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Alexandre NM, Cameron AC, Tian D, Chatla K, Kolora SRR, Whiteman NK, Turner TF, Reinthal PN. Chromosome-level reference genomes of two imperiled desert fishes: spikedace (Meda fulgida) and loach minnow (Tiaroga cobitis). G3 (BETHESDA, MD.) 2023; 13:jkad157. [PMID: 37466215 PMCID: PMC10542311 DOI: 10.1093/g3journal/jkad157] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/21/2023] [Accepted: 06/28/2023] [Indexed: 07/20/2023]
Abstract
North American minnows (Cypriniformes: Leuciscidae) comprise a diverse taxonomic group, but many members, particularly those inhabiting deserts, face elevated extinction risks. Despite conservation concerns, leuciscids remain under sampled for reference assemblies relative to other groups of freshwater fishes. Here, we present 2 chromosome-scale reference genome assemblies spikedace (Meda fulgida) and loach minnow (Tiaroga cobitis) using PacBio, Illumina and Omni-C technologies. The complete assembly for spikedace was 882.1 Mb in total length comprised of 83 scaffolds with N50 = 34.8 Mb, L50 = 11, N75 = 32.3 Mb, and L75 = 18. The complete assembly for loach minnow was 1.3 Gb in total length comprised of 550 scaffolds with N50 = 48.6 Mb, L50 = 13, N75 = 42.3 Mb, and L75 = 20. Completeness assessed via Benchmarking Universal Single-Copy Orthologues (BUSCO) metrics using the Actinopterygii BUSCO database showed ∼97% for spikedace and ∼98% for loach minnow of complete BUSCO proportions. Annotation revealed approximately 32.58 and 29.04% of spikedace and loach minnow total genome lengths to be comprised of protein-coding genes, respectively. Comparative genomic analyses of these endangered and co-distributed fishes revealed widespread structural variants, gene family expansions, and evidence of positive selection in both genomes.
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Affiliation(s)
- Nicolas M Alexandre
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, Berkeley, CA 94720, USA
| | - Alexander C Cameron
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - David Tian
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, Berkeley, CA 94720, USA
| | - Kamalakar Chatla
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, Berkeley, CA 94720, USA
| | - Sree R R Kolora
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, Berkeley, CA 94720, USA
| | - Noah K Whiteman
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, Berkeley, CA 94720, USA
| | - Thomas F Turner
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Peter N Reinthal
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
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2
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Otero-Tarrazón A, Perelló-Amorós M, Jorge-Pedraza V, Moshayedi F, Sánchez-Moya A, García-Pérez I, Fernández-Borràs J, García de la serrana D, Navarro I, Blasco J, Capilla E, Gutierrez J. Muscle regeneration in gilthead sea bream: Implications of endocrine and local regulatory factors and the crosstalk with bone. Front Endocrinol (Lausanne) 2023; 14:1101356. [PMID: 36755925 PMCID: PMC9899866 DOI: 10.3389/fendo.2023.1101356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/03/2023] [Indexed: 01/24/2023] Open
Abstract
Fish muscle regeneration is still a poorly known process. In the present study, an injury was done into the left anterior epaxial skeletal muscle of seventy 15 g gilthead sea bream (Sparus aurata) juveniles to evaluate at days 0, 1, 2, 4, 8, 16 and 30 post-wound, the expression of several muscle genes. Moreover, transcripts' expression in the bone (uninjured tissue) was also analyzed. Histology of the muscle showed the presence of dead tissue the first day after injury and how the damaged fibers were removed and replaced by new muscle fibers by day 16 that kept growing up to day 30. Gene expression results showed in muscle an early upregulation of igf-2 and a downregulation of ghr-1 and igf-1. Proteolytic systems expression increased with capn2 and ctsl peaking at 1 and 2 days post-injury, respectively and mafbx at day 8. A pattern of expression that fitted well with active myogenesis progression 16 days after the injury was then observed, with the recovery of igf-1, pax7, cmet, and cav1 expression; and later on, that of cav3 as well. Furthermore, the first days post-injury, the cytokines il-6 and il-15 were also upregulated confirming the tissue inflammation, while tnfα was only upregulated at days 16 and 30 to induce satellite cells recruitment; overall suggesting a possible role for these molecules as myokines. The results of the bone transcripts showed an upregulation first, of bmp2 and ctsk at days 1 and 2, respectively; then, ogn1 and ocn peaked at day 4 in parallel to mstn2 downregulation, and runx2 and ogn2 increased after 8 days of muscle injury, suggesting a possible tissue crosstalk during the regenerative process. Overall, the present model allows studying the sequential involvement of different regulatory molecules during muscle regeneration, as well as the potential relationship between muscle and other tissues such as bone to control musculoskeletal development and growth, pointing out an interesting new line of research in this group of vertebrates.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Joaquin Gutierrez
