 PMCID: PMC4756668 DOI: 10.1038/srep21111] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 01/18/2016] [Indexed: 01/06/2023] Open
Abstract
Horns are a cranial appendage found exclusively in Bovidae, and play important roles in accessing resources and mates. In sheep (Ovies aries), horns vary from polled to six-horned, and human have been selecting polled animals in farming and breeding. Here, we conducted a genome-wide association study on 24 two-horned versus 22 four-horned phenotypes in a native Chinese breed of Sishui Fur sheep. Together with linkage disequilibrium (LD) analyses and haplotype-based association tests, we identified a genomic region comprising 132.0–133.1 Mb on chromosome 2 that contained the top 10 SNPs (including 4 significant SNPs) and 5 most significant haplotypes associated with the polycerate phenotype. In humans and mice, this genomic region contains the HOXD gene cluster and adjacent functional genes EVX2 and KIAA1715, which have a close association with the formation of limbs and genital buds. Our results provide new insights into the genetic basis underlying variable numbers of horns and represent a new resource for use in sheep genetics and breeding.
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Affiliation(s)
- Xue Ren
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China.,University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Guang-Li Yang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China.,Department of Life Sciences, Shangqiu Normal University, Shangqiu 476000, China
| | - Wei-Feng Peng
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China.,University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Yong-Xin Zhao
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China.,University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Min Zhang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Ze-Hui Chen
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China.,University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Fu-An Wu
- Bureau of Animal Husbandry and Veterinary Medicine, Sishui County, Jining 273200, China
| | - Juha Kantanen
- Green Technology, Natural Resources Institute Finland (Luke), Jokioinen 31600, Finland.,Department of Biology, University of Eastern Finland, Kuopio 70211, Finland
| | - Min Shen
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China.,Key Laboratory of Sheep Breeding and Development Technology of Xinjiang Production and Construction Crops (XPCC), Shihezi 832000, China
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China
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21
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Independent regulation of vertebral number and vertebral identity by microRNA-196 paralogs. Proc Natl Acad Sci U S A 2015; 112:E4884-93. [PMID: 26283362 DOI: 10.1073/pnas.1512655112] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The Hox genes play a central role in patterning the embryonic anterior-to-posterior axis. An important function of Hox activity in vertebrates is the specification of different vertebral morphologies, with an additional role in axis elongation emerging. The miR-196 family of microRNAs (miRNAs) are predicted to extensively target Hox 3' UTRs, although the full extent to which miR-196 regulates Hox expression dynamics and influences mammalian development remains to be elucidated. Here we used an extensive allelic series of mouse knockouts to show that the miR-196 family of miRNAs is essential both for properly patterning vertebral identity at different axial levels and for modulating the total number of vertebrae. All three miR-196 paralogs, 196a1, 196a2, and 196b, act redundantly to pattern the midthoracic region, whereas 196a2 and 196b have an additive role in controlling the number of rib-bearing vertebra and positioning of the sacrum. Independent of this, 196a1, 196a2, and 196b act redundantly to constrain total vertebral number. Loss of miR-196 leads to a collective up-regulation of numerous trunk Hox target genes with a concomitant delay in activation of caudal Hox genes, which are proposed to signal the end of axis extension. Additionally, we identified altered molecular signatures associated with the Wnt, Fgf, and Notch/segmentation pathways and demonstrate that miR-196 has the potential to regulate Wnt activity by multiple mechanisms. By feeding into, and thereby integrating, multiple genetic networks controlling vertebral number and identity, miR-196 is a critical player defining axial formulae.
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22
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Srivastava S, Dhawan J, Mishra RK. Epigenetic mechanisms and boundaries in the regulation of mammalian Hox clusters. Mech Dev 2015; 138 Pt 2:160-169. [PMID: 26254900 DOI: 10.1016/j.mod.2015.07.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 07/29/2015] [Accepted: 07/30/2015] [Indexed: 01/07/2023]
Abstract
Hox gene expression imparts segment identity to body structures along the anterior-posterior axis and is tightly governed by higher order chromatin mechanisms. Chromatin regulatory features of the homeotic complex are best defined in Drosophila melanogaster, where multiple cis-regulatory elements have been identified that ensure collinear Hox gene expression patterns in accordance with their genomic organization. Recent studies focused on delineating the epigenetic features of the vertebrate Hox clusters have helped reveal their dynamic chromatin organization and its impact on gene expression. Enrichment for the 'activating' H3K4me3 and 'repressive' H3K27me3 histone modifications is a particularly strong read-out for transcriptional status and correlates well with the evidence for chromatin loop domain structures and stage specific topological changes at these loci. However, it is not clear how such distinct domains are imposed and regulated independent of each other. Comparative analysis of the chromatin structure and organization of the homeotic gene clusters in fly and mammals is increasingly revealing the functional conservation of chromatin mediated mechanisms. Here we discuss the case for interspersed boundary elements existing within mammalian Hox clusters along with their possible roles and mechanisms of action. Recent studies suggest a role for factors other than the well characterized vertebrate boundary factor CTCF, such as the GAGA binding factor (GAF), in maintaining chromatin domains at the Hox loci. We also present data demonstrating how such regulatory elements may be involved in organizing higher order structure and demarcating active domains of gene expression at the mammalian Hox clusters.
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Affiliation(s)
- Surabhi Srivastava
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India.
| | - Jyotsna Dhawan
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
| | - Rakesh K Mishra
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
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23
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Overcoming resistance to BRAF inhibition in BRAF-mutated metastatic melanoma. Oncotarget 2015; 5:10206-21. [PMID: 25344914 PMCID: PMC4279367 DOI: 10.18632/oncotarget.2602] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 10/18/2014] [Indexed: 12/29/2022] Open
Abstract
Almost 50% of metastatic melanoma patients harbor a BRAF(V600) mutation and the introduction of BRAF inhibitors has improved their treatment options. BRAF inhibitors vemurafenib and dabrafenib achieved improved overall survival over chemotherapy and have been approved for the treatment of BRAF-mutated metastatic melanoma. However, most patients develop mechanisms of acquired resistance and about 15% of them do not achieve tumor regression at all, due to intrinsic resistance to therapy. Moreover, early adaptive responses limit the initial efficacy of BRAF inhibition, leading mostly to incomplete responses that may favor the selection of a sub-population of resistant clones and the acquisition of alterations that cause tumor regrowth and progressive disease. The purpose of this paper is to review the mechanisms of resistance to therapy with BRAF inhibitors and to discuss the strategies to overcome them based on pre-clinical and clinical evidences.
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24
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Structure, function and evolution of topologically associating domains (TADs) at HOX loci. FEBS Lett 2015; 589:2869-76. [PMID: 25913784 DOI: 10.1016/j.febslet.2015.04.024] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 04/16/2015] [Accepted: 04/17/2015] [Indexed: 11/24/2022]
Abstract
Hox genes encode transcription factors necessary for patterning the major developing anterior to posterior embryonic axis. In addition, during vertebrate evolution, various subsets of this gene family were co-opted along with the emergence of novel body structures, such as the limbs or the external genitalia. The morphogenesis of these axial structures thus relies in part upon the precisely controlled transcription of specific Hox genes, a mechanism involving multiple long-range enhancers. Recently, it was reported that such regulatory mechanisms were largely shared between different developing tissues, though with some specificities, suggesting the recruitment of ancestral regulatory modalities from one tissue to another. The analysis of chromatin architectures at HoxD and HoxA loci revealed the existence of two flanking topologically associating domains (TADs), precisely encompassing the adjacent regulatory landscapes. Here, we discuss the function of these TADs in the control of Hox gene regulation and we speculate about their capacity to serve as structural frameworks for the emergence of novel enhancers. In this view, TADs may have been used as genomic niches to evolve pleiotropic regulations found at many developmental loci.
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25
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Denans N, Iimura T, Pourquié O. Hox genes control vertebrate body elongation by collinear Wnt repression. eLife 2015; 4. [PMID: 25719209 PMCID: PMC4384752 DOI: 10.7554/elife.04379] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 02/20/2015] [Indexed: 12/23/2022] Open
Abstract
In vertebrates, the total number of vertebrae is precisely defined. Vertebrae derive
from embryonic somites that are continuously produced posteriorly from the presomitic
mesoderm (PSM) during body formation. We show that in the chicken embryo, activation
of posterior Hox genes (paralogs 9–13) in the tail-bud
correlates with the slowing down of axis elongation. Our data indicate that a subset
of progressively more posterior Hox genes, which are collinearly
activated in vertebral precursors, repress Wnt activity with increasing strength.
This leads to a graded repression of the Brachyury/T transcription
factor, reducing mesoderm ingression and slowing down the elongation process. Due to
the continuation of somite formation, this mechanism leads to the progressive
reduction of PSM size. This ultimately brings the retinoic acid (RA)-producing
segmented region in close vicinity to the tail bud, potentially accounting for the
termination of segmentation and axis elongation. DOI:http://dx.doi.org/10.7554/eLife.04379.001 In humans and other vertebrates, the number of bones (vertebrae) in the spine is
determined early in development. The vertebrae form from blocks of tissue called
somites that make segments along the body axis—a virtual line running from the
head to the tail-end—of the embryo. The somites form as the embryo increases
in length, with new somites forming periodically at the back near the embryo's
tail-end. A family of genes called the Hox genes are involved in controlling
the formation of the somites. However, it is not known whether they directly control
the number of somites that form, or whether they control the length of the body of
the embryo. Denans et al. studied the Hox genes in chicken embryos. The
experiments suggest that the activation of some of the Hox genes in
a structure called the tail-bud, which is found at the tail-end of the embryo, slow
down the elongation of the body. The Hox genes achieve this by
repressing the activity of a signaling pathway called Wnt so that Wnt activity in the
tail-bud progressively decreases as the embryo develops. The elongation of the body stops when the levels of a molecule called retinoic acid
increase in the tail-bud, which causes the loss of the stem cells that are needed to
make the somites. Denans et al.'s findings suggest that Hox
genes influence the timing of the halt in elongation, which in turn is important for
determining the total number of somites that form. Understanding how
Hox genes control the formation of the cells that will make up
the somites and influence Wnt signaling is a major challenge for the future. DOI:http://dx.doi.org/10.7554/eLife.04379.002
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Affiliation(s)
- Nicolas Denans
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, University of Strasbourg, Illkirch, France
| | - Tadahiro Iimura
- Stowers Institute for Medical Research, Kansas City, United States
| | - Olivier Pourquié
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, University of Strasbourg, Illkirch, France
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26
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YAP regulates the expression of Hoxa1 and Hoxc13 in mouse and human oral and skin epithelial tissues. Mol Cell Biol 2015; 35:1449-61. [PMID: 25691658 DOI: 10.1128/mcb.00765-14] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Yes-associated protein (YAP) is a Hippo signaling transcriptional coactivator that plays pivotal roles in stem cell proliferation, organ size control, and tumor development. The downstream targets of YAP have been shown to be highly context dependent. In this study, we used the embryonic mouse tooth germ as a tool to search for the downstream targets of YAP in ectoderm-derived tissues. Yap deficiency in the dental epithelium resulted in a small tooth germ with reduced epithelial cell proliferation. We compared the gene expression profiles of embryonic day 14.5 (E14.5) Yap conditional knockout and YAP transgenic mouse tooth germs using transcriptome sequencing (RNA-Seq) and further confirmed the differentially expressed genes using real-time PCR and in situ hybridization. We found that YAP regulates the expression of Hoxa1 and Hoxc13 in oral and dental epithelial tissues as well as in the epidermis of skin during embryonic and adult stages. Sphere formation assay suggested that Hoxa1 and Hoxc13 are functionally involved in YAP-regulated epithelial progenitor cell proliferation, and chromatin immunoprecipitation (ChIP) assay implies that YAP may regulate Hoxa1 and Hoxc13 expression through TEAD transcription factors. These results provide mechanistic insights into abnormal YAP activities in mice and humans.
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27
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Genetic interactions between Shox2 and Hox genes during the regional growth and development of the mouse limb. Genetics 2014; 198:1117-26. [PMID: 25217052 DOI: 10.1534/genetics.114.167460] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The growth and development of the vertebrate limb relies on homeobox genes of the Hox and Shox families, with their independent mutation often giving dose-dependent effects. Here we investigate whether Shox2 and Hox genes function together during mouse limb development by modulating their relative dosage and examining the limb for nonadditive effects on growth. Using double mRNA fluorescence in situ hybridization (FISH) in single embryos, we first show that Shox2 and Hox genes have associated spatial expression dynamics, with Shox2 expression restricted to the proximal limb along with Hoxd9 and Hoxa11 expression, juxtaposing the distal expression of Hoxa13 and Hoxd13. By generating mice with all possible dosage combinations of mutant Shox2 alleles and HoxA/D cluster deletions, we then show that their coordinated proximal limb expression is critical to generate normally proportioned limb segments. These epistatic interactions tune limb length, where Shox2 underexpression enhances, and Shox2 overexpression suppresses, Hox-mutant phenotypes. Disruption of either Shox2 or Hox genes leads to a similar reduction in Runx2 expression in the developing humerus, suggesting their concerted action drives cartilage maturation during normal development. While we furthermore provide evidence that Hox gene function influences Shox2 expression, this regulation is limited in extent and is unlikely on its own to be a major explanation for their genetic interaction. Given the similar effect of human SHOX mutations on regional limb growth, Shox and Hox genes may generally function as genetic interaction partners during the growth and development of the proximal vertebrate limb.
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28
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Noordermeer D, Leleu M, Schorderet P, Joye E, Chabaud F, Duboule D. Temporal dynamics and developmental memory of 3D chromatin architecture at Hox gene loci. eLife 2014; 3:e02557. [PMID: 24843030 PMCID: PMC4017647 DOI: 10.7554/elife.02557] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Hox genes are essential regulators of embryonic development. Their step-wise transcriptional activation follows their genomic topology and the various states of activation are subsequently memorized into domains of progressively overlapping gene products. We have analyzed the 3D chromatin organization of Hox clusters during their early activation in vivo, using high-resolution circular chromosome conformation capture. Initially, Hox clusters are organized as single chromatin compartments containing all genes and bivalent chromatin marks. Transcriptional activation is associated with a dynamic bi-modal 3D organization, whereby the genes switch autonomously from an inactive to an active compartment. These local 3D dynamics occur within a framework of constitutive interactions within the surrounding Topological Associated Domains, indicating that this regulation process is mostly cluster intrinsic. The step-wise progression in time is fixed at various body levels and thus can account for the chromatin architectures previously described at a later stage for different anterior to posterior levels.DOI: http://dx.doi.org/10.7554/eLife.02557.001.
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Affiliation(s)
- Daan Noordermeer
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Marion Leleu
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Patrick Schorderet
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland Department of Molecular Biology, Harvard University, Boston, United States
| | - Elisabeth Joye
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Fabienne Chabaud
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Denis Duboule
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
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29
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Bhatia S, Kleinjan DA. Disruption of long-range gene regulation in human genetic disease: a kaleidoscope of general principles, diverse mechanisms and unique phenotypic consequences. Hum Genet 2014; 133:815-45. [DOI: 10.1007/s00439-014-1424-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 01/18/2014] [Indexed: 01/05/2023]
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30
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Tschopp P, Duboule D. The genetics of murine Hox loci: TAMERE, STRING, and PANTHERE to engineer chromosome variants. Methods Mol Biol 2014; 1196:89-102. [PMID: 25151159 DOI: 10.1007/978-1-4939-1242-1_6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Following their duplications at the base of the vertebrate clade, Hox gene clusters underwent remarkable sub- and neo-functionalization events. Many of these evolutionary innovations can be associated with changes in the transcriptional regulation of their genes, where an intricate relationship between the structure of the gene cluster and the architecture of the surrounding genomic landscape is at play. Here, we report on a portfolio of in vivo genome engineering strategies in mice, which have been used to probe and decipher the genetic and molecular underpinnings of the complex regulatory mechanisms implemented at these loci.
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Affiliation(s)
- Patrick Tschopp
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
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31
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Berlivet S, Paquette D, Dumouchel A, Langlais D, Dostie J, Kmita M. Clustering of tissue-specific sub-TADs accompanies the regulation of HoxA genes in developing limbs. PLoS Genet 2013; 9:e1004018. [PMID: 24385922 PMCID: PMC3873244 DOI: 10.1371/journal.pgen.1004018] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 10/25/2013] [Indexed: 12/19/2022] Open
Abstract
HoxA genes exhibit central roles during development and causal mutations have been found in several human syndromes including limb malformation. Despite their importance, information on how these genes are regulated is lacking. Here, we report on the first identification of bona fide transcriptional enhancers controlling HoxA genes in developing limbs and show that these enhancers are grouped into distinct topological domains at the sub-megabase scale (sub-TADs). We provide evidence that target genes and regulatory elements physically interact with each other through contacts between sub-TADs rather than by the formation of discreet “DNA loops”. Interestingly, there is no obvious relationship between the functional domains of the enhancers within the limb and how they are partitioned among the topological domains, suggesting that sub-TAD formation does not rely on enhancer activity. Moreover, we show that suppressing the transcriptional activity of enhancers does not abrogate their contacts with HoxA genes. Based on these data, we propose a model whereby chromatin architecture defines the functional landscapes of enhancers. From an evolutionary standpoint, our data points to the convergent evolution of HoxA and HoxD regulation in the fin-to-limb transition, one of the major morphological innovations in vertebrates. Hox genes encode transcription factors with crucial roles during development. These genes are grouped in four different clusters names HoxA, B, C, and D. Mutations in genes of the HoxA and D clusters have been found in several human syndromes, affecting in some cases limb development. Despite their essential role and contrary to the genes of the HoxD cluster, little is known about how the HoxA genes are regulated. Here, we identified a large set of regulatory elements controlling HoxA genes during limb development. By studying spatial chromatin organization at the HoxA region, we found that the regulatory elements are spatially clustered regardless of their activity. Clustering of enhancers define tissue-specific chromatin domains that interact specifically with each other and with active genes in the limb. Our findings give support to the emerging concept that chromatin architecture defines the functional properties of genomes. Additionally, our study suggests a common constraint of the chromatin topology in the evolution of HoxA and HoxD regulation in the emergence of the hand/foot, which is one of the major morphological innovations in vertebrates.
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Affiliation(s)
- Soizik Berlivet
- Unité de génétique et développement, Institut de recherches cliniques de Montréal, Montréal, Québec, Canada
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montréal, Québec, Canada
| | - Denis Paquette
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montréal, Québec, Canada
| | - Annie Dumouchel
- Unité de génétique et développement, Institut de recherches cliniques de Montréal, Montréal, Québec, Canada
| | - David Langlais
- Unité de génétique moléculaire, Institut de recherches cliniques de Montréal, Montréal, Québec, Canada
| | - Josée Dostie
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montréal, Québec, Canada
- * E-mail: (JD); (MK)
| | - Marie Kmita
- Unité de génétique et développement, Institut de recherches cliniques de Montréal, Montréal, Québec, Canada
- Department of Medicine, University of Montréal, Montréal, Québec, Canada
- * E-mail: (JD); (MK)
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32
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Brison N, Debeer P, Tylzanowski P. Joining the fingers: AHOXD13story. Dev Dyn 2013; 243:37-48. [DOI: 10.1002/dvdy.24037] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 06/27/2013] [Accepted: 07/01/2013] [Indexed: 12/21/2022] Open
Affiliation(s)
- Nathalie Brison
- Center for Human Genetics; University Hospitals Leuven, University of Leuven; Belgium
| | - Philippe Debeer
- Department of Development and Regeneration; University of Leuven; Belgium
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33
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Van Allen EM, Wagle N, Sucker A, Treacy DJ, Johannessen CM, Goetz EM, Place CS, Taylor-Weiner A, Whittaker S, Kryukov GV, Hodis E, Rosenberg M, McKenna A, Cibulskis K, Farlow D, Zimmer L, Hillen U, Gutzmer R, Goldinger SM, Ugurel S, Gogas HJ, Egberts F, Berking C, Trefzer U, Loquai C, Weide B, Hassel JC, Gabriel SB, Carter SL, Getz G, Garraway LA, Schadendorf D. The genetic landscape of clinical resistance to RAF inhibition in metastatic melanoma. Cancer Discov 2013; 4:94-109. [PMID: 24265153 DOI: 10.1158/2159-8290.cd-13-0617] [Citation(s) in RCA: 692] [Impact Index Per Article: 62.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Most patients with BRAF(V600)-mutant metastatic melanoma develop resistance to selective RAF kinase inhibitors. The spectrum of clinical genetic resistance mechanisms to RAF inhibitors and options for salvage therapy are incompletely understood. We performed whole-exome sequencing on formalin-fixed, paraffin-embedded tumors from 45 patients with BRAF(V600)-mutant metastatic melanoma who received vemurafenib or dabrafenib monotherapy. Genetic alterations in known or putative RAF inhibitor resistance genes were observed in 23 of 45 patients (51%). Besides previously characterized alterations, we discovered a "long tail" of new mitogen-activated protein kinase (MAPK) pathway alterations (MAP2K2, MITF) that confer RAF inhibitor resistance. In three cases, multiple resistance gene alterations were observed within the same tumor biopsy. Overall, RAF inhibitor therapy leads to diverse clinical genetic resistance mechanisms, mostly involving MAPK pathway reactivation. Novel therapeutic combinations may be needed to achieve durable clinical control of BRAF(V600)-mutant melanoma. Integrating clinical genomics with preclinical screens may model subsequent resistance studies.
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Affiliation(s)
- Eliezer M Van Allen
- 1Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School; 2Department of Pathology, Massachusetts General Hospital Cancer Center, Boston; 3Broad Institute of MIT and Harvard; 4Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts; 5Department of Dermatology, University Hospital, West German Cancer Center, University Duisburg-Essen, Essen; 6German Cancer Consortium (DKTK); 7Department of Dermatology, Heidelberg University Hospital, Heidelberg; 8Department of Dermatology and Allergy, Hannover Medical School, Hannover; 9Department of Dermatology, University of Wuerzburg, Wuerzburg; 10Department of Dermatology, Venerology and Allergology, University of Schleswig-Holstein Hospital, Kiel; 11Department of Dermatology and Allergology, Ludwig-Maximilian University, Munich; 12Department of Dermatology, Venerology and Allergy, Charité Universitätsmedizin Berlin, Humboldt University, Berlin; 13Department of Dermatology, University of Mainz, Mainz; 14University Medical Center, University of Tübingen, Tübingen, Germany; 15Department of Genome Sciences, University of Washington, Seattle, Washington; 16Department of Dermatology, University Hospital Zurich, Zurich, Switzerland; and 17First Department of Medicine, Medical School, University of Athens, Athens, Greece
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34
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Multiple Enhancers Regulate Hoxd Genes and the Hotdog LncRNA during Cecum Budding. Cell Rep 2013; 5:137-50. [DOI: 10.1016/j.celrep.2013.09.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 08/07/2013] [Accepted: 09/05/2013] [Indexed: 11/23/2022] Open
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35
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Li L, Liu B, Wapinski OL, Tsai MC, Qu K, Zhang J, Carlson JC, Lin M, Fang F, Gupta RA, Helms JA, Chang HY. Targeted disruption of Hotair leads to homeotic transformation and gene derepression. Cell Rep 2013; 5:3-12. [PMID: 24075995 DOI: 10.1016/j.celrep.2013.09.003] [Citation(s) in RCA: 258] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 08/30/2013] [Accepted: 09/02/2013] [Indexed: 12/22/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are thought to be prevalent regulators of gene expression, but the consequences of lncRNA inactivation in vivo are mostly unknown. Here, we show that targeted deletion of mouse Hotair lncRNA leads to derepression of hundreds of genes, resulting in homeotic transformation of the spine and malformation of metacarpal-carpal bones. RNA sequencing and conditional inactivation reveal an ongoing requirement of Hotair to repress HoxD genes and several imprinted loci such as Dlk1-Meg3 and Igf2-H19 without affecting imprinting choice. Hotair binds to both Polycomb repressive complex 2, which methylates histone H3 at lysine 27 (H3K27), and Lsd1 complex, which demethylates histone H3 at lysine 4 (H3K4) in vivo. Hotair inactivation causes H3K4me3 gain and, to a lesser extent, H3K27me3 loss at target genes. These results reveal the function and mechanisms of Hotair lncRNA in enforcing a silent chromatin state at Hox and additional genes.
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Affiliation(s)
- Lingjie Li
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
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36
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Soshnikova N. Hox genes regulation in vertebrates. Dev Dyn 2013; 243:49-58. [PMID: 23832853 DOI: 10.1002/dvdy.24014] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 06/30/2013] [Accepted: 07/01/2013] [Indexed: 12/16/2022] Open
Abstract
Hox genes encode transcription factors defining cellular identities along the major and secondary body axes. Their coordinated expression in both space and time is critical for embryonic patterning. Accordingly, Hox genes transcription is tightly controlled at multiple levels, and involves an intricate combination of local and long-range cis-regulatory elements. Recent studies revealed that in addition to transcription factors, dynamic patterns of histone marks and higher-order chromatin structure are important determinants of Hox gene regulation. Furthermore, the emerging picture suggests an involvement of various species of non-coding RNA in targeting activating and repressive complexes to Hox clusters. I review these recent developments and discuss their relevance to the control of Hox gene expression in vivo, as well as to our understanding of transcriptional regulatory mechanisms.
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37
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Transgene- and locus-dependent imprinting reveals allele-specific chromosome conformations. Proc Natl Acad Sci U S A 2013; 110:11946-51. [PMID: 23818637 DOI: 10.1073/pnas.1310704110] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
When positioned into the integrin α-6 gene, an Hoxd9lacZ reporter transgene displayed parental imprinting in mouse embryos. While the expression from the paternal allele was comparable with patterns seen for the same transgene when present at the neighboring HoxD locus, almost no signal was scored at this integration site when the transgene was inherited from the mother, although the Itga6 locus itself is not imprinted. The transgene exhibited maternal allele-specific DNA hypermethylation acquired during oogenesis, and its expression silencing was reversible on passage through the male germ line. Histone modifications also corresponded to profiles described at known imprinted loci. Chromosome conformation analyses revealed distinct chromatin microarchitectures, with a more compact structure characterizing the maternally inherited repressed allele. Such genetic analyses of well-characterized transgene insertions associated with a de novo-induced parental imprint may help us understand the molecular determinants of imprinting.
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38
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Sheth R, Grégoire D, Dumouchel A, Scotti M, Pham JMT, Nemec S, Bastida MF, Ros MA, Kmita M. Decoupling the function of Hox and Shh in developing limb reveals multiple inputs of Hox genes on limb growth. Development 2013; 140:2130-8. [PMID: 23633510 DOI: 10.1242/dev.089409] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Limb development relies on an exquisite coordination between growth and patterning, but the underlying mechanisms remain elusive. Anterior-posterior and proximal-distal specification initiates in early limb bud concomitantly with the proliferative expansion of limb cells. Previous studies have shown that limb bud growth initially relies on fibroblast growth factors (FGFs) produced in the apical ectodermal ridge (AER-FGFs), the maintenance of which relies on a positive-feedback loop involving sonic hedgehog (Shh) and the BMP antagonist gremlin 1 (Grem1). The positive cross-regulation between Shh and the HoxA and HoxD clustered genes identified an indirect effect of Hox genes on the maintenance of AER-FGFs but the respective function of Shh and Hox genes in this process remains unknown. Here, by uncoupling Hox and Shh function, we show that HoxA and HoxD genes are required for proper AER-FGFs expression, independently of their function in controlling Shh expression. In addition, we provide evidence that the Hox-dependent control of AER-FGF expression is achieved through the regulation of key mesenchymal signals, namely Grem1 and Fgf10, ensuring proper epithelial-mesenchymal interactions. Notably, HoxA and HoxD genes contribute to both the initial activation of Grem1 and the subsequent anterior expansion of its expression domain. We propose that the intricate interactions between Hox genes and the FGF and Shh signaling pathways act as a molecular network that ensures proper limb bud growth and patterning, probably contributing to the coordination of these two processes.
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Affiliation(s)
- Rushikesh Sheth
- Laboratory of Genetics and Development, Institut de Recherches Cliniques de Montréal (IRCM, Québec, Canada
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39
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Montavon T, Duboule D. Chromatin organization and global regulation of Hox gene clusters. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120367. [PMID: 23650639 PMCID: PMC3682730 DOI: 10.1098/rstb.2012.0367] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
During development, a properly coordinated expression of Hox genes, within their different genomic clusters is critical for patterning the body plans of many animals with a bilateral symmetry. The fascinating correspondence between the topological organization of Hox clusters and their transcriptional activation in space and time has served as a paradigm for understanding the relationships between genome structure and function. Here, we review some recent observations, which revealed highly dynamic changes in the structure of chromatin at Hox clusters, in parallel with their activation during embryonic development. We discuss the relevance of these findings for our understanding of large-scale gene regulation.
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Affiliation(s)
- Thomas Montavon
- National Research Centre 'Frontiers in Genetics', School of Life Sciences, Ecole Polytechnique Fédérale, Lausanne, Switzerland
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40
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Davis MC. The Deep Homology of the Autopod: Insights from Hox Gene Regulation. Integr Comp Biol 2013; 53:224-32. [DOI: 10.1093/icb/ict029] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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41
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Soshnikova N, Dewaele R, Janvier P, Krumlauf R, Duboule D. Duplications of hox gene clusters and the emergence of vertebrates. Dev Biol 2013; 378:194-9. [PMID: 23501471 DOI: 10.1016/j.ydbio.2013.03.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 03/05/2013] [Indexed: 11/27/2022]
Abstract
The vertebrate body plan is characterized by an increased complexity relative to that of all other chordates and large-scale gene amplifications have been associated with key morphological innovations leading to their remarkable evolutionary success. Here, we use compound full Hox clusters deletions to investigate how Hox genes duplications may have contributed to the emergence of vertebrate-specific innovations. We show that the combined deletion of HoxA and HoxB leads to an atavistic heart phenotype, suggesting that the ancestral HoxA/B cluster was co-opted to help in diversifying the complex organ in vertebrates. Other phenotypic effects observed seem to illustrate the resurgence of ancestral (plesiomorphic) features. This indicates that the duplications of Hox clusters were associated with the recruitment or formation of novel cis-regulatory controls, which were key to the evolution of many vertebrate features and hence to the evolutionary radiation of this group.
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Affiliation(s)
- Natalia Soshnikova
- Department of Genetics and Evolution, University of Geneva, Sciences III, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
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42
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Lin C, Yin Y, Bell SM, Veith GM, Chen H, Huh SH, Ornitz DM, Ma L. Delineating a conserved genetic cassette promoting outgrowth of body appendages. PLoS Genet 2013; 9:e1003231. [PMID: 23358455 PMCID: PMC3554569 DOI: 10.1371/journal.pgen.1003231] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 11/26/2012] [Indexed: 12/27/2022] Open
Abstract
The acquisition of the external genitalia allowed mammals to cope with terrestrial-specific reproductive needs for internal fertilization, and thus it represents one of the most fundamental steps in evolution towards a life on land. How genitalia evolved remains obscure, and the key to understanding this process may lie in the developmental genetics that underpins the early establishment of the genital primordium, the genital tubercle (GT). Development of the GT is similar to that of the limb, which requires precise regulation from a distal signaling epithelium. However, whether outgrowth of the GT and limbs is mediated by common instructive signals remains unknown. In this study, we used comprehensive genetic approaches to interrogate the signaling cascade involved in GT formation in comparison with limb formation. We demonstrate that the FGF ligand responsible for GT development is FGF8 expressed in the cloacal endoderm. We further showed that forced Fgf8 expression can rescue limb and GT reduction in embryos deficient in WNT signaling activity. Our studies show that the regulation of Fgf8 by the canonical WNT signaling pathway is mediated in part by the transcription factor SP8. Sp8 mutants elicit appendage defects mirroring WNT and FGF mutants, and abolishing Sp8 attenuates ectopic appendage development caused by a gain-of-function β-catenin mutation. These observations indicate that a conserved WNT-SP8-FGF8 genetic cassette is employed by both appendages for promoting outgrowth, and suggest a deep homology shared by the limb and external genitalia. Mammalian limbs and external genitalia are body appendages specialized for locomotion and internal fertilization, respectively. Despite their marked anatomical and functional differences, development of the limb and external genitalia appears to involve similar genetic controls, and some have suggested that regulatory mechanisms common to both might be evolutionarily linked. One essential aspect for appendage development is the establishment and maintenance of a separated proximodistal developmental axis apart from the main body axis, which is often instructed by a distal signaling epithelium. Herein, we adopted comprehensive mouse genetic approaches to investigate regulatory mechanisms underlying the distal signaling center in the limb and the GT, and uncovered a conserved genetic cassette that is utilized by both paired and unpaired appendages to establish a distal signaling center in the epithelium that mediates subsequent proximodistal outgrowth. Our results further suggested that the evolution of the external genital organ involved co-option of the same genetic program underpinning limb development.
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Affiliation(s)
- Congxing Lin
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Yan Yin
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Sheila M. Bell
- Perinatal Institute of Cincinnati Children's Hospital Medical Center, Division of Neonatology-and Pulmonary Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - G. Michael Veith
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Hong Chen
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Sung-Ho Huh
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - David M. Ornitz
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Liang Ma
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
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Gross S, Krause Y, Wuelling M, Vortkamp A. Hoxa11 and Hoxd11 regulate chondrocyte differentiation upstream of Runx2 and Shox2 in mice. PLoS One 2012; 7:e43553. [PMID: 22916278 PMCID: PMC3423364 DOI: 10.1371/journal.pone.0043553] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 07/23/2012] [Indexed: 11/18/2022] Open
Abstract
During limb development, posterior Hox genes of the Hoxa- and Hoxd cluster provide positional information along the limb axis. Here we report a new function for Hoxa11 and Hoxd11 in regulating the early steps of chondrocyte differentiation. We analyzed forelimbs of Hoxa11−/−;d11−/− and Ulnaless mice, which are characterized by specifically shortened zeugopods. By detailed morphological and molecular analyses, we show that loss of Hoxa11 and Hoxd11 in the ulna of both mutants leads to an arrest of chondrocyte differentiation at a step before the separation into round and columnar cells takes place. Furthermore, we demonstrate that Hoxa11 and Hoxd11 act upstream of Runx2 and Shox2, two key regulators of chondrocyte differentiation. We hypothesize that Runx2 activates Shox2 in early chondrocytes, which at later stages induces Runx2 expression to regulate hypertrophic differentiation. These results give insight into mechanisms by which positional information might be translated into a specific bone pattern.
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Affiliation(s)
- Stefanie Gross
- Department of Developmental Biology, Center for Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Yvonne Krause
- Department of Developmental Biology, Center for Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Manuela Wuelling
- Department of Developmental Biology, Center for Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Andrea Vortkamp
- Department of Developmental Biology, Center for Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
- * E-mail:
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Eng D, Ma HY, Xu J, Shih HP, Gross MK, Kiouss C. Loss of abdominal muscle in Pitx2 mutants associated with altered axial specification of lateral plate mesoderm. PLoS One 2012; 7:e42228. [PMID: 22860089 PMCID: PMC3409154 DOI: 10.1371/journal.pone.0042228] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Accepted: 07/05/2012] [Indexed: 11/19/2022] Open
Abstract
Sequence specific transcription factors (SSTFs) combinatorially define cell types during development by forming recursively linked network kernels. Pitx2 expression begins during gastrulation, together with Hox genes, and becomes localized to the abdominal lateral plate mesoderm (LPM) before the onset of myogenesis in somites. The somatopleure of Pitx2 null embryos begins to grow abnormally outward before muscle regulatory factors (MRFs) or Pitx2 begin expression in the dermomyotome/myotome. Abdominal somites become deformed and stunted as they elongate into the mutant body wall, but maintain normal MRF expression domains. Subsequent loss of abdominal muscles is therefore not due to defects in specification, determination, or commitment of the myogenic lineage. Microarray analysis was used to identify SSTF families whose expression levels change in E10.5 interlimb body wall biopsies. All Hox9-11 paralogs had lower RNA levels in mutants, whereas genes expressed selectively in the hypaxial dermomyotome/myotome and sclerotome had higher RNA levels in mutants. In situ hybridization analyses indicate that Hox gene expression was reduced in parts of the LPM and intermediate mesoderm of mutants. Chromatin occupancy studies conducted on E10.5 interlimb body wall biopsies showed that Pitx2 protein occupied chromatin sites containing conserved bicoid core motifs in the vicinity of Hox 9-11 and MRF genes. Taken together, the data indicate that Pitx2 protein in LPM cells acts, presumably in combination with other SSTFs, to repress gene expression, that are normally expressed in physically adjoining cell types. Pitx2 thereby prevents cells in the interlimb LPM from adopting the stable network kernels that define sclerotomal, dermomyotomal, or myotomal mesenchymal cell types. This mechanism may be viewed either as lineage restriction or specification.
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Affiliation(s)
- Diana Eng
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, United States of America
| | - Hsiao-Yen Ma
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, United States of America
| | - Jun Xu
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, United States of America
| | - Hung-Ping Shih
- Department of Pediatrics, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Michael K. Gross
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, United States of America
| | - Chrissa Kiouss
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, United States of America
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Kamiyama N, Seki R, Yokoyama H, Tamura K. Heterochronically early decline of Hox expression prior to cartilage formation in the avian hindlimb zeugopod. Dev Growth Differ 2012; 54:619-32. [PMID: 22708793 DOI: 10.1111/j.1440-169x.2012.01359.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 05/01/2012] [Accepted: 05/01/2012] [Indexed: 12/19/2022]
Abstract
The fibula, a zeugopod bone in the hindlimb, exhibits various morphologies in tetrapod species. The fibula in some species has a similar length with the other zeugopod element, the tibia, while other species have obvious differences in the sizes of the two elements. In the avian hindlimb, for example, the fibula is extremely short, thin, and truncated. Basic morphology of the fibula is established during development, and cartilage primordium of the bone emerges in a certain region defined by a distinct combination of expression of Hox genes (Hox code). In order to elucidate how the different morphologies are produced from a region that is defined as the fixed Hox code, we examined spatial and temporal patterns of Hoxd11/Hoxd12 expression in the developing limb bud, which defines the region from which the fibula emerges, in comparison with the sites of precartilaginous mesenchymal condensations representing regions for cartilage formation among chick, mouse, and gecko embryos. We found that in the chick hindlimb, expression of Hoxd11/Hoxd12 decreased and disappeared from the presumptive zeugopod region before cartilage formation. This heterochronically early decline of expression of Hox genes is strongly correlated with the peculiar trait of the fibula in the avian hindlimb, since in the other species examined, expression of those genes continued after the onset of cartilage formation. This is morphological phenotype-related because the early disappearance was not seen in the chick forelimb. Our results suggest that temporal change of the Hox code governs diversification in morphology of homologous structures among related species.
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Affiliation(s)
- Namiko Kamiyama
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Aobayama Aoba-ku, Sendai, 980-8578, Japan
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Stranger BE, Montgomery SB, Dimas AS, Parts L, Stegle O, Ingle CE, Sekowska M, Smith GD, Evans D, Gutierrez-Arcelus M, Price A, Raj T, Nisbett J, Nica AC, Beazley C, Durbin R, Deloukas P, Dermitzakis ET. Patterns of cis regulatory variation in diverse human populations. PLoS Genet 2012; 8:e1002639. [PMID: 22532805 PMCID: PMC3330104 DOI: 10.1371/journal.pgen.1002639] [Citation(s) in RCA: 360] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 02/18/2012] [Indexed: 01/18/2023] Open
Abstract
The genetic basis of gene expression variation has long been studied with the aim to understand the landscape of regulatory variants, but also more recently to assist in the interpretation and elucidation of disease signals. To date, many studies have looked in specific tissues and population-based samples, but there has been limited assessment of the degree of inter-population variability in regulatory variation. We analyzed genome-wide gene expression in lymphoblastoid cell lines from a total of 726 individuals from 8 global populations from the HapMap3 project and correlated gene expression levels with HapMap3 SNPs located in cis to the genes. We describe the influence of ancestry on gene expression levels within and between these diverse human populations and uncover a non-negligible impact on global patterns of gene expression. We further dissect the specific functional pathways differentiated between populations. We also identify 5,691 expression quantitative trait loci (eQTLs) after controlling for both non-genetic factors and population admixture and observe that half of the cis-eQTLs are replicated in one or more of the populations. We highlight patterns of eQTL-sharing between populations, which are partially determined by population genetic relatedness, and discover significant sharing of eQTL effects between Asians, European-admixed, and African subpopulations. Specifically, we observe that both the effect size and the direction of effect for eQTLs are highly conserved across populations. We observe an increasing proximity of eQTLs toward the transcription start site as sharing of eQTLs among populations increases, highlighting that variants close to TSS have stronger effects and therefore are more likely to be detected across a wider panel of populations. Together these results offer a unique picture and resource of the degree of differentiation among human populations in functional regulatory variation and provide an estimate for the transferability of complex trait variants across populations.
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Affiliation(s)
- Barbara E. Stranger
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Stephen B. Montgomery
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
| | - Antigone S. Dimas
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
- Max Planck Institute Intelligent Systems and Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Leopold Parts
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Oliver Stegle
- Max Planck Institute Intelligent Systems and Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Catherine E. Ingle
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Magda Sekowska
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - George Davey Smith
- MRC CAiTE centre, School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - David Evans
- MRC CAiTE centre, School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Maria Gutierrez-Arcelus
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
| | - Alkes Price
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Epidemiology and Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Towfique Raj
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - James Nisbett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Alexandra C. Nica
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
| | - Claude Beazley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Richard Durbin
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Panos Deloukas
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Emmanouil T. Dermitzakis
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
- * E-mail:
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Delpretti S, Zakany J, Duboule D. A function for all posterior Hoxd genes during digit development? Dev Dyn 2012; 241:792-802. [PMID: 22374744 DOI: 10.1002/dvdy.23756] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2012] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Four posterior Hoxd genes, from Hoxd13 to Hoxd10, are collectively regulated during the development of tetrapod digits. Besides the well-documented role of Hoxd13, the function of the neighboring genes has been difficult to evaluate due to the close genetic linkage and potential regulatory interferences. We used a combination of five small nested deletions in cis, involving from two to four consecutive genes of the Hoxd13 to Hoxd9 loci, in mice, to evaluate their combined functional importance. RESULTS We show that deletions leading to a gain of function of Hoxd13, via regulatory re-allocation, generate abnormal phenotypes, in agreement with the dominant negative role of this gene. We also show that Hoxd10, Hoxd11, and Hoxd12 all seem to play a genuine role in digit development, though less compelling than that of Hoxd13. In contrast, the nearby Hoxd9 contributed no measurable function in digits. CONCLUSIONS We conclude that a slight and transient deregulation of Hoxd13 expression can readily affect the relative lengths of limb segments and that all posterior Hoxd genes likely contribute to the final limb morphology. We discuss the difficulty to clearly assess the functional share of individual genes within such a gene family, where closely located neighbors, coding for homologous proteins, are regulated by a unique circuitry and all contribute to shape the distal parts of our appendages.
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Affiliation(s)
- Saskia Delpretti
- National Research Centre Frontiers in Genetics, School of Life Sciences, Ecole Polytechnique Fédérale, Lausanne, Switzerland
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Tschopp P, Duboule D. A genetic approach to the transcriptional regulation of Hox gene clusters. Annu Rev Genet 2012; 45:145-66. [PMID: 22060042 DOI: 10.1146/annurev-genet-102209-163429] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The evolution of vertebrate genomes was accompanied by an astounding increase in the complexity of their regulatory modalities. Genetic redundancy resulting from large-scale genome duplications at the base of the chordate tree was repeatedly exploited by the functional redeployment of paralogous genes via innovations in their regulatory circuits. As a paradigm of such regulatory evolution, we have extensively studied those control mechanisms at work in-cis over vertebrate Hox gene clusters. Here, we review the portfolio of genetic strategies that have been developed to tackle the intricate relationship between genomic topography and the transcriptional activities in this gene family, and we describe some of the mechanistic insights we gained by using the HoxD cluster as an example. We discuss the high heuristic value of this system in our general understanding of how changes in transcriptional regulation can diversify gene function and thereby fuel morphological evolution.
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Affiliation(s)
- Patrick Tschopp
- National Center of Competence in Research, Frontiers in Genetics, Department of Genetics and Evolution, University of Geneva, 1211 Geneva 4, Switzerland
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Scotti M, Kmita M. Recruitment of 5' Hoxa genes in the allantois is essential for proper extra-embryonic function in placental mammals. Development 2012; 139:731-9. [PMID: 22219351 DOI: 10.1242/dev.075408] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Hox gene family is well known for its functions in establishing morphological diversity along the anterior-posterior axis of developing embryos. In mammals, one of these genes, Hoxa13, is crucial for embryonic survival, as its function is required for the proper expansion of the fetal vasculature in the placenta. Thus, it appears that the developmental strategy specific to placental mammals is linked, at least in part, to the recruitment of Hoxa13 function in developing extra-embryonic tissues. Yet, the mechanism underlying this extra-embryonic recruitment is unknown. Here, we provide evidence that this functional novelty is not exclusive to Hoxa13 but is shared with its neighboring Hoxa11 and Hoxa10 genes. We show that the extra-embryonic function of these three Hoxa genes stems from their specific expression in the allantois, an extra-embryonic hallmark of amniote vertebrates. Interestingly, Hoxa10-13 expression in the allantois is conserved in chick embryos, which are non-placental amniotes, suggesting that the extra-embryonic recruitment of Hoxa10, Hoxa11 and Hoxa13 most likely arose in amniotes, i.e. prior to the emergence of placental mammals. Finally, using a series of targeted recombination and transgenic assays, we provide evidence that the regulatory mechanism underlying Hoxa expression in the allantois is extremely complex and relies on several cis-regulatory sequences.
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Affiliation(s)
- Martina Scotti
- Laboratory of Genetics and Development, Institut de Recherches Cliniques de Montréal, Université de Montréal, 110 avenue des Pins Ouest, Montréal, Québec, Canada
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