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Andersson L. White horses - non-coding sequences drive premature hair greying and predisposition to melanoma. Ups J Med Sci 2024; 129:10626. [PMID: 38571883 PMCID: PMC10989212 DOI: 10.48101/ujms.v129.10626] [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] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 04/05/2024] Open
Abstract
The Grey allele in horses is causing premature hair greying and susceptibility to melanoma. The causal mutation is a 4.6 kb tandem duplication in intron 6 of the Syntaxin 17 gene. A recent study demonstrated that the most common allele at the Grey locus (G3) involves three tandem copies of this sequence, whilst a more rare allele (G2) has two tandem copies and the wild-type allele (G1) only one copy. The G3 allele is causing fast greying and high incidence of skin melanoma, whereas the G2 allele is causing slow greying and no obvious increase in melanoma incidence. Further somatic copy number expansion has been documented in melanoma tissue from Grey horses. Functional studies showed that this intronic sequence acts as a weak melanocyte-specific enhancer that becomes substantially stronger by the copy number expansion. The Grey mutation is associated with upregulated expression of both Syntaxin 17 and the neighbouring NR4A3 gene in Grey horse melanomas. It is still an open question which of these genes is most important for the phenotypic effects or if causality is due to the combined effect of upregulation of both genes. Interestingly, RNAseq data in the Human Protein Atlas give support for a possible role of NR4A3 because it is particularly upregulated in human skin cancer, and it belongs to a cluster of genes associated with skin cancer and melanin biosynthesis. The Grey mutation and its association with melanoma provide a possibility to study the path to tumour development in numerous Grey horses carrying exactly the same predisposing mutation.
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Affiliation(s)
- Leif Andersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
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2
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Siegel PB, Honaker CF, Andersson L. Research Note: Phenotypic trends for the multigenerational advanced intercross of the Virginia body weight lines of chickens. Poult Sci 2024; 103:103480. [PMID: 38330887 PMCID: PMC10864792 DOI: 10.1016/j.psj.2024.103480] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/05/2024] [Accepted: 01/15/2024] [Indexed: 02/10/2024] Open
Abstract
Random samples from generation S41 of the Virginia high and low 8-week body weight lines formed the base population for producing a multigenerational reciprocal intercross population. Although genetic mapping from this intercross has been reported, lacking are phenotypic trends across multiple generations. Here, we provide phenotypic information for the parental base population, the F1 reciprocal cross, and subsequent segregating recombinant generations F2 to F17. Heterosis for the selected trait in the F1 was negative for both reciprocal crosses. Phenotypic correlations for the selected trait in the recombinant generations were essentially nil for both males and females as was percent sexual dimorphism and coefficients of variation.
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Affiliation(s)
- P B Siegel
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 USA.
| | - C F Honaker
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 USA
| | - L Andersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, S-75123 Uppsala, Sweden; Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
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3
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Fuentes‐Pardo AP, Stanley R, Bourne C, Singh R, Emond K, Pinkham L, McDermid JL, Andersson L, Ruzzante DE. Adaptation to seasonal reproduction and environment-associated factors drive temporal and spatial differentiation in northwest Atlantic herring despite gene flow. Evol Appl 2024; 17:e13675. [PMID: 38495946 PMCID: PMC10940790 DOI: 10.1111/eva.13675] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/19/2024] Open
Abstract
Understanding how marine organisms adapt to local environments is crucial for predicting how populations will respond to global climate change. The genomic basis, environmental factors and evolutionary processes involved in local adaptation are however not well understood. Here we use Atlantic herring, an abundant, migratory and widely distributed marine fish with substantial genomic resources, as a model organism to evaluate local adaptation. We examined genomic variation and its correlation with environmental variables across a broad environmental gradient, for 15 spawning aggregations in Atlantic Canada and the United States. We then compared our results with available genomic data of northeast Atlantic populations. We confirmed that population structure lies in a fraction of the genome including likely adaptive genetic variants of functional importance. We discovered 10 highly differentiated genomic regions distributed across four chromosomes. Nine regions show strong association with seasonal reproduction. One region, corresponding to a known inversion on chromosome 12, underlies a latitudinal pattern discriminating populations north and south of a biogeographic transition zone on the Scotian Shelf. Genome-environment associations indicate that winter seawater temperature best correlates with the latitudinal pattern of this inversion. The variation at two so-called 'islands of divergence' related to seasonal reproduction appear to be private to the northwest Atlantic. Populations in the northwest and northeast Atlantic share variation at four of these divergent regions, simultaneously displaying significant diversity in haplotype composition at another four regions, which includes an undescribed structural variant approximately 7.7 Mb long on chromosome 8. Our results suggest that the timing and geographic location of spawning and early development may be under diverse selective pressures related to allelic fitness across environments. Our study highlights the role of genomic architecture, ancestral haplotypes and selection in maintaining adaptive divergence in species with large population sizes and presumably high gene flow.
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Affiliation(s)
- Angela P. Fuentes‐Pardo
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
| | - Ryan Stanley
- Fisheries and Oceans CanadaMaritimes RegionDartmouthNova ScotiaCanada
| | - Christina Bourne
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt John'sNewfoundland and LabradorCanada
| | - Rabindra Singh
- Fisheries and Oceans CanadaSt. Andrews Biological StationSt. AndrewsNew BrunswickCanada
| | - Kim Emond
- Fisheries and Oceans CanadaMaurice Lamontagne InstituteMont‐JoliQuebecCanada
| | - Lisa Pinkham
- Department of Marine ResourcesWest Boothbay HarborMaineUSA
| | - Jenni L. McDermid
- Fisheries and Oceans CanadaGulf Fisheries CentreMonctonNew BrunswickCanada
| | - Leif Andersson
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
- Department of Veterinary Integrative BiosciencesTexas A&M UniversityCollege StationTexasUSA
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4
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Andersson L, Bekkevold D, Berg F, Farrell ED, Felkel S, Ferreira MS, Fuentes-Pardo AP, Goodall J, Pettersson M. How Fish Population Genomics Can Promote Sustainable Fisheries: A Road Map. Annu Rev Anim Biosci 2024; 12:1-20. [PMID: 37906837 DOI: 10.1146/annurev-animal-021122-102933] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Maintenance of genetic diversity in marine fishes targeted by commercial fishing is a grand challenge for the future. Most of these species are abundant and therefore important for marine ecosystems and food security. Here, we present a road map of how population genomics can promote sustainable fisheries. In these species, the development of reference genomes and whole genome sequencing is key, because genetic differentiation at neutral loci is usually low due to large population sizes and gene flow. First, baseline allele frequencies representing genetically differentiated populations within species must be established. These can then be used to accurately determine the composition of mixed samples, forming the basis for population demographic analysis to inform sustainably set fish quotas. SNP-chip analysis is a cost-effective method for determining baseline allele frequencies and for population identification in mixed samples. Finally, we describe how genetic marker analysis can transform stock identification and management.
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Affiliation(s)
- Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden;
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, USA
| | - Dorte Bekkevold
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | | | - Edward D Farrell
- Killybegs Fishermen's Organisation, Killybegs, County Donegal, Ireland
| | - Sabine Felkel
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden;
| | - Mafalda S Ferreira
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden;
| | - Angela P Fuentes-Pardo
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden;
| | - Jake Goodall
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden;
| | - Mats Pettersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden;
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5
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Mihalič F, Arcila D, Pettersson ME, Farkhondehkish P, Andersson E, Andersson L, Betancur-R R, Jemth P. Conservation of Affinity Rather Than Sequence Underlies a Dynamic Evolution of the Motif-Mediated p53/MDM2 Interaction in Ray-Finned Fishes. Mol Biol Evol 2024; 41:msae018. [PMID: 38301272 PMCID: PMC10901556 DOI: 10.1093/molbev/msae018] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 12/12/2023] [Accepted: 01/22/2024] [Indexed: 02/03/2024] Open
Abstract
The transcription factor and cell cycle regulator p53 is marked for degradation by the ubiquitin ligase MDM2. The interaction between these 2 proteins is mediated by a conserved binding motif in the disordered p53 transactivation domain (p53TAD) and the folded SWIB domain in MDM2. The conserved motif in p53TAD from zebrafish displays a 20-fold weaker interaction with MDM2, compared to the interaction in human and chicken. To investigate this apparent difference, we tracked the molecular evolution of the p53TAD/MDM2 interaction among ray-finned fishes (Actinopterygii), the largest vertebrate clade. Intriguingly, phylogenetic analyses, ancestral sequence reconstructions, and binding experiments showed that different loss-of-affinity changes in the canonical binding motif within p53TAD have occurred repeatedly and convergently in different fish lineages, resulting in relatively low extant affinities (KD = 0.5 to 5 μM). However, for 11 different fish p53TAD/MDM2 interactions, nonconserved regions flanking the canonical motif increased the affinity 4- to 73-fold to be on par with the human interaction. Our findings suggest that compensating changes at conserved and nonconserved positions within the motif, as well as in flanking regions of low conservation, underlie a stabilizing selection of "functional affinity" in the p53TAD/MDM2 interaction. Such interplay complicates bioinformatic prediction of binding and calls for experimental validation. Motif-mediated protein-protein interactions involving short binding motifs and folded interaction domains are very common across multicellular life. It is likely that the evolution of affinity in motif-mediated interactions often involves an interplay between specific interactions made by conserved motif residues and nonspecific interactions by nonconserved disordered regions.
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Affiliation(s)
- Filip Mihalič
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Uppsala SE-75123, Sweden
| | - Dahiana Arcila
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Mats E Pettersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Uppsala SE-75123, Sweden
| | - Pouria Farkhondehkish
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Uppsala SE-75123, Sweden
| | - Eva Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Uppsala SE-75123, Sweden
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Uppsala SE-75123, Sweden
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77483, USA
| | - Ricardo Betancur-R
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Uppsala SE-75123, Sweden
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6
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Hill J, Enbody ED, Bi H, Lamichhaney S, Lei W, Chen J, Wei C, Liu Y, Schwochow D, Younis S, Widemo F, Andersson L. Low Mutation Load in a Supergene Underpinning Alternative Male Mating Strategies in Ruff (Calidris pugnax). Mol Biol Evol 2023; 40:msad224. [PMID: 37804117 DOI: 10.1093/molbev/msad224] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/23/2023] [Accepted: 09/28/2023] [Indexed: 10/08/2023] Open
Abstract
A paradox in evolutionary biology is how supergenes can maintain high fitness despite reduced effective population size, the suppression of recombination, and the expected accumulation of mutational load. The ruff supergene involves 2 rare inversion haplotypes (satellite and faeder). These are recessive lethals but with dominant effects on male mating strategies, plumage, and body size. Sequence divergence to the wild-type (independent) haplotype indicates that the inversion could be as old as 4 million years. Here, we have constructed a highly contiguous genome assembly of the inversion region for both the independent and satellite haplotypes. Based on the new data, we estimate that the recombination event(s) creating the satellite haplotype occurred only about 70,000 yr ago. Contrary to expectations for supergenes, we find no substantial expansion of repeats and only a modest mutation load on the satellite and faeder haplotypes despite high sequence divergence to the non-inverted haplotype (1.46%). The essential centromere protein N (CENPN) gene is disrupted by the inversion and is as well conserved on the inversion haplotypes as on the noninversion haplotype. These results suggest that the inversion may be much younger than previously thought. The low mutation load, despite recessive lethality, may be explained by the introgression of the inversion from a now extinct lineage.
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Affiliation(s)
- Jason Hill
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
| | - Erik D Enbody
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Huijuan Bi
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
| | - Sangeet Lamichhaney
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
- Department of Biological Sciences, Kent State University, Kent, OH 44241, USA
| | - Weipan Lei
- Key Laboratory for Biodiversity Science and Ecological Engineering, National Demonstration Center for Experimental Life Sciences and Biotechnology Education, College of Life Sciences, Beijing Normal University, 100875 Beijing, China
| | - Juexin Chen
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, 510275 Guangzhou, China
| | - Chentao Wei
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, 510275 Guangzhou, China
| | - Yang Liu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, 510275 Guangzhou, China
| | - Doreen Schwochow
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
| | - Shady Younis
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
- Division of Immunology and Rheumatology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Fredrik Widemo
- Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
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7
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Sendell-Price AT, Tulenko FJ, Pettersson M, Kang D, Montandon M, Winkler S, Kulb K, Naylor GP, Phillippy A, Fedrigo O, Mountcastle J, Balacco JR, Dutra A, Dale RE, Haase B, Jarvis ED, Myers G, Burgess SM, Currie PD, Andersson L, Schartl M. Low mutation rate in epaulette sharks is consistent with a slow rate of evolution in sharks. Nat Commun 2023; 14:6628. [PMID: 37857613 PMCID: PMC10587355 DOI: 10.1038/s41467-023-42238-x] [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: 03/31/2023] [Accepted: 10/03/2023] [Indexed: 10/21/2023] Open
Abstract
Sharks occupy diverse ecological niches and play critical roles in marine ecosystems, often acting as apex predators. They are considered a slow-evolving lineage and have been suggested to exhibit exceptionally low cancer rates. These two features could be explained by a low nuclear mutation rate. Here, we provide a direct estimate of the nuclear mutation rate in the epaulette shark (Hemiscyllium ocellatum). We generate a high-quality reference genome, and resequence the whole genomes of parents and nine offspring to detect de novo mutations. Using stringent criteria, we estimate a mutation rate of 7×10-10 per base pair, per generation. This represents one of the lowest directly estimated mutation rates for any vertebrate clade, indicating that this basal vertebrate group is indeed a slowly evolving lineage whose ability to restore genetic diversity following a sustained population bottleneck may be hampered by a low mutation rate.
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Affiliation(s)
- Ashley T Sendell-Price
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE75123, Uppsala, Sweden
- Bioinformatics Research Technology Platform, University of Warwick, Coventry, UK
| | - Frank J Tulenko
- Australian Regenerative Medicine Institute, Monash University, Victoria, 3800, Australia
| | - Mats Pettersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE75123, Uppsala, Sweden
| | - Du Kang
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, 78666, USA
| | - Margo Montandon
- Australian Regenerative Medicine Institute, Monash University, Victoria, 3800, Australia
| | - Sylke Winkler
- Max-Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
| | - Kathleen Kulb
- Max-Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
| | - Gavin P Naylor
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Adam Phillippy
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health Bethesda, Bethesda, MD, 20892, USA
| | - Olivier Fedrigo
- Vertebrate Genome Laboratory, Rockefeller University, New York, NY, 10065, USA
| | - Jacquelyn Mountcastle
- Research Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA
| | - Jennifer R Balacco
- Research Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA
| | - Amalia Dutra
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health Bethesda, Bethesda, MD, 20892, USA
| | - Rebecca E Dale
- Australian Regenerative Medicine Institute, Monash University, Victoria, 3800, Australia
| | - Bettina Haase
- Vertebrate Genome Laboratory, Rockefeller University, New York, NY, 10065, USA
| | - Erich D Jarvis
- Vertebrate Genome Laboratory, Rockefeller University, New York, NY, 10065, USA
| | - Gene Myers
- Max-Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
- Center of Systems Biology Dresden, 01307, Dresden, Germany
| | - Shawn M Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health Bethesda, Bethesda, MD, 20892, USA.
| | - Peter D Currie
- Australian Regenerative Medicine Institute, Monash University, Victoria, 3800, Australia.
- EMBL Australia, Victorian Node, Monash University, Clayton, Victoria, 3800, Australia.
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE75123, Uppsala, Sweden.
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX77483, USA.
| | - Manfred Schartl
- Developmental Biochemistry, Theodor-Boveri Institute, Biocenter, University of Würzburg, 97074, Würzburg, Germany.
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8
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Rancilhac L, Enbody ED, Harris R, Saitoh T, Irestedt M, Liu Y, Lei F, Andersson L, Alström P. Introgression underlies phylogenetic uncertainty but not parallel plumage evolution in a recent songbird radiation. Syst Biol 2023:syad062. [PMID: 37801684 DOI: 10.1093/sysbio/syad062] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Indexed: 10/08/2023] Open
Abstract
Instances of parallel phenotypic evolution offer great opportunities to understand the evolutionary processes underlying phenotypic changes. However, confirming parallel phenotypic evolution and studying its causes requires a robust phylogenetic framework. One such example is the "black-and-white wagtails", a group of five species in the songbird genus Motacilla: one species, Motacilla alba, shows wide intra-specific plumage variation, while the four others form two pairs of very similar-looking species (M. aguimp + M. samveasnae and M. grandis + M. maderaspatensis, respectively). However, the two species in each of these pairs were not recovered as sisters in previous phylogenetic inferences. Their relationships varied depending on the markers used, suggesting that gene tree heterogeneity might have hampered accurate phylogenetic inference. Here, we use whole genome resequencing data to explore the phylogenetic relationships within this group, with a special emphasis on characterizing the extent of gene tree heterogeneity and its underlying causes. We first used multispecies coalescent methods to generate a "complete evidence" phylogenetic hypothesis based on genome-wide variants, while accounting for incomplete lineage sorting (ILS) and introgression. We then investigated the variation in phylogenetic signal across the genome, to quantify the extent of discordance across genomic regions, and test its underlying causes. We found that wagtail genomes are mosaics of regions supporting variable genealogies, because of ILS and inter-specific introgression. The most common topology across the genome, supporting M. alba and M. aguimp as sister species, appears to be influenced by ancient introgression. Additionally, we inferred another ancient introgression event, between M. alba and M. grandis. By combining results from multiple analyses, we propose a phylogenetic network for the black-and-white wagtails that confirms that similar phenotypes evolved in non-sister lineages, supporting parallel plumage evolution. Furthermore, the inferred reticulations do not connect species with similar plumage coloration, suggesting that introgression does not underlie parallel plumage evolution in this group. Our results demonstrate the importance of investigation of genome-wide patterns of gene tree heterogeneity to help understanding the mechanisms underlying phenotypic evolution.
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Affiliation(s)
- Loïs Rancilhac
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, 752 36 Uppsala, Sweden
| | - Erik D Enbody
- Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
- Biomolecular Engineering, University of California, Santa Cruz, California, USA
| | | | - Takema Saitoh
- Yamashina Institute for Ornithology, 115 Konoyama, Abiko, Chiba 270-1145, Japan
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, 104 05 Stockholm, Sweden
| | - Yang Liu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen 518107, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Per Alström
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, 752 36 Uppsala, Sweden
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
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9
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Enbody ED, Sendell-Price AT, Sprehn CG, Rubin CJ, Visscher PM, Grant BR, Grant PR, Andersson L. Community-wide genome sequencing reveals 30 years of Darwin's finch evolution. Science 2023; 381:eadf6218. [PMID: 37769091 DOI: 10.1126/science.adf6218] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 08/22/2023] [Indexed: 09/30/2023]
Abstract
A fundamental goal in evolutionary biology is to understand the genetic architecture of adaptive traits. Using whole-genome data of 3955 of Darwin's finches on the Galápagos Island of Daphne Major, we identified six loci of large effect that explain 45% of the variation in the highly heritable beak size of Geospiza fortis, a key ecological trait. The major locus is a supergene comprising four genes. Abrupt changes in allele frequencies at the loci accompanied a strong change in beak size caused by natural selection during a drought. A gradual change in Geospiza scandens occurred across 30 years as a result of introgressive hybridization with G. fortis. This study shows how a few loci with large effect on a fitness-related trait contribute to the genetic potential for rapid adaptive radiation.
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Affiliation(s)
- Erik D Enbody
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 751 23 Uppsala, Sweden
| | - Ashley T Sendell-Price
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 751 23 Uppsala, Sweden
| | - C Grace Sprehn
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 751 23 Uppsala, Sweden
| | - Carl-Johan Rubin
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 751 23 Uppsala, Sweden
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Rd., St. Lucia QLD 4072, Australia
| | - B Rosemary Grant
- Department of Ecology and Evolutionary Biology, Princeton University, 106A Guyot Hall, Princeton, NJ 08544, USA
| | - Peter R Grant
- Department of Ecology and Evolutionary Biology, Princeton University, 106A Guyot Hall, Princeton, NJ 08544, USA
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 751 23 Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, Texas A&M University, 402 Raymond Stotzer Pkwy Building 2, College Station, TX 77843, USA
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10
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Kases K, Schubert E, Hajikhezri Z, Larsson M, Devi P, Darweesh M, Andersson L, Akusjärvi G, Punga T, Younis S. The RNA-binding protein ZC3H11A interacts with the nuclear poly(A)-binding protein PABPN1 and alters polyadenylation of viral transcripts. J Biol Chem 2023; 299:104959. [PMID: 37356722 PMCID: PMC10371797 DOI: 10.1016/j.jbc.2023.104959] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/09/2023] [Accepted: 06/14/2023] [Indexed: 06/27/2023] Open
Abstract
Nuclear mRNA metabolism is regulated by multiple proteins, which either directly bind to RNA or form multiprotein complexes. The RNA-binding protein ZC3H11A is involved in nuclear mRNA export, NF-κB signaling, and is essential during mouse embryo development. Furthermore, previous studies have shown that ZC3H11A is important for nuclear-replicating viruses. However, detailed biochemical characterization of the ZC3H11A protein has been lacking. In this study, we established the ZC3H11A protein interactome in human and mouse cells. We demonstrate that the nuclear poly(A)-binding protein PABPN1 interacts specifically with the ZC3H11A protein and controls ZC3H11A localization into nuclear speckles. We report that ZC3H11A specifically interacts with the human adenovirus type 5 (HAdV-5) capsid mRNA in a PABPN1-dependent manner. Notably, ZC3H11A uses the same zinc finger motifs to interact with PABPN1 and viral mRNA. Further, we demonstrate that the lack of ZC3H11A alters the polyadenylation of HAdV-5 capsid mRNA. Taken together, our results suggest that the ZC3H11A protein may act as a novel regulator of polyadenylation of nuclear mRNA.
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Affiliation(s)
- Katharina Kases
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Erik Schubert
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Zamaneh Hajikhezri
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Mårten Larsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Priya Devi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Mahmoud Darweesh
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden; Department of Microbiology and Immunology, Al-Azhr University, Assiut, Egypt
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Göran Akusjärvi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Tanel Punga
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
| | - Shady Younis
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden; Division of Immunology and Rheumatology, Stanford University, Stanford, California, USA.
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11
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Younis S, Jouneau A, Larsson M, Oudin JF, Adenot P, Omar J, Brochard V, Andersson L. Ablation of ZC3H11A causes early embryonic lethality and dysregulation of metabolic processes. Proc Natl Acad Sci U S A 2023; 120:e2216799120. [PMID: 37252988 DOI: 10.1073/pnas.2216799120] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023] Open
Abstract
ZC3H11A (zinc finger CCCH domain-containing protein 11A) is a stress-induced mRNA-binding protein required for efficient growth of nuclear-replicating viruses. The cellular functions of ZC3H11A during embryonic development are unknown. Here, we report the generation and phenotypic characterization of Zc3h11a knockout (KO) mice. Heterozygous null Zc3h11a mice were born at the expected frequency without distinguishable phenotypic differences compared with wild-type mice. In contrast, homozygous null Zc3h11a mice were missing, indicating that Zc3h11a is crucial for embryonic viability and survival. Zc3h11a -/- embryos were detected at the expected Mendelian ratios up to late preimplantation stage (E4.5). However, phenotypic characterization at E6.5 revealed degeneration of Zc3h11a -/- embryos, indicating developmental defects around the time of implantation. Transcriptomic analyses documented a dysregulation of glycolysis and fatty acid metabolic pathways in Zc3h11a-/- embryos at E4.5. Proteomic analysis indicated a tight interaction between ZC3H11A and mRNA-export proteins in embryonic stem cells. CLIP-seq analysis demonstrated that ZC3H11A binds a subset of mRNA transcripts that are critical for metabolic regulation of embryonic cells. Furthermore, embryonic stem cells with an induced deletion of Zc3h11a display an impaired differentiation toward epiblast-like cells and impaired mitochondrial membrane potential. Altogether, the results show that ZC3H11A is participating in export and posttranscriptional regulation of selected mRNA transcripts required to maintain metabolic processes in embryonic cells. While ZC3H11A is essential for the viability of the early mouse embryo, inactivation of Zc3h11a expression in adult tissues using a conditional KO did not lead to obvious phenotypic defects.
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Affiliation(s)
- Shady Younis
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University SE-751 23, Uppsala, Sweden
- Division of Immunology and Rheumatology, Stanford University, Stanford, CA 94305
| | - Alice Jouneau
- Université Paris-Saclay, Université Saint-Quentin-en-Yvelines, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Biologie de la Reproduction, Epigénétique, Environnement et Développement 78350, Jouy-en-Josas, France
| | - Mårten Larsson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University SE-751 23, Uppsala, Sweden
| | - Jean-Francois Oudin
- Université Paris-Saclay, Université Saint-Quentin-en-Yvelines, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Biologie de la Reproduction, Epigénétique, Environnement et Développement 78350, Jouy-en-Josas, France
| | - Pierre Adenot
- Université Paris-Saclay, Université Saint-Quentin-en-Yvelines, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Biologie de la Reproduction, Epigénétique, Environnement et Développement 78350, Jouy-en-Josas, France
| | - Jihad Omar
- Université Paris-Saclay, Université Saint-Quentin-en-Yvelines, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Biologie de la Reproduction, Epigénétique, Environnement et Développement 78350, Jouy-en-Josas, France
| | - Vincent Brochard
- Université Paris-Saclay, Université Saint-Quentin-en-Yvelines, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Biologie de la Reproduction, Epigénétique, Environnement et Développement 78350, Jouy-en-Josas, France
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University SE-751 23, Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843
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12
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Fuentes‐Pardo AP, Farrell ED, Pettersson ME, Sprehn CG, Andersson L. The genomic basis and environmental correlates of local adaptation in the Atlantic horse mackerel ( Trachurus trachurus). Evol Appl 2023; 16:1201-1219. [PMID: 37360028 PMCID: PMC10286234 DOI: 10.1111/eva.13559] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 04/21/2023] [Accepted: 05/07/2023] [Indexed: 06/28/2023] Open
Abstract
Understanding how populations adapt to their environment is increasingly important to prevent biodiversity loss due to overexploitation and climate change. Here we studied the population structure and genetic basis of local adaptation of Atlantic horse mackerel, a commercially and ecologically important marine fish that has one of the widest distributions in the eastern Atlantic. We analyzed whole-genome sequencing and environmental data of samples collected from the North Sea to North Africa and the western Mediterranean Sea. Our genomic approach indicated low population structure with a major split between the Mediterranean Sea and the Atlantic Ocean and between locations north and south of mid-Portugal. Populations from the North Sea are the most genetically distinct in the Atlantic. We discovered that most population structure patterns are driven by a few highly differentiated putatively adaptive loci. Seven loci discriminate the North Sea, two the Mediterranean Sea, and a large putative inversion (9.9 Mb) on chromosome 21 underlines the north-south divide and distinguishes North Africa. A genome-environment association analysis indicates that mean seawater temperature and temperature range, or factors correlated to them, are likely the main environmental drivers of local adaptation. Our genomic data broadly support the current stock divisions, but highlight areas of potential mixing, which require further investigation. Moreover, we demonstrate that as few as 17 highly informative SNPs can genetically discriminate the North Sea and North African samples from neighboring populations. Our study highlights the importance of both, life history and climate-related selective pressures in shaping population structure patterns in marine fish. It also supports that chromosomal rearrangements play a key role in local adaptation with gene flow. This study provides the basis for more accurate delineation of the horse mackerel stocks and paves the way for improving stock assessments.
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Affiliation(s)
| | - Edward D. Farrell
- EDF Scientific LimitedCorkIreland
- Killybegs Fishermen's OrganisationDonegalIreland
| | - Mats E. Pettersson
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
| | - C. Grace Sprehn
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
| | - Leif Andersson
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
- Department of Veterinary Integrative BiosciencesTexas A&M UniversityCollege StationTexasUSA
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13
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Pettersson ME, Fuentes-Pardo AP, Rochus CM, Enbody ED, Bi H, Väinölä R, Andersson L. A long-standing hybrid population between Pacific and Atlantic herring in a subarctic fjord of Norway. Genome Biol Evol 2023; 15:7147330. [PMID: 37120751 PMCID: PMC10182735 DOI: 10.1093/gbe/evad069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/12/2023] [Accepted: 04/21/2023] [Indexed: 05/01/2023] Open
Abstract
Atlantic herring (Clupea harengus) and Pacific herring (C. pallasii) are sister species that split from a common ancestor about 2 million years ago. Balsfjord, a subarctic fjord in Northern Norway, harbors an outpost population of Pacific herring within the range of the Atlantic herring. We used whole genome sequencing to show that gene flow from Atlantic herring into the Balsfjord population has generated a stable hybrid population that has persisted for thousands of generations. The Atlantic herring ancestry in Balsfjord was estimated in the range 25-26%. The old age and large proportion of introgressed regions suggest there are no obvious genetic incompatibilities between species. Introgressed regions were widespread in the genome and large, with some in excess of 1 Mb, and they were overrepresented in low-recombination regions. We show that the distribution of introgressed material is non-random; introgressed sequence blocks in different individuals are shared more often than expected by chance. Furthermore, introgressed regions tend to show elevated divergence (FST) between Atlantic and Pacific herring. Together, our results suggest that introgression of genetic material has facilitated adaptation in the Balsfjord population. The Balsfjord population provides a rare example of a stable interspecies hybrid population that has persisted over thousands of years.
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Affiliation(s)
- Mats E Pettersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Angela P Fuentes-Pardo
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Christina M Rochus
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Erik D Enbody
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Huijuan Bi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Risto Väinölä
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
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14
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Bi H, Tranell J, Harper DC, Lin W, Li J, Hellström AR, Larsson M, Rubin CJ, Wang C, Sayyab S, Kerje S, Bed'hom B, Gourichon D, Ito S, Wakamatsu K, Tixier-Boichard M, Marks MS, Globisch D, Andersson L. A frame-shift mutation in COMTD1 is associated with impaired pheomelanin pigmentation in chicken. PLoS Genet 2023; 19:e1010724. [PMID: 37068079 PMCID: PMC10138217 DOI: 10.1371/journal.pgen.1010724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/27/2023] [Accepted: 03/28/2023] [Indexed: 04/18/2023] Open
Abstract
The biochemical pathway regulating the synthesis of yellow/red pheomelanin is less well characterized than the synthesis of black/brown eumelanin. Inhibitor of gold (IG phenotype) is a plumage colour variant in chicken that provides an opportunity to further explore this pathway since the recessive allele (IG) at this locus is associated with a defect in the production of pheomelanin. IG/IG homozygotes display a marked dilution of red pheomelanin pigmentation, whilst black pigmentation (eumelanin) is only slightly affected. Here we show that a 2-base pair insertion (frame-shift mutation) in the 5th exon of the Catechol-O-methyltransferase containing domain 1 gene (COMTD1), expected to cause a complete or partial loss-of-function of the COMTD1 enzyme, shows complete concordance with the IG phenotype within and across breeds. We show that the COMTD1 protein is localized to mitochondria in pigment cells. Knockout of Comtd1 in a mouse melanocytic cell line results in a reduction in pheomelanin metabolites and significant alterations in metabolites of glutamate/glutathione, riboflavin, and the tricarboxylic acid cycle. Furthermore, COMTD1 overexpression enhanced cellular proliferation following chemical-induced transfection, a potential inducer of oxidative stress. These observations suggest that COMTD1 plays a protective role for melanocytes against oxidative stress and that this supports their ability to produce pheomelanin.
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Affiliation(s)
- Huijuan Bi
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Jonas Tranell
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Dawn C Harper
- Department of Pathology & Laboratory Medicine and Department of Physiology, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, United States of America
| | - Weifeng Lin
- Department of Chemistry, Uppsala University, Uppsala, Sweden
| | - Jingyi Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Anders R Hellström
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Mårten Larsson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Carl-Johan Rubin
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Chao Wang
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Shumaila Sayyab
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Susanne Kerje
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Bertrand Bed'hom
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, F-78350 Jouy-en-Josas, France
| | | | - Shosuke Ito
- Institute for Melanin Chemistry, Fujita Health University, Toyoake, Aichi, Japan
| | - Kazumasa Wakamatsu
- Institute for Melanin Chemistry, Fujita Health University, Toyoake, Aichi, Japan
| | | | - Michael S Marks
- Department of Pathology & Laboratory Medicine and Department of Physiology, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, United States of America
| | - Daniel Globisch
- Department of Chemistry, Uppsala University, Uppsala, Sweden
| | - Leif Andersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, United States of America
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15
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Darweesh M, Younis S, Hajikhezri Z, Ali A, Jin C, Punga T, Gupta S, Essand M, Andersson L, Akusjärvi G. ZC3H11A loss of function enhances NF-κB signaling through defective IκBα protein expression. Front Immunol 2022; 13:1002823. [PMID: 36439101 PMCID: PMC9681899 DOI: 10.3389/fimmu.2022.1002823] [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] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/05/2022] [Indexed: 12/02/2023] Open
Abstract
ZC3H11A is a cellular protein associated with the transcription export (TREX) complex that is induced during heat-shock. Several nuclear-replicating viruses exploit the mRNA export mechanism of ZC3H11A protein for their efficient replication. Here we show that ZC3H11A protein plays a role in regulation of NF-κB signal transduction. Depletion of ZC3H11A resulted in enhanced NF-κB mediated signaling, with upregulation of numerous innate immune related mRNAs, including IL-6 and a large group of interferon-stimulated genes. IL-6 upregulation in the absence of the ZC3H11A protein correlated with an increased NF-κB transcription factor binding to the IL-6 promoter and decreased IL-6 mRNA decay. The enhanced NF-κB signaling pathway in ZC3H11A deficient cells correlated with a defect in IκBα inhibitory mRNA and protein accumulation. Upon ZC3H11A depletion The IκBα mRNA was retained in the cell nucleus resulting in failure to maintain normal levels of the cytoplasmic IκBα mRNA and protein that is essential for its inhibitory feedback loop on NF-κB activity. These findings indicate towards a previously unknown mechanism of ZC3H11A in regulating the NF-κB pathway at the level of IkBα mRNA export.
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Affiliation(s)
- Mahmoud Darweesh
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Microbiology and Immunology, Faculty of Pharmacy, Alazhr University, Assiut, Egypt
| | - Shady Younis
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Division of Immunology and Rheumatology, Stanford University, Stanford, CA, United States
| | - Zamaneh Hajikhezri
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Arwa Ali
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Chuan Jin
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Tanel Punga
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Soham Gupta
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Magnus Essand
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
| | - Göran Akusjärvi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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16
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Hill J, Lillie M, Pettersson ME, Rubin CJ, Grant BR, Grant PR, Andersson L, Jern P. Spatiotemporal variations in retrovirus-host interactions among Darwin's finches. Nat Commun 2022; 13:6033. [PMID: 36229469 PMCID: PMC9562234 DOI: 10.1038/s41467-022-33723-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 03/10/2022] [Accepted: 09/29/2022] [Indexed: 11/24/2022] Open
Abstract
Endogenous retroviruses (ERVs) are inherited remnants of retroviruses that colonized host germline over millions of years, providing a sampling of retroviral diversity across time. Here, we utilize the strength of Darwin’s finches, a system synonymous with evolutionary studies, for investigating ERV history, revealing recent retrovirus-host interactions in natural populations. By mapping ERV variation across all species of Darwin’s finches and comparing with outgroup species, we highlight geographical and historical patterns of retrovirus-host occurrence, utilizing the system for evaluating the extent and timing of retroviral activity in hosts undergoing adaptive radiation and colonization of new environments. We find shared ERVs among all samples indicating retrovirus-host associations pre-dating host speciation, as well as considerable ERV variation across populations of the entire Darwin’s finches’ radiation. Unexpected ERV variation in finch species on different islands suggests historical changes in gene flow and selection. Non-random distribution of ERVs along and between chromosomes, and across finch species, suggests association between ERV accumulation and the rapid speciation of Darwin’s finches. Endogenous retroviruses (ERV) are inherited remains of retroviruses that have colonized host genomes during evolution. Here the authors observe considerable species-specific ERV variation among Darwin’s finches, reflecting historic retrovirus-host interactions.
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Affiliation(s)
- Jason Hill
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23, Uppsala, Sweden.
| | - Mette Lillie
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23, Uppsala, Sweden.
| | - Mats E Pettersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Carl-Johan Rubin
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23, Uppsala, Sweden.,Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - B Rosemary Grant
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Peter R Grant
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Leif Andersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23, Uppsala, Sweden.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden.,Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843, USA
| | - Patric Jern
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23, Uppsala, Sweden.
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17
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Farrell ED, Andersson L, Bekkevold D, Campbell N, Carlsson J, Clarke MW, Egan A, Folkvord A, Gras M, Lusseau SM, Mackinson S, Nolan C, O'Connell S, O'Malley M, Pastoors M, Pettersson ME, White E. A baseline for the genetic stock identification of Atlantic herring, Clupea harengus, in ICES Divisions 6.a, 7.b-c. R Soc Open Sci 2022; 9:220453. [PMID: 36133150 PMCID: PMC9449477 DOI: 10.1098/rsos.220453] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/19/2022] [Indexed: 06/16/2023]
Abstract
Atlantic herring in International Council for Exploration of the Sea (ICES) Divisions 6.a, 7.b-c comprises at least three populations, distinguished by temporal and spatial differences in spawning, which have until recently been managed as two stocks defined by geographical delineators. Outside of spawning the populations form mixed aggregations, which are the subject of acoustic surveys. The inability to distinguish the populations has prevented the development of separate survey indices and separate stock assessments. A panel of 45 single-nucleotide polymorphisms, derived from whole-genome sequencing, were used to genotype 3480 baseline spawning samples (2014-2021). A temporally stable baseline comprising 2316 herring from populations known to inhabit Division 6.a was used to develop a genetic assignment method, with a self-assignment accuracy greater than 90%. The long-term temporal stability of the assignment model was validated by assigning archive (2003-2004) baseline samples (270 individuals) with a high level of accuracy. Assignment of non-baseline samples (1514 individuals) from Divisions 6.a, 7.b-c indicated previously unrecognized levels of mixing of populations outside of the spawning season. The genetic markers and assignment models presented constitute a 'toolbox' that can be used for the assignment of herring caught in mixed survey and commercial catches in Division 6.a into their population of origin with a high level of accuracy.
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Affiliation(s)
- Edward D. Farrell
- EDF Scientific Limited, Rathaha, Ladysbridge, Cork, Ireland
- Area 52 Research Group, School of Biology and Environmental Science/Earth Institute, Science Centre West, University College Dublin, Dublin, Ireland
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, USA
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Dorte Bekkevold
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | - Neil Campbell
- Marine Scotland Science, 375 Victoria Road, Aberdeen AB11 9DB, Scotland
| | - Jens Carlsson
- Area 52 Research Group, School of Biology and Environmental Science/Earth Institute, Science Centre West, University College Dublin, Dublin, Ireland
| | | | - Afra Egan
- Marine Institute, Rinville, Oranmore, Co. Galway, Ireland
| | - Arild Folkvord
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Michaël Gras
- Marine Institute, Rinville, Oranmore, Co. Galway, Ireland
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Susan Mærsk Lusseau
- Marine Scotland Science, 375 Victoria Road, Aberdeen AB11 9DB, Scotland
- National Institute of Aquatic Resources, Willemoesvej 2, Hovedbygning, 067, 9850 Hirtshals, Denmark
| | - Steven Mackinson
- Scottish Pelagic Fishermen's Association, Heritage House, 135-139 Shore Street, Fraserburgh, Aberdeenshire, Scotland
| | - Cormac Nolan
- Marine Institute, Rinville, Oranmore, Co. Galway, Ireland
| | - Steven O'Connell
- Marine Scotland Science, 375 Victoria Road, Aberdeen AB11 9DB, Scotland
| | | | - Martin Pastoors
- Pelagic Freezer-trawler Association, Louis Braillelaan 80, 2719 EK Zoetermeer, The Netherlands
| | - Mats E. Pettersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Emma White
- Marine Institute, Rinville, Oranmore, Co. Galway, Ireland
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18
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Rubin CJ, Enbody ED, Dobreva MP, Abzhanov A, Davis BW, Lamichhaney S, Pettersson M, Sendell-Price AT, Sprehn CG, Valle CA, Vasco K, Wallerman O, Grant BR, Grant PR, Andersson L. Rapid adaptive radiation of Darwin's finches depends on ancestral genetic modules. Sci Adv 2022; 8:eabm5982. [PMID: 35857449 PMCID: PMC9269886 DOI: 10.1126/sciadv.abm5982] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 05/25/2022] [Indexed: 05/21/2023]
Abstract
Recent adaptive radiations are models for investigating mechanisms contributing to the evolution of biodiversity. An unresolved question is the relative importance of new mutations, ancestral variants, and introgressive hybridization for phenotypic evolution and speciation. Here, we address this issue using Darwin's finches and investigate the genomic architecture underlying their phenotypic diversity. Admixture mapping for beak and body size in the small, medium, and large ground finches revealed 28 loci showing strong genetic differentiation. These loci represent ancestral haplotype blocks with origins predating speciation events during the Darwin's finch radiation. Genes expressed in the developing beak are overrepresented in these genomic regions. Ancestral haplotypes constitute genetic modules for selection and act as key determinants of the unusual phenotypic diversity of Darwin's finches. Such ancestral haplotype blocks can be critical for how species adapt to environmental variability and change.
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Affiliation(s)
- Carl-Johan Rubin
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Institute of Marine Research, Nordnesgaten 50, 5005 Bergen, Norway
| | - Erik D. Enbody
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Mariya P. Dobreva
- Department of Life Sciences, Imperial College London, Silwood Park Campus, SL5 7PY Ascot, UK
| | - Arhat Abzhanov
- Department of Life Sciences, Imperial College London, Silwood Park Campus, SL5 7PY Ascot, UK
| | - Brian W. Davis
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | | | - Mats Pettersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Ashley T. Sendell-Price
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Edward Grey Institute, Department of Zoology, University of Oxford, Oxford, UK
| | - C. Grace Sprehn
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Carlos A. Valle
- Colegio de Ciencias Biológicas y Ambientales, Galápagos Science Center GSC, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Karla Vasco
- Colegio de Ciencias Biológicas y Ambientales, Galápagos Science Center GSC, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Ola Wallerman
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - B. Rosemary Grant
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Peter R. Grant
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Corresponding author.
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19
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Lee MO, Li J, Davis BW, Upadhyay S, Al Muhisen HM, Suva LJ, Clement TM, Andersson L. Hmga2 deficiency is associated with allometric growth retardation, infertility, and behavioral abnormalities in mice. G3 (Bethesda) 2022; 12:6456304. [PMID: 34878116 PMCID: PMC9210324 DOI: 10.1093/g3journal/jkab417] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/23/2021] [Indexed: 05/13/2023]
Abstract
The high mobility group AT-hook 2 (HMGA2) protein works as an architectural regulator by binding AT-rich DNA sequences to induce conformational changes affecting transcription. Genomic deletions disrupting HMGA2 coding sequences and flanking noncoding sequences cause dwarfism in mice and rabbits. Here, CRISPR/Cas9 was used in mice to generate an Hmga2 null allele that specifically disrupts only the coding sequence. The loss of one or both alleles of Hmga2 resulted in reduced body size of 20% and 60%, respectively, compared to wild-type littermates as well as an allometric reduction in skull length in Hmga2-/- mice. Both male and female Hmga2-/- mice are infertile, whereas Hmga2+/- mice are fertile. Examination of reproductive tissues of Hmga2-/- males revealed a significantly reduced size of testis, epididymis, and seminal vesicle compared to controls, and 70% of knock-out males showed externalized penis, but no cryptorchidism was observed. Sperm analyses revealed severe oligospermia in mutant males and slightly decreased sperm viability, increased DNA damage but normal sperm chromatin compaction. Testis histology surprisingly revealed a normal seminiferous epithelium, despite the significant reduction in testis size. In addition, Hmga2-/- mice showed a significantly reduced exploratory behavior. In summary, the phenotypic effects in mouse using targeted mutagenesis confirmed that Hmga2 is affecting prenatal and postnatal growth regulation, male reproductive tissue development, and presents the first indication that Hmga2 function is required for normal mouse behavior. No specific effect, despite an allometric reduction, on craniofacial development was noted in contrast to previous reports of an altered craniofacial development in mice and rabbits carrying deletions of both coding and noncoding sequences at the 5' part of Hmga2.
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Affiliation(s)
- Mi Ok Lee
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Jingyi Li
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Srijana Upadhyay
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX 77843, USA
| | - Hadil M Al Muhisen
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX 77843, USA
- Interdisciplinary Program in Toxicology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Larry J Suva
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX 77843, USA
| | - Tracy M Clement
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX 77843, USA
- Interdisciplinary Program in Toxicology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Leif Andersson
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
- Corresponding author: Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, Vet Med Research Bldg., 588 Raymond Stotzer Pw, TX 77843, USA.
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20
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Li J, Lee MO, Davis BW, Wu P, Hsieh Li SM, Chuong CM, Andersson L. Corrigendum to “The crest phenotype in domestic chicken is caused by a 195 bp duplication in the intron of HOXC10”. G3 Genes|Genomes|Genetics 2022; 12:6495528. [PMID: 35100383 PMCID: PMC8824791 DOI: 10.1093/g3journal/jkab425] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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21
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Hanley KG, McFadden JP, Mitchell DL, Fowler CM, Stone SW, Yelle RV, Mayyasi M, Ergun RE, Andersson L, Benna M, Elrod MK, Jakosky BM. In Situ Measurements of Thermal Ion Temperature in the Martian Ionosphere. J Geophys Res Space Phys 2021; 126:e2021JA029531. [PMID: 35865356 PMCID: PMC9286691 DOI: 10.1029/2021ja029531] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 10/22/2021] [Accepted: 11/19/2021] [Indexed: 06/15/2023]
Abstract
In situ measurements of ionospheric and thermospheric temperatures are experimentally challenging because orbiting spacecraft typically travel supersonically with respect to the cold gas and plasma. We present O 2 + temperatures in Mars' ionosphere derived from data measured by the SupraThermal And Thermal Ion Composition instrument onboard the Mars Atmosphere and Volatile EvolutioN spacecraft. We focus on data obtained during nine special orbit maneuvers known as Deep Dips, during which MAVEN lowered its periapsis altitude from the nominal 150 to 120 km for 1 week in order to sample the ionospheric main peak and approach the homopause. We use two independent techniques to calculate ion temperatures from the measured energy and angular widths of the supersonic ram ion beam. After correcting for background and instrument response, we are able to measure ion temperatures as low as 100 K with associated uncertainties as low as 10%. It is theoretically expected that ion temperatures will converge to the neutral temperature at altitudes below the exobase region (∼180-200 km) due to strong collisional coupling; however, no evidence of the expected thermalization is observed. We have eliminated several possible explanations for the observed temperature difference between ions and neutrals, including Coulomb collisions with electrons, Joule heating, and heating caused by interactions with the spacecraft. The source of the energy maintaining the high ion temperatures remains unclear, suggesting that a fundamental piece of physics is missing from existing models of the Martian ionosphere.
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Affiliation(s)
- K. G. Hanley
- Space Sciences LaboratoryUniversity of California BerkeleyBerkeleyCAUSA
| | - J. P. McFadden
- Space Sciences LaboratoryUniversity of California BerkeleyBerkeleyCAUSA
| | - D. L. Mitchell
- Space Sciences LaboratoryUniversity of California BerkeleyBerkeleyCAUSA
| | - C. M. Fowler
- Space Sciences LaboratoryUniversity of California BerkeleyBerkeleyCAUSA
- Department of Physics and AstronomyWest Virginia UniversityMorgantownWVUSA
| | - S. W. Stone
- Lunar and Planetary LaboratoryUniversity of ArizonaTucsonAZUSA
| | - R. V. Yelle
- Lunar and Planetary LaboratoryUniversity of ArizonaTucsonAZUSA
| | - M. Mayyasi
- Astronomy DepartmentBoston UniversityBostonMAUSA
| | - R. E. Ergun
- Laboratory for Atmospheric and Space PhysicsUniversity of Colorado BoulderBoulderCOUSA
| | - L. Andersson
- Laboratory for Atmospheric and Space PhysicsUniversity of Colorado BoulderBoulderCOUSA
| | - M. Benna
- Center for Research and Exploration in Space Science and TechnologyNASA Goddard Space Flight CenterGreenbeltMDUSA
- University of MarylandBaltimore CountyMDUSA
| | - M. K. Elrod
- Center for Research and Exploration in Space Science and TechnologyNASA Goddard Space Flight CenterGreenbeltMDUSA
- University of MarylandCollege ParkMDUSA
| | - B. M. Jakosky
- Laboratory for Atmospheric and Space PhysicsUniversity of Colorado BoulderBoulderCOUSA
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22
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Schwochow D, Bornelöv S, Jiang T, Li J, Gourichon D, Bed’Hom B, Dorshorst BJ, Chuong CM, Tixier-Boichard M, Andersson L. The feather pattern autosomal barring in chicken is strongly associated with segregation at the MC1R locus. Pigment Cell Melanoma Res 2021; 34:1015-1028. [PMID: 33793042 PMCID: PMC8484376 DOI: 10.1111/pcmr.12975] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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] [Received: 02/18/2021] [Accepted: 03/26/2021] [Indexed: 01/14/2023]
Abstract
Color patterns within individual feathers are common in birds but little is known about the genetic mechanisms causing such patterns. Here, we investigate the genetic basis for autosomal barring in chicken, a horizontal striping pattern on individual feathers. Using an informative backcross, we demonstrate that the MC1R locus is strongly associated with this phenotype. A deletion at SOX10, underlying the dark brown phenotype on its own, affects the manifestation of the barring pattern. The coding variant L133Q in MC1R is the most likely causal mutation for autosomal barring in this pedigree. Furthermore, a genetic screen across six different breeds showing different patterning phenotypes revealed that the most striking shared characteristics among these breeds were that they all carried the MC1R alleles Birchen or brown. Our data suggest that the presence of activating MC1R mutations enhancing pigment synthesis is an important mechanism underlying pigmentation patterns on individual feathers in chicken. We propose that MC1R and its antagonist ASIP play a critical role for determining within-feather pigmentation patterns in birds by acting as activator and inhibitor possibly in a Turing reaction-diffusion model.
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Affiliation(s)
- Doreen Schwochow
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Susanne Bornelöv
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Tingxing Jiang
- Department of Pathology, University of Southern California, Los Angeles, CS, USA
| | - Jingyi Li
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA, USA
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | | | - Bertrand Bed’Hom
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Ben J. Dorshorst
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Cheng-Ming Chuong
- Department of Pathology, University of Southern California, Los Angeles, CS, USA
| | | | - Leif Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
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23
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Wang D, Pan D, Xie B, Wang S, Xing X, Liu X, Ma Y, Andersson L, Wu J, Jiang L. Porcine ZBED6 regulates growth of skeletal muscle and internal organs via multiple targets. PLoS Genet 2021; 17:e1009862. [PMID: 34710100 PMCID: PMC8577783 DOI: 10.1371/journal.pgen.1009862] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 07/30/2021] [Revised: 11/09/2021] [Accepted: 10/06/2021] [Indexed: 11/20/2022] Open
Abstract
ZBED6 (zinc finger BED domain containing protein 6) is a transcription factor unique to placental mammals and its interaction with the IGF2 (insulin-like growth factor 2) locus plays a prominent role in the regulation of postnatal skeletal muscle growth. Here, we generated lean Bama miniature pigs by generating ZBED6-knockout (ZBED6−/−) and investigated the mechanism underlying ZBED6 in growth of muscle and internal organs of placental mammals. ZBED6−/− pigs show markedly higher lean mass, lean mass rate, larger muscle fiber area and heavier internal organs (heart and liver) than wild-type (WT) pigs. The striking phenotypic changes of ZBED6-/- pigs coincided with remarkable upregulation of IGF2 mRNA and protein expression across three tissues (gastrocnemius muscle, longissimus dorsi, heart). Despite a significant increase in liver weight, ZBED6-/- pigs show comparable levels of IGF2 expression to those of WT controls. A mechanistic study revealed that elevated methylation in the liver abrogates ZBED6 binding at the IGF2 locus, explaining the unaltered hepatic IGF2 expression in ZBED6-/- pigs. These results indicate that a ZBED6-IGF2-independent regulatory pathway exists in the liver. Transcriptome analysis and ChIP-PCR revealed new ZBED6 target genes other than IGF2, including cyclin dependent kinase inhibitor 1A (CDKN1A) and tsukushi, small leucine rich proteoglycan (TSKU), that regulates growth of muscle and liver, respectively. The lean meat rate is an important economic trait for the swine industry and it is determined by muscle growth and development. A single base change in intron 3 of the insulin-like growth factor 2 (IGF2) gene increases meat production in pigs by disrupting a binding site for zinc finger BED domain containing protein 6 (ZBED6). Chinese indigenous pig breeds carrying the homozygous IGF2 wild-type allele produce low lean meat. We thus generate a lean pig model in Chinese Bama pig by knocking out ZBED6. In this model, we demonstrate that ZBED6 KO increases muscle and internal organ growth through ZBED6-IGF2 axis and other target genes. These results not only open new strategies for lean meat breeding in Chinese indigenous pigs, but also provide new insights to the global function of ZBED6 in organ growth and development.