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain
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Kubra K, Gaddu GK, Liongue C, Heidary S, Ward AC, Dhillon AS, Basheer F. Phylogenetic and Expression Analysis of Fos Transcription Factors in Zebrafish. Int J Mol Sci 2022; 23:ijms231710098. [PMID: 36077499 PMCID: PMC9456341 DOI: 10.3390/ijms231710098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 08/28/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
Members of the FOS protein family regulate gene expression responses to a multitude of extracellular signals and are dysregulated in several pathological states. Whilst mouse genetic models have provided key insights into the tissue-specific functions of these proteins in vivo, little is known about their roles during early vertebrate embryonic development. This study examined the potential of using zebrafish as a model for such studies and, more broadly, for investigating the mechanisms regulating the functions of Fos proteins in vivo. Through phylogenetic and sequence analysis, we identified six zebrafish FOS orthologues, fosaa, fosab, fosb, fosl1a, fosl1b, and fosl2, which show high conservation in key regulatory domains and post-translational modification sites compared to their equivalent human proteins. During embryogenesis, zebrafish fos genes exhibit both overlapping and distinct spatiotemporal patterns of expression in specific cell types and tissues. Most fos genes are also expressed in a variety of adult zebrafish tissues. As in humans, we also found that expression of zebrafish FOS orthologs is induced by oncogenic BRAF-ERK signalling in zebrafish melanomas. These findings suggest that zebrafish represent an alternate model to mice for investigating the regulation and functions of Fos proteins in vertebrate embryonic and adult tissues, and cancer.
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Affiliation(s)
- Khadizatul Kubra
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia
| | - Gurveer K. Gaddu
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia
| | - Clifford Liongue
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia
- Institute of Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC 3216, Australia
| | - Somayyeh Heidary
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia
| | - Alister C. Ward
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia
- Institute of Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC 3216, Australia
| | - Amardeep S. Dhillon
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia
- Institute of Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC 3216, Australia
- Olivia Newton-John Cancer Research Institute, Melbourne, VIC 3084, Australia
- School of Cancer Medicine, LaTrobe University, Melbourne, VIC 3086, Australia
- Correspondence: (A.S.D.); (F.B.)
| | - Faiza Basheer
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia
- Institute of Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC 3216, Australia
- Correspondence: (A.S.D.); (F.B.)
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Midkine-a functions as a universal regulator of proliferation during epimorphic regeneration in adult zebrafish. PLoS One 2020; 15:e0232308. [PMID: 32530962 PMCID: PMC7292404 DOI: 10.1371/journal.pone.0232308] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 05/28/2020] [Indexed: 12/20/2022] Open
Abstract
Zebrafish have the ability to regenerate damaged cells and tissues by activating quiescent stem and progenitor cells or reprogramming differentiated cells into regeneration-competent precursors. Proliferation among the cells that will functionally restore injured tissues is a fundamental biological process underlying regeneration. Midkine-a is a cytokine growth factor, whose expression is strongly induced by injury in a variety of tissues across a range of vertebrate classes. Using a zebrafish Midkine-a loss of function mutant, we evaluated regeneration of caudal fin, extraocular muscle and retinal neurons to investigate the function of Midkine-a during epimorphic regeneration. In wildtype zebrafish, injury among these tissues induces robust proliferation and rapid regeneration. In Midkine-a mutants, the initial proliferation in each of these tissues is significantly diminished or absent. Regeneration of the caudal fin and extraocular muscle is delayed; regeneration of the retina is nearly completely absent. These data demonstrate that Midkine-a is universally required in the signaling pathways that convert tissue injury into the initial burst of cell proliferation. Further, these data highlight differences in the molecular mechanisms that regulate epimorphic regeneration in zebrafish.
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Tingle CF, Magnuson B, Zhao Y, Heisel CJ, Kish PE, Kahana A. Paradoxical Changes Underscore Epigenetic Reprogramming During Adult Zebrafish Extraocular Muscle Regeneration. Invest Ophthalmol Vis Sci 2020; 60:4991-4999. [PMID: 31794598 PMCID: PMC6890397 DOI: 10.1167/iovs.19-27556] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Purpose Genomic reprogramming and cellular dedifferentiation are critical to the success of de novo tissue regeneration in lower vertebrates such as zebrafish and axolotl. In tissue regeneration following injury or disease, differentiated cells must retain lineage while assuming a progenitor-like identity in order to repopulate the damaged tissue. Understanding the epigenetic regulation of programmed cellular dedifferentiation provides unique insights into the biology of stem cells and cancer and may lead to novel approaches for treating human degenerative conditions. Methods Using a zebrafish in vivo model of adult muscle regeneration, we utilized chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq) to characterize early changes in epigenetic signals, focusing on three well-studied histone modifications-histone H3 trimethylated at lysine 4 (H3K4me3), and histone H3 trimethylated or acetylated at lysine 27 (H3K27me3 and H3K27Ac, respectively). Results We discovered that zebrafish myocytes undergo a global, rapid, and transient program to drive genomic remodeling. The timing of these epigenetic changes suggests that genomic reprogramming itself represents a distinct sequence of events, with predetermined checkpoints, to generate cells capable of de novo regeneration. Importantly, we uncovered subsets of genes that maintain epigenetic marks paradoxical to changes in expression, underscoring the complexity of epigenetic reprogramming. Conclusions Within our model, histone modifications previously associated with gene expression act for the most part as expected, with exceptions suggesting that zebrafish chromatin maintains an easily editable state with a number of genes paradoxically marked for transcriptional activity despite downregulation.
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Affiliation(s)
- Christina F Tingle
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan, United States
| | - Brian Magnuson
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, United States.,Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States
| | - Yi Zhao
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan, United States
| | - Curtis J Heisel
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan, United States.,University of Michigan Medical School, Ann Arbor, Michigan, United States
| | - Phillip E Kish
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan, United States
| | - Alon Kahana
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan, United States.,Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, United States
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Paatero I, Veikkolainen V, Mäenpää M, Schmelzer E, Belting HG, Pelliniemi LJ, Elenius K. ErbB4 tyrosine kinase inhibition impairs neuromuscular development in zebrafish embryos. Mol Biol Cell 2018; 30:209-218. [PMID: 30462579 PMCID: PMC6589560 DOI: 10.1091/mbc.e18-07-0460] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Tyrosine kinase inhibitors are widely used in the clinic, but limited information is available about their toxicity in developing organisms. Here, we tested the effect of tyrosine kinase inhibitors targeting the ErbB receptors for their effects on developing zebrafish (Danio rerio) embryos. Embryos treated with wide-spectrum pan-ErbB inhibitors or erbb4a-targeting antisense oligonucleotides demonstrated reduced locomotion, reduced diameter of skeletal muscle fibers, and reduced expression of muscle-specific genes, as well as reduced motoneuron length. The phenotypes in the skeletal muscle, as well as the defect in motility, were rescued both by microinjection of human ERBB4 mRNA and by transposon-mediated muscle-specific ERBB4 overexpression. The role of ErbB4 in regulating motility was further controlled by targeted mutation of the endogenous erbb4a locus in the zebrafish genome by CRISPR/Cas9. These observations demonstrate a potential for the ErbB tyrosine kinase inhibitors to induce neuromuscular toxicity in a developing organism via a mechanism involving inhibition of ErbB4 function.
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Affiliation(s)
- Ilkka Paatero
- Institute of Biomedicine, University of Turku, FIN-20520 Turku, Finland.,Medicity Research Laboratory, University of Turku, FIN-20520 Turku, Finland.,Laboratory of Animal Physiology, Department of Biology, University of Turku, FIN-20520 Turku, Finland.,Biozentrum der Universität Basel, CH-4056 Basel, Switzerland.,Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FIN-20520 Turku, Finland
| | - Ville Veikkolainen
- Institute of Biomedicine, University of Turku, FIN-20520 Turku, Finland.,Medicity Research Laboratory, University of Turku, FIN-20520 Turku, Finland
| | - Matias Mäenpää
- Institute of Biomedicine, University of Turku, FIN-20520 Turku, Finland
| | | | | | | | - Klaus Elenius
- Institute of Biomedicine, University of Turku, FIN-20520 Turku, Finland.,Medicity Research Laboratory, University of Turku, FIN-20520 Turku, Finland.,Department of Oncology, University of Turku, FIN-20520 Turku, Finland
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7
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Saera-Vila A, Louie KW, Sha C, Kelly RM, Kish PE, Kahana A. Extraocular muscle regeneration in zebrafish requires late signals from Insulin-like growth factors. PLoS One 2018; 13:e0192214. [PMID: 29415074 PMCID: PMC5802911 DOI: 10.1371/journal.pone.0192214] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 01/19/2018] [Indexed: 12/22/2022] Open
Abstract
Insulin-like growth factors (Igfs) are key regulators of key biological processes such as embryonic development, growth, and tissue repair and regeneration. The role of Igf in myogenesis is well documented and, in zebrafish, promotes fin and heart regeneration. However, the mechanism of action of Igf in muscle repair and regeneration is not well understood. Using adult zebrafish extraocular muscle (EOM) regeneration as an experimental model, we show that Igf1 receptor blockage using either chemical inhibitors (BMS754807 and NVP-AEW541) or translation-blocking morpholino oligonucleotides (MOs) reduced EOM regeneration. Zebrafish EOMs regeneration depends on myocyte dedifferentiation, which is driven by early epigenetic reprogramming and requires autophagy activation and cell cycle reentry. Inhibition of Igf signaling had no effect on either autophagy activation or cell proliferation, indicating that Igf signaling was not involved in the early reprogramming steps of regeneration. Instead, blocking Igf signaling produced hypercellularity of regenerating EOMs and diminished myosin expression, resulting in lack of mature differentiated muscle fibers even many days after injury, indicating that Igf was involved in late re-differentiation steps. Although it is considered the main mediator of myogenic Igf actions, Akt activation decreased in regenerating EOMs, suggesting that alternative signaling pathways mediate Igf activity in muscle regeneration. In conclusion, Igf signaling is critical for re-differentiation of reprogrammed myoblasts during late steps of zebrafish EOM regeneration, suggesting a regulatory mechanism for determining regenerated muscle size and timing of differentiation, and a potential target for regenerative therapy.
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Affiliation(s)
- Alfonso Saera-Vila
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Ke’ale W. Louie
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Biologic and Materials Sciences, School of Dentistry, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Cuilee Sha
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Ryan M. Kelly
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Phillip E. Kish
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Alon Kahana
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan, United States of America
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Abstract
Zebrafish extraocular muscles regenerate after severe injury. Injured myocytes dedifferentiate to a mesenchymal progenitor state and reenter the cell cycle to proliferate, migrate, and redifferentiate into functional muscles. A dedifferentiation process that begins with a multinucleated syncytial myofiber filled with sarcomeres and ends with proliferating mononucleated myoblasts must include significant remodeling of the protein machinery and organelle content of the cell. It turns out that autophagy plays a key role early in this process, to degrade the sarcomeres as well as the excess nuclei of the syncytial multinucleated myofibers. Because of the robustness of the zebrafish reprogramming process, and its relative synchrony, it can serve as a useful in vivo model for studying the biology of autophagy. In this chapter, we describe the surgical muscle injury model as well as the experimental protocols for assessing and manipulating autophagy activation.
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