1
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Poss KD, Tanaka EM. Hallmarks of regeneration. Cell Stem Cell 2024; 31:1244-1261. [PMID: 39163854 PMCID: PMC11410156 DOI: 10.1016/j.stem.2024.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/12/2024] [Accepted: 07/24/2024] [Indexed: 08/22/2024]
Abstract
Regeneration is a heroic biological process that restores tissue architecture and function in the face of day-to-day cell loss or the aftershock of injury. Capacities and mechanisms for regeneration can vary widely among species, organs, and injury contexts. Here, we describe "hallmarks" of regeneration found in diverse settings of the animal kingdom, including activation of a cell source, initiation of regenerative programs in the source, interplay with supporting cell types, and control of tissue size and function. We discuss these hallmarks with an eye toward major challenges and applications of regenerative biology.
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Affiliation(s)
- Kenneth D Poss
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA.
| | - Elly M Tanaka
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria.
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2
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Kawaguchi A, Wang J, Knapp D, Murawala P, Nowoshilow S, Masselink W, Taniguchi-Sugiura Y, Fei JF, Tanaka EM. A chromatin code for limb segment identity in axolotl limb regeneration. Dev Cell 2024; 59:2239-2253.e9. [PMID: 38788714 DOI: 10.1016/j.devcel.2024.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 07/25/2023] [Accepted: 05/03/2024] [Indexed: 05/26/2024]
Abstract
The salamander limb correctly regenerates missing limb segments because connective tissue cells have segment-specific identities, termed "positional information". How positional information is molecularly encoded at the chromatin level has been unknown. Here, we performed genome-wide chromatin profiling in mature and regenerating axolotl limb connective tissue cells. We find segment-specific levels of histone H3K27me3 as the major positional mark, especially at limb homeoprotein gene loci but not their upstream regulators, constituting an intrinsic segment information code. During regeneration, regeneration-specific regulatory elements became active prior to the re-appearance of developmental regulatory elements. In the hand, the permissive chromatin state of the homeoprotein gene HoxA13 engages with the regeneration program bypassing the upper limb program. Comparison of regeneration regulatory elements with those found in other regenerative animals identified a core shared set of transcription factors, supporting an ancient, conserved regeneration program.
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Affiliation(s)
- Akane Kawaguchi
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Jingkui Wang
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Dunja Knapp
- DFG Research Center for Regenerative Therapies, Technische Universität Dresden, 01307 Dresden, Germany
| | - Prayag Murawala
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria; DFG Research Center for Regenerative Therapies, Technische Universität Dresden, 01307 Dresden, Germany
| | - Sergej Nowoshilow
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria; DFG Research Center for Regenerative Therapies, Technische Universität Dresden, 01307 Dresden, Germany
| | - Wouter Masselink
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Yuka Taniguchi-Sugiura
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Ji-Feng Fei
- Department of Pathology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
| | - Elly M Tanaka
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria.
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3
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Alvarado K, Tang WJ, Watson CJ, Ahmed AR, Gomez AE, Donaka R, Amemiya C, Karasik D, Hsu YH, Kwon RY. Loss of cped1 does not affect bone and lean tissue in zebrafish. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.10.601974. [PMID: 39026892 PMCID: PMC11257572 DOI: 10.1101/2024.07.10.601974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Human genetic studies have nominated Cadherin-like and PC-esterase Domain-containing 1 (CPED1) as a candidate target gene mediating bone mineral density (BMD) and fracture risk heritability. Recent efforts to define the role of CPED1 in bone in mouse and human models have revealed complex alternative splicing and inconsistent results arising from gene targeting, making its function in bone difficult to interpret. To better understand the role of CPED1 in adult bone mass and morphology, we conducted a comprehensive genetic and phenotypic analysis of cped1 in zebrafish, an emerging model for bone and mineral research. We analyzed two different cped1 mutant lines and performed deep phenotyping to characterize more than 200 measures of adult vertebral, craniofacial, and lean tissue morphology. We also examined alternative splicing of zebrafish cped1 and gene expression in various cell/tissue types. Our studies fail to support an essential role of cped1 in adult zebrafish bone. Specifically, homozygous mutants for both cped1 mutant alleles, which are expected to result in loss-of-function and impact all cped1 isoforms, exhibited no significant differences in the measures examined when compared to their respective wildtype controls, suggesting that cped1 does not significantly contribute to these traits. We identified sequence differences in critical residues of the catalytic triad between the zebrafish and mouse orthologs of CPED1, suggesting that differences in key residues, as well as distinct alternative splicing, could underlie different functions of CPED1 orthologs in the two species. Our studies fail to support a requirement of cped1 in zebrafish bone and lean tissue, adding to evidence that variants at 7q31.31 can act independently of CPED1 to influence BMD and fracture risk.
