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DeLorenzo L, Powder KE. Epigenetics and the evolution of form: Experimental manipulation of a chromatin modification causes species-specific changes to the craniofacial skeleton. Evol Dev 2024; 26:e12461. [PMID: 37850843 PMCID: PMC10842503 DOI: 10.1111/ede.12461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 08/18/2023] [Accepted: 10/05/2023] [Indexed: 10/19/2023]
Abstract
A central question in biology is the molecular origins of phenotypic diversity. While genetic changes are key to the genotype-phenotype relationship, alterations to chromatin structure and the physical packaging of histone proteins may also be important drivers of vertebrate divergence. We investigate the impact of such an epigenetic mechanism, histone acetylation, within a textbook example of an adaptive radiation. Cichlids of Lake Malawi have adapted diverse craniofacial structures, and here we investigate how histone acetylation influences morphological variation in these fishes. Specifically, we assessed the effect of inhibiting histone deacetylation using the drug trichostatin A (TSA) on developing facial structures. We examined this during three critical developmental windows in two cichlid species with alternate adult morphologies. Exposure to TSA during neural crest cell (NCC) migration and as postmigratory NCCs proliferate in the pharyngeal arches resulted in significant changes in lateral and ventral shape in Maylandia, but not in Tropheops. This included an overall shortening of the head, widening of the lower jaw, and steeper craniofacial profile, all of which are paedomorphic morphologies. In contrast, treatment with TSA during early chondrogenesis did not result in significant morphological changes in either species. Together, these data suggest a sensitivity to epigenetic alterations that are both time- and species-dependent. We find that morphologies are due to nonautonomous or potentially indirect effects on NCC development, including in part a global developmental delay. Our research bolsters the understanding that proper histone acetylation is essential for early craniofacial development and identifies a species-specific robustness to developmental change. Overall, this study demonstrates how epigenetic regulation may play an important role in both generating and buffering morphological variation.
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Affiliation(s)
- Leah DeLorenzo
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Kara E Powder
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
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2
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Kundu S, De Alwis PS, Kim AR, Lee SR, Kang HE, Go Y, Gietbong FZ, Wibowo A, Kim HW. Mitogenomic Characterization of Cameroonian Endemic Coptodon camerunensis (Cichliformes: Cichlidae) and Matrilineal Phylogeny of Old-World Cichlids. Genes (Basel) 2023; 14:1591. [PMID: 37628642 PMCID: PMC10454717 DOI: 10.3390/genes14081591] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/02/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
The mitogenomic evolution of old-world cichlids is still largely incomplete in Western Africa. In this present study, the complete mitogenome of the Cameroon endemic cichlid, Coptodon camerunensis, was determined by next-generation sequencing. The mitogenome was 16,557 bp long and encoded with 37 genes (13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a control region). The C. camerunensis mitogenome is AT-biased (52.63%), as exhibited in its congener, Coptodon zillii (52.76% and 53.04%). The majority of PCGs start with an ATG initiation codon, except COI, which starts with a GTG codon and five PCGs and ends with the TAA termination codon and except seven PCGs with an incomplete termination codon. In C. camerunensis mitogenome, most tRNAs showed classical cloverleaf secondary structures, except tRNA-serine with a lack of DHU stem. Comparative analyses of the conserved blocks of two Coptodonini species control regions revealed that the CSB-II block was longer than other blocks and contained highly variable sites. Using 13 concatenated PCGs, the mitogenome-based Bayesian phylogeny easily distinguished all the examined old-world cichlids. Except for Oreochromini and Coptodinini tribe members, the majority of the taxa exhibited monophyletic clustering within their respective lineages. C. camerunensis clustered closely with Heterotilapia buttikoferi (tribe Heterotilapiini) and had paraphyletic clustering with its congener, C. zillii. The Oreochromini species also displayed paraphyletic grouping, and the genus Oreochromis showed a close relationship with Coptodinini and Heterotilapiini species. In addition, illustrating the known distribution patterns of old-world cichlids, the present study is congruent with the previous hypothesis and proclaims that prehistoric geological evolution plays a key role in the hydroclimate of the African continent during Mesozoic, which simultaneously disperses and/or colonizes cichlids in different ichthyological provinces and Rift Lake systems in Africa. The present study suggests that further mitogenomes of cichlid species are required, especially from western Africa, to understand their unique evolution and adaptation.
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Affiliation(s)
- Shantanu Kundu
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea; (S.K.); (P.S.D.A.)
| | - Piyumi S. De Alwis
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea; (S.K.); (P.S.D.A.)
| | - Ah Ran Kim
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; (A.R.K.); (S.R.L.)
| | - Soo Rin Lee
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; (A.R.K.); (S.R.L.)
| | - Hye-Eun Kang
- Institute of Marine Life Science, Pukyong National University, Busan 48513, Republic of Korea;
| | - Yunji Go
- Industry 4.0 Convergence Bionics Engineering, Pukyong National University, Busan 48513, Republic of Korea;
| | | | - Arif Wibowo
- Research Center for Conservation of Marine and Inland Water Resources, National Research and Innovation Agency (BRIN), South Tangerang 15314, Indonesia;
| | - Hyun-Woo Kim
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea; (S.K.); (P.S.D.A.)
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; (A.R.K.); (S.R.L.)
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3
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Santos ME, Lopes JF, Kratochwil CF. East African cichlid fishes. EvoDevo 2023; 14:1. [PMID: 36604760 PMCID: PMC9814215 DOI: 10.1186/s13227-022-00205-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 11/29/2022] [Indexed: 01/06/2023] Open
Abstract
Cichlid fishes are a very diverse and species-rich family of teleost fishes that inhabit lakes and rivers of India, Africa, and South and Central America. Research has largely focused on East African cichlids of the Rift Lakes Tanganyika, Malawi, and Victoria that constitute the biodiversity hotspots of cichlid fishes. Here, we give an overview of the study system, research questions, and methodologies. Research on cichlid fishes spans many disciplines including ecology, evolution, physiology, genetics, development, and behavioral biology. In this review, we focus on a range of organismal traits, including coloration phenotypes, trophic adaptations, appendages like fins and scales, sensory systems, sex, brains, and behaviors. Moreover, we discuss studies on cichlid phylogenies, plasticity, and general evolutionary patterns, ranging from convergence to speciation rates and the proximate and ultimate mechanisms underlying these processes. From a methodological viewpoint, the last decade has brought great advances in cichlid fish research, particularly through the advent of affordable deep sequencing and advances in genetic manipulations. The ability to integrate across traits and research disciplines, ranging from developmental biology to ecology and evolution, makes cichlid fishes a fascinating research system.
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Affiliation(s)
- M. Emília Santos
- grid.5335.00000000121885934Department of Zoology, University of Cambridge, Cambridge, UK
| | - João F. Lopes
- grid.7737.40000 0004 0410 2071Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Claudius F. Kratochwil
- grid.7737.40000 0004 0410 2071Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
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4
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Mehta TK, Penso-Dolfin L, Nash W, Roy S, Di-Palma F, Haerty W. Evolution of miRNA binding sites and regulatory networks in cichlids. Mol Biol Evol 2022; 39:6617238. [PMID: 35748824 PMCID: PMC9260339 DOI: 10.1093/molbev/msac146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The divergence of regulatory regions and gene regulatory network (GRN) rewiring is a key driver of cichlid phenotypic diversity. However, the contribution of miRNA binding site turnover has yet to be linked to GRN evolution across cichlids. Here, we extend our previous studies by analysing the selective constraints driving evolution of miRNA and transcription factor (TF) binding sites of target genes, to infer instances of cichlid GRN rewiring associated with regulatory binding site turnover. Comparative analyses identified increased species-specific networks that are functionally associated to traits of cichlid phenotypic diversity. The evolutionary rewiring is associated with differential models of miRNA and TF binding site turnover, driven by a high proportion of fast-evolving polymorphic sites in adaptive trait genes compared to subsets of random genes. Positive selection acting upon discrete mutations in these regulatory regions is likely to be an important mechanism in rewiring GRNs in rapidly radiating cichlids. Regulatory variants of functionally associated miRNA and TF binding sites of visual opsin genes differentially segregate according to phylogeny and ecology of Lake Malawi species, identifying both rewired e.g. clade-specific and conserved network motifs of adaptive trait associated GRNs. Our approach revealed several novel candidate regulators, regulatory regions and three-node motifs across cichlid genomes with previously reported associations to known adaptive evolutionary traits.
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Affiliation(s)
| | - Luca Penso-Dolfin
- Silence Therapeutics GmbH, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | | | - Sushmita Roy
- Dept. of Biostatistics and Medical Informatics, UW Madison, Madison, USA.,Wisconsin Institute for Discovery (WID), Madison, USA.,Dept. of Computer Sciences, UW Madison, Madison, USA
| | - Federica Di-Palma
- School of Biological Sciences, University of East Anglia, Norwich, UK.,Genome British Columbia, Vancouver, Canada
| | - Wilfried Haerty
- Earlham Institute (EI), Norwich, UK.,School of Biological Sciences, University of East Anglia, Norwich, UK
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5
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Schäfer N, Kaya Y, Rebl H, Stüeken M, Rebl A, Nguinkal JA, Franz GP, Brunner RM, Goldammer T, Grunow B, Verleih M. Insights into early ontogenesis: characterization of stress and development key genes of pikeperch (Sander lucioperca) in vivo and in vitro. FISH PHYSIOLOGY AND BIOCHEMISTRY 2021; 47:515-532. [PMID: 33559015 PMCID: PMC8026417 DOI: 10.1007/s10695-021-00929-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 01/18/2021] [Indexed: 05/11/2023]
Abstract
There are still numerous difficulties in the successful farming of pikeperch in the anthropogenic environment of various aquaculture systems, especially during early developmental steps in the hatchery. To investigate the physiological processes involved on the molecular level, we determined the basal expression patterns of 21 genes involved in stress and immune responses and early ontogenesis of pikeperch between 0 and 175 days post hatch (dph). Their transcription patterns most likely reflect the challenges of growth and feed conversion. The gene coding for apolipoprotein A (APOE) was strongly expressed at 0 dph, indicating its importance for yolk sac utilization. Genes encoding bone morphogenetic proteins 4 and 7 (BMP4, BMP7), creatine kinase M (CKM), and SRY-box transcription factor 9 (SOX9) were highly abundant during the peak phases of morphological changes and acclimatization processes at 4-18 dph. The high expression of genes coding for peroxisome proliferator-activated receptors alpha and delta (PPARA, PPARD) at 121 and 175 dph, respectively, suggests their importance during this strong growth phase of juvenile stages. As an alternative experimental model to replace further in vivo investigations of ontogenetically important processes, we initiated the first approach towards a long-lasting primary cell culture from whole pikeperch embryos. The present study provides a set of possible biomarkers to support the monitoring of pikeperch farming and provides a first basis for the establishment of a suitable cell model of this emerging aquaculture species.
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Affiliation(s)
- Nadine Schäfer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Yagmur Kaya
- Institute of Muscle Biology and Growth, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Henrike Rebl
- Department of Cell Biology, Rostock University Medical Center, 18059, Rostock, Germany
| | - Marcus Stüeken
- Institute of Fisheries, Department of Aquaculture, Mecklenburg-Vorpommern Research Centre for Agriculture and Fisheries, 17194, Hohen Wangelin, Germany
| | - Alexander Rebl
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Julien A Nguinkal
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - George P Franz
- Institute of Muscle Biology and Growth, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Ronald M Brunner
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Tom Goldammer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
- Faculty of Agriculture and Environmental Sciences, University of Rostock, 18059, Rostock, Germany
| | - Bianka Grunow
- Institute of Muscle Biology and Growth, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany.
| | - Marieke Verleih
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany.
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6
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Mehta TK, Koch C, Nash W, Knaack SA, Sudhakar P, Olbei M, Bastkowski S, Penso-Dolfin L, Korcsmaros T, Haerty W, Roy S, Di-Palma F. Evolution of regulatory networks associated with traits under selection in cichlids. Genome Biol 2021; 22:25. [PMID: 33419455 PMCID: PMC7791837 DOI: 10.1186/s13059-020-02208-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 11/18/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Seminal studies of vertebrate protein evolution speculated that gene regulatory changes can drive anatomical innovations. However, very little is known about gene regulatory network (GRN) evolution associated with phenotypic effect across ecologically diverse species. Here we use a novel approach for comparative GRN analysis in vertebrate species to study GRN evolution in representative species of the most striking examples of adaptive radiations, the East African cichlids. We previously demonstrated how the explosive phenotypic diversification of East African cichlids can be attributed to diverse molecular mechanisms, including accelerated regulatory sequence evolution and gene expression divergence. RESULTS To investigate these mechanisms across species at a genome-wide scale, we develop a novel computational pipeline that predicts regulators for co-extant and ancestral co-expression modules along a phylogeny, and candidate regulatory regions associated with traits under selection in cichlids. As a case study, we apply our approach to a well-studied adaptive trait-the visual system-for which we report striking cases of network rewiring for visual opsin genes, identify discrete regulatory variants, and investigate their association with cichlid visual system evolution. In regulatory regions of visual opsin genes, in vitro assays confirm that transcription factor binding site mutations disrupt regulatory edges across species and segregate according to lake species phylogeny and ecology, suggesting GRN rewiring in radiating cichlids. CONCLUSIONS Our approach reveals numerous novel potential candidate regulators and regulatory regions across cichlid genomes, including some novel and some previously reported associations to known adaptive evolutionary traits.
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Affiliation(s)
| | - Christopher Koch
- Department of Biostatistics and Medical Informatics, UW Madison, Madison, USA
| | | | - Sara A Knaack
- Wisconsin Institute for Discovery (WID), Madison, USA
| | | | - Marton Olbei
- Earlham Institute (EI), Norwich, UK
- Quadram Institute, Norwich, UK
| | - Sarah Bastkowski
- Earlham Institute (EI), Norwich, UK
- Quadram Institute, Norwich, UK
| | | | - Tamas Korcsmaros
- Earlham Institute (EI), Norwich, UK
- Quadram Institute, Norwich, UK
| | | | - Sushmita Roy
- Department of Biostatistics and Medical Informatics, UW Madison, Madison, USA.
- Wisconsin Institute for Discovery (WID), Madison, USA.
- Department of Computer Sciences, UW Madison, Madison, USA.
| | - Federica Di-Palma
- Earlham Institute (EI), Norwich, UK.
- Norwich Medical School, University of East Anglia, Norwich, UK.
- School of Biological Sciences, University of East Anglia, Norwich, UK.
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7
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Penso-Dolfin L, Man A, Mehta T, Haerty W, Di Palma F. Analysis of structural variants in four African cichlids highlights an association with developmental and immune related genes. BMC Evol Biol 2020; 20:69. [PMID: 32564776 PMCID: PMC7309985 DOI: 10.1186/s12862-020-01629-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 05/18/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND East African lake cichlids are one of the most impressive examples of an adaptive radiation. Independently in Lake Victoria, Tanganyika, and Malawi, several hundreds of species arose within the last 10 million to 100,000 years. Whereas most analyses in cichlids focused on nucleotide substitutions across species to investigate the genetic bases of this explosive radiation, to date, no study has investigated the contribution of structural variants (SVs) in the evolution of adaptive traits across the three Great Lakes of East Africa. RESULTS Here, we annotate and characterize the repertoires and evolutionary potential of different SV classes (deletion, duplication, inversion, insertions and translocations) in four cichlid species: Haplochromis burtoni, Metriaclima zebra, Neolamprologus brichardi and Pundamilia nyererei. We investigate the patterns of gain and loss evolution for each SV type, enabling the identification of lineage specific events. Both deletions and inversions show a significant overlap with SINE elements, while inversions additionally show a limited, but significant association with DNA transposons. Inverted regions are enriched for genes regulating behaviour, or involved in skeletal and visual system development. We also find that duplicated regions show enrichment for genes associated with "antigen processing and presentation" and other immune related categories. Our pipeline and results were further tested by PCR validation of selected deletions and inversions, which confirmed respectively 7 out of 10 and 6 out of 9 events. CONCLUSIONS Altogether, we provide the first comprehensive overview of rearrangement evolution in East African cichlids, and some important insights into their likely contribution to adaptation.