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Affiliation(s)
- Dandan Wang
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Dengke Pan
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Clinical Immunology Translational Medicine Key Laboratory of Sichuan Province, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, Chengdu, China
| | - Baocai Xie
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Shengnan Wang
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | | | - Xuexue Liu
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Yuehui Ma
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Leif Andersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, United States of America
| | - Jiangwei Wu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
- * E-mail: (JW); (LJ)
| | - Lin Jiang
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- * E-mail: (JW); (LJ)
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24
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Enbody ED, Sprehn CG, Abzhanov A, Bi H, Dobreva MP, Osborne OG, Rubin CJ, Grant PR, Grant BR, Andersson L. A multispecies BCO2 beak color polymorphism in the Darwin's finch radiation. Curr Biol 2021; 31:5597-5604.e7. [PMID: 34687609 DOI: 10.1016/j.cub.2021.09.085] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 05/08/2021] [Revised: 08/25/2021] [Accepted: 09/29/2021] [Indexed: 10/20/2022]
Abstract
Carotenoid-based polymorphisms are widespread in populations of birds, fish, and reptiles,1 but generally little is known about the factors affecting their maintenance in populations.2 We report a combined field and molecular-genetic investigation of a nestling beak color polymorphism in Darwin's finches. Beaks are pink or yellow, and yellow is recessive.3 Here we show that the polymorphism arose in the Galápagos half a million years ago through a mutation associated with regulatory change in the BCO2 gene and is shared by 14 descendant species. The polymorphism is probably a balanced polymorphism, maintained by ecological selection associated with survival and diet. In cactus finches, the frequency of the yellow genotype is correlated with cactus fruit abundance and greater hatching success and may be altered by introgressive hybridization. Polymorphisms that are hidden as adults, as here, may be far more common than is currently recognized, and contribute to diversification in ways that are yet to be discovered.
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Affiliation(s)
- Erik D Enbody
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden.
| | - C Grace Sprehn
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden
| | - Arhat Abzhanov
- Department of Life Sciences, Imperial College London, Silwood Park Campus, SL5 7PY Ascot, UK
| | - Huijuan Bi
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden
| | - Mariya P Dobreva
- Department of Life Sciences, Imperial College London, Silwood Park Campus, SL5 7PY Ascot, UK
| | - Owen G Osborne
- School of Natural Sciences, Bangor University, Environment Centre Wales, Deiniol Road, Bangor LL57 2UW, UK
| | - Carl-Johan Rubin
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden
| | - Peter R Grant
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - B Rosemary Grant
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden; Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden; Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843-4458, USA.
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25
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Li J, Lee MO, Chen J, Davis BW, Dorshorst BJ, Siegel PB, Inaba M, Jiang TX, Chuong CM, Andersson L. Cis-acting mutation affecting GJA5 transcription is underlying the Melanotic within-feather pigmentation pattern in chickens. Proc Natl Acad Sci U S A 2021; 118:e2109363118. [PMID: 34607956 PMCID: PMC8521658 DOI: 10.1073/pnas.2109363118] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2021] [Indexed: 11/18/2022] Open
Abstract
Melanotic (Ml) is a mutation in chickens that extends black (eumelanin) pigmentation in normally brown or red (pheomelanin) areas, thus affecting multiple within-feather patterns [J. W. Moore, J. R. Smyth Jr, J. Hered. 62, 215-219 (1971)]. In the present study, linkage mapping using a back-cross between Dark Cornish (Ml/Ml) and Partridge Plymouth Rock (ml+/ml+ ) chickens assigned Ml to an 820-kb region on chromosome 1. Identity-by-descent mapping, via whole-genome sequencing and diagnostic tests using a diverse set of chickens, refined the localization to the genomic region harboring GJA5 encoding gap-junction protein 5 (alias connexin 40) previously associated with pigmentation patterns in zebrafish. An insertion/deletion polymorphism located in the vicinity of the GJA5 promoter region was identified as the candidate causal mutation. Four different GJA5 transcripts were found to be expressed in feather follicles and at least two showed differential expression between genotypes. The results showed that Melanotic constitutes a cis-acting regulatory mutation affecting GJA5 expression. A recent study established the melanocortin-1 receptor (MC1R) locus and the interaction between the MC1R receptor and its antagonist agouti-signaling protein as the primary mechanism underlying variation in within-feather pigmentation patterns in chickens. The present study advances understanding the mechanisms underlying variation in plumage color in birds because it demonstrates that the activity of connexin 40/GJA5 can modulate the periodic pigmentation patterns within individual feathers.
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Affiliation(s)
- Jingyi Li
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Mi-Ok Lee
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843
| | - Junfeng Chen
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843
| | - Benjamin J Dorshorst
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Paul B Siegel
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Masafumi Inaba
- Department of Pathology, University of Southern California, Los Angeles, CA 90033
| | - Ting-Xin Jiang
- Department of Pathology, University of Southern California, Los Angeles, CA 90033
| | - Cheng-Ming Chuong
- Department of Pathology, University of Southern California, Los Angeles, CA 90033
| | - Leif Andersson
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843;
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden
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26
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Wang X, Younis S, Cen J, Wang Y, Krizhanovskii C, Andersson L, Welsh N. ZBED6 counteracts high-fat diet-induced glucose intolerance by maintaining beta cell area and reducing excess mitochondrial activation. Diabetologia 2021; 64:2292-2305. [PMID: 34296320 PMCID: PMC8423654 DOI: 10.1007/s00125-021-05517-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 04/01/2021] [Indexed: 12/31/2022]
Abstract
AIMS/HYPOTHESIS ZBED6 (zinc finger, BED-type containing 6) is known to regulate muscle mass by suppression of Igf2 gene transcription. In insulin-producing cell lines, ZBED6 maintains proliferative capacity at the expense of differentiation and beta cell function. The aim was to study the impact of Zbed6 knockout on beta cell function and glucose tolerance in C57BL/6 mice. METHODS Beta cell area and proliferation were determined in Zbed6 knockout mice using immunohistochemical analysis. Muscle and fat distribution were assessed using micro-computed tomography. Islet gene expression was assessed by RNA sequencing. Effects of a high-fat diet were analysed by glucose tolerance and insulin tolerance tests. ZBED6 was overexpressed in EndoC-βH1 cells and human islet cells using an adenoviral vector. Beta cell cell-cycle analysis, insulin release and mitochondrial function were studied in vitro using propidium iodide staining and flow cytometry, ELISA, the Seahorse technique, and the fluorescent probes JC-1 and MitoSox. RESULTS Islets from Zbed6 knockout mice showed lowered expression of the cell cycle gene Pttg1, decreased beta cell proliferation and decreased beta cell area, which occurred independently from ZBED6 effects on Igf2 gene expression. Zbed6 knockout mice, but not wild-type mice, developed glucose intolerance when given a high-fat diet. The high-fat diet Zbed6 knockout islets displayed upregulated expression of oxidative phosphorylation genes and genes associated with beta cell differentiation. In vitro, ZBED6 overexpression resulted in increased EndoC-βH1 cell proliferation and a reduced glucose-stimulated insulin release in human islets. ZBED6 also reduced mitochondrial JC-1 J-aggregate formation, mitochondrial oxygen consumption rates (OCR) and mitochondrial reactive oxygen species (ROS) production, both at basal and palmitate + high glucose-stimulated conditions. ZBED6-induced inhibition of OCR was not rescued by IGF2 addition. ZBED6 reduced levels of the mitochondrial regulator PPAR-γ related coactivator 1 protein (PRC) and bound its promoter/enhancer region. Knockdown of PRC resulted in a lowered OCR. CONCLUSIONS/INTERPRETATION It is concluded that ZBED6 is required for normal beta cell replication and also limits excessive beta cell mitochondrial activation in response to an increased functional demand. ZBED6 may act, at least in part, by restricting PRC-mediated mitochondrial activation/ROS production, which may lead to protection against beta cell dysfunction and glucose intolerance in vivo.
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Affiliation(s)
- Xuan Wang
- Science for Life Laboratory, Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Shady Younis
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Division of Immunology and Rheumatology, Stanford University, Stanford, CA, USA
| | - Jing Cen
- Science for Life Laboratory, Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Yun Wang
- Science for Life Laboratory, Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Camilla Krizhanovskii
- Science for Life Laboratory, Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Leif Andersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
- Department of Veterinary Integrative Biosciences, Texas A & M University, College Station, TX, USA.
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | - Nils Welsh
- Science for Life Laboratory, Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden.
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Naboulsi R, Larsson M, Andersson L, Younis S. ZBED6 regulates Igf2 expression partially through its regulation of miR483 expression. Sci Rep 2021; 11:19484. [PMID: 34593874 PMCID: PMC8484269 DOI: 10.1038/s41598-021-98777-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 11/06/2020] [Accepted: 09/14/2021] [Indexed: 02/06/2023] Open
Abstract
The expression of Igf2 in mammals shows a complex regulation involving multiple promoters and epigenetic mechanisms. We previously identified a novel regulatory mechanism based on the interaction between the transcriptional factor ZBED6 and Igf2 intron. Disruption of the ZBED6-Igf2 interaction leads to a dramatic up-regulation of IGF2 expression postnatally. In the current study we characterize an additional layer of regulation involving miR483 encoded by another Igf2 intron. We found a highly significant up-regulation of miR483 expression when the ZBED6-Igf2 axis is disrupted in transgenic mice. Furthermore, CRISPR/Cas9 mediated knock-out of miR483 in C2C12 myoblast cells, both wild-type and cells with disrupted ZBED6-Igf2 axis (Igf2dGGCT), resulted in down-regulation of Igf2 expression and a reduced proliferation rate. This was further validated using miR483 mimics and inhibitors. RNA-seq analysis revealed a significant enrichment of genes involved in the PI3K-Akt signaling pathway among genes down-regulated in miR483-/- cells, including Igf2 down-regulation. The opposite pattern was observed in Igf2dGGCT cells, where Igf2 is up-regulated. Our data suggest a positive feedback between miR483 and Igf2 promoter activity, strongly affecting how ZBED6 controls Igf2 expression in various cell types.
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Affiliation(s)
- Rakan Naboulsi
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23, Uppsala, Sweden
| | - Mårten Larsson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23, Uppsala, Sweden
| | - Leif Andersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23, Uppsala, Sweden.
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 750 07, Uppsala, Sweden.
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843, USA.
| | - Shady Younis
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23, Uppsala, Sweden.
- Department of Animal Breeding and Genetics, Ain Shams University, Shoubra El-Kheima, Cairo, 11241, Egypt.
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA, 94305, USA.
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Sato DX, Rafati N, Ring H, Younis S, Feng C, Blanco-Aguiar JA, Rubin CJ, Villafuerte R, Hallböök F, Carneiro M, Andersson L. Brain Transcriptomics of Wild and Domestic Rabbits Suggests That Changes in Dopamine Signaling and Ciliary Function Contributed to Evolution of Tameness. Genome Biol Evol 2021; 12:1918-1928. [PMID: 32835359 DOI: 10.1093/gbe/evaa158] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2020] [Indexed: 12/13/2022] Open
Abstract
Domestication has resulted in immense phenotypic changes in animals despite their relatively short evolutionary history. The European rabbit is one of the most recently domesticated animals, but exhibits distinct morphological, physiological, and behavioral differences from their wild conspecifics. A previous study revealed that sequence variants with striking allele frequency differences between wild and domestic rabbits were enriched in conserved noncoding regions, in the vicinity of genes involved in nervous system development. This suggests that a large proportion of the genetic changes targeted by selection during domestication might affect gene regulation. Here, we generated RNA-sequencing data for four brain regions (amygdala, hypothalamus, hippocampus, and parietal/temporal cortex) sampled at birth and revealed hundreds of differentially expressed genes (DEGs) between wild and domestic rabbits. DEGs in amygdala were significantly enriched for genes associated with dopaminergic function and all 12 DEGs in this category showed higher expression in domestic rabbits. DEGs in hippocampus were enriched for genes associated with ciliary function, all 21 genes in this category showed lower expression in domestic rabbits. These results indicate an important role of dopamine signaling and ciliary function in the evolution of tameness during rabbit domestication. Our study shows that gene expression in specific pathways has been profoundly altered during domestication, but that the majority of genes showing differential expression in this study have not been the direct targets of selection.
