26
|
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] [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.
Collapse
|
27
|
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] [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/.
Collapse
|
28
|
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] [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.
Collapse
|
29
|
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: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [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.
Collapse
|
30
|
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] [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.
Collapse
|
31
|
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] [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.
Collapse
|
32
|
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] [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.
Collapse
|
33
|
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] [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.
Collapse
|
34
|
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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
35
|
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 PMCID: PMC9202818 DOI: 10.1002/bit.25987] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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.
Collapse
|
36
|
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] [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.
Collapse
|
37
|
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] [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
Collapse
|
38
|
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] [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.
Collapse
|
39
|
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: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [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.
Collapse
|
40
|
Dias AD, Kingsley DM, Corr DT. Recent advances in bioprinting and applications for biosensing. BIOSENSORS 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] [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.
Collapse
|
41
|
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] [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.
Collapse
|
42
|
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] [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.
Collapse
|
43
|
Kingsley DM, Dias AD, Chrisey DB, Corr DT. Single-step laser-based fabrication and patterning of cell-encapsulated alginate microbeads. Biofabrication 2013; 5:045006. [PMID: 24192221 PMCID: PMC3890439 DOI: 10.1088/1758-5082/5/4/045006] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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.
Collapse
|
44
|
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] [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.
Collapse
|
45
|
Infante CR, Park S, Mihala AG, Kingsley DM, Menke DB. Pitx1 broadly associates with limb enhancers and is enriched on hindlimb cis-regulatory elements. Dev Biol 2012. [PMID: 23201014 DOI: 10.1016/j.ydbio.2012.11.017] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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.
Collapse
|
46
|
Rogers SM, Tamkee P, Summers B, Balabahadra S, Marks M, Kingsley DM, Schluter D. Genetic signature of adaptive peak shift in threespine stickleback. Evolution 2012; 66:2439-50. [PMID: 22834743 PMCID: PMC4433314 DOI: 10.1111/j.1558-5646.2012.01622.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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.
Collapse
|
47
|
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] [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.
Collapse
|
48
|
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] [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.
Collapse
|
49
|
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] [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.
Collapse
|
50
|
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] [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.
Collapse
|