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Affiliation(s)
- Luca Penso-Dolfin
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR47UZ UK
| | - Angela Man
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR47UZ UK
| | - Tarang Mehta
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR47UZ UK
| | - Wilfried Haerty
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR47UZ UK
| | - Federica Di Palma
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR47UZ UK
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8
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Abstract
Nearly one-third of adults over the age of 65 have lost all their teeth. We set out to understand tooth renewal in animals that have replacement and regeneration capabilities. Using cichlid fishes and mouse models, we discovered plasticity between tooth and taste bud progenitor cell derivatives, mediated by BMP. Our results suggest that oral organs have surprising regenerative capabilities and can be manipulated to express characteristics of different tissue types. In Lake Malawi cichlids, each tooth is replaced in one-for-one fashion every ∼20 to 50 d, and taste buds (TBs) are continuously renewed as in mammals. These structures are colocalized in the fish mouth and throat, from the point of initiation through adulthood. Here, we found that replacement teeth (RT) share a continuous band of epithelium with adjacent TBs and that both organs coexpress stem cell factors in subsets of label-retaining cells. We used RNA-seq to characterize transcriptomes of RT germs and TB-bearing oral epithelium. Analysis revealed differential usage of developmental pathways in RT compared to TB oral epithelia, as well as a repertoire of genome paralogues expressed complimentarily in each organ. Notably, BMP ligands were expressed in RT but excluded from TBs. Morphant fishes bathed in a BMP chemical antagonist exhibited RT with abrogated shh expression in the inner dental epithelium (IDE) and ectopic expression of calb2 (a TB marker) in these very cells. In the mouse, teeth are located on the jaw margin while TBs and other oral papillae are located on the tongue. Previous study reported that tongue intermolar eminence (IE) oral papillae of Follistatin (a BMP antagonist) mouse mutants exhibited dysmorphic invagination. We used these mutants to demonstrate altered transcriptomes and ectopic expression of dental markers in tongue IE. Our results suggest that vertebrate oral epithelium retains inherent plasticity to form tooth and taste-like cell types, mediated by BMP specification of progenitor cells. These findings indicate underappreciated epithelial cell populations with promising potential in bioengineering and dental therapeutics.
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9
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Abstract
PURPOSE OF REVIEW This article reviews the past 2 years of research on Notch signaling as it relates to bone physiology, with the goal of reconciling seemingly discrepant findings and identifying fruitful areas of potential future research. RECENT FINDINGS Conditional animal models and high-throughput omics have contributed to a greater understanding of the context-dependent role of Notch signaling in bone. However, significant gaps remain in our understanding of how spatiotemporal context and epigenetic state dictate downstream Notch phenotypes. Biphasic activation of Notch signaling orchestrates progression of mesenchymal progenitor cells through the osteoblast lineage, but there is a limited understanding of ligand- and receptor-specific functions. Paracrine Notch signaling through non-osteoblastic cell types contributes additional layers of complexity, and we anticipate impactful future work related to the integration of these cell types and signaling mechanisms.
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Affiliation(s)
- Daniel W Youngstrom
- Department of Orthopaedic Surgery, University of Michigan Medical School, 109 Zina Pitcher Pl, Ann Arbor, MI, 48872, USA.
| | - Kurt D Hankenson
- Department of Orthopaedic Surgery, University of Michigan Medical School, 109 Zina Pitcher Pl, Ann Arbor, MI, 48872, USA
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10
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Kratochwil CF, Urban S, Meyer A. Genome of the Malawi golden cichlid fish (Melanochromis auratus) reveals exon loss of oca2 in an amelanistic morph. Pigment Cell Melanoma Res 2019; 32:719-723. [PMID: 31131985 DOI: 10.1111/pcmr.12799] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 04/26/2019] [Accepted: 05/17/2019] [Indexed: 11/26/2022]
Abstract
The tropical freshwater fish family Cichlidae is famous for its record-breaking rates of speciation and diversity in colors and color patterns. Here, we sequenced the genome of the Lake Malawi cichlid Melanochromis auratus to study the genetic basis of an amelanistic morph of this species that lacks the typical melanic stripes and markings. Genome sequencing of the amelanistic and wild-type morph revealed the loss of the second exon of the known pigmentation gene oculocutaneous albinism II (oca2), also known as p(ink-eyed dilution) gene or melanocyte-specific transporter gene. Additional genotyping confirms the complete association with this recessive Mendelian phenotype. The deletion results in a shorter transcript, lacking an acidic di-leucine domain that is crucial for trafficking of the Oca2 protein to melanosomes. The fact that oca2 is involved in a wide range of amelanistic morphs across vertebrates demonstrates its highly conserved function.
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Affiliation(s)
- Claudius F Kratochwil
- Department of Biology, Zoology and Evolutionary Biology, University of Konstanz, Konstanz, Germany.,Zukunftskolleg, University of Konstanz, Konstanz, Germany.,International Max Planck Research School for Organismal Biology (IMPRS), Max Planck Institute for Ornithology, Radolfzell, Germany
| | - Sabine Urban
- Department of Biology, Zoology and Evolutionary Biology, University of Konstanz, Konstanz, Germany.,International Max Planck Research School for Organismal Biology (IMPRS), Max Planck Institute for Ornithology, Radolfzell, Germany
| | - Axel Meyer
- Department of Biology, Zoology and Evolutionary Biology, University of Konstanz, Konstanz, Germany.,International Max Planck Research School for Organismal Biology (IMPRS), Max Planck Institute for Ornithology, Radolfzell, Germany
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11
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Rostampour N, Appelt CM, Abid A, Boughner JC. Expression of new genes in vertebrate tooth development and p63 signaling. Dev Dyn 2019; 248:744-755. [PMID: 30875130 DOI: 10.1002/dvdy.26] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 02/15/2019] [Accepted: 03/11/2019] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND p63 is an evolutionarily ancient transcription factor essential to vertebrate tooth development. Our recent gene expression screen comparing wild-type and "toothless" p63-/- mouse embryos implicated in tooth development several new genes that we hypothesized act downstream of p63 in dental epithelium, where p63 is also expressed. RESULTS Via in situ hybridization and immunohistochemistry, we probed mouse embryos (embryonic days 10.5-14.5) and spotted gar fish embryos (14 days postfertilization) for these newly linked genes, Cbln1, Cldn23, Fermt1, Krt15, Pltp and Prss8, which were expressed in mouse and gar dental epithelium. Loss of p63 altered expression levels but not domains. Expression was comparable between murine upper and lower tooth organs, implying conserved gene functions in maxillary and mandibular dentitions. Our meta-analysis of gene expression databases supported that these genes act within a p63-driven gene regulatory network important to tooth development in mammals and more evolutionary ancient vertebrates (fish, amphibians). CONCLUSIONS Cbln1, Cldn23, Fermt1, Krt15, Pltp, and Prss8 were expressed in mouse and fish dental epithelium at placode, bud, and/or cap stages. We theorize that these genes participate in cell-cell adhesion, cell polarity, and extracellular matrix signaling to support dental epithelium integrity, folding, and epithelial-mesenchymal cross talk during tooth development.
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Affiliation(s)
- Nasim Rostampour
- Department of Anatomy & Cell Biology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Cassy M Appelt
- Department of Anatomy & Cell Biology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Aunum Abid
- Department of Anatomy & Cell Biology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Julia C Boughner
- Department of Anatomy & Cell Biology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
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