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Affiliation(s)
- Daiki X Sato
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan.,Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala Biomedical Centre, Sweden
| | - Nima Rafati
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala Biomedical Centre, Sweden.,Science for Life Laboratory, Uppsala University, National Bioinformatics Infrastructure Sweden (NBIS), Sweden
| | - Henrik Ring
- Department of Neuroscience, Uppsala University, Uppsala Biomedical Centre, Sweden
| | - Shady Younis
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala Biomedical Centre, Sweden
| | - Chungang Feng
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala Biomedical Centre, Sweden
| | - José A Blanco-Aguiar
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Instituto de Investigación en Recursos Cinegéticos, IREC (CSIC, UCLM, JCCM), Ciudad Real, Spain
| | - Carl-Johan Rubin
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala Biomedical Centre, Sweden
| | | | - Finn Hallböök
- Department of Neuroscience, Uppsala University, Uppsala Biomedical Centre, Sweden
| | - Miguel Carneiro
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Portugal
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala Biomedical Centre, Sweden.,Department of Veterinary Integrative Biosciences, Texas A&M University.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Nielsen A, Lundgaard K, Jacobsen K, Hansen K, Søltoft K, Sten L, Gullander L, Sibolt P, Calmels L, Andersson L, Geertsen P. PO-1988 Designing a radiation therapy technologist training program for online adaptive Radiation Therapy. Radiother Oncol 2021. [DOI: 10.1016/s0167-8140(21)08439-5] [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: 11/16/2022]
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Li J, Lee MO, Davis BW, Wu P, Hsieh Li SM, Chuong CM, Andersson L. The crest phenotype in domestic chicken is caused by a 197 bp duplication in the intron of HOXC10. G3 (Bethesda) 2021; 11:6062401. [PMID: 33704432 PMCID: PMC8022956 DOI: 10.1093/g3journal/jkaa048] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 11/01/2020] [Indexed: 11/12/2022]
Abstract
The Crest mutation in chicken shows incomplete dominance and causes a spectacular phenotype in which the small feathers normally present on the head are replaced by much larger feathers normally present only in dorsal skin. Using whole-genome sequencing, we show that the crest phenotype is caused by a 197 bp duplication of an evolutionarily conserved sequence located in the intron of HOXC10 on chromosome 33. A diagnostic test showed that the duplication was present in all 54 crested chickens representing eight breeds and absent from all 433 non-crested chickens representing 214 populations. The mutation causes ectopic expression of at least five closely linked HOXC genes, including HOXC10, in cranial skin of crested chickens. The result is consistent with the interpretation that the crest feathers are caused by an altered body region identity. The upregulated HOXC gene expression is expanded to skull tissue of Polish chickens showing a large crest often associated with cerebral hernia, but not in Silkie chickens characterized by a small crest, both homozygous for the duplication. Thus, the 197 bp duplication is required for the development of a large crest and susceptibility to cerebral hernia because only crested chicken show this malformation. However, this mutation is not sufficient to cause herniation because this malformation is not present in breeds with a small crest, like Silkie chickens.
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Affiliation(s)
- Jingyi Li
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA.,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, 430070 Wuhan, Hubei, China
| | - Mi-Ok Lee
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Ping Wu
- Department of Pathology, University of Southern California, Los Angeles, CA 90033, USA
| | - Shu-Man Hsieh Li
- Department of Pathology, University of Southern California, Los Angeles, CA 90033, USA.,Center for Craniofacial Molecular Biology, Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, USA.,Department of Biochemistry, National Defense Medical Center, Taipei 114, Taiwan
| | - Cheng-Ming Chuong
- Department of Pathology, University of Southern California, Los Angeles, CA 90033, USA
| | - Leif Andersson
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA.,Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden
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Wimalarathna AAAK, Herath EMUCK, Senarath NH, Fonseka MCN, Manathunga MMKM, Nawarathna LS, Andersson L. Introduction of an interactive tool (the Dental Trauma Guide) in the undergraduate dental teaching to manage traumatic dental injuries. Dent Traumatol 2021; 37:717-724. [PMID: 34120401 DOI: 10.1111/edt.12687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 11/02/2020] [Revised: 05/03/2021] [Accepted: 05/03/2021] [Indexed: 12/01/2022]
Abstract
BACKGROUND/AIMS Traumatic dental injuries (TDI) are complex problems where lack of proper care may result in serious complications. The need to improve the management of TDI is a frequently addressed concern. Methods of improvement in their diagnosis and management are continuously evolving. The interactive Internet tool, the Dental Trauma Guide (DTG), helps to simplify diagnostic and management dilemmas. However, it is not a freely available tool. The aim of the current study was to assess the knowledge and diagnostic skills of undergraduate dental students with access to the DTG compared with students without such access, in order to validate and promote this tool in dental education. MATERIALS AND METHODS Two groups of students were randomly selected where one group of final year dental undergraduate students were exposed to lectures, demonstrations, discussions and tutorials on the management of TDI according to the standard undergraduate curriculum in Sri Lanka. Another test group of 21 students were provided with access to DTG during their training in paediatric dentistry. At the end of the study period, students were assessed on their knowledge of TDI using MCQs (Multiple Choice Questions) and OSCEs (Objective Structured Clinical Examination), based on the DTG. RESULTS The students with access to the DTG were more knowledgeable in providing the correct answers to three out of the seven OSCE questions. Evaluation based on the MCQs did not reveal a significant difference (p = .913). However, users of the DTG showed a statistically significant difference with better overall knowledge based on their answers (p = .028). Following this period of evaluation, all of the students were provided with access to the DTG to supplement their learning experience. CONCLUSION The Dental Trauma Guide is a useful supplementary tool for undergraduate students to arrive at a correct diagnosis and treatment plan for TDI.
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Affiliation(s)
- A A A K Wimalarathna
- Department of Prosthetic Dentistry, Faculty of Dental Sciences, University of Peradeniya, Peradeniya, Sri Lanka
| | - E M U C K Herath
- Division of Paedodontics, Faculty of Dental Sciences, University of Peradeniya, Peradeniya, Sri Lanka
| | - N H Senarath
- Division of Paedodontics, Faculty of Dental Sciences, University of Peradeniya, Peradeniya, Sri Lanka
| | - M C N Fonseka
- Department of Restorative Dentistry, Faculty of Dental Sciences, University of Peradeniya, Peradeniya, Sri Lanka
| | - M M K M Manathunga
- Technical Officer, Faculty of Dental Sciences, University of Peradeniya, Peradeniya, Sri Lanka
| | - L S Nawarathna
- Department of Statistics & Computer Science, Faculty of Science, University of Peradeniya, Peradeniya, Sri Lanka
| | - L Andersson
- Oral & Maxillofacial Surgery, Faculty of Odontology, Malmö University, Malmo, Sweden
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Liu H, Chen C, Lv M, Liu N, Hu Y, Zhang H, Enbody ED, Gao Z, Andersson L, Wang W. A chromosome-level assembly of blunt snout bream (Megalobrama amblycephala) reveals an expansion of olfactory receptor genes in freshwater fish. Mol Biol Evol 2021; 38:4238-4251. [PMID: 34003267 PMCID: PMC8476165 DOI: 10.1093/molbev/msab152] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The number of olfactory receptor genes (ORs), which are responsible for detecting diverse odor molecules varies extensively among mammals as a result of frequent gene gains and losses that contribute to olfactory specialization. However, how OR expansions/contractions in fish are influenced by habitat and feeding habit and which OR subfamilies are important in each ecological niche is unknown. Here, we report a major OR expansion in a freshwater herbivorous fish, Megalobrama amblycephala, using a highly contiguous, chromosome-level assembly. We evaluate the possible contribution of OR expansion to habitat and feeding specialization by comparing the OR repertoire in 28 phylogenetically and ecologically diverse teleosts. In total, we analyzed > 4,000 ORs including 3,253 intact, 122 truncated, and 913 pseudogenes. The number of intact ORs is highly variable ranging from 20 to 279. We estimate that the most recent common ancestor of Osteichthyes had 62 intact ORs, which declined in most lineages except the freshwater Otophysa clade that has a substantial expansion in subfamily β and ε ORs. Across teleosts, we found a strong association between duplications of β and ε ORs and freshwater habitat. Nearly, all ORs were expressed in the olfactory epithelium (OE) in three tested fish species. Specifically, all the expanded β and ε ORs were highly expressed in OE of M. amblycephala. Together, we provide molecular and functional evidence for how OR repertoires in fish have undergone gain and loss with respect to ecological factors and highlight the role of β and ε OR in freshwater adaptation.
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Affiliation(s)
- Han Liu
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China.,Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education/Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, Wuhan, 430070, China
| | - Chunhai Chen
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Maolin Lv
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ning Liu
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yafei Hu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Hailin Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Erik D Enbody
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, SE75237, Sweden
| | - Zexia Gao
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China.,Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education/Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, Wuhan, 430070, China
| | - Leif Andersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, SE75237, Sweden.,Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, USA.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Weimin Wang
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
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Li J, Lee M, Davis BW, Lamichhaney S, Dorshorst BJ, Siegel PB, Andersson L. Mutations Upstream of the TBX5 and PITX1 Transcription Factor Genes Are Associated with Feathered Legs in the Domestic Chicken. Mol Biol Evol 2021; 37:2477-2486. [PMID: 32344431 PMCID: PMC7475036 DOI: 10.1093/molbev/msaa093] [Citation(s) in RCA: 12] [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] [Indexed: 12/12/2022] Open
Abstract
Feathered leg is a trait in domestic chickens that has undergone intense selection by fancy breeders. Previous studies have shown that two major loci controlling feathered leg are located on chromosomes 13 and 15. Here, we present genetic evidence for the identification of candidate causal mutations at these loci. This was accomplished by combining classical linkage mapping using an experimental cross segregating for feathered leg and high-resolution identical-by-descent mapping using whole-genome sequence data from 167 samples of chicken with or without feathered legs. The first predicted causal mutation is a single-base change located 25 kb upstream of the gene for the forelimb-specific transcription factor TBX5 on chromosome 15. The second is a 17.7-kb deletion located ∼200 kb upstream of the gene for the hindlimb-specific transcription factor PITX1 on chromosome 13. These mutations are predicted to activate TBX5 and repress PITX1 expression, respectively. The study reveals a remarkable convergence in the evolution of the feathered-leg phenotype in domestic chickens and domestic pigeons, as this phenotype is caused by noncoding mutations upstream of the same two genes. Furthermore, the PITX1 causal variants are large overlapping deletions, 17.7 kb in chicken and 44 kb in pigeons. The results of the present study are consistent with the previously proposed model for pigeon that feathered leg is caused by reduced PITX1 expression and ectopic expression of TBX5 in hindlimb buds resulting in a shift of limb identity from hindlimb to more forelimb-like identity.
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Affiliation(s)
- Jingyi Li
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX.,Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA
| | - MiOk Lee
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX
| | - Sangeet Lamichhaney
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Ben J Dorshorst
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA
| | - Paul B Siegel
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA
| | - Leif Andersson
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX.,Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Carneiro M, Vieillard J, Andrade P, Boucher S, Afonso S, Blanco-Aguiar JA, Santos N, Branco J, Esteves PJ, Ferrand N, Kullander K, Andersson L. A loss-of-function mutation in RORB disrupts saltatorial locomotion in rabbits. PLoS Genet 2021; 17:e1009429. [PMID: 33764968 PMCID: PMC7993613 DOI: 10.1371/journal.pgen.1009429] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 09/29/2020] [Accepted: 02/17/2021] [Indexed: 11/18/2022] Open
Abstract
Saltatorial locomotion is a type of hopping gait that in mammals can be found in rabbits, hares, kangaroos, and some species of rodents. The molecular mechanisms that control and fine-tune the formation of this type of gait are unknown. Here, we take advantage of one strain of domesticated rabbits, the sauteur d'Alfort, that exhibits an abnormal locomotion behavior defined by the loss of the typical jumping that characterizes wild-type rabbits. Strikingly, individuals from this strain frequently adopt a bipedal gait using their front legs. Using a combination of experimental crosses and whole genome sequencing, we show that a single locus containing the RAR related orphan receptor B gene (RORB) explains the atypical gait of these rabbits. We found that a splice-site mutation in an evolutionary conserved site of RORB results in several aberrant transcript isoforms incorporating intronic sequence. This mutation leads to a drastic reduction of RORB-positive neurons in the spinal cord, as well as defects in differentiation of populations of spinal cord interneurons. Our results show that RORB function is required for the performance of saltatorial locomotion in rabbits.
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Affiliation(s)
- Miguel Carneiro
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- * E-mail: (MC); (LA)
| | | | - Pedro Andrade
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Samuel Boucher
- Labovet Conseil (Réseau Cristal), Les Herbiers Cedex, France
| | - Sandra Afonso
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - José A. Blanco-Aguiar
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Nuno Santos
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - João Branco
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Pedro J. Esteves
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Nuno Ferrand
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- Department of Zoology, Faculty of Sciences, University of Johannesburg, Auckland, South Africa
| | - Klas Kullander
- Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Leif Andersson
- Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- * E-mail: (MC); (LA)
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Semenov GA, Linck E, Enbody ED, Harris RB, Khaydarov DR, Alström P, Andersson L, Taylor SA. Asymmetric introgression reveals the genetic architecture of a plumage trait. Nat Commun 2021; 12:1019. [PMID: 33589637 PMCID: PMC7884433 DOI: 10.1038/s41467-021-21340-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 06/28/2020] [Accepted: 01/20/2021] [Indexed: 01/04/2023] Open
Abstract
Genome-wide variation in introgression rates across hybrid zones offers a powerful opportunity for studying population differentiation. One poorly understood pattern of introgression is the geographic displacement of a trait implicated in lineage divergence from genome-wide population boundaries. While difficult to interpret, this pattern can facilitate the dissection of trait genetic architecture because traits become uncoupled from their ancestral genomic background. We studied an example of trait displacement generated by the introgression of head plumage coloration from personata to alba subspecies of the white wagtail. A previous study of their hybrid zone in Siberia revealed that the geographic transition in this sexual signal that mediates assortative mating was offset from other traits and genetic markers. Here we show that head plumage is associated with two small genetic regions. Despite having a simple genetic architecture, head plumage inheritance is consistent with partial dominance and epistasis, which could contribute to its asymmetric introgression. Hybrid zones are windows into the evolutionary process. Semenov et al. find that the head plumage differences between white wagtail subspecies have a simple genetic basis involving two small genetic regions, in which partially dominant and epistatic interactions help to explain how this sexual signal has become decoupled from other plumage traits.
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Affiliation(s)
- Georgy A Semenov
- Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA.
| | - Ethan Linck
- UNM Biology, University of New Mexico, Albuquerque, NM, Mexico
| | - Erik D Enbody
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | | | | | - Per Alström
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.,Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Scott A Taylor
- Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
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Abstract
The relative role of genetic adaptation and phenotypic plasticity is of fundamental importance in evolutionary ecology [M. J. West-Eberhard, Proc. Natl. Acad. Sci. U.S.A. 102 (suppl. 1), 6543-6549 (2005)]. European eels have a complex life cycle, including transitions between life stages across ecological conditions in the Sargasso Sea, where spawning occurs, and those in brackish and freshwater bodies from northern Europe to northern Africa. Whether continental eel populations consist of locally adapted and genetically distinct populations or comprise a single panmictic population has received conflicting support. Here we use whole-genome sequencing and show that European eels belong to one panmictic population. A complete lack of geographical genetic differentiation is demonstrated. We postulate that this is possible because the most critical life stages-spawning and embryonic development-take place under near-identical conditions in the Sargasso Sea. We further show that within-generation selection, which has recently been proposed as a mechanism for genetic adaptation in eels, can only marginally change allele frequencies between cohorts of eels from different geographic regions. Our results strongly indicate plasticity as the predominant mechanism for how eels respond to diverse environmental conditions during postlarval stages, ultimately solving a long-standing question for a classically enigmatic species.
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Affiliation(s)
- Erik D Enbody
- Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
| | - Mats E Pettersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
| | - C Grace Sprehn
- Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
| | - Stefan Palm
- Department of Aquatic Resources, Institute of Freshwater Research, Swedish University of Agricultural Sciences, 178 93 Drottningholm, Sweden
| | - Håkan Wickström
- Department of Aquatic Resources, Institute of Freshwater Research, Swedish University of Agricultural Sciences, 178 93 Drottningholm, Sweden
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden;
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
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Han F, Jamsandekar M, Pettersson ME, Su L, Fuentes-Pardo AP, Davis BW, Bekkevold D, Berg F, Casini M, Dahle G, Farrell ED, Folkvord A, Andersson L. Ecological adaptation in Atlantic herring is associated with large shifts in allele frequencies at hundreds of loci. eLife 2020; 9:e61076. [PMID: 33274714 PMCID: PMC7738190 DOI: 10.7554/elife.61076] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [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: 07/15/2020] [Accepted: 12/03/2020] [Indexed: 12/23/2022] Open
Abstract
Atlantic herring is widespread in North Atlantic and adjacent waters and is one of the most abundant vertebrates on earth. This species is well suited to explore genetic adaptation due to minute genetic differentiation at selectively neutral loci. Here, we report hundreds of loci underlying ecological adaptation to different geographic areas and spawning conditions. Four of these represent megabase inversions confirmed by long read sequencing. The genetic architecture underlying ecological adaptation in herring deviates from expectation under a classical infinitesimal model for complex traits because of large shifts in allele frequencies at hundreds of loci under selection.
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Affiliation(s)
- Fan Han
- Department of Medical Biochemistry and Microbiology, Uppsala UniversityUppsalaSweden
| | - Minal Jamsandekar
- Department of Veterinary Integrative Biosciences, Texas A&M UniversityCollege StationUnited States
| | - Mats E Pettersson
- Department of Medical Biochemistry and Microbiology, Uppsala UniversityUppsalaSweden
| | - Leyi Su
- Department of Medical Biochemistry and Microbiology, Uppsala UniversityUppsalaSweden
| | | | - Brian W Davis
- Department of Veterinary Integrative Biosciences, Texas A&M UniversityCollege StationUnited States
| | - Dorte Bekkevold
- National Institute of Aquatic Resources, Technical University of DenmarkSilkeborgDenmark
| | - Florian Berg
- Department of Biological Sciences, University of BergenBergenNorway
- Institute of Marine ResearchBergenNorway
| | - Michele Casini
- Department of Aquatic Resources, Institute of Marine Research, Swedish University of Agricultural SciencesLysekilSweden
- Department of Biological, Geological and Environmental Sciences, University of BolognaBolognaItaly
| | - Geir Dahle
- Institute of Marine ResearchBergenNorway
| | - Edward D Farrell
- School of Biology and Environmental Science, Science Centre West, University College DublinDublinIreland
| | - Arild Folkvord
- Department of Biological Sciences, University of BergenBergenNorway
- Institute of Marine ResearchBergenNorway
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala UniversityUppsalaSweden
- Department of Veterinary Integrative Biosciences, Texas A&M UniversityCollege StationUnited States
- Department of Animal Breeding and Genetics, Swedish University of Agricultural SciencesUppsalaSweden
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Gustafsson R, Eckhard U, Ye W, Enbody ED, Pettersson M, Jemth P, Andersson L, Selmer M. Structure and Characterization of Phosphoglucomutase 5 from Atlantic and Baltic Herring-An Inactive Enzyme with Intact Substrate Binding. Biomolecules 2020; 10:E1631. [PMID: 33287293 PMCID: PMC7761743 DOI: 10.3390/biom10121631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 11/08/2020] [Revised: 11/27/2020] [Accepted: 11/30/2020] [Indexed: 12/31/2022] Open
Abstract
Phosphoglucomutase 5 (PGM5) in humans is known as a structural muscle protein without enzymatic activity, but detailed understanding of its function is lacking. PGM5 belongs to the alpha-D-phosphohexomutase family and is closely related to the enzymatically active metabolic enzyme PGM1. In the Atlantic herring, Clupea harengus, PGM5 is one of the genes strongly associated with ecological adaptation to the brackish Baltic Sea. We here present the first crystal structures of PGM5, from the Atlantic and Baltic herring, differing by a single substitution Ala330Val. The structure of PGM5 is overall highly similar to structures of PGM1. The structure of the Baltic herring PGM5 in complex with the substrate glucose-1-phosphate shows conserved substrate binding and active site compared to human PGM1, but both PGM5 variants lack phosphoglucomutase activity under the tested conditions. Structure comparison and sequence analysis of PGM5 and PGM1 from fish and mammals suggest that the lacking enzymatic activity of PGM5 is related to differences in active-site loops that are important for flipping of the reaction intermediate. The Ala330Val substitution does not alter structure or biophysical properties of PGM5 but, due to its surface-exposed location, could affect interactions with protein-binding partners.
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Affiliation(s)
- Robert Gustafsson
- Department of Cell and Molecular Biology, Uppsala University, BMC, Box 596, SE-751 24 Uppsala, Sweden; (R.G.); (U.E.)
| | - Ulrich Eckhard
- Department of Cell and Molecular Biology, Uppsala University, BMC, Box 596, SE-751 24 Uppsala, Sweden; (R.G.); (U.E.)
| | - Weihua Ye
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Box 582, SE-751 23 Uppsala, Sweden; (W.Y.); (E.D.E.); (M.P.); (P.J.); (L.A.)
| | - Erik D. Enbody
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Box 582, SE-751 23 Uppsala, Sweden; (W.Y.); (E.D.E.); (M.P.); (P.J.); (L.A.)
| | - Mats Pettersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Box 582, SE-751 23 Uppsala, Sweden; (W.Y.); (E.D.E.); (M.P.); (P.J.); (L.A.)
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Box 582, SE-751 23 Uppsala, Sweden; (W.Y.); (E.D.E.); (M.P.); (P.J.); (L.A.)
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Box 582, SE-751 23 Uppsala, Sweden; (W.Y.); (E.D.E.); (M.P.); (P.J.); (L.A.)
- Department of Veterinary Integrative Biosciences, Texas A & M University, College Station, TX 77843, USA
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
| | - Maria Selmer
- Department of Cell and Molecular Biology, Uppsala University, BMC, Box 596, SE-751 24 Uppsala, Sweden; (R.G.); (U.E.)
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Sibolt P, Andersson L, Calmels L, Behrens C, Serup-Hansen E, Lindberg H, Mouritsen LS, Sjöström D, Geertsen P. PD-0308: First clinical experience of online adaptive radiotherapy driven by CBCT and artificial intelligence. Radiother Oncol 2020. [DOI: 10.1016/s0167-8140(21)00332-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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40
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Sibolt P, Andersson L, Calmels L, Sjostrom D, Behrens C, Lindberg H, Mouritsen L, Geertsen P. Results of a Pilot Study on Online Adaptive Radiotherapy of Bladder Cancer with Artificial Intelligence-driven Full Re-optimization on the Anatomy of the Day. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.2231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Calmels L, Andersson L, Sjöström D, Sjölin M, Sibolt P. PO-1483: Evaluation of an artificial intelligence driven planning system for online adaptive radiotherapy. Radiother Oncol 2020. [DOI: 10.1016/s0167-8140(21)01501-2] [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: 10/22/2022]
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Sibolt P, Bjelkengren U, Calmels L, Santurio G, Andersson L, Sjölin M, Sjöström D. PO-1415: Validating a commercial solution for calculation-based QA of AI-driven online adaptive radiotherapy. Radiother Oncol 2020. [DOI: 10.1016/s0167-8140(21)01433-x] [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: 11/26/2022]
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43
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Björnson E, Packard CJ, Adiels M, Andersson L, Matikainen N, Söderlund S, Kahri J, Hakkarainen A, Lundbom N, Lundbom J, Sihlbom C, Thorsell A, Zhou H, Taskinen MR, Borén J. Apolipoprotein B48 metabolism in chylomicrons and very low-density lipoproteins and its role in triglyceride transport in normo- and hypertriglyceridemic human subjects. J Intern Med 2020; 288:422-438. [PMID: 31846520 DOI: 10.1111/joim.13017] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND Renewed interest in triglyceride-rich lipoproteins as causative agents in cardiovascular disease mandates further exploration of the integrated metabolism of chylomicrons and very low-density lipoproteins (VLDL). METHODS Novel tracer techniques and an integrated multi-compartmental model were used to determine the kinetics of apoB48- and apoB100-containing particles in the chylomicron and VLDL density intervals in 15 subjects with a wide range of plasma triglyceride levels. RESULTS Following a fat-rich meal, apoB48 appeared in the chylomicron, VLDL1 and VLDL2 fractions in all subjects. Chylomicrons cleared rapidly from the circulation but apoB48-containing VLDL accumulated, and over the day were 3-fold higher in those with high versus low plasma triglyceride. ApoB48-containing particles were secreted directly into both the chylomicron and VLDL fractions at rates that were similar across the plasma triglyceride range studied. During fat absorption, whilst most triglyceride entered the circulation in chylomicrons, the majority of apoB48 particles were secreted into the VLDL density range. CONCLUSION The intestine secretes apoB48-containing particles not only as chylomicrons but also directly into the VLDL1 and VLDL2 density ranges both in the basal state and during dietary lipid absorption. Over the day, apoB48-containing particles appear to comprise about 20-25% of circulating VLDL and, especially in those with elevated triglycerides, form part of a slowly cleared 'remnant' particle population, thereby potentially increasing CHD risk. These findings provide a metabolic understanding of the potential consequences for increased CHD risk when slowed lipolysis leads to the accumulation of remnants, especially in individuals with hypertriglyceridemia.
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Affiliation(s)
- E Björnson
- Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, Sweden
| | - C J Packard
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - M Adiels
- Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, Sweden
| | - L Andersson
- Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, Sweden
| | - N Matikainen
- Research Programs Unit, Clinical and Molecular Metabolism, University of Helsinki, Helsinki, Finland.,Endocrinology, Abdominal Center, Helsinki University Hospital, Helsinki, Finland
| | - S Söderlund
- Research Programs Unit, Clinical and Molecular Metabolism, University of Helsinki, Helsinki, Finland.,Endocrinology, Abdominal Center, Helsinki University Hospital, Helsinki, Finland
| | - J Kahri
- Department of Internal Medicine and Rehabilitation, Helsinki University Hospital, Helsinki, Finland
| | - A Hakkarainen
- Radiology, HUS Medical Imaging Center, Helsinki University Hospital, University of Helsinki, Helsinki, Finland.,Department of Neuroscience and Biomedical Engineering, Aalto University School of Science, Espoo, Finland
| | - N Lundbom
- Radiology, HUS Medical Imaging Center, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - J Lundbom
- Radiology, HUS Medical Imaging Center, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - C Sihlbom
- Proteomics Facility, University of Gothenburg, Gothenburg, Sweden
| | - A Thorsell
- Proteomics Facility, University of Gothenburg, Gothenburg, Sweden
| | - H Zhou
- Merck Research Laboratories, Merck & Co. Inc., Kenilworth, NJ, USA
| | - M-R Taskinen
- Research Programs Unit, Clinical and Molecular Metabolism, University of Helsinki, Helsinki, Finland
| | - J Borén
- Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, Sweden.,Sahlgrenska University Hospital, Gothenburg, Sweden
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Younis S, Naboulsi R, Wang X, Cao X, Larsson M, Sargsyan E, Bergsten P, Welsh N, Andersson L. The importance of the ZBED6-IGF2 axis for metabolic regulation in mouse myoblast cells. FASEB J 2020; 34:10250-10266. [PMID: 32557799 DOI: 10.1096/fj.201901321r] [Citation(s) in RCA: 7] [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: 06/21/2019] [Revised: 05/12/2020] [Accepted: 05/19/2020] [Indexed: 12/13/2022]
Abstract
The transcription factor ZBED6 acts as a repressor of Igf2 and affects directly or indirectly the transcriptional regulation of thousands of genes. Here, we use gene editing in mouse C2C12 myoblasts and show that ZBED6 regulates Igf2 exclusively through its binding site 5'-GGCTCG-3' in intron 1 of Igf2. Deletion of this motif (Igf2ΔGGCT ) or complete ablation of Zbed6 leads to ~20-fold upregulation of the IGF2 protein. Quantitative proteomics revealed an activation of Ras signaling pathway in both Zbed6-/- and Igf2ΔGGCT myoblasts, and a significant enrichment of mitochondrial membrane proteins among proteins showing altered expression in Zbed6-/- myoblasts. Both Zbed6-/- and Igf2ΔGGCT myoblasts showed a faster growth rate and developed myotube hypertrophy. These cells exhibited an increased O2 consumption rate, due to IGF2 upregulation. Transcriptome analysis revealed ~30% overlap between differentially expressed genes in Zbed6-/- and Igf2ΔGGCT myotubes, with an enrichment of upregulated genes involved in muscle development. In contrast, ZBED6-overexpression in myoblasts led to cell apoptosis, cell cycle arrest, reduced mitochondrial activities, and ceased myoblast differentiation. The similarities in growth and differentiation phenotypes observed in Zbed6-/- and Igf2ΔGGCT myoblasts demonstrates that ZBED6 affects mitochondrial activity and myogenesis largely through its regulation of IGF2 expression. This study adds new insights how the ZBED6-Igf2 axis affects muscle metabolism.
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Affiliation(s)
- Shady Younis
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Rakan Naboulsi
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Xuan Wang
- Science for Life Laboratory, Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Xiaofang Cao
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Mårten Larsson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Ernest Sargsyan
- Science for Life Laboratory, Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Peter Bergsten
- Science for Life Laboratory, Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Nils Welsh
- Science for Life Laboratory, Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Leif Andersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
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46
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Lamichhaney S, Han F, Webster MT, Grant BR, Grant PR, Andersson L. Female-biased gene flow between two species of Darwin’s finches. Nat Ecol Evol 2020; 4:979-986. [DOI: 10.1038/s41559-020-1183-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 03/20/2020] [Indexed: 01/29/2023]
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Pettersson ME, Rochus CM, Han F, Chen J, Hill J, Wallerman O, Fan G, Hong X, Xu Q, Zhang H, Liu S, Liu X, Haggerty L, Hunt T, Martin FJ, Flicek P, Bunikis I, Folkvord A, Andersson L. A chromosome-level assembly of the Atlantic herring genome-detection of a supergene and other signals of selection. Genome Res 2019; 29:1919-1928. [PMID: 31649060 PMCID: PMC6836730 DOI: 10.1101/gr.253435.119] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [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: 06/11/2019] [Accepted: 09/27/2019] [Indexed: 01/27/2023]
Abstract
The Atlantic herring is a model species for exploring the genetic basis for ecological adaptation, due to its huge population size and extremely low genetic differentiation at selectively neutral loci. However, such studies have so far been hampered because of a highly fragmented genome assembly. Here, we deliver a chromosome-level genome assembly based on a hybrid approach combining a de novo Pacific Biosciences (PacBio) assembly with Hi-C-supported scaffolding. The assembly comprises 26 autosomes with sizes ranging from 12.4 to 33.1 Mb and a total size, in chromosomes, of 726 Mb, which has been corroborated by a high-resolution linkage map. A comparison between the herring genome assembly with other high-quality assemblies from bony fishes revealed few inter-chromosomal but frequent intra-chromosomal rearrangements. The improved assembly facilitates analysis of previously intractable large-scale structural variation, allowing, for example, the detection of a 7.8-Mb inversion on Chromosome 12 underlying ecological adaptation. This supergene shows strong genetic differentiation between populations. The chromosome-based assembly also markedly improves the interpretation of previously detected signals of selection, allowing us to reveal hundreds of independent loci associated with ecological adaptation.
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Affiliation(s)
- Mats E Pettersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
| | - Christina M Rochus
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
| | - Fan Han
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
| | - Junfeng Chen
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
| | - Jason Hill
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
| | - Ola Wallerman
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao 999078, China
| | - Xiaoning Hong
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | - Qiwu Xu
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - He Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Shanshan Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Xin Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Leanne Haggerty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Toby Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Ignas Bunikis
- Science for Life Laboratory Uppsala, Department of Immunology, Genetics and Pathology, Uppsala University, SE-75123 Uppsala, Sweden
| | - Arild Folkvord
- Department of Biological Sciences, University of Bergen, 5020 Bergen, Norway.,Institute of Marine Research, 5018 Bergen, Norway
| | - Leif Andersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden.,Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA
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Kurland S, Wheat CW, de la Paz Celorio Mancera M, Kutschera VE, Hill J, Andersson A, Rubin C, Andersson L, Ryman N, Laikre L. Exploring a Pool-seq-only approach for gaining population genomic insights in nonmodel species. Ecol Evol 2019; 9:11448-11463. [PMID: 31641485 PMCID: PMC6802065 DOI: 10.1002/ece3.5646] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 12/12/2022] Open
Abstract
Developing genomic insights is challenging in nonmodel species for which resources are often scarce and prohibitively costly. Here, we explore the potential of a recently established approach using Pool-seq data to generate a de novo genome assembly for mining exons, upon which Pool-seq data are used to estimate population divergence and diversity. We do this for two pairs of sympatric populations of brown trout (Salmo trutta): one naturally sympatric set of populations and another pair of populations introduced to a common environment. We validate our approach by comparing the results to those from markers previously used to describe the populations (allozymes and individual-based single nucleotide polymorphisms [SNPs]) and from mapping the Pool-seq data to a reference genome of the closely related Atlantic salmon (Salmo salar). We find that genomic differentiation (F ST) between the two introduced populations exceeds that of the naturally sympatric populations (F ST = 0.13 and 0.03 between the introduced and the naturally sympatric populations, respectively), in concordance with estimates from the previously used SNPs. The same level of population divergence is found for the two genome assemblies, but estimates of average nucleotide diversity differ ( π ¯ ≈ 0.002 and π ¯ ≈ 0.001 when mapping to S. trutta and S. salar, respectively), although the relationships between population values are largely consistent. This discrepancy might be attributed to biases when mapping to a haploid condensed assembly made of highly fragmented read data compared to using a high-quality reference assembly from a divergent species. We conclude that the Pool-seq-only approach can be suitable for detecting and quantifying genome-wide population differentiation, and for comparing genomic diversity in populations of nonmodel species where reference genomes are lacking.
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Affiliation(s)
- Sara Kurland
- Division of Population GeneticsDepartment of ZoologyStockholm UniversityStockholmSweden
| | - Christopher W. Wheat
- Division of Population GeneticsDepartment of ZoologyStockholm UniversityStockholmSweden
| | | | - Verena E. Kutschera
- Science for Life Laboratory and Department for Biochemistry and BiophysicsStockholm UniversitySolnaSweden
| | - Jason Hill
- Division of Population GeneticsDepartment of ZoologyStockholm UniversityStockholmSweden
| | - Anastasia Andersson
- Division of Population GeneticsDepartment of ZoologyStockholm UniversityStockholmSweden
| | - Carl‐Johan Rubin
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
| | - Leif Andersson
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
- Department of Animal Breeding and GeneticsSwedish University of Agricultural SciencesUppsalaSweden
- Department of Veterinary Integrative BiosciencesTexas A&M UniversityCollege StationTXUSA
| | - Nils Ryman
- Division of Population GeneticsDepartment of ZoologyStockholm UniversityStockholmSweden
| | - Linda Laikre
- Division of Population GeneticsDepartment of ZoologyStockholm UniversityStockholmSweden
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Li J, Davis BW, Jern P, Dorshorst BJ, Siegel PB, Andersson L. Characterization of the endogenous retrovirus insertion in CYP19A1 associated with henny feathering in chicken. Mob DNA 2019; 10:38. [PMID: 31467598 PMCID: PMC6712707 DOI: 10.1186/s13100-019-0181-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 05/20/2019] [Accepted: 08/14/2019] [Indexed: 11/10/2022] Open
Abstract
Background Henny feathering in chickens is determined by a dominant mutation that transforms male-specific plumage to female-like plumage. Previous studies indicated that this phenotype is caused by ectopic expression in skin of CYP19A1 encoding aromatase that converts androgens to estrogen and thereby inhibits the development of male-specific plumage. A long terminal repeat (LTR) from an uncharacterized endogenous retrovirus (ERV) insertion was found in an isoform of the CYP19A1 transcript from henny feathering chicken. However, the complete sequence and the genomic position of the insertion were not determined. Results We used publicly available whole genome sequence data to determine the flanking sequences of the ERV, and then PCR amplified the entire insertion and sequenced it using Nanopore long reads and Sanger sequencing. The 7524 bp insertion contains an intact endogenous retrovirus that was not found in chickens representing 31 different breeds not showing henny feathering or in samples of the ancestral red junglefowl. The sequence shows over 99% sequence identity to the avian leukosis virus ev-1 and ev-21 strains, suggesting a recent integration. The ERV 3’LTR, containing a powerful transcriptional enhancer and core promoter with TATA box together with binding sites for EFIII and Ig/EBP inside the CYP19A1 5′ untranslated region, was detected partially in an aromatase transcript, which present a plausible explanation for ectopic expression of aromatase in non-ovarian tissues underlying the henny feathering phenotype. Conclusions We demonstrate that the henny feathering allele harbors an insertion of an intact avian leukosis virus at the 5’end of CYP19A1. The presence of this ERV showed complete concordance with the henny feathering phenotype both within a pedigree segregating for this phenotype and across breeds. Electronic supplementary material The online version of this article (10.1186/s13100-019-0181-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jingyi Li
- 1Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Brian W Davis
- 1Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Patric Jern
- 2Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden
| | - Ben J Dorshorst
- 4Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, 24061 USA
| | - Paul B Siegel
- 4Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, 24061 USA
| | - Leif Andersson
- 1Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843 USA.,2Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden.,3Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-7507 Uppsala, Sweden
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McCoy AM, Beeson SK, Rubin CJ, Andersson L, Caputo P, Lykkjen S, Moore A, Piercy RJ, Mickelson JR, McCue ME. Identification and validation of genetic variants predictive of gait in standardbred horses. PLoS Genet 2019; 15:e1008146. [PMID: 31136578 PMCID: PMC6555539 DOI: 10.1371/journal.pgen.1008146] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 04/30/2018] [Revised: 06/07/2019] [Accepted: 04/17/2019] [Indexed: 12/30/2022] Open
Abstract
Several horse breeds have been specifically selected for the ability to exhibit alternative patterns of locomotion, or gaits. A premature stop codon in the gene DMRT3 is permissive for “gaitedness” across breeds. However, this mutation is nearly fixed in both American Standardbred trotters and pacers, which perform a diagonal and lateral gait, respectively, during harness racing. This suggests that modifying alleles must influence the preferred gait at racing speeds in these populations. A genome-wide association analysis for the ability to pace was performed in 542 Standardbred horses (n = 176 pacers, n = 366 trotters) with genotype data imputed to ~74,000 single nucleotide polymorphisms (SNPs). Nineteen SNPs on nine chromosomes (ECA1, 2, 6, 9, 17, 19, 23, 25, 31) reached genome-wide significance (p < 1.44 x 10−6). Variant discovery in regions of interest was carried out via whole-genome sequencing. A set of 303 variants from 22 chromosomes with putative modifying effects on gait was genotyped in 659 Standardbreds (n = 231 pacers, n = 428 trotters) using a high-throughput assay. Random forest classification analysis resulted in an out-of-box error rate of 0.61%. A conditional inference tree algorithm containing seven SNPs predicted status as a pacer or trotter with 99.1% accuracy and subsequently performed with 99.4% accuracy in an independently sampled population of 166 Standardbreds (n = 83 pacers, n = 83 trotters). This highly accurate algorithm could be used by owners/trainers to identify Standardbred horses with the potential to race as pacers or as trotters, according to the genotype identified, prior to initiating training and would enable fine-tuning of breeding programs with designed matings. Additional work is needed to determine both the algorithm’s utility in other gaited breeds and whether any of the predictive SNPs play a physiologically functional role in the tendency to pace or tag true functional alleles. Certain horse breeds have been developed over generations specifically for the ability to perform alternative patterns of movement, or gaits. Current understanding of the genetic basis for these gaits is limited to one known mutation apparently necessary, but not sufficient, for explaining variability in “gaitedness.” The Standardbred breed includes two distinct groups, trotters, which exhibit a two-beat gait in which the opposite forelimb and hind limb move together, and pacers, which exhibit an alternative two-beat gait where the legs on the same side of the body move together. Our long-term objective is to identify variants underlying the ability of certain Standardbreds to pace. In this study, we were able to identify several regions of the genome highly associated with pacing and, within these regions, a number of specific highly associated variants. Although the biological function of these variants has yet to be determined, we developed a model based on seven variants that was > 99% accurate in predicting whether an individual was a pacer or a trotter in two independent populations. This predictive model can be used by horse owners to make breeding and training decisions related to this economically important trait, and by scientists interested in understanding the biology of coordinated gait development.
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Affiliation(s)
- Annette M McCoy
- Department of Veterinary Clinical Medicine, University of Illinois, Urbana, Illinois, United States of America
| | - Samantha K Beeson
- Veterinary Population Medicine Department, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Carl-Johan Rubin
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, United States of America
| | - Paul Caputo
- Paul Caputo, DVM, Pompano Beach, Florida, United States of America
| | - Sigrid Lykkjen
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Alison Moore
- Moore Equine Services, Cambridge, Ontario, Canada
| | - Richard J Piercy
- Department of Clinical Sciences and Services, Royal Veterinary College, London, United Kingdom
| | - James R Mickelson
- Veterinary and Biomedical Sciences Department, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Molly E McCue
- Veterinary Population Medicine Department, University of Minnesota, St. Paul, Minnesota, United States of America
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