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Affiliation(s)
- Kurtis Alvarado
- Department of Orthopaedic Surgery and Sports Medicine, University of Washington School of Medicine, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - W. Joyce Tang
- Department of Orthopaedic Surgery and Sports Medicine, University of Washington School of Medicine, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Claire J. Watson
- Department of Orthopaedic Surgery and Sports Medicine, University of Washington School of Medicine, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Ali R. Ahmed
- Department of Orthopaedic Surgery and Sports Medicine, University of Washington School of Medicine, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Arianna Ericka Gomez
- Department of Orthopaedic Surgery and Sports Medicine, University of Washington School of Medicine, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | | | - Chris Amemiya
- Department of Molecular and Cell Biology and Quantitative and Systems Biology Program, University of California, Merced, CA, USA
| | - David Karasik
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
- Hebrew SeniorLife, Hinda and Arthur Marcus Institute for Aging Research, Boston, MA, USA
| | - Yi-Hsiang Hsu
- Hebrew SeniorLife, Hinda and Arthur Marcus Institute for Aging Research, Boston, MA, USA
| | - Ronald Young Kwon
- Department of Orthopaedic Surgery and Sports Medicine, University of Washington School of Medicine, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
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4
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Duong P, Rodriguez-Parks A, Kang J, Murphy PJ. CUT&Tag applied to zebrafish adult tail fins reveals a return of embryonic H3K4me3 patterns during regeneration. Epigenetics Chromatin 2024; 17:22. [PMID: 39033118 PMCID: PMC11264793 DOI: 10.1186/s13072-024-00547-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 07/10/2024] [Indexed: 07/23/2024] Open
Abstract
Regenerative potential is governed by a complex process of transcriptional reprogramming, involving chromatin reorganization and dynamics in transcription factor binding patterns throughout the genome. The degree to which chromatin and epigenetic changes contribute to this process remains only partially understood. Here we provide a modified CUT&Tag protocol suitable for improved characterization and interrogation of changes in chromatin modifications during adult fin regeneration in zebrafish. Our protocol generates data that recapitulates results from previously published ChIP-Seq methods, requires far fewer cells as input, and significantly improves signal to noise ratios. We deliver high-resolution enrichment maps for H3K4me3 of uninjured and regenerating fin tissues. During regeneration, we find that H3K4me3 levels increase over gene promoters which become transcriptionally active and genes which lose H3K4me3 become silenced. Interestingly, these reprogramming events recapitulate the H3K4me3 patterns observed in developing fin folds of 24-h old zebrafish embryos. Our results indicate that changes in genomic H3K4me3 patterns during fin regeneration occur in a manner consistent with reactivation of developmental programs, demonstrating CUT&Tag to be an effective tool for profiling chromatin landscapes in regenerating tissues.
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Affiliation(s)
- Phu Duong
- Department of Biomedical Genetics, University of Rochester, Rochester, USA
| | | | - Junsu Kang
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, USA.
| | - Patrick J Murphy
- Department of Biomedical Genetics, University of Rochester, Rochester, USA.
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5
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Duong P, Rodriguez-Parks A, Kang J, Murphy PJ. CUT&Tag Applied to Zebrafish Adult Tail Fins Reveals a Return of Embryonic H3K4me3 Patterns During Regeneration. RESEARCH SQUARE 2024:rs.3.rs-4189493. [PMID: 38645155 PMCID: PMC11030498 DOI: 10.21203/rs.3.rs-4189493/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Regenerative potential is governed by a complex process of transcriptional reprogramming, involving chromatin reorganization and dynamics in transcription factor binding patterns throughout the genome. The degree to which chromatin and epigenetic changes contribute to this process remains partially understood. Here we provide a modified CUT&Tag protocol suitable for improved characterization and interrogation of epigenetic changes during adult fin regeneration in zebrafish. Our protocol generates data that recapitulates results from previously published ChIP-Seq methods, requires far fewer cells as input, and significantly improves signal to noise ratios. We deliver high-resolution enrichment maps for H3K4me3 of uninjured and regenerating fin tissues. During regeneration, we find that H3K4me3 levels increase over gene promoters which become transcriptionally active and genes which lose H3K4me3 become silenced. Interestingly, these epigenetic reprogramming events recapitulate the H3K4me3 patterns observed in developing fin folds of 24-hour old zebrafish embryos. Our results indicate that changes in genomic H3K4me3 patterns during fin regeneration occur in a manner consistent with reactivation of developmental programs, demonstrating CUT&Tag to be an effective tool for profiling chromatin landscapes in regenerating tissues.
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6
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Ando K, Ou J, Thompson JD, Welsby J, Bangru S, Shen J, Wei X, Diao Y, Poss KD. A screen for regeneration-associated silencer regulatory elements in zebrafish. Dev Cell 2024; 59:676-691.e5. [PMID: 38290519 PMCID: PMC10939760 DOI: 10.1016/j.devcel.2024.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 11/03/2023] [Accepted: 01/08/2024] [Indexed: 02/01/2024]
Abstract
Regeneration involves gene expression changes explained in part by context-dependent recruitment of transcriptional activators to distal enhancers. Silencers that engage repressive transcriptional complexes are less studied than enhancers and more technically challenging to validate, but they potentially have profound biological importance for regeneration. Here, we identified candidate silencers through a screening process that examined the ability of DNA sequences to limit injury-induced gene expression in larval zebrafish after fin amputation. A short sequence (s1) on chromosome 5 near several genes that reduce expression during adult fin regeneration could suppress promoter activity in stable transgenic lines and diminish nearby gene expression in knockin lines. High-resolution analysis of chromatin organization identified physical associations of s1 with gene promoters occurring preferentially during fin regeneration, and genomic deletion of s1 elevated the expression of these genes after fin amputation. Our study provides methods to identify "tissue regeneration silencer elements" (TRSEs) with the potential to reduce unnecessary or deleterious gene expression during regeneration.
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Affiliation(s)
- Kazunori Ando
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jianhong Ou
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - John D Thompson
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - John Welsby
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sushant Bangru
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jingwen Shen
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xiaolin Wei
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Yarui Diao
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kenneth D Poss
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA.
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7
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Rao A, Lyu B, Jahan I, Lubertozzi A, Zhou G, Tedeschi F, Jankowsky E, Kang J, Carstens B, Poss KD, Baskin K, Goldman JA. The translation initiation factor homolog eif4e1c regulates cardiomyocyte metabolism and proliferation during heart regeneration. Development 2023; 150:dev201376. [PMID: 37306388 PMCID: PMC10281269 DOI: 10.1242/dev.201376] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 04/28/2023] [Indexed: 05/25/2023]
Abstract
The eIF4E family of translation initiation factors bind 5' methylated caps and act as the limiting step for mRNA translation. The canonical eIF4E1A is required for cell viability, yet other related eIF4E families exist and are utilized in specific contexts or tissues. Here, we describe a family called Eif4e1c, for which we find roles during heart development and regeneration in zebrafish. The Eif4e1c family is present in all aquatic vertebrates but is lost in all terrestrial species. A core group of amino acids shared over 500 million years of evolution forms an interface along the protein surface, suggesting that Eif4e1c functions in a novel pathway. Deletion of eif4e1c in zebrafish caused growth deficits and impaired survival in juveniles. Mutants surviving to adulthood had fewer cardiomyocytes and reduced proliferative responses to cardiac injury. Ribosome profiling of mutant hearts demonstrated changes in translation efficiency of mRNA for genes known to regulate cardiomyocyte proliferation. Although eif4e1c is broadly expressed, its disruption had most notable impact on the heart and at juvenile stages. Our findings reveal context-dependent requirements for translation initiation regulators during heart regeneration.
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Affiliation(s)
- Anupama Rao
- Department of Biological Chemistry and Pharmacology, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Baken Lyu
- Department of Biological Chemistry and Pharmacology, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Ishrat Jahan
- Department of Biological Chemistry and Pharmacology, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Anna Lubertozzi
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Gao Zhou
- Center for RNA Molecular Biology, Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106USA
| | - Frank Tedeschi
- Center for RNA Molecular Biology, Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106USA
| | - Eckhard Jankowsky
- Center for RNA Molecular Biology, Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106USA
| | - Junsu Kang
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Bryan Carstens
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Kenneth D. Poss
- Department of Cell Biology, Duke Regeneration Center, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kedryn Baskin
- Department of Cell Biology and Physiology, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Joseph Aaron Goldman
- Department of Biological Chemistry and Pharmacology, The Ohio State University Medical Center, Columbus, OH 43210, USA
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8
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Du J, Liao W, Wang H, Hou G, Liao M, Xu L, Huang J, Yuan K, Chen X, Zeng Y. MDIG-mediated H3K9me3 demethylation upregulates Myc by activating OTX2 and facilitates liver regeneration. Signal Transduct Target Ther 2023; 8:351. [PMID: 37709738 PMCID: PMC10502063 DOI: 10.1038/s41392-023-01575-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 07/04/2023] [Accepted: 07/20/2023] [Indexed: 09/16/2023] Open
Abstract
The mineral dust-induced gene (MDIG) comprises a conserved JmjC domain and has the ability to demethylate histone H3 lysine 9 trimethylation (H3K9me3). Previous studies have indicated the significance of MDIG in promoting cell proliferation by modulating cell-cycle transition. However, its involvement in liver regeneration has not been extensively investigated. In this study, we generated mice with liver-specific knockout of MDIG and applied partial hepatectomy or carbon tetrachloride mouse models to investigate the biological contribution of MDIG in liver regeneration. The MDIG levels showed initial upregulation followed by downregulation as the recovery progressed. Genetic MDIG deficiency resulted in dramatically impaired liver regeneration and delayed cell cycle progression. However, the MDIG-deleted liver was eventually restored over a long latency. RNA-seq analysis revealed Myc as a crucial effector downstream of MDIG. However, ATAC-seq identified the reduced chromatin accessibility of OTX2 locus in MDIG-ablated regenerating liver, with unaltered chromatin accessibility of Myc locus. Mechanistically, MDIG altered chromatin accessibility to allow transcription by demethylating H3K9me3 at the OTX2 promoter region. As a consequence, the transcription factor OTX2 binding at the Myc promoter region was decreased in MDIG-deficient hepatocytes, which in turn repressed Myc expression. Reciprocally, Myc enhanced MDIG expression by regulating MDIG promoter activity, forming a positive feedback loop to sustain hepatocyte proliferation. Altogether, our results prove the essential role of MDIG in facilitating liver regeneration via regulating histone methylation to alter chromatin accessibility and provide valuable insights into the epi-transcriptomic regulation during liver regeneration.
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Affiliation(s)
- Jinpeng Du
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Wenwei Liao
- Department of Thoracic Surgery, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, 518020, China
- The First Affiliated Hospital, Jinan University, Guangzhou, Guangdong, 510630, China
| | - Haichuan Wang
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Guimin Hou
- Department of Hepato-Biliary-Pancreatic Surgery, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, The Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, Sichuan, 610041, China
| | - Min Liao
- Department of Medical Ultrasound, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Lin Xu
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Jiwei Huang
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Kefei Yuan
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Xiangzheng Chen
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
| | - Yong Zeng
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
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9
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Catalán A, Merondun J, Knief U, Wolf JBW. Chromatin accessibility, not 5mC methylation covaries with partial dosage compensation in crows. PLoS Genet 2023; 19:e1010901. [PMID: 37747941 PMCID: PMC10575545 DOI: 10.1371/journal.pgen.1010901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 10/13/2023] [Accepted: 08/07/2023] [Indexed: 09/27/2023] Open
Abstract
The evolution of genetic sex determination is often accompanied by degradation of the sex-limited chromosome. Male heterogametic systems have evolved convergent, epigenetic mechanisms restoring the resulting imbalance in gene dosage between diploid autosomes (AA) and the hemizygous sex chromosome (X). Female heterogametic systems (AAf Zf, AAm ZZm) tend to only show partial dosage compensation (0.5 < Zf:AAf < 1) and dosage balance (0.5
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Affiliation(s)
- Ana Catalán
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
- Division of Evolutionary Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Justin Merondun
- Division of Evolutionary Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Ulrich Knief
- Division of Evolutionary Biology, LMU Munich, Planegg-Martinsried, Germany
- Evolutionary Biology & Ecology,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Jochen B. W. Wolf
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
- Division of Evolutionary Biology, LMU Munich, Planegg-Martinsried, Germany
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10
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Jia X, Lin W, Wang W. Regulation of chromatin organization during animal regeneration. CELL REGENERATION (LONDON, ENGLAND) 2023; 12:19. [PMID: 37259007 DOI: 10.1186/s13619-023-00162-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/21/2023] [Indexed: 06/02/2023]
Abstract
Activation of regeneration upon tissue damages requires the activation of many developmental genes responsible for cell proliferation, migration, differentiation, and tissue patterning. Ample evidence revealed that the regulation of chromatin organization functions as a crucial mechanism for establishing and maintaining cellular identity through precise control of gene transcription. The alteration of chromatin organization can lead to changes in chromatin accessibility and/or enhancer-promoter interactions. Like embryogenesis, each stage of tissue regeneration is accompanied by dynamic changes of chromatin organization in regeneration-responsive cells. In the past decade, many studies have been conducted to investigate the contribution of chromatin organization during regeneration in various tissues, organs, and organisms. A collection of chromatin regulators were demonstrated to play critical roles in regeneration. In this review, we will summarize the progress in the understanding of chromatin organization during regeneration in different research organisms and discuss potential common mechanisms responsible for the activation of regeneration response program.
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Affiliation(s)
- Xiaohui Jia
- National Institute of Biological Sciences, Beijing, 102206, China
- China Agricultural University, Beijing, 100083, China
| | - Weifeng Lin
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 100084, China
| | - Wei Wang
- National Institute of Biological Sciences, Beijing, 102206, China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 100084, China.
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11
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Russell SK, Harrison JK, Olson BS, Lee HJ, O'Brien VP, Xing X, Livny J, Yu L, Roberson EDO, Bomjan R, Fan C, Sha M, Estfanous S, Amer AO, Colonna M, Stappenbeck TS, Wang T, Hannan TJ, Hultgren SJ. Uropathogenic Escherichia coli infection-induced epithelial trained immunity impacts urinary tract disease outcome. Nat Microbiol 2023; 8:875-888. [PMID: 37037942 PMCID: PMC10159856 DOI: 10.1038/s41564-023-01346-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/20/2023] [Indexed: 04/12/2023]
Abstract
Previous urinary tract infections (UTIs) can predispose one to future infections; however, the underlying mechanisms affecting recurrence are poorly understood. We previously found that UTIs in mice cause differential bladder epithelial (urothelial) remodelling, depending on disease outcome, that impacts susceptibility to recurrent UTI. Here we compared urothelial stem cell (USC) lines isolated from mice with a history of either resolved or chronic uropathogenic Escherichia coli (UPEC) infection, elucidating evidence of molecular imprinting that involved epigenetic changes, including differences in chromatin accessibility, DNA methylation and histone modification. Epigenetic marks in USCs from chronically infected mice enhanced caspase-1-mediated cell death upon UPEC infection, promoting bacterial clearance. Increased Ptgs2os2 expression also occurred, potentially contributing to sustained cyclooxygenase-2 expression, bladder inflammation and mucosal wounding-responses associated with severe recurrent cystitis. Thus, UPEC infection acts as an epi-mutagen reprogramming the urothelial epigenome, leading to urothelial-intrinsic remodelling and training of the innate response to subsequent infection.
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Affiliation(s)
- Seongmi K Russell
- Department of Molecular Microbiology and Center for Women's Infectious Disease Research, Washington University School of Medicine, St Louis, MO, USA
| | - Jessica K Harrison
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Benjamin S Olson
- Department of Molecular Microbiology and Center for Women's Infectious Disease Research, Washington University School of Medicine, St Louis, MO, USA
| | - Hyung Joo Lee
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Valerie P O'Brien
- Department of Molecular Microbiology and Center for Women's Infectious Disease Research, Washington University School of Medicine, St Louis, MO, USA
- Fred Hutchinson Cancer Center, Human Biology Division, Seattle, WA, USA
| | - Xiaoyun Xing
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Jonathan Livny
- Infectious Disease and Microbiome Program, The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Lu Yu
- Department of Molecular Microbiology and Center for Women's Infectious Disease Research, Washington University School of Medicine, St Louis, MO, USA
| | - Elisha D O Roberson
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- Department of Medicine, Division of Rheumatology, Washington University School of Medicine, St Louis, MO, USA
| | - Rajdeep Bomjan
- Department of Molecular Microbiology and Center for Women's Infectious Disease Research, Washington University School of Medicine, St Louis, MO, USA
| | - Changxu Fan
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Marina Sha
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Shady Estfanous
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, Ohio State University, Columbus, OH, USA
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy Helwan University, Cairo, Egypt
| | - Amal O Amer
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, Ohio State University, Columbus, OH, USA
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Thaddeus S Stappenbeck
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA.
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA.
| | - Thomas J Hannan
- Department of Molecular Microbiology and Center for Women's Infectious Disease Research, Washington University School of Medicine, St Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.
| | - Scott J Hultgren
- Department of Molecular Microbiology and Center for Women's Infectious Disease Research, Washington University School of Medicine, St Louis, MO, USA.
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12
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Bergen DJM, Maurizi A, Formosa MM, McDonald GLK, El-Gazzar A, Hassan N, Brandi ML, Riancho JA, Rivadeneira F, Ntzani E, Duncan EL, Gregson CL, Kiel DP, Zillikens MC, Sangiorgi L, Högler W, Duran I, Mäkitie O, Van Hul W, Hendrickx G. High Bone Mass Disorders: New Insights From Connecting the Clinic and the Bench. J Bone Miner Res 2023; 38:229-247. [PMID: 36161343 PMCID: PMC10092806 DOI: 10.1002/jbmr.4715] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 09/05/2022] [Accepted: 09/22/2022] [Indexed: 02/04/2023]
Abstract
Monogenