1
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Hung TC, Kingsley DM, Boettiger AN. Boundary stacking interactions enable cross-TAD enhancer-promoter communication during limb development. Nat Genet 2024; 56:306-314. [PMID: 38238628 DOI: 10.1038/s41588-023-01641-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 12/06/2023] [Indexed: 02/15/2024]
Abstract
Although promoters and their enhancers are frequently contained within a topologically associating domain (TAD), some developmentally important genes have their promoter and enhancers within different TADs. Hypotheses about molecular mechanisms enabling cross-TAD interactions remain to be assessed. To test these hypotheses, we used optical reconstruction of chromatin architecture to characterize the conformations of the Pitx1 locus on single chromosomes in developing mouse limbs. Our data support a model in which neighboring boundaries are stacked as a result of loop extrusion, bringing boundary-proximal cis-elements into contact. This stacking interaction also contributes to the appearance of architectural stripes in the population average maps. Through molecular dynamics simulations, we found that increasing boundary strengths facilitates the formation of the stacked boundary conformation, counter-intuitively facilitating border bypass. This work provides a revised view of the TAD borders' function, both facilitating and preventing cis-regulatory interactions, and introduces a framework to distinguish border-crossing from border-respecting enhancer-promoter pairs.
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Affiliation(s)
- Tzu-Chiao Hung
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Alistair N Boettiger
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.
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2
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Herbert AL, Allard CAH, McCoy MJ, Wucherpfennig JI, Krueger SP, Chen HI, Gourlay AN, Jackson KD, Abbo LA, Bennett SH, Sears JD, Rhyne AL, Bellono NW, Kingsley DM. The genetic basis of novel trait gain in walking fish. bioRxiv 2023:2023.10.14.562356. [PMID: 37873105 PMCID: PMC10592820 DOI: 10.1101/2023.10.14.562356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
A major goal in biology is to understand how organisms evolve novel traits. Multiple studies have identified genes contributing to regressive evolution, the loss of structures that existed in a recent ancestor. However, fewer examples exist for genes underlying constructive evolution, the gain of novel structures and capabilities in lineages that previously lacked them. Sea robins are fish that have evolved enlarged pectoral fins, six mobile locomotory fin rays (legs) and six novel macroscopic lobes in the central nervous system (CNS) that innervate the corresponding legs. Here, we establish successful husbandry and use a combination of transcriptomics, CRISPR-Cas9 editing, and behavioral assays to identify key transcription factors that are required for leg formation and function in sea robins. We also generate hybrids between two sea robin species with distinct leg morphologies and use allele-specific expression analysis and gene editing to explore the genetic basis of species-specific trait diversity, including a novel sensory gain of function. Collectively, our study establishes sea robins as a new model for studying the genetic basis of novel organ formation, and demonstrates a crucial role for the conserved limb gene tbx3a in the evolution of chemosensory legs in walking fish.
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Affiliation(s)
- Amy L Herbert
- Department of Developmental Biology, Stanford University School of Medicine, Stanford CA 94305 USA
| | - Corey AH Allard
- Department of Molecular and Cellular Biology, Harvard University, Cambridge MA 02138 USA
| | - Matthew J McCoy
- Department of Pathology, Stanford University School of Medicine, Stanford CA 94305 USA
| | - Julia I Wucherpfennig
- Department of Developmental Biology, Stanford University School of Medicine, Stanford CA 94305 USA
| | - Stephanie P Krueger
- Department of Molecular and Cellular Biology, Harvard University, Cambridge MA 02138 USA
| | - Heidi I Chen
- Department of Developmental Biology, Stanford University School of Medicine, Stanford CA 94305 USA
| | | | - Kohle D Jackson
- Department of Developmental Biology, Stanford University School of Medicine, Stanford CA 94305 USA
| | - Lisa A Abbo
- Marine Biological Laboratory, Woods Hole, MA, 02543 USA
| | | | | | | | - Nicholas W Bellono
- Department of Molecular and Cellular Biology, Harvard University, Cambridge MA 02138 USA
| | - David M Kingsley
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford CA 94305 USA
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3
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Chen HI, Turakhia Y, Bejerano G, Kingsley DM. Whole-genome Comparisons Identify Repeated Regulatory Changes Underlying Convergent Appendage Evolution in Diverse Fish Lineages. Mol Biol Evol 2023; 40:msad188. [PMID: 37739926 PMCID: PMC10516590 DOI: 10.1093/molbev/msad188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023] Open
Abstract
Fins are major functional appendages of fish that have been repeatedly modified in different lineages. To search for genomic changes underlying natural fin diversity, we compared the genomes of 36 percomorph fish species that span over 100 million years of evolution and either have complete or reduced pelvic and caudal fins. We identify 1,614 genomic regions that are well-conserved in fin-complete species but missing from multiple fin-reduced lineages. Recurrent deletions of conserved sequences in wild fin-reduced species are enriched for functions related to appendage development, suggesting that convergent fin reduction at the organismal level is associated with repeated genomic deletions near fin-appendage development genes. We used sequencing and functional enhancer assays to confirm that PelA, a Pitx1 enhancer previously linked to recurrent pelvic loss in sticklebacks, has also been independently deleted and may have contributed to the fin morphology in distantly related pelvic-reduced species. We also identify a novel enhancer that is conserved in the majority of percomorphs, drives caudal fin expression in transgenic stickleback, is missing in tetraodontiform, syngnathid, and synbranchid species with caudal fin reduction, and alters caudal fin development when targeted by genome editing. Our study illustrates a broadly applicable strategy for mapping phenotypes to genotypes across a tree of vertebrate species and highlights notable new examples of regulatory genomic hotspots that have been used to evolve recurrent phenotypes across 100 million years of fish evolution.
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Affiliation(s)
- Heidi I Chen
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yatish Turakhia
- Department of Electrical and Computer Engineering, University of California, San Diego, CA, USA
| | - Gill Bejerano
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
- Department of Computer Science, Stanford University School of Engineering, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
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4
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Allard CAH, Herbert AL, Kingsley DM, Bellono NW. Sea robins. Curr Biol 2023; 33:R704-R706. [PMID: 37433267 PMCID: PMC11073509 DOI: 10.1016/j.cub.2023.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
Allard et al. provide an overview of sea robins, a group of benthic fish that have evolved leg-like appendages that they use to walk on the sea floor and find prey.
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Affiliation(s)
- Corey A H Allard
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Amy L Herbert
- Department of Developmental Biology and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - David M Kingsley
- Department of Developmental Biology and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nicholas W Bellono
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
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5
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Roberge CL, Miceli RT, Murphy LR, Kingsley DM, Gross RA, Corr DT. Sophorolipid Candidates Demonstrate Cytotoxic Efficacy against 2D and 3D Breast Cancer Models. J Nat Prod 2023; 86:1159-1170. [PMID: 37104545 PMCID: PMC10760934 DOI: 10.1021/acs.jnatprod.2c00804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Sophorolipids are biosurfactants derived from the nonpathogenic yeasts such as Starmerella bombicola with potential efficacy in anticancer applications. Simple and cost-effective synthesis of these drugs makes them a promising alternative to traditional chemotherapeutics, pending their success in preliminary drug-screening. Drug-screening typically utilizes 2D cell monolayers due to their simplicity and ease of high-throughput assessment. However, 2D assays fail to capture the complexity and 3D context of the tumor microenvironment and have consequently been implicated in the high percentage of drugs investigated in vitro that later fail in clinical trials. Herein, we screened two sophorolipid candidates and a clinically-used chemotherapeutic, doxorubicin, on in vitro breast cancer models ranging from 2D monolayers to 3D spheroids, employing optical coherence tomography to confirm these morphologies. We calculated corresponding IC50 values for these drugs and found one of the sophorolipids to have comparable toxicities to the chemotherapeutic control. Our findings show increased drug resistance associated with model dimensionality, such that all drugs tested showed that 3D spheroids exhibited higher IC50 values than their 2D counterparts. These findings demonstrate promising preliminary data to support the use of sophorolipids as a more affordable alternative to traditional clinical interventions and demonstrate the importance of 3D tumor models in assessing drug response.
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Affiliation(s)
- Cassandra L Roberge
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Rebecca T Miceli
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Lillian R Murphy
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - David M Kingsley
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Richard A Gross
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - David T Corr
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
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6
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Roberge CL, Kingsley DM, Cornely LR, Spain CJ, Fortin AG, Corr DT. Viscoelastic Properties of Bioprinted Alginate Microbeads Compared to Their Bulk Hydrogel Analogs. J Biomech Eng 2023; 145:031002. [PMID: 36149022 PMCID: PMC9791675 DOI: 10.1115/1.4055757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 09/14/2022] [Indexed: 12/30/2022]
Abstract
Hydrogel microbeads are engineered spherical microgels widely used for biomedical applications in cell cultures, tissue engineering, and drug delivery. Their mechanical and physical properties (i.e., modulus, porosity, diffusion) heavily influence their utility by affecting encapsulated cellular behavior, biopayload elution kinetics, and stability for longer term cultures. There is a need to quantify these properties to guide microbead design for effective application. However, there are few techniques with the μN-level resolution required to evaluate these relatively small, compliant constructs. To circumvent mechanically testing individual microbeads, researchers often approximate microbead properties by characterizing larger bulk gel analogs of the same material formulation. This approach provides some insight into the hydrogel properties. However, bulk gels possess key structural and mechanical differences compared to their microbead equivalents, which may limit their accuracy and utility as analogs for estimating microbead properties. Herein, we explore how microbead properties are influenced by hydrogel formulation (i.e., alginate concentration, divalent cation crosslinker, and crosslinker concentration), and whether these trends are accurately reflected in bulk gel analogs. To accomplish this, we utilize laser direct-write bioprinting to create 12 × 12 arrays of alginate microbeads and characterize all 144 microbeads in parallel using a commercially available microcompression system. In this way, the compressive load is distributed across a large number of beads, thus amplifying sample signal. Comparing microbead properties to those of their bulk gel analogs, we found that their trends in modulus, porosity, and diffusion with hydrogel formulation are consistent, yet bulk gels exhibit significant discrepancies in their measured values.
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Affiliation(s)
- Cassandra L. Roberge
- Biomedical Engineering Department, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, NY 12180
| | - David M. Kingsley
- Biomedical Engineering Department, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, NY 12180
| | - Lexie R. Cornely
- Biomedical Engineering Department, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, NY 12180
| | - Connor J. Spain
- Rensselaer Polytechnic Institute, Biomedical Engineering Department, 110 Eighth Street, Troy, NY 12180
| | - Aiyana G. Fortin
- Biomedical Engineering Department, University of Vermont, 590 Main Street, Burlington, VT 05401
| | - David T. Corr
- Biomedical Engineering Department, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, NY 12180
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7
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Chen HI, Turakhia Y, Bejerano G, Kingsley DM. Whole-genome comparisons identify repeated regulatory changes underlying convergent appendage evolution in diverse fish lineages. bioRxiv 2023:2023.01.30.526059. [PMID: 36778215 PMCID: PMC9915506 DOI: 10.1101/2023.01.30.526059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Fins are major functional appendages of fish that have been repeatedly modified in different lineages. To search for genomic changes underlying natural fin diversity, we compared the genomes of 36 wild fish species that either have complete or reduced pelvic and caudal fins. We identify 1,614 genomic regions that are well-conserved in fin-complete species but missing from multiple fin-reduced lineages. Recurrent deletions of conserved sequences (CONDELs) in wild fin-reduced species are enriched for functions related to appendage development, suggesting that convergent fin reduction at the organismal level is associated with repeated genomic deletions near fin-appendage development genes. We used sequencing and functional enhancer assays to confirm that PelA , a Pitx1 enhancer previously linked to recurrent pelvic loss in sticklebacks, has also been independently deleted and may have contributed to the fin morphology in distantly related pelvic-reduced species. We also identify a novel enhancer that is conserved in the majority of percomorphs, drives caudal fin expression in transgenic stickleback, is missing in tetraodontiform, s yngnathid, and synbranchid species with caudal fin reduction, and which alters caudal fin development when targeted by genome editing. Our study illustrates a general strategy for mapping phenotypes to genotypes across a tree of vertebrate species, and highlights notable new examples of regulatory genomic hotspots that have been used to evolve recurrent phenotypes during 100 million years of fish evolution.
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Affiliation(s)
- Heidi I. Chen
- Department of Developmental Biology, Stanford University School of Medicine, CA
| | - Yatish Turakhia
- Department of Electrical and Computer Engineering, University of California, San Diego, San Diego, CA
| | - Gill Bejerano
- Department of Developmental Biology, Stanford University School of Medicine, CA
- Department of Biomedical Data Science, Stanford University School of Medicine, CA
- Department of Computer Science, Stanford University School of Engineering, CA
- Department of Pediatrics, Stanford University School of Medicine, CA
| | - David M. Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, CA
- Howard Hughes Medical Institute, Stanford University, CA
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8
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Wucherpfennig JI, Howes TR, Au JN, Au EH, Roberts Kingman GA, Brady SD, Herbert AL, Reimchen TE, Bell MA, Lowe CB, Dalziel AC, Kingsley DM. Evolution of stickleback spines through independent cis-regulatory changes at HOXDB. Nat Ecol Evol 2022; 6:1537-1552. [PMID: 36050398 PMCID: PMC9525239 DOI: 10.1038/s41559-022-01855-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 07/19/2022] [Indexed: 11/10/2022]
Abstract
Understanding the mechanisms leading to new traits or additional features in organisms is a fundamental goal of evolutionary biology. We show that HOXDB regulatory changes have been used repeatedly in different fish genera to alter the length and number of the prominent dorsal spines used to classify stickleback species. In Gasterosteus aculeatus (typically 'three-spine sticklebacks'), a variant HOXDB allele is genetically linked to shortening an existing spine and adding an additional spine. In Apeltes quadracus (typically 'four-spine sticklebacks'), a variant HOXDB allele is associated with lengthening a spine and adding an additional spine in natural populations. The variant alleles alter the same non-coding enhancer region in the HOXDB locus but do so by diverse mechanisms, including single-nucleotide polymorphisms, deletions and transposable element insertions. The independent regulatory changes are linked to anterior expansion or contraction of HOXDB expression. We propose that associated changes in spine lengths and numbers are partial identity transformations in a repeating skeletal series that forms major defensive structures in fish. Our findings support the long-standing hypothesis that natural Hox gene variation underlies key patterning changes in wild populations and illustrate how different mutational mechanisms affecting the same region may produce opposite gene expression changes with similar phenotypic outcomes.
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Affiliation(s)
- Julia I Wucherpfennig
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Timothy R Howes
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jessica N Au
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Eric H Au
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | | | - Shannon D Brady
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Amy L Herbert
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Thomas E Reimchen
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Michael A Bell
- University of California Museum of Paleontology, University of California, Berkeley, CA, USA
| | - Craig B Lowe
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Anne C Dalziel
- Department of Biology, Saint Mary's University, Halifax, Nova Scotia, Canada
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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9
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Marques DA, Jones FC, Di Palma F, Kingsley DM, Reimchen TE. Genomic changes underlying repeated niche shifts in an adaptive radiation. Evolution 2022; 76:1301-1319. [PMID: 35398888 PMCID: PMC9320971 DOI: 10.1111/evo.14490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 02/28/2022] [Accepted: 03/09/2022] [Indexed: 01/21/2023]
Abstract
In adaptive radiations, single lineages rapidly diversify by adapting to many new niches. Little is known yet about the genomic mechanisms involved, that is, the source of genetic variation or genomic architecture facilitating or constraining adaptive radiation. Here, we investigate genomic changes associated with repeated invasion of many different freshwater niches by threespine stickleback in the Haida Gwaii archipelago, Canada, by resequencing single genomes from one marine and 28 freshwater populations. We find 89 likely targets of parallel selection in the genome that are enriched for old standing genetic variation. In contrast to theoretical expectations, their genomic architecture is highly dispersed with little clustering. Candidate genes and genotype-environment correlations match the three major environmental axes predation regime, light environment, and ecosystem size. In a niche space with these three dimensions, we find that the more divergent a new niche from the ancestral marine habitat, the more loci show signatures of parallel selection. Our findings suggest that the genomic architecture of parallel adaptation in adaptive radiation depends on the steepness of ecological gradients and the dimensionality of the niche space.
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Affiliation(s)
- David A. Marques
- Department of BiologyUniversity of VictoriaVictoriaBCV8W 3N5Canada,Aquatic Ecology and Evolution, Institute of Ecology and EvolutionUniversity of BernBernCH‐3012Switzerland,Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and BiogeochemistrySwiss Federal Institute of Aquatic Science and Technology (EAWAG), Eawag ‐ Swiss Federal Institute of Aquatic Science and TechnologyKastanienbaumCH‐6047Switzerland,Natural History Museum BaselBaselCH‐4051Switzerland
| | - Felicity C. Jones
- Howard Hughes Medical Institute, Stanford University School of MedicineStanfordCalifornia94305USA,Department of Developmental BiologyStanford University School of MedicineStanfordCalifornia94305USA,Friedrich Miescher Laboratory of the Max Planck SocietyTübingen72076Germany
| | - Federica Di Palma
- Earlham InstituteNorwichNR4 7UZUnited Kingdom,Department of Biological SciencesUniversity of East AngliaNorwichNR4 7TJUnited Kingdom
| | - David M. Kingsley
- Howard Hughes Medical Institute, Stanford University School of MedicineStanfordCalifornia94305USA,Department of Developmental BiologyStanford University School of MedicineStanfordCalifornia94305USA
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10
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Heller IS, Guenther CA, Meireles AM, Talbot WS, Kingsley DM. Characterization of mouse Bmp5 regulatory injury element in zebrafish wound models. Bone 2022; 155:116263. [PMID: 34826632 PMCID: PMC9007314 DOI: 10.1016/j.bone.2021.116263] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 11/17/2021] [Accepted: 11/18/2021] [Indexed: 11/21/2022]
Abstract
Many key signaling molecules used to build tissues during embryonic development are re-activated at injury sites to stimulate tissue regeneration and repair. Bone morphogenetic proteins provide a classic example, but the mechanisms that lead to reactivation of BMPs following injury are still unknown. Previous studies have mapped a large "injury response element" (IRE) in the mouse Bmp5 gene that drives gene expression following bone fractures and other types of injury. Here we show that the large mouse IRE region is also activated in both zebrafish tail resection and mechanosensory hair cell injury models. Using the ability to test multiple constructs and image temporal and spatial dynamics following injury responses, we have narrowed the original size of the mouse IRE region by over 100 fold and identified a small 142 bp minimal enhancer that is rapidly induced in both mesenchymal and epithelial tissues after injury. These studies identify a small sequence that responds to evolutionarily conserved local signals in wounded tissues and suggest candidate pathways that contribute to BMP reactivation after injury.
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Affiliation(s)
- Ian S Heller
- Department of Developmental Biology, Stanford University School of Medicine, United States of America
| | - Catherine A Guenther
- Department of Developmental Biology, Stanford University School of Medicine, United States of America; Howard Hughes Medical Institute, Stanford University School of Medicine, United States of America
| | - Ana M Meireles
- Department of Developmental Biology, Stanford University School of Medicine, United States of America
| | - William S Talbot
- Department of Developmental Biology, Stanford University School of Medicine, United States of America
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, United States of America; Howard Hughes Medical Institute, Stanford University School of Medicine, United States of America.
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11
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Roberts Kingman GA, Lee D, Jones FC, Desmet D, Bell MA, Kingsley DM. Longer or shorter spines: Reciprocal trait evolution in stickleback via triallelic regulatory changes in Stanniocalcin2a. Proc Natl Acad Sci U S A 2021; 118:e2100694118. [PMID: 34321354 PMCID: PMC8346906 DOI: 10.1073/pnas.2100694118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Vertebrates have repeatedly modified skeletal structures to adapt to their environments. The threespine stickleback is an excellent system for studying skeletal modifications, as different wild populations have either increased or decreased the lengths of their prominent dorsal and pelvic spines in different freshwater environments. Here we identify a regulatory locus that has a major morphological effect on the length of stickleback dorsal and pelvic spines, which we term Maser (major spine enhancer). Maser maps in a closely linked supergene complex that controls multiple armor, feeding, and behavioral traits on chromosome IV. Natural alleles in Maser are differentiated between marine and freshwater sticklebacks; however, alleles found among freshwater populations are also differentiated, with distinct alleles found in short- and long-spined freshwater populations. The distinct freshwater alleles either increase or decrease expression of the bone growth inhibitor gene Stanniocalcin2a in developing spines, providing a simple genetic mechanism for either increasing or decreasing spine lengths in natural populations. Genomic surveys suggest many recurrently differentiated loci in sticklebacks are similarly specialized into three or more distinct alleles, providing multiple ancient standing variants in particular genes that may contribute to a range of phenotypes in different environments.
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Affiliation(s)
| | - David Lee
- Stanford University School of Humanities and Sciences, Stanford University, Stanford, CA 94305
| | - Felicity C Jones
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Danielle Desmet
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Michael A Bell
- University of California Museum of Paleontology, University of California, Berkeley, CA 94720
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305;
- HHMI, Stanford University School of Medicine, Stanford, CA 94305
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12
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Roberts Kingman GA, Vyas DN, Jones FC, Brady SD, Chen HI, Reid K, Milhaven M, Bertino TS, Aguirre WE, Heins DC, von Hippel FA, Park PJ, Kirch M, Absher DM, Myers RM, Di Palma F, Bell MA, Kingsley DM, Veeramah KR. Predicting future from past: The genomic basis of recurrent and rapid stickleback evolution. Sci Adv 2021; 7:7/25/eabg5285. [PMID: 34144992 PMCID: PMC8213234 DOI: 10.1126/sciadv.abg5285] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/05/2021] [Indexed: 05/30/2023]
Abstract
Similar forms often evolve repeatedly in nature, raising long-standing questions about the underlying mechanisms. Here, we use repeated evolution in stickleback to identify a large set of genomic loci that change recurrently during colonization of freshwater habitats by marine fish. The same loci used repeatedly in extant populations also show rapid allele frequency changes when new freshwater populations are experimentally established from marine ancestors. Marked genotypic and phenotypic changes arise within 5 years, facilitated by standing genetic variation and linkage between adaptive regions. Both the speed and location of changes can be predicted using empirical observations of recurrence in natural populations or fundamental genomic features like allelic age, recombination rates, density of divergent loci, and overlap with mapped traits. A composite model trained on these stickleback features can also predict the location of key evolutionary loci in Darwin's finches, suggesting that similar features are important for evolution across diverse taxa.
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Affiliation(s)
- Garrett A Roberts Kingman
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329, USA
| | - Deven N Vyas
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA
| | - Felicity C Jones
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring, Tübingen, Germany
| | - Shannon D Brady
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329, USA
| | - Heidi I Chen
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329, USA
| | - Kerry Reid
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA
| | - Mark Milhaven
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Thomas S Bertino
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA
| | - Windsor E Aguirre
- Department of Biological Sciences, DePaul University, Chicago, IL 60614-3207, USA
| | - David C Heins
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA 70118, USA
| | - Frank A von Hippel
- Department of Community, Environment and Policy, Mel & Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ 85724, USA
| | - Peter J Park
- Department of Biology, Farmingdale State College, Farmingdale, NY 11735-1021, USA
| | - Melanie Kirch
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring, Tübingen, Germany
| | - Devin M Absher
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA
| | - Federica Di Palma
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Michael A Bell
- University of California Museum of Paleontology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Krishna R Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA.
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13
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Schluter D, Marchinko KB, Arnegard ME, Zhang H, Brady SD, Jones FC, Bell MA, Kingsley DM. Fitness maps to a large-effect locus in introduced stickleback populations. Proc Natl Acad Sci U S A 2021; 118:e1914889118. [PMID: 33414274 PMCID: PMC7826376 DOI: 10.1073/pnas.1914889118] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Mutations of small effect underlie most adaptation to new environments, but beneficial variants with large fitness effects are expected to contribute under certain conditions. Genes and genomic regions having large effects on phenotypic differences between populations are known from numerous taxa, but fitness effect sizes have rarely been estimated. We mapped fitness over a generation in an F2 intercross between a marine and a lake stickleback population introduced to a freshwater pond. A quantitative trait locus map of the number of surviving offspring per F2 female detected a single, large-effect locus near Ectodysplasin (Eda), a gene having an ancient freshwater allele causing reduced bony armor and other changes. F2 females homozygous for the freshwater allele had twice the number of surviving offspring as homozygotes for the marine allele, producing a large selection coefficient, s = 0.50 ± 0.09 SE. Correspondingly, the frequency of the freshwater allele increased from 0.50 in F2 mothers to 0.58 in surviving offspring. We compare these results to allele frequency changes at the Eda gene in an Alaskan lake population colonized by marine stickleback in the 1980s. The frequency of the freshwater Eda allele rose steadily over multiple generations and reached 95% within 20 y, yielding a similar estimate of selection, s = 0.49 ± 0.05, but a different degree of dominance. These findings are consistent with other studies suggesting strong selection on this gene (and/or linked genes) in fresh water. Selection on ancient genetic variants carried by colonizing ancestors is likely to increase the prevalence of large-effect fitness variants in adaptive evolution.
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Affiliation(s)
- Dolph Schluter
- Biodiversity Research Centre, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4;
- Department of Zoology, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Kerry B Marchinko
- Biodiversity Research Centre, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4
- Department of Zoology, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Matthew E Arnegard
- Biodiversity Research Centre, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4
- Department of Zoology, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Haili Zhang
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Shannon D Brady
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305
| | - Felicity C Jones
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Michael A Bell
- University of California Museum of Paleontology, Berkeley, CA 94720
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305;
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305
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14
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Roberge CL, Kingsley DM, Faulkner DE, Sloat CJ, Wang L, Barroso M, Intes X, Corr DT. Non-Destructive Tumor Aggregate Morphology and Viability Quantification at Cellular Resolution, During Development and in Response to Drug. Acta Biomater 2020; 117:322-334. [PMID: 33007490 DOI: 10.1016/j.actbio.2020.09.042] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/15/2020] [Accepted: 09/22/2020] [Indexed: 12/15/2022]
Abstract
Three-dimensional (3D) tissue-engineered in vitro models, particularly multicellular spheroids and organoids, have become important tools to explore disease progression and guide the development of novel therapeutic strategies. These avascular constructs are particularly powerful in oncological research due to their ability to mimic several key aspects of in vivo tumors, such as 3D structure and pathophysiologic gradients. Advancement of spheroid models requires characterization of critical features (i.e., size, shape, cellular density, and viability) during model development, and in response to treatment. However, evaluation of these characteristics longitudinally, quantitatively and non-invasively remains a challenge. Herein, Optical Coherence Tomography (OCT) is used as a label-free tool to assess 3D morphologies and cellular densities of tumor spheroids generated via the liquid overlay technique. We utilize this quantitative tool to assess Matrigel's influence on spheroid morphologic development, finding that the absence of Matrigel produces flattened, disk-like aggregates rather than 3D spheroids with physiologically-relevant features. Furthermore, this technology is adapted to quantify cell number within tumor spheroids, and to discern between live and dead cells, to non-destructively provide valuable information on tissue/construct viability, as well as a proof-of-concept for longitudinal drug efficacy studies. Together, these findings demonstrate OCT as a promising noninvasive, quantitative, label-free, longitudinal and cell-based method that can assess development and drug response in 3D cellular aggregates at a mesoscopic scale.
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Affiliation(s)
- Cassandra L Roberge
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 Eighth St., Troy, NY 12180, USA.
| | - David M Kingsley
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 Eighth St., Troy, NY 12180, USA.
| | - Denzel E Faulkner
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 Eighth St., Troy, NY 12180, USA.
| | - Charles J Sloat
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 Eighth St., Troy, NY 12180, USA.
| | - Ling Wang
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, 12208, USA.
| | - Margarida Barroso
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, 12208, USA.
| | - Xavier Intes
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 Eighth St., Troy, NY 12180, USA.
| | - David T Corr
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 Eighth St., Troy, NY 12180, USA.
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15
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Peichel CL, McCann SR, Ross JA, Naftaly AFS, Urton JR, Cech JN, Grimwood J, Schmutz J, Myers RM, Kingsley DM, White MA. Assembly of the threespine stickleback Y chromosome reveals convergent signatures of sex chromosome evolution. Genome Biol 2020; 21:177. [PMID: 32684159 PMCID: PMC7368989 DOI: 10.1186/s13059-020-02097-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 07/08/2020] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Heteromorphic sex chromosomes have evolved repeatedly across diverse species. Suppression of recombination between X and Y chromosomes leads to degeneration of the Y chromosome. The progression of degeneration is not well understood, as complete sequence assemblies of heteromorphic Y chromosomes have only been generated across a handful of taxa with highly degenerate sex chromosomes. Here, we describe the assembly of the threespine stickleback (Gasterosteus aculeatus) Y chromosome, which is less than 26 million years old and at an intermediate stage of degeneration. Our previous work identified that the non-recombining region between the X and the Y spans approximately 17.5 Mb on the X chromosome. RESULTS We combine long-read sequencing with a Hi-C-based proximity guided assembly to generate a 15.87 Mb assembly of the Y chromosome. Our assembly is concordant with cytogenetic maps and Sanger sequences of over 90 Y chromosome BAC clones. We find three evolutionary strata on the Y chromosome, consistent with the three inversions identified by our previous cytogenetic analyses. The threespine stickleback Y shows convergence with more degenerate sex chromosomes in the retention of haploinsufficient genes and the accumulation of genes with testis-biased expression, many of which are recent duplicates. However, we find no evidence for large amplicons identified in other sex chromosome systems. We also report an excellent candidate for the master sex-determination gene: a translocated copy of Amh (Amhy). CONCLUSIONS Together, our work shows that the evolutionary forces shaping sex chromosomes can cause relatively rapid changes in the overall genetic architecture of Y chromosomes.
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Affiliation(s)
- Catherine L. Peichel
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
| | - Shaugnessy R. McCann
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
| | - Joseph A. Ross
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195 USA
| | | | - James R. Urton
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195 USA
| | - Jennifer N. Cech
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195 USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806 USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806 USA
| | - Richard M. Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806 USA
| | - David M. Kingsley
- Department of Developmental Biology and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Michael A. White
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
- Department of Genetics, University of Georgia, Athens, GA 30602 USA
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16
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Kingsley DM, Roberge CL, Rudkouskaya A, Faulkner DE, Barroso M, Intes X, Corr DT. Laser-based 3D bioprinting for spatial and size control of tumor spheroids and embryoid bodies. Acta Biomater 2019; 95:357-370. [PMID: 30776506 PMCID: PMC7171976 DOI: 10.1016/j.actbio.2019.02.014] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 02/08/2019] [Accepted: 02/12/2019] [Indexed: 12/17/2022]
Abstract
3D multicellular aggregates, and more advanced organotypic systems, have become central tools in recent years to study a wide variety of complex biological processes. Most notably, these model systems have become mainstream within oncology (multicellular tumor spheroids) and regenerative medicine (embryoid bodies) research. However, the biological behavior of these in vitro tissue surrogates is extremely sensitive to their aggregate size and geometry. Indeed, both of these geometrical parameters are key in producing pathophysiological gradients responsible for cellular and structural heterogeneity, replicating in vivo observations. Moreover, the fabrication techniques most widely used for producing these models lack the ability to accurately control cellular spatial location, an essential component for regulating homotypic and heterotypic cell signaling. Herein, we report on a 3D bioprinting technique, laser direct-write (LDW), that enables precise control of both spatial patterning and size of cell-encapsulating microbeads. The generated cell-laden beads are further processed into core-shelled structures, allowing for the growth and formation of self-contained, self-aggregating cells (e.g., breast cancer cells, embryonic stem cells). Within these structures we demonstrate our ability to produce multicellular tumor spheroids (MCTSs) and embryoid bodies (EBs) with well-controlled overall size and shape, that can be designed on demand. Furthermore, we investigated the impact of aggregate size on the uptake of a commonly employed ligand for receptor-mediated drug delivery, Transferrin, indicating that larger tumor spheroids exhibit greater spatial heterogeneity in ligand uptake. Taken together, these findings establish LDW as a versatile biomanufacturing platform for bioprinting and patterning core-shelled structures to generate size-controlled 3D multicellular aggregates. STATEMENT OF SIGNIFICANCE: Multicellular 3D aggregates are powerful in vitro models used to study a wide variety of complex biological processes, particularly within oncology and regenerative medicine. These tissue surrogates are fabricated using environments that encourage cellular self-assembly. However, specific applications require control of aggregate size and position to recapitulate key in vivo parameters (e.g., pathophysiological gradients and homotypic/heterotypic cell signaling). Herein, we demonstrate the ability to create and spatially pattern size-controlled embryoid bodies and tumor spheroids, using laser-based 3D bioprinting. Furthermore, we investigated the effect of tumor spheroid size on internalization of Transferrin, a common ligand for targeted therapy, finding greater spatial heterogeneity in our large aggregates. Overall, this technique offers incredible promise and flexibility for fabricating idealized 3D in vitro models.
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Affiliation(s)
- David M Kingsley
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 Eighth St., Troy, NY 12180, USA.
| | - Cassandra L Roberge
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 Eighth St., Troy, NY 12180, USA.
| | - Alena Rudkouskaya
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA.
| | - Denzel E Faulkner
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 Eighth St., Troy, NY 12180, USA.
| | - Margarida Barroso
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA.
| | - Xavier Intes
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 Eighth St., Troy, NY 12180, USA.
| | - David T Corr
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 Eighth St., Troy, NY 12180, USA.
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17
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Abstract
We present an electrodeposition technique for fabricating tubular alginate structures. In this technique, two electrodes (anode and cathode) are suspended in a solution of alginate and insoluble calcium carbonate particles, and the application of an electrical potential produces a localized pH change at the anode surface causing suspended divalent cations to become soluble and cross-link the alginate. We robustly characterize how the fabrication parameters influence the rate of radial deposition on the anode, including deposition time, applied voltage, alginate concentration, type of divalent cation and concentration, and anode diameter. Furthermore, we produce gels with a range of tailorable features, including mechanical properties, dimensions (thick-ness and lumen size), customizable tubular geometries, and radial compositional heterogeneity.
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Affiliation(s)
- David M Kingsley
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
| | - Jared A Capuano
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States.,Biomedical Engineering, Clemson University, 301 Rhodes Research Center, Clemson, South Carolina 29634, United States
| | - David T Corr
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
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18
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Kingsley DM, McCleery CH, Johnson CDL, Bramson MTK, Rende D, Gilbert RJ, Corr DT. Multi-modal characterization of polymeric gels to determine the influence of testing method on observed elastic modulus. J Mech Behav Biomed Mater 2019; 92:152-161. [PMID: 30703738 PMCID: PMC6387847 DOI: 10.1016/j.jmbbm.2019.01.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 12/29/2018] [Accepted: 01/07/2019] [Indexed: 12/25/2022]
Abstract
Demand for materials that mechanically replicate native tissue has driven development and characterization of various new biomaterials. However, a consequence of materials and characterization technique diversity is a lack of consensus within the field, with no clear way to compare values measured via different modalities. This likely contributes to the difficulty in replicating findings across the research community; recent evidence suggests that different modalities do not yield the same mechanical measurements within a material, and direct comparisons cannot be made across different testing platforms. Herein, we examine whether "material properties" are characterization modality-specific by analyzing the elastic moduli determined by five typical biomaterial mechanical characterization techniques: unconfined-compression, tensiometry, rheometry, and micro-indentation at the macroscopic level, and microscopically using nanoindentation. These analyses were performed in two different polymeric gels frequently used for biological applications, polydimethylsiloxane (PDMS) and agarose. Each was fabricated to span a range of moduli, from physiologic to supraphysiologic values. All five techniques identified the same overall trend within each material group, supporting their ability to appreciate relative moduli differences. However, significant differences were found across modalities, illustrating a difference in absolute moduli values, and thereby precluding direct comparison of measurements from different characterization modalities. These observed differences may depend on material compliance, viscoelasticity, and microstructure. While determining the underlying mechanism(s) of these differences was beyond the scope of this work, these results demonstrate how each modality affects the measured moduli of the same material, and the sensitivity of each modality to changes in sample material composition.
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Affiliation(s)
- David M Kingsley
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 Eighth St., Troy, NY 12180, USA.
| | - Caitlin H McCleery
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 Eighth St., Troy, NY 12180, USA.
| | - Christopher D L Johnson
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 Eighth St., Troy, NY 12180, USA.
| | - Michael T K Bramson
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 Eighth St., Troy, NY 12180, USA.
| | - Deniz Rende
- Center for Materials, Devices and Integrated Systems, Rensselaer Polytechnic Institute, 110 Eighth St., Troy, NY 12180, USA.
| | - Ryan J Gilbert
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 Eighth St., Troy, NY 12180, USA.
| | - David T Corr
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 Eighth St., Troy, NY 12180, USA.
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19
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Xie KT, Wang G, Thompson AC, Wucherpfennig JI, Reimchen TE, MacColl ADC, Schluter D, Bell MA, Vasquez KM, Kingsley DM. DNA fragility in the parallel evolution of pelvic reduction in stickleback fish. Science 2019; 363:81-84. [PMID: 30606845 DOI: 10.1126/science.aan1425] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 04/18/2018] [Accepted: 11/28/2018] [Indexed: 01/22/2023]
Abstract
Evolution generates a remarkable breadth of living forms, but many traits evolve repeatedly, by mechanisms that are still poorly understood. A classic example of repeated evolution is the loss of pelvic hindfins in stickleback fish (Gasterosteus aculeatus). Repeated pelvic loss maps to recurrent deletions of a pelvic enhancer of the Pitx1 gene. Here, we identify molecular features contributing to these recurrent deletions. Pitx1 enhancer sequences form alternative DNA structures in vitro and increase double-strand breaks and deletions in vivo. Enhancer mutability depends on DNA replication direction and is caused by TG-dinucleotide repeats. Modeling shows that elevated mutation rates can influence evolution under demographic conditions relevant for sticklebacks and humans. DNA fragility may thus help explain why the same loci are often used repeatedly during parallel adaptive evolution.
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Affiliation(s)
- Kathleen T Xie
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Guliang Wang
- Division of Pharmacology and Toxicology, University of Texas at Austin, Austin, TX, USA
| | - Abbey C Thompson
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia I Wucherpfennig
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - Dolph Schluter
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Michael A Bell
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA.
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, University of Texas at Austin, Austin, TX, USA
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA. .,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
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20
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Wucherpfennig JI, Miller CT, Kingsley DM. Efficient CRISPR-Cas9 editing of major evolutionary loci in sticklebacks. Evol Ecol Res 2019; 20:107-132. [PMID: 34899072 PMCID: PMC8664273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
BACKGROUND Stickleback fish are widely used to study the genetic and ecological basis of phenotypic evolution. Although several major loci have now been identified that contribute to evolutionary differences between wild populations, further study of the phenotypes associated with particular genes and mutations has been limited by the difficulty of generating targeted mutations at precise locations in the stickleback genome. APPROACH AND AIMS We compared different methods of expressing single-guide RNAs (sgRNAs) and Cas9 activity in fertilized stickleback eggs. We used an easily scored pigmentation gene (SLC24A5) to screen for molecular lesions, phenotypic effects, and possible germline transmission of newly induced alleles. We then used the optimized CRISPR methods to target two major evolutionary loci in sticklebacks, KITLG and EDA. We hypothesized that coding region mutations in the KITLG gene would alter body pigmentation and possibly sex determination, and that mutations in the EDA gene would disrupt the formation of most armor plates, fin rays, spines, teeth, and gill rakers. RESULTS Targeted deletions were successfully induced at each target locus by co-injecting one-cell stage stickleback embryos with either Cas9 mRNA or Cas9 protein, together with sgRNAs designed to protein-coding exons. Founder animals were typically mosaic for multiple mutations, which they transmitted through the germline at overall rates of 21 to 100%. We found that the copy of KITLG on the X chromosome (KITLGX) has diverged from the KITLG on the Y chromosome (KITLGY). Predicted loss-of-function mutations in the KITLGX gene dramatically altered pigmentation in both external skin and internal organ, but the same was not true for KITLGY mutations. Predicted loss-of-function mutations in either the KITLGX or KITLGY genes did not lead to sex reversal or prevent fertility. Homozygous loss-of-function mutations in the EDA gene led to complete loss of armor plates, severe reduction or loss of most soft rays in the dorsal, anal, and caudal fins, and severe reductions in tooth and gill raker number. In contrast, long dorsal and pelvic spines remained intact in EDA mutant animals, suggesting that common co-segregation of plate loss and spine reduction in wild populations is unlikely to be due to pleiotropic effects of EDA mutations. CONCLUSION CRISPR-Cas9 approaches can be used to induce germline mutations in key evolutionary loci in sticklebacks. Targeted coding region mutations confirm an important role for KITLG and EDA in skin pigmentation and armor plate reduction, respectively. They also provide new information about the functions of these genes in other body structures.
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Affiliation(s)
- Julia I Wucherpfennig
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305-5329, USA
| | - Craig T Miller
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, California 94720, USA
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305-5329, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305-5329, USA
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21
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Thompson AC, Capellini TD, Guenther CA, Chan YF, Infante CR, Menke DB, Kingsley DM. A novel enhancer near the Pitx1 gene influences development and evolution of pelvic appendages in vertebrates. eLife 2018; 7:38555. [PMID: 30499775 PMCID: PMC6269122 DOI: 10.7554/elife.38555] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 11/12/2018] [Indexed: 12/29/2022] Open
Abstract
Vertebrate pelvic reduction is a classic example of repeated evolution. Recurrent loss of pelvic appendages in sticklebacks has previously been linked to natural mutations in a pelvic enhancer that maps upstream of Pitx1. The sequence of this upstream PelA enhancer is not conserved to mammals, so we have surveyed a large region surrounding the mouse Pitx1 gene for other possible hind limb control sequences. Here we identify a new pelvic enhancer, PelB, that maps downstream rather than upstream of Pitx1. PelB drives expression in the posterior portion of the developing hind limb, and deleting the sequence from mice alters the size of several hind limb structures. PelB sequences are broadly conserved from fish to mammals. A wild stickleback population lacking the pelvis has an insertion/deletion mutation that disrupts the structure and function of PelB, suggesting that changes in this ancient enhancer contribute to evolutionary modification of pelvic appendages in nature.
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Affiliation(s)
- Abbey C Thompson
- Department of Developmental Biology, Stanford University School of Medicine, California, United States.,Department of Genetics, Stanford University School of Medicine, California, United States
| | - Terence D Capellini
- Department of Developmental Biology, Stanford University School of Medicine, California, United States
| | - Catherine A Guenther
- Department of Developmental Biology, Stanford University School of Medicine, California, United States.,Howard Hughes Medical Institute, Stanford University, California, United States
| | - Yingguang Frank Chan
- Department of Developmental Biology, Stanford University School of Medicine, California, United States
| | - Carlos R Infante
- Department of Genetics, University of Georgia, Georgia, United States
| | - Douglas B Menke
- Department of Genetics, University of Georgia, Georgia, United States
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, California, United States.,Howard Hughes Medical Institute, Stanford University, California, United States
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22
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Song JHT, Lowe CB, Kingsley DM. Characterization of a Human-Specific Tandem Repeat Associated with Bipolar Disorder and Schizophrenia. Am J Hum Genet 2018; 103:421-430. [PMID: 30100087 PMCID: PMC6128321 DOI: 10.1016/j.ajhg.2018.07.011] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 07/13/2018] [Indexed: 10/28/2022] Open
Abstract
Bipolar disorder (BD) and schizophrenia (SCZ) are highly heritable diseases that affect more than 3% of individuals worldwide. Genome-wide association studies have strongly and repeatedly linked risk for both of these neuropsychiatric diseases to a 100 kb interval in the third intron of the human calcium channel gene CACNA1C. However, the causative mutation is not yet known. We have identified a human-specific tandem repeat in this region that is composed of 30 bp units, often repeated hundreds of times. This large tandem repeat is unstable using standard polymerase chain reaction and bacterial cloning techniques, which may have resulted in its incorrect size in the human reference genome. The large 30-mer repeat region is polymorphic in both size and sequence in human populations. Particular sequence variants of the 30-mer are associated with risk status at several flanking single-nucleotide polymorphisms in the third intron of CACNA1C that have previously been linked to BD and SCZ. The tandem repeat arrays function as enhancers that increase reporter gene expression in a human neural progenitor cell line. Different human arrays vary in the magnitude of enhancer activity, and the 30-mer arrays associated with increased psychiatric disease risk status have decreased enhancer activity. Changes in the structure and sequence of these arrays likely contribute to changes in CACNA1C function during human evolution and may modulate neuropsychiatric disease risk in modern human populations.
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Affiliation(s)
- Janet H T Song
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Craig B Lowe
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - David M Kingsley
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
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Marques DA, Jones FC, Di Palma F, Kingsley DM, Reimchen TE. Experimental evidence for rapid genomic adaptation to a new niche in an adaptive radiation. Nat Ecol Evol 2018; 2:1128-1138. [PMID: 29942074 PMCID: PMC6519129 DOI: 10.1038/s41559-018-0581-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 05/17/2018] [Indexed: 12/20/2022]
Abstract
A substantial part of biodiversity is thought to have arisen from adaptive radiations in which one lineage rapidly diversified into multiple lineages adapted to many different niches. However, selection and drift reduce genetic variation during adaptation to new niches and may thus prevent or slow down further niche shifts. We tested whether rapid adaptation is still possible from a highly derived ecotype in the adaptive radiation of threespine stickleback on the Haida Gwaii archipelago, Western Canada. In a 19-years selection experiment, we let giant stickleback from a large blackwater lake evolve in a small clearwater pond without vertebrate predators. 56 whole genomes from the experiment and 26 natural populations revealed that adaptive genomic change was rapid in many small genomic regions and encompassed 75% of the adaptive genomic change between 12,000 years old ecotypes. Adaptive genomic change was as fast as phenotypic change in defence and trophic morphology and both were largely parallel between the short-term selection experiment and long-term natural adaptive radiation. Our results show that functionally relevant standing genetic variation can persist in derived adaptive radiation members, allowing adaptive radiations to unfold very rapidly.
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Affiliation(s)
- David A Marques
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada. .,Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland. .,Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland.
| | - Felicity C Jones
- Department of Developmental Biology, HHMI and Stanford University School of Medicine, Stanford, CA, USA.,Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Federica Di Palma
- Earlham Institute, Norwich Research Park, Norwich, UK.,Department of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - David M Kingsley
- Department of Developmental Biology, HHMI and Stanford University School of Medicine, Stanford, CA, USA
| | - Thomas E Reimchen
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
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24
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Lowe CB, Sanchez-Luege N, Howes TR, Brady SD, Daugherty RR, Jones FC, Bell MA, Kingsley DM. Corrigendum: Detecting differential copy number variation between groups of samples. Genome Res 2018; 28:766.1. [DOI: 10.1101/gr.237370.118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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25
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Howes TR, Summers BR, Kingsley DM. Dorsal spine evolution in threespine sticklebacks via a splicing change in MSX2A. BMC Biol 2017; 15:115. [PMID: 29212540 PMCID: PMC5719529 DOI: 10.1186/s12915-017-0456-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Accepted: 11/09/2017] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Dorsal spine reduction in threespine sticklebacks (Gasterosteus aculeatus) is a classic example of recurrent skeletal evolution in nature. Sticklebacks in marine environments typically have long spines that form part of their skeletal armor. Many derived freshwater populations have evolved shorter spines. Changes in spine length are controlled in part by a quantitative trait locus (QTL) previously mapped to chromosome 4, but the causative gene and mutations underlying the repeated evolution of this interesting skeletal trait have not been identified. RESULTS Refined mapping of the spine length QTL shows that it lies near the MSX2A transcription factor gene. MSX2A is expressed in developing spines. In F1 marine × freshwater fish, the marine allele is preferentially expressed. Differences in expression can be attributed to splicing regulation. Due to the use of an alternative 5 ' splice site within the first exon, the freshwater allele produces greater amounts of a shortened, non-functional transcript and makes less of the full-length transcript. Sequence changes in the MSX2A region are shared by many freshwater fish, suggesting that repeated evolution occurs by reuse of a spine-reduction variant. To demonstrate the effect of full-length MSX2A on spine length, we produced transgenic freshwater fish expressing a copy of marine MSX2A. The spines of the transgenic fish were significantly longer on average than those of their non-transgenic siblings, partially reversing the reduced spine lengths that have evolved in freshwater populations. CONCLUSIONS MSX2A is a major gene underlying dorsal spine reduction in freshwater sticklebacks. The gene is linked to a separate gene controlling bony plate loss, helping explain the concerted effects of chromosome 4 on multiple armor-reduction traits. The nature of the molecular changes provides an interesting example of morphological evolution occurring not through a simple amino acid change, nor through a change only in gene expression levels, but through a change in the ratio of splice products encoding both normal and truncated proteins.
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Affiliation(s)
- Timothy R Howes
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Brian R Summers
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA. .,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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26
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Kingsley DM. Beautiful Piles of Bones: An Interview with 2017 Genetics Society of America Medal Recipient David M. Kingsley. Genetics 2017; 207:1221-1222. [PMID: 29203698 PMCID: PMC5714440 DOI: 10.1534/genetics.117.300415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023] Open
Abstract
The Genetics Society of America Medal is awarded to an individual for outstanding contributions to the field of genetics in the last 15 years. Recipients of the GSA Medal are recognized for elegant and highly meaningful contributions to modern genetics, exemplifying the ingenuity of GSA membership. The 2017 recipient is David M. Kingsley, whose work in mouse, sticklebacks, and humans has shifted paradigms about how vertebrates evolve. Kingsley first fell in love with genetics in graduate school, where he worked on receptor mediated endocytosis with Monty Krieger. In his postdoctoral training he was able to unite genetics with his first scientific love: vertebrate morphology. He joined the group of Neal Copeland and Nancy Jenkins, where he led efforts to map the classical mouse skeletal mutation short ear Convinced that experimental genetics had a unique power to reveal the inner workings of evolution, Kingsley then established the stickleback fish as an extraordinarily productive model of quantitative trait evolution in wild species. He and his colleagues revealed many important insights, including the discoveries that major morphological differences can map to key loci with large effects, that regulatory changes in essential developmental control genes have produced advantageous new traits, and that nature has selected the same genes over and over again to drive the stickleback's skeletal evolution. Recently, Kingsley's group has been using these lessons to reveal more about how our own species evolved.This is an abridged version of the interview. The full interview is available on the Genes to Genomes blog, at genestogenomes.org/kingsley/.
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Affiliation(s)
- David M Kingsley
- Department of Developmental Biology and Howard Hughes Medical Institute, Stanford University School of Medicine, California 94305-5329
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27
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Martin AR, Lin M, Granka JM, Myrick JW, Liu X, Sockell A, Atkinson EG, Werely CJ, Möller M, Sandhu MS, Kingsley DM, Hoal EG, Liu X, Daly MJ, Feldman MW, Gignoux CR, Bustamante CD, Henn BM. An Unexpectedly Complex Architecture for Skin Pigmentation in Africans. Cell 2017; 171:1340-1353.e14. [PMID: 29195075 PMCID: PMC5884124 DOI: 10.1016/j.cell.2017.11.015] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 08/13/2017] [Accepted: 11/08/2017] [Indexed: 01/17/2023]
Abstract
Approximately 15 genes have been directly associated with skin pigmentation variation in humans, leading to its characterization as a relatively simple trait. However, by assembling a global survey of quantitative skin pigmentation phenotypes, we demonstrate that pigmentation is more complex than previously assumed, with genetic architecture varying by latitude. We investigate polygenicity in the KhoeSan populations indigenous to southern Africa who have considerably lighter skin than equatorial Africans. We demonstrate that skin pigmentation is highly heritable, but known pigmentation loci explain only a small fraction of the variance. Rather, baseline skin pigmentation is a complex, polygenic trait in the KhoeSan. Despite this, we identify canonical and non-canonical skin pigmentation loci, including near SLC24A5, TYRP1, SMARCA2/VLDLR, and SNX13, using a genome-wide association approach complemented by targeted resequencing. By considering diverse, under-studied African populations, we show how the architecture of skin pigmentation can vary across humans subject to different local evolutionary pressures.
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Affiliation(s)
- Alicia R Martin
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02141, USA; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA 02141, USA.
| | - Meng Lin
- Department of Ecology and Evolution, SUNY Stony Brook, NY 11794, USA
| | - Julie M Granka
- Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA
| | - Justin W Myrick
- Department of Ecology and Evolution, SUNY Stony Brook, NY 11794, USA
| | | | - Alexandra Sockell
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | | | - Cedric J Werely
- SA MRC Centre for Tuberculosis Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Marlo Möller
- SA MRC Centre for Tuberculosis Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | | | - David M Kingsley
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Eileen G Hoal
- SA MRC Centre for Tuberculosis Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Xiao Liu
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02141, USA; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA 02141, USA
| | - Marcus W Feldman
- Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA
| | | | | | - Brenna M Henn
- Department of Ecology and Evolution, SUNY Stony Brook, NY 11794, USA.
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28
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Bay RA, Arnegard ME, Conte GL, Best J, Bedford NL, McCann SR, Dubin ME, Chan YF, Jones FC, Kingsley DM, Schluter D, Peichel CL. Genetic Coupling of Female Mate Choice with Polygenic Ecological Divergence Facilitates Stickleback Speciation. Curr Biol 2017; 27:3344-3349.e4. [PMID: 29056455 DOI: 10.1016/j.cub.2017.09.037] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 08/12/2017] [Accepted: 09/15/2017] [Indexed: 11/28/2022]
Abstract
Ecological speciation with gene flow is widespread in nature [1], but it presents a conundrum: how are associations between traits under divergent natural selection and traits that contribute to assortative mating maintained? Theoretical models suggest that genetic mechanisms inhibiting free recombination between loci underlying these two types of traits (hereafter, "genetic coupling") can facilitate speciation [2-4]. Here, we perform a direct test for genetic coupling by mapping both divergent traits and female mate choice in a classic model of ecological speciation: sympatric benthic and limnetic threespine stickleback (Gasterosteus aculeatus). By measuring mate choice in F2 hybrid females, we allowed for recombination between loci underlying assortative mating and those under divergent ecological selection. In semi-natural mating arenas in which females had access to both benthic and limnetic males, we found that F2 females mated with males similar to themselves in body size and shape. In addition, we found two quantitative trait loci (QTLs) associated with female mate choice that also predicted female morphology along the benthic-limnetic trait axis. Furthermore, a polygenic genetic model that explains adaptation to contrasting benthic and limnetic feeding niches [5] also predicted F2 female mate choice. Together, these results provide empirical evidence that genetic coupling of assortative mating with traits under divergent ecological selection helps maintain species in the face of gene flow, despite a polygenic basis for adaptation to divergent environments.
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Affiliation(s)
- Rachael A Bay
- Biodiversity Research Centre and Zoology Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada; Institute of the Environment and Sustainability, University of California, Los Angeles, 619 Charles E. Young Drive #300, Los Angeles, CA 90024, USA
| | - Matthew E Arnegard
- Biodiversity Research Centre and Zoology Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada; Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Gina L Conte
- Biodiversity Research Centre and Zoology Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Jacob Best
- Biodiversity Research Centre and Zoology Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Nicole L Bedford
- Biodiversity Research Centre and Zoology Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Shaugnessy R McCann
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Matthew E Dubin
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Yingguang Frank Chan
- Department of Developmental Biology and Howard Hughes Medical Institute, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA
| | - Felicity C Jones
- Department of Developmental Biology and Howard Hughes Medical Institute, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA
| | - David M Kingsley
- Department of Developmental Biology and Howard Hughes Medical Institute, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA
| | - Dolph Schluter
- Biodiversity Research Centre and Zoology Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Catherine L Peichel
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA.
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29
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Lickwar CR, Camp JG, Weiser M, Cocchiaro JL, Kingsley DM, Furey TS, Sheikh SZ, Rawls JF. Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells. PLoS Biol 2017; 15:e2002054. [PMID: 28850571 PMCID: PMC5574553 DOI: 10.1371/journal.pbio.2002054] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 07/31/2017] [Indexed: 12/17/2022] Open
Abstract
The intestinal epithelium serves critical physiologic functions that are shared among all vertebrates. However, it is unknown how the transcriptional regulatory mechanisms underlying these functions have changed over the course of vertebrate evolution. We generated genome-wide mRNA and accessible chromatin data from adult intestinal epithelial cells (IECs) in zebrafish, stickleback, mouse, and human species to determine if conserved IEC functions are achieved through common transcriptional regulation. We found evidence for substantial common regulation and conservation of gene expression regionally along the length of the intestine from fish to mammals and identified a core set of genes comprising a vertebrate IEC signature. We also identified transcriptional start sites and other putative regulatory regions that are differentially accessible in IECs in all 4 species. Although these sites rarely showed sequence conservation from fish to mammals, surprisingly, they drove highly conserved IEC expression in a zebrafish reporter assay. Common putative transcription factor binding sites (TFBS) found at these sites in multiple species indicate that sequence conservation alone is insufficient to identify much of the functionally conserved IEC regulatory information. Among the rare, highly sequence-conserved, IEC-specific regulatory regions, we discovered an ancient enhancer upstream from her6/HES1 that is active in a distinct population of Notch-positive cells in the intestinal epithelium. Together, these results show how combining accessible chromatin and mRNA datasets with TFBS prediction and in vivo reporter assays can reveal tissue-specific regulatory information conserved across 420 million years of vertebrate evolution. We define an IEC transcriptional regulatory network that is shared between fish and mammals and establish an experimental platform for studying how evolutionarily distilled regulatory information commonly controls IEC development and physiology. The epithelium lining the intestine is an ancient animal tissue that serves as a primary site of nutrient absorption and interaction with microbiota. Its formation and function require complex patterns of gene transcription that vary along the intestine and in specialized intestinal epithelial cell (IEC) subtypes. However, it is unknown how the underlying transcriptional regulatory mechanisms have changed over the course of vertebrate evolution. Here, we used genome-wide profiling of mRNA levels and chromatin accessibility to identify conserved IEC genes and regulatory regions in 4 vertebrate species (zebrafish, stickleback, mouse, and human) separated from a common ancestor by 420 million years. We identified substantial similarities in genes expressed along the vertebrate intestine. These data disclosed putative conserved transcription factor binding sites (TFBS) enriched in accessible chromatin near IEC genes and in regulatory sites with accessibility restricted to IECs. Fluorescent reporter assays in transparent zebrafish showed that these regions, which frequently lacked sequence conservation, were still capable of driving conserved expression patterns. We also found a highly conserved region near mammalian and fish hes1 sufficient to drive expression in a specific population of IECs with active Notch signaling. These results establish a platform to define the conserved transcriptional networks underlying vertebrate IEC physiology.
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Affiliation(s)
- Colin R. Lickwar
- Department of Molecular Genetics and Microbiology, Center for the Genomics of Microbial Systems, Duke University, Durham, North Carolina, United States of America
- Department of Cell Biology and Physiology, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - J. Gray Camp
- Department of Cell Biology and Physiology, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Developmental Biology, Stanford University, Stanford, California, United States of America
| | - Matthew Weiser
- Departments of Genetics and Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jordan L. Cocchiaro
- Department of Molecular Genetics and Microbiology, Center for the Genomics of Microbial Systems, Duke University, Durham, North Carolina, United States of America
- Department of Cell Biology and Physiology, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - David M. Kingsley
- Department of Developmental Biology, Stanford University, Stanford, California, United States of America
| | - Terrence S. Furey
- Departments of Genetics and Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Shehzad Z. Sheikh
- Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - John F. Rawls
- Department of Molecular Genetics and Microbiology, Center for the Genomics of Microbial Systems, Duke University, Durham, North Carolina, United States of America
- Department of Cell Biology and Physiology, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
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30
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Capellini TD, Chen H, Cao J, Doxey AC, Kiapour AM, Schoor M, Kingsley DM. Ancient selection for derived alleles at a GDF5 enhancer influencing human growth and osteoarthritis risk. Nat Genet 2017; 49:1202-1210. [PMID: 28671685 PMCID: PMC6556117 DOI: 10.1038/ng.3911] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 06/12/2017] [Indexed: 12/19/2022]
Abstract
Variants in GDF5 are associated with human arthritis and decreased height, but the causal mutations are still unknown. We surveyed the Gdf5 locus for regulatory regions in transgenic mice and fine-mapped separate enhancers controlling expression in joints versus growing ends of long bones. A large downstream regulatory region contains a novel growth enhancer (GROW1), which is required for normal Gdf5 expression at ends of developing bones and for normal bone lengths in vivo. Human GROW1 contains a common base-pair change that decreases enhancer activity and colocalizes with peaks of positive selection in humans. The derived allele is rare in Africa but common in Eurasia and is found in Neandertals and Denisovans. Our results suggest that an ancient regulatory variant in GROW1 has been repeatedly selected in northern environments and that past selection on growth phenotypes explains the high frequency of a GDF5 haplotype that also increases arthritis susceptibility in many human populations.
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Affiliation(s)
- Terence D Capellini
- Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.,Department of Developmental Biology, Stanford University, Stanford, California, USA
| | - Hao Chen
- Department of Developmental Biology, Stanford University, Stanford, California, USA
| | - Jiaxue Cao
- Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Andrew C Doxey
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Ata M Kiapour
- Department of Orthopedic Surgery, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael Schoor
- Department of Developmental Biology, Stanford University, Stanford, California, USA
| | - David M Kingsley
- Department of Developmental Biology, Stanford University, Stanford, California, USA.,Howard Hughes Medical Institute, Stanford University, Stanford, California, USA
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31
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Marques DA, Taylor JS, Jones FC, Di Palma F, Kingsley DM, Reimchen TE. Convergent evolution of SWS2 opsin facilitates adaptive radiation of threespine stickleback into different light environments. PLoS Biol 2017; 15:e2001627. [PMID: 28399148 PMCID: PMC5388470 DOI: 10.1371/journal.pbio.2001627] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 03/06/2017] [Indexed: 11/18/2022] Open
Abstract
Repeated adaptation to a new environment often leads to convergent phenotypic changes whose underlying genetic mechanisms are rarely known. Here, we study adaptation of color vision in threespine stickleback during the repeated postglacial colonization of clearwater and blackwater lakes in the Haida Gwaii archipelago. We use whole genomes from 16 clearwater and 12 blackwater populations, and a selection experiment, in which stickleback were transplanted from a blackwater lake into an uninhabited clearwater pond and resampled after 19 y to test for selection on cone opsin genes. Patterns of haplotype homozygosity, genetic diversity, site frequency spectra, and allele-frequency change support a selective sweep centered on the adjacent blue- and red-light sensitive opsins SWS2 and LWS. The haplotype under selection carries seven amino acid changes in SWS2, including two changes known to cause a red-shift in light absorption, and is favored in blackwater lakes but disfavored in the clearwater habitat of the transplant population. Remarkably, the same red-shifting amino acid changes occurred after the duplication of SWS2 198 million years ago, in the ancestor of most spiny-rayed fish. Two distantly related fish species, bluefin killifish and black bream, express these old paralogs divergently in black- and clearwater habitats, while sticklebacks lost one paralog. Our study thus shows that convergent adaptation to the same environment can involve the same genetic changes on very different evolutionary time scales by reevolving lost mutations and reusing them repeatedly from standing genetic variation.
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Affiliation(s)
- David A. Marques
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
- * E-mail:
| | - John S. Taylor
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Felicity C. Jones
- Stanford University School of Medicine, Department of Developmental Biology, Stanford, California, United States of America
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Federica Di Palma
- Earlham Institute and University of East Anglia, Department of Biological Sciences, Norwich, United Kingdom
| | - David M. Kingsley
- Stanford University School of Medicine, Department of Developmental Biology, Stanford, California, United States of America
| | - Thomas E. Reimchen
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
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32
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Chen H, Capellini TD, Schoor M, Mortlock DP, Reddi AH, Kingsley DM. Heads, Shoulders, Elbows, Knees, and Toes: Modular Gdf5 Enhancers Control Different Joints in the Vertebrate Skeleton. PLoS Genet 2016; 12:e1006454. [PMID: 27902701 PMCID: PMC5130176 DOI: 10.1371/journal.pgen.1006454] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 11/02/2016] [Indexed: 11/18/2022] Open
Abstract
Synovial joints are crucial for support and locomotion in vertebrates, and are the frequent site of serious skeletal defects and degenerative diseases in humans. Growth and differentiation factor 5 (Gdf5) is one of the earliest markers of joint formation, is required for normal joint development in both mice and humans, and has been genetically linked to risk of common osteoarthritis in Eurasian populations. Here, we systematically survey the mouse Gdf5 gene for regulatory elements controlling expression in synovial joints. We identify separate regions of the locus that control expression in axial tissues, in proximal versus distal joints in the limbs, and in remarkably specific sub-sets of composite joints like the elbow. Predicted transcription factor binding sites within Gdf5 regulatory enhancers are required for expression in particular joints. The multiple enhancers that control Gdf5 expression in different joints are distributed over a hundred kilobases of DNA, including regions both upstream and downstream of Gdf5 coding exons. Functional rescue tests in mice confirm that the large flanking regions are required to restore normal joint formation and patterning. Orthologs of these enhancers are located throughout the large genomic region previously associated with common osteoarthritis risk in humans. The large array of modular enhancers for Gdf5 provide a new foundation for studying the spatial specificity of joint patterning in vertebrates, as well as new candidates for regulatory regions that may also influence osteoarthritis risk in human populations. Joints, such as the hip and knee, are crucial for support and locomotion in animals, and are the frequent sites of serious human diseases such as arthritis. The Growth and differentiation factor 5 (Gdf5) gene is required for normal joint formation, and has been linked to risk of common arthritis in Eurasians. Here, we surveyed the mouse gene for the regulatory information that controls Gdf5's expression pattern in stripes at sites of joint formation. The gene does not have a single regulatory sequence that drives expression in all joints. Instead, Gdf5 has multiple different control sequences that show striking specificity for joints in the head, vertebral column, shoulder, elbow, wrist, hip, knee, and digits. Rescue experiments show that multiple control sequences are required to restore normal joint formation in Gdf5 mutants. The joint control sequences originally found in mice are also present in humans, where they are marked as active regions during fetal development and post-natal life, and map to a large region associated with arthritis risk in human populations. Regulatory variants in the human GDF5 control sequences can now be studied for their potential role in altering joint development or disease risk at particular locations in the skeleton.
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Affiliation(s)
- Hao Chen
- Department of Developmental Biology, Beckman Center B300, Stanford University School of Medicine, Stanford, California, United States of America
| | - Terence D. Capellini
- Department of Developmental Biology, Beckman Center B300, Stanford University School of Medicine, Stanford, California, United States of America
- Human Evolutionary Biology, Peabody Museum, Harvard University, Cambridge, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | | | - Doug P. Mortlock
- Molecular Physiology and Biophysics and Vanderbilt Genetics Institute, Vanderbilt University, Nashville, Tennessee, United States of America
| | - A. Hari Reddi
- Center for Tissue Regeneration and Repair, University of California Davis Medical Center, Sacramento, California, United States of America
| | - David M. Kingsley
- Department of Developmental Biology, Beckman Center B300, Stanford University School of Medicine, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford University, Stanford, California, United States of America
- * E-mail:
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Heng K, Thompson A, Chu D, Kingsley DM. Three cheers for the three-spined stickleback. Lab Anim (NY) 2016; 45:421. [PMID: 27763600 DOI: 10.1038/laban.1142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Kingsley DM, Dias AD, Corr DT. Microcapsules and 3D customizable shelled microenvironments from laser direct-written microbeads. Biotechnol Bioeng 2016; 113:2264-74. [PMID: 27070458 DOI: 10.1002/bit.25987] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 04/07/2016] [Indexed: 01/05/2023]
Abstract
Microcapsules are shelled 3D microenvironments, with a liquid core. These core-shelled structures enable cell-cell contact, cellular proliferation and aggregation within the capsule, and can be utilized for controlled release of encapsulated contents. Traditional microcapsule fabrication methods provide limited control of capsule size, and are unable to control capsule placement. To overcome these limitations, we demonstrate size and spatial control of poly-l-lysine and chitosan microcapsules, using laser direct-write (LDW) printing, and subsequent processing, of alginate microbeads. Additionally, microbeads were used as volume pixels (voxels) to form continuous 3D hydrogel structures, which were processed like capsules, to form custom shelled aqueous-core 3D structures of prescribed geometry; such as strands, rings, and bifurcations. Heterogeneous structures were also created with controlled initial locations of different cell types, to demonstrate the ability to prescribe cell signaling (heterotypic and homotypic) in co-culture conditions. Herein, we demonstrate LDW's ability to fabricate intricate 3D structures, essentially with "printed macroporosity," and to precisely control structural composition by bottom-up fabrication in a bead-by-bead manner. The structural and compositional control afforded by this process enables the creation of a wide range of new constructs, with many potential applications in tissue engineering and regenerative medicine. Biotechnol. Bioeng. 2016;113: 2264-2274. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- David M Kingsley
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 Eighth St., Troy, New York 12180
| | - Andrew D Dias
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 Eighth St., Troy, New York 12180
| | - David T Corr
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 Eighth St., Troy, New York 12180.
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Guenther CA, Wang Z, Li E, Tran MC, Logan CY, Nusse R, Pantalena-Filho L, Yang GP, Kingsley DM. A distinct regulatory region of the Bmp5 locus activates gene expression following adult bone fracture or soft tissue injury. Bone 2015; 77:31-41. [PMID: 25886903 PMCID: PMC4447581 DOI: 10.1016/j.bone.2015.04.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Revised: 04/02/2015] [Accepted: 04/04/2015] [Indexed: 12/25/2022]
Abstract
Bone morphogenetic proteins (BMPs) are key signaling molecules required for normal development of bones and other tissues. Previous studies have shown that null mutations in the mouse Bmp5 gene alter the size, shape and number of multiple bone and cartilage structures during development. Bmp5 mutations also delay healing of rib fractures in adult mutants, suggesting that the same signals used to pattern embryonic bone and cartilage are also reused during skeletal regeneration and repair. Despite intense interest in BMPs as agents for stimulating bone formation in clinical applications, little is known about the regulatory elements that control developmental or injury-induced BMP expression. To compare the DNA sequences that activate gene expression during embryonic bone formation and following acute injuries in adult animals, we assayed regions surrounding the Bmp5 gene for their ability to stimulate lacZ reporter gene expression in transgenic mice. Multiple genomic fragments, distributed across the Bmp5 locus, collectively coordinate expression in discrete anatomic domains during normal development, including in embryonic ribs. In contrast, a distinct regulatory region activated expression following rib fracture in adult animals. The same injury control region triggered gene expression in mesenchymal cells following tibia fracture, in migrating keratinocytes following dorsal skin wounding, and in regenerating epithelial cells following lung injury. The Bmp5 gene thus contains an "injury response" control region that is distinct from embryonic enhancers, and that is activated by multiple types of injury in adult animals.
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Affiliation(s)
- Catherine A Guenther
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Zhen Wang
- Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Emma Li
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Misha C Tran
- Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Catriona Y Logan
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Roel Nusse
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Luiz Pantalena-Filho
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - George P Yang
- Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA; Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA.
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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O'Brown NM, Summers BR, Jones FC, Brady SD, Kingsley DM. A recurrent regulatory change underlying altered expression and Wnt response of the stickleback armor plates gene EDA. eLife 2015; 4:e05290. [PMID: 25629660 PMCID: PMC4384742 DOI: 10.7554/elife.05290] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 01/26/2015] [Indexed: 12/15/2022] Open
Abstract
Armor plate changes in sticklebacks are a classic example of repeated adaptive
evolution. Previous studies identified ectodysplasin (EDA) gene as
the major locus controlling recurrent plate loss in freshwater fish, though the
causative DNA alterations were not known. Here we show that freshwater
EDA alleles have cis-acting regulatory changes
that reduce expression in developing plates and spines. An identical T → G
base pair change is found in EDA enhancers of divergent low-plated
fish. Recreation of the T → G change in a marine enhancer strongly reduces
expression in posterior armor plates. Bead implantation and cell culture experiments
show that Wnt signaling strongly activates the marine EDA enhancer,
and the freshwater T → G change reduces Wnt responsiveness. Thus parallel
evolution of low-plated sticklebacks has occurred through a shared DNA regulatory
change, which reduces the sensitivity of an EDA enhancer to Wnt
signaling, and alters expression in developing armor plates while preserving
expression in other tissues. DOI:http://dx.doi.org/10.7554/eLife.05290.001 Stickleback fish develop bony plates on their surface to protect themselves from
predators. The extent and pattern of their bony armor depends on their habitat:
marine sticklebacks are typically covered from head to tail with bony plates, but
freshwater sticklebacks retain only a few plates on their sides. One gene that promotes the formation of the bony plates is called
ectodysplasin (EDA). This encodes a signaling
protein that is important for the development of the skeleton, skin and many other
tissues. Variations in the sequence of this gene are shared among different
stickleback populations worldwide. However, it has not been clear which genetic
changes can explain how lightly armored freshwater sticklebacks could have evolved
from their well-armored marine ancestors on several separate occasions. Here, O'Brown et al. studied EDA in marine and groups of
freshwater sticklebacks that have evolved in different locations around the world.
The experiments show that the level of expression of EDA in the
developing plates and spines is lower in the freshwater fish. O'Brown et al.
thought this could be due to genetic changes in regions of EDA that
lie outside the region that encodes the protein, so called ‘regulatory
elements’. Indeed, further experiments found that all freshwater fish have a small change in the
DNA of a regulatory element that switches on the gene in plate-forming regions of the
body. When this change was introduced into marine sticklebacks, the fish had lower
levels of gene expression in these plate-forming regions. These findings demonstrate that lightly armored sticklebacks have evolved multiple
times from their well-armored marine ancestors through the same small change in their
DNA that alters the expression of the EDA gene. The next challenge
will be to understand why this particular small change in DNA appears to be favored
over all the other changes that could occur in the regulatory element, and to see if
factors that act through this regulatory switch also modify armor structures in
natural populations. DOI:http://dx.doi.org/10.7554/eLife.05290.002
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Affiliation(s)
- Natasha M O'Brown
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, United States
| | - Brian R Summers
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, United States
| | - Felicity C Jones
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, United States
| | - Shannon D Brady
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, United States
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, United States
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Kumar ME, Bogard PE, Espinoza FH, Menke DB, Kingsley DM, Krasnow MA. Mesenchymal cells. Defining a mesenchymal progenitor niche at single-cell resolution. Science 2014; 346:1258810. [PMID: 25395543 DOI: 10.1126/science.1258810] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Most vertebrate organs are composed of epithelium surrounded by support and stromal tissues formed from mesenchyme cells, which are not generally thought to form organized progenitor pools. Here, we use clonal cell labeling with multicolor reporters to characterize individual mesenchymal progenitors in the developing mouse lung. We observe a diversity of mesenchymal progenitor populations with different locations, movements, and lineage boundaries. Airway smooth muscle (ASM) progenitors map exclusively to mesenchyme ahead of budding airways. Progenitors recruited from these tip pools differentiate into ASM around airway stalks; flanking stalk mesenchyme can be induced to form an ASM niche by a lateral bud or by an airway tip plus focal Wnt signal. Thus, mesenchymal progenitors can be organized into localized and carefully controlled domains that rival epithelial progenitor niches in regulatory sophistication.
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Affiliation(s)
- Maya E Kumar
- Howard Hughes Medical Institute and Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA
| | - Patrick E Bogard
- Howard Hughes Medical Institute and Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA
| | - F Hernán Espinoza
- Howard Hughes Medical Institute and Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA
| | - Douglas B Menke
- Department of Genetics, University of Georgia, Athens, GA 30602-2607, USA. Howard Hughes Medical Institute and Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329, USA
| | - David M Kingsley
- Howard Hughes Medical Institute and Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329, USA
| | - Mark A Krasnow
- Howard Hughes Medical Institute and Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA.
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Arnegard ME, McGee MD, Matthews B, Marchinko KB, Conte GL, Kabir S, Bedford N, Bergek S, Chan YF, Jones FC, Kingsley DM, Peichel CL, Schluter D. Genetics of ecological divergence during speciation. Nature 2014; 511:307-11. [PMID: 24909991 PMCID: PMC4149549 DOI: 10.1038/nature13301] [Citation(s) in RCA: 199] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 04/01/2014] [Indexed: 01/15/2023]
Abstract
Ecological differences often evolve early in speciation as divergent natural selection drives adaptation to distinct ecological niches, leading ultimately to reproductive isolation. Although this process is a major generator of biodiversity, its genetic basis is still poorly understood. Here we investigate the genetic architecture of niche differentiation in a sympatric species pair of threespine stickleback fish by mapping the environment-dependent effects of phenotypic traits on hybrid feeding and performance under semi-natural conditions. We show that multiple, unlinked loci act largely additively to determine position along the major niche axis separating these recently diverged species. We also find that functional mismatch between phenotypic traits reduces the growth of some stickleback hybrids beyond that expected from an intermediate phenotype, suggesting a role for epistasis between the underlying genes. This functional mismatch might lead to hybrid incompatibilities that are analogous to those underlying intrinsic reproductive isolation but depend on the ecological context.
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Affiliation(s)
- Matthew E Arnegard
- 1] Fred Hutchinson Cancer Research Center, Human Biology and Basic Sciences Divisions, 1100 Fairview Avenue North, Seattle, Washington 98109, USA [2] University of British Columbia, Biodiversity Research Centre and Zoology Department, 6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
| | - Matthew D McGee
- University of California at Davis, Department of Evolution and Ecology, One Shields Avenue, Davis, California 95616, USA
| | - Blake Matthews
- EAWAG, Department of Aquatic Ecology, Center for Ecology, Evolution, and Biogeochemistry, Seestrasse 79, 6047 Kastanienbaum, Switzerland
| | - Kerry B Marchinko
- University of British Columbia, Biodiversity Research Centre and Zoology Department, 6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
| | - Gina L Conte
- University of British Columbia, Biodiversity Research Centre and Zoology Department, 6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
| | - Sahriar Kabir
- University of British Columbia, Biodiversity Research Centre and Zoology Department, 6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
| | - Nicole Bedford
- University of British Columbia, Biodiversity Research Centre and Zoology Department, 6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
| | - Sara Bergek
- 1] Uppsala University, Department of Animal Ecology, Evolutionary Biology Centre (EBC), Norbyvägen 18D, SE-75236 Uppsala, Sweden [2] Swedish University of Agricultural Sciences, Department of Aquatic Resources, Stångholmsvägen 2, SE-17893 Drottningholm, Sweden
| | - Yingguang Frank Chan
- Stanford University School of Medicine, Department of Developmental Biology and Howard Hughes Medical Institute, 279 Campus Drive, Stanford, California 94305, USA
| | - Felicity C Jones
- Stanford University School of Medicine, Department of Developmental Biology and Howard Hughes Medical Institute, 279 Campus Drive, Stanford, California 94305, USA
| | - David M Kingsley
- Stanford University School of Medicine, Department of Developmental Biology and Howard Hughes Medical Institute, 279 Campus Drive, Stanford, California 94305, USA
| | - Catherine L Peichel
- Fred Hutchinson Cancer Research Center, Human Biology and Basic Sciences Divisions, 1100 Fairview Avenue North, Seattle, Washington 98109, USA
| | - Dolph Schluter
- University of British Columbia, Biodiversity Research Centre and Zoology Department, 6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
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Dias AD, Kingsley DM, Corr DT. Recent advances in bioprinting and applications for biosensing. Biosensors (Basel) 2014; 4:111-36. [PMID: 25587413 PMCID: PMC4264374 DOI: 10.3390/bios4020111] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 04/12/2014] [Accepted: 04/18/2014] [Indexed: 12/19/2022]
Abstract
Future biosensing applications will require high performance, including real-time monitoring of physiological events, incorporation of biosensors into feedback-based devices, detection of toxins, and advanced diagnostics. Such functionality will necessitate biosensors with increased sensitivity, specificity, and throughput, as well as the ability to simultaneously detect multiple analytes. While these demands have yet to be fully realized, recent advances in biofabrication may allow sensors to achieve the high spatial sensitivity required, and bring us closer to achieving devices with these capabilities. To this end, we review recent advances in biofabrication techniques that may enable cutting-edge biosensors. In particular, we focus on bioprinting techniques (e.g., microcontact printing, inkjet printing, and laser direct-write) that may prove pivotal to biosensor fabrication and scaling. Recent biosensors have employed these fabrication techniques with success, and further development may enable higher performance, including multiplexing multiple analytes or cell types within a single biosensor. We also review recent advances in 3D bioprinting, and explore their potential to create biosensors with live cells encapsulated in 3D microenvironments. Such advances in biofabrication will expand biosensor utility and availability, with impact realized in many interdisciplinary fields, as well as in the clinic.
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Affiliation(s)
- Andrew D Dias
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 Eighth St., Troy, NY 12180, USA; E-Mails: (A.D.D.); (D.M.K.)
| | - David M Kingsley
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 Eighth St., Troy, NY 12180, USA; E-Mails: (A.D.D.); (D.M.K.)
| | - David T Corr
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 Eighth St., Troy, NY 12180, USA; E-Mails: (A.D.D.); (D.M.K.)
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Miller CT, Glazer AM, Summers BR, Blackman BK, Norman AR, Shapiro MD, Cole BL, Peichel CL, Schluter D, Kingsley DM. Modular skeletal evolution in sticklebacks is controlled by additive and clustered quantitative trait Loci. Genetics 2014; 197:405-20. [PMID: 24652999 PMCID: PMC4012497 DOI: 10.1534/genetics.114.162420] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 02/22/2014] [Indexed: 11/18/2022] Open
Abstract
Understanding the genetic architecture of evolutionary change remains a long-standing goal in biology. In vertebrates, skeletal evolution has contributed greatly to adaptation in body form and function in response to changing ecological variables like diet and predation. Here we use genome-wide linkage mapping in threespine stickleback fish to investigate the genetic architecture of evolved changes in many armor and trophic traits. We identify >100 quantitative trait loci (QTL) controlling the pattern of serially repeating skeletal elements, including gill rakers, teeth, branchial bones, jaws, median fin spines, and vertebrae. We use this large collection of QTL to address long-standing questions about the anatomical specificity, genetic dominance, and genomic clustering of loci controlling skeletal differences in evolving populations. We find that most QTL (76%) that influence serially repeating skeletal elements have anatomically regional effects. In addition, most QTL (71%) have at least partially additive effects, regardless of whether the QTL controls evolved loss or gain of skeletal elements. Finally, many QTL with high LOD scores cluster on chromosomes 4, 20, and 21. These results identify a modular system that can control highly specific aspects of skeletal form. Because of the general additivity and genomic clustering of major QTL, concerted changes in both protective armor and trophic traits may occur when sticklebacks inherit either marine or freshwater alleles at linked or possible "supergene" regions of the stickleback genome. Further study of these regions will help identify the molecular basis of both modular and coordinated changes in the vertebrate skeleton.
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Affiliation(s)
- Craig T. Miller
- Molecular and Cell Biology Department, University of California, Berkeley, California 94720
- Department of Developmental Biology and Howard Hughes Medical Institute, Stanford University, Stanford, California 94305
| | - Andrew M. Glazer
- Molecular and Cell Biology Department, University of California, Berkeley, California 94720
| | - Brian R. Summers
- Department of Developmental Biology and Howard Hughes Medical Institute, Stanford University, Stanford, California 94305
| | - Benjamin K. Blackman
- Department of Developmental Biology and Howard Hughes Medical Institute, Stanford University, Stanford, California 94305
| | - Andrew R. Norman
- Department of Developmental Biology and Howard Hughes Medical Institute, Stanford University, Stanford, California 94305
| | - Michael D. Shapiro
- Department of Developmental Biology and Howard Hughes Medical Institute, Stanford University, Stanford, California 94305
| | - Bonnie L. Cole
- Department of Developmental Biology and Howard Hughes Medical Institute, Stanford University, Stanford, California 94305
| | - Catherine L. Peichel
- Department of Developmental Biology and Howard Hughes Medical Institute, Stanford University, Stanford, California 94305
| | - Dolph Schluter
- Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - David M. Kingsley
- Department of Developmental Biology and Howard Hughes Medical Institute, Stanford University, Stanford, California 94305
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Reno PL, McLean CY, Hines JE, Capellini TD, Bejerano G, Kingsley DM. A penile spine/vibrissa enhancer sequence is missing in modern and extinct humans but is retained in multiple primates with penile spines and sensory vibrissae. PLoS One 2013; 8:e84258. [PMID: 24367647 PMCID: PMC3868586 DOI: 10.1371/journal.pone.0084258] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 11/04/2013] [Indexed: 11/18/2022] Open
Abstract
Previous studies show that humans have a large genomic deletion downstream of the Androgen Receptor gene that eliminates an ancestral mammalian regulatory enhancer that drives expression in developing penile spines and sensory vibrissae. Here we use a combination of large-scale sequence analysis and PCR amplification to demonstrate that the penile spine/vibrissa enhancer is missing in all humans surveyed and in the Neandertal and Denisovan genomes, but is present in DNA samples of chimpanzees and bonobos, as well as in multiple other great apes and primates that maintain some form of penile integumentary appendage and facial vibrissae. These results further strengthen the association between the presence of the penile spine/vibrissa enhancer and the presence of penile spines and macro- or micro- vibrissae in non-human primates as well as show that loss of the enhancer is both a distinctive and characteristic feature of the human lineage.
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Affiliation(s)
- Philip L. Reno
- Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail: (PLR); (CYM)
| | - Cory Y. McLean
- Department of Computer Science, Stanford University, Stanford, California, United States of America
- * E-mail: (PLR); (CYM)
| | - Jasmine E. Hines
- Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Terence D. Capellini
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Gill Bejerano
- Department of Computer Science, Stanford University, Stanford, California, United States of America
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - David M. Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford, California, United States of America
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Abstract
Alginate can be used to encapsulate mammalian cells and for the slow release of small molecules. Packaging alginate as microbead structures allows customizable delivery for tissue engineering, drug release, or contrast agents for imaging. However, state-of-the-art microbead fabrication has a limited range in achievable bead sizes, and poor control over bead placement, which may be desired to localize cellular signaling or delivery. Herein, we present a novel, laser-based method for single-step fabrication and precise planar placement of alginate microbeads. Our results show that bead size is controllable within 8%, and fabricated microbeads can remain immobilized within 2% of their target placement. Demonstration of this technique using human breast cancer cells shows that cells encapsulated within these microbeads survive at a rate of 89.6%, decreasing to 84.3% after five days in culture. Infusing rhodamine dye into microbeads prior to fluorescent microscopy shows their 3D spheroidal geometry and the ability to sequester small molecules. Microbead fabrication and patterning is compatible with conventional cellular transfer and patterning by laser direct-write, allowing location-based cellular studies. While this method can also be used to fabricate microbeads en masse for collection, the greatest value to tissue engineering and drug delivery studies and applications lies in the pattern registry of printed microbeads.
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Affiliation(s)
- DM Kingsley
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 Eighth St., Troy, NY 12180, USA
| | - AD Dias
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 Eighth St., Troy, NY 12180, USA
| | - DB Chrisey
- Department of Physics, Tulane University, 6823 St. Charles Avenue New Orleans, LA 70118, USA
| | - DT Corr
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 Eighth St., Troy, NY 12180, USA
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Deagle BE, Jones FC, Absher DM, Kingsley DM, Reimchen TE. Phylogeography and adaptation genetics of stickleback from the Haida Gwaii archipelago revealed using genome-wide single nucleotide polymorphism genotyping. Mol Ecol 2013; 22:1917-32. [PMID: 23452150 PMCID: PMC3604130 DOI: 10.1111/mec.12215] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 12/12/2012] [Accepted: 12/13/2012] [Indexed: 01/26/2023]
Abstract
Threespine stickleback populations are model systems for studying adaptive evolution and the underlying genetics. In lakes on the Haida Gwaii archipelago (off western Canada), stickleback have undergone a remarkable local radiation and show phenotypic diversity matching that seen throughout the species distribution. To provide a historical context for this radiation, we surveyed genetic variation at >1000 single nucleotide polymorphism (SNP) loci in stickleback from over 100 populations. SNPs included markers evenly distributed throughout genome and candidate SNPs tagging adaptive genomic regions. Based on evenly distributed SNPs, the phylogeographic pattern differs substantially from the disjunct pattern previously observed between two highly divergent mtDNA lineages. The SNP tree instead shows extensive within watershed population clustering and different watersheds separated by short branches deep in the tree. These data are consistent with separate colonizations of most watersheds, despite underlying genetic connections between some independent drainages. This supports previous suppositions that morphological diversity observed between watersheds has been shaped independently, with populations exhibiting complete loss of lateral plates and giant size each occurring in several distinct clades. Throughout the archipelago, we see repeated selection of SNPs tagging candidate freshwater adaptive variants at several genomic regions differentiated between marine-freshwater populations on a global scale (e.g. EDA, Na/K ATPase). In estuarine sites, both marine and freshwater allelic variants were commonly detected. We also found typically marine alleles present in a few freshwater lakes, especially those with completely plated morphology. These results provide a general model for postglacial colonization of freshwater habitat by sticklebacks and illustrate the tremendous potential of genome-wide SNP data sets hold for resolving patterns and processes underlying recent adaptive divergences.
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Affiliation(s)
- Bruce E Deagle
- Department of Biology, University of Victoria, Victoria, British Colombia, Canada.
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Abstract
Extensive functional analyses have demonstrated that the pituitary homeodomain transcription factor Pitx1 plays a critical role in specifying hindlimb morphology in vertebrates. However, much less is known regarding the target genes and cis-regulatory elements through which Pitx1 acts. Earlier studies suggested that the hindlimb transcription factors Tbx4, HoxC10, and HoxC11 might be transcriptional targets of Pitx1, but definitive evidence for direct regulatory interactions has been lacking. Using ChIP-Seq on embryonic mouse hindlimbs, we have pinpointed the genome-wide location of Pitx1 binding sites during mouse hindlimb development and identified potential gene targets for Pitx1. We determined that Pitx1 binding is significantly enriched near genes involved in limb morphogenesis, including Tbx4, HoxC10, and HoxC11. Notably, Pitx1 is bound to the previously identified HLEA and HLEB hindlimb enhancers of the Tbx4 gene and to a newly identified Tbx2 hindlimb enhancer. Moreover, Pitx1 binding is significantly enriched on hindlimb relative to forelimb-specific cis-regulatory features that are differentially marked by H3K27ac. However, our analysis revealed that Pitx1 also strongly associates with many functionally verified limb enhancers that exhibit similar levels of activity in the embryonic mesenchyme of forelimbs and hindlimbs. We speculate that Pitx1 influences hindlimb morphology both through the activation of hindlimb-specific enhancers as well as through the hindlimb-specific modulation of enhancers that are active in both sets of limbs.
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Affiliation(s)
- Carlos R Infante
- Department of Genetics, University of Georgia, Coverdell Building, Room 250A, 500 DW Brooks Drive, Athens, GA 30602, USA
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45
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Abstract
Transition of an evolving population to a new adaptive optimum is predicted to leave a signature in the distribution of effect sizes of fixed mutations. If they affect many traits (are pleiotropic), large effect mutations should contribute more when a population evolves to a farther adaptive peak than to a nearer peak. We tested this prediction in wild threespine stickleback fish (Gasterosteus aculeatus) by comparing the estimated frequency of large effect genetic changes underlying evolution as the same ancestor adapted to two lake types since the end of the ice age. A higher frequency of large effect genetic changes (quantitative trait loci) contributed to adaptive evolution in populations that adapted to lakes representing a more distant optimum than to lakes in which the optimum phenotype was nearer to the ancestral state. Our results also indicate that pleiotropy, not just optimum overshoot, contributes to this difference. These results suggest that a series of adaptive improvements to a new environment leaves a detectable mark in the genome of wild populations. Although not all assumptions of the theory are likely met in natural systems, the prediction may be robust enough to the complexities of natural environments to be useful when forecasting adaptive responses to large environmental changes.
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Affiliation(s)
- Sean M Rogers
- Department of Biological Sciences, University of Calgary, 2500 University Drive N.W., Calgary, Alberta, T2N 1N4, Canada.
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Jones FC, Chan YF, Schmutz J, Grimwood J, Brady SD, Southwick AM, Absher DM, Myers RM, Reimchen TE, Deagle BE, Schluter D, Kingsley DM. A genome-wide SNP genotyping array reveals patterns of global and repeated species-pair divergence in sticklebacks. Curr Biol 2011; 22:83-90. [PMID: 22197244 DOI: 10.1016/j.cub.2011.11.045] [Citation(s) in RCA: 171] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Revised: 10/04/2011] [Accepted: 11/21/2011] [Indexed: 12/28/2022]
Abstract
Genes underlying repeated adaptive evolution in natural populations are still largely unknown. Stickleback fish (Gasterosteus aculeatus) have undergone a recent dramatic evolutionary radiation, generating numerous examples of marine-freshwater species pairs and a small number of benthic-limnetic species pairs found within single lakes [1]. We have developed a new genome-wide SNP genotyping array to study patterns of genetic variation in sticklebacks over a wide geographic range, and to scan the genome for regions that contribute to repeated evolution of marine-freshwater or benthic-limnetic species pairs. Surveying 34 global populations with 1,159 informative markers revealed substantial genetic variation, with predominant patterns reflecting demographic history and geographic structure. After correcting for geographic structure and filtering for neutral markers, we detected large repeated shifts in allele frequency at some loci, identifying both known and novel loci likely contributing to marine-freshwater and benthic-limnetic divergence. Several novel loci fall close to genes implicated in epithelial barrier or immune functions, which have likely changed as sticklebacks adapt to contrasting environments. Specific alleles differentiating sympatric benthic-limnetic species pairs are shared in nearby solitary populations, suggesting an allopatric origin for adaptive variants and selection pressures unrelated to sympatry in the initial formation of these classic vertebrate species pairs.
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Affiliation(s)
- Felicity C Jones
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
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47
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Deagle BE, Jones FC, Chan YF, Absher DM, Kingsley DM, Reimchen TE. Population genomics of parallel phenotypic evolution in stickleback across stream-lake ecological transitions. Proc Biol Sci 2011; 279:1277-86. [PMID: 21976692 DOI: 10.1098/rspb.2011.1552] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Understanding the genetics of adaptation is a central focus in evolutionary biology. Here, we use a population genomics approach to examine striking parallel morphological divergences of parapatric stream-lake ecotypes of threespine stickleback fish in three watersheds on the Haida Gwaii archipelago, western Canada. Genome-wide variation at greater than 1000 single nucleotide polymorphism loci indicate separate origin of giant lake and small-bodied stream fish within each watershed (mean F(ST) between watersheds = 0.244 and within = 0.114). Genome scans within watersheds identified a total of 21 genomic regions that are highly differentiated between ecotypes and are probably subject to directional selection. Most outliers were watershed-specific, but genomic regions undergoing parallel genetic changes in multiple watersheds were also identified. Interestingly, several of the stream-lake outlier regions match those previously identified in marine-freshwater and benthic-limnetic genome scans, indicating reuse of the same genetic loci in different adaptive scenarios. We also identified multiple new outlier loci, which may contribute to unique aspects of differentiation in stream-lake environments. Overall, our data emphasize the important role of ecological boundaries in driving both local and broadly occurring parallel genetic changes during adaptation.
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Affiliation(s)
- Bruce E Deagle
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada.
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Lowe CB, Kellis M, Siepel A, Raney BJ, Clamp M, Salama SR, Kingsley DM, Lindblad-Toh K, Haussler D. Three periods of regulatory innovation during vertebrate evolution. Science 2011; 333:1019-24. [PMID: 21852499 PMCID: PMC3511857 DOI: 10.1126/science.1202702] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The gain, loss, and modification of gene regulatory elements may underlie a substantial proportion of phenotypic changes on animal lineages. To investigate the gain of regulatory elements throughout vertebrate evolution, we identified genome-wide sets of putative regulatory regions for five vertebrates, including humans. These putative regulatory regions are conserved nonexonic elements (CNEEs), which are evolutionarily conserved yet do not overlap any coding or noncoding mature transcript. We then inferred the branch on which each CNEE came under selective constraint. Our analysis identified three extended periods in the evolution of gene regulatory elements. Early vertebrate evolution was characterized by regulatory gains near transcription factors and developmental genes, but this trend was replaced by innovations near extracellular signaling genes, and then innovations near posttranslational protein modifiers.
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Affiliation(s)
- Craig B. Lowe
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064
- Department of Developmental Biology, Stanford University, Stanford, CA 94305
- Howard Hughes Medical Institute
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Adam Siepel
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853
| | - Brian J. Raney
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064
| | - Michele Clamp
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Sofie R. Salama
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064
- Howard Hughes Medical Institute
| | - David M. Kingsley
- Department of Developmental Biology, Stanford University, Stanford, CA 94305
- Howard Hughes Medical Institute
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - David Haussler
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064
- Howard Hughes Medical Institute
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Foster BL, Nagatomo KJ, Bamashmous SO, Tompkins KA, Fong H, Dunn D, Chu EY, Guenther C, Kingsley DM, Rutherford RB, Somerman MJ. The progressive ankylosis protein regulates cementum apposition and extracellular matrix composition. Cells Tissues Organs 2011; 194:382-405. [PMID: 21389671 DOI: 10.1159/000323457] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2010] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND/AIMS Tooth root cementum is sensitive to modulation of inorganic pyrophosphate (PP(i)), an inhibitor of hydroxyapatite precipitation. Factors increasing PP(i) include progressive ankylosis protein (ANK) and ectonucleotide pyrophosphatase/phosphodiesterase 1 (NPP1) while tissue nonspecific alkaline phosphatase hydrolyzes PP(i). Studies here aimed to define the role of ANK in root and cementum by analyzing tooth development in Ank knock-out (KO) mice versus wild type. MATERIALS AND METHODS Periodontal development in KO versus control mice was analyzed by histology, histomorphometry, immunohistochemistry, in situ hybridization, electron microscopy, and nanoindentation. Cementoblast cultures were used in vitro to provide mechanistic underpinnings for PP(i) modulation of cell function. RESULTS Over the course of root development, Ank KO cervical cementum became 8- to 12-fold thicker than control cervical cementum. Periodontal ligament width was maintained and other dentoalveolar tissues, including apical cementum, were unaltered. Cervical cementum uncharacteristically included numerous cells, from rapid cementogenesis. Ank KO increased osteopontin and dentin matrix protein 1 gene and protein expression, and markedly increased NPP1 protein expression in cementoblasts but not in other cell types. Conditional ablation of Ank in joints and periodontia confirmed a local role for ANK in cementogenesis. In vitro studies employing cementoblasts indicated that Ank and Enpp1 mRNA levels increased in step with mineral nodule formation, supporting a role for these factors in regulation of cementum matrix mineralization. CONCLUSION ANK, by modulating local PP(i), controls cervical cementum apposition and extracellular matrix. Loss of ANK created a local environment conducive to rapid cementogenesis; therefore, approaches modulating PP(i) in periodontal tissues have potential to promote cementum regeneration.
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Affiliation(s)
- B L Foster
- Department of Periodontics, University of Washington School of Dentistry, Seattle, Wash. 98195, USA.
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50
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Greenwood AK, Jones FC, Chan YF, Brady SD, Absher DM, Grimwood J, Schmutz J, Myers RM, Kingsley DM, Peichel CL. The genetic basis of divergent pigment patterns in juvenile threespine sticklebacks. Heredity (Edinb) 2011; 107:155-66. [PMID: 21304547 DOI: 10.1038/hdy.2011.1] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Animal pigment patterns are important for a range of functions, including camouflage and communication. Repeating pigment patterns, such as stripes, bars and spots have been of particular interest to developmental and theoretical biologists, but the genetic basis of natural variation in such patterns is largely unexplored. In this study, we identify a difference in a periodic pigment pattern among juvenile threespine sticklebacks (Gasterosteus aculeatus) from different environments. Freshwater sticklebacks exhibit prominent vertical bars that visually break up the body shape, but sticklebacks from marine populations do not. We hypothesize that these distinct pigment patterns are tuned to provide crypsis in different habitats. This phenotypic difference is widespread and appears in most of the freshwater populations that we sampled. We used quantitative trait locus (QTL) mapping in freshwater-marine F2 hybrids to elucidate the genetic architecture underlying divergence in this pigmentation pattern. We identified two QTL that were significantly associated with variation in barring. Interestingly, these QTL were associated with two distinct aspects of the pigment pattern: melanophore number and overall pigment level. We compared the QTL locations with positions of known pigment candidate genes in the stickleback genome. We also identified two major QTL for juvenile body size, providing new insights into the genetic basis of juvenile growth rates in natural populations. In summary, although there is a growing literature describing simple genetic bases for adaptive coloration differences, this study emphasizes that pigment patterns can also possess a more complex genetic architecture.
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Affiliation(s)
- A K Greenwood
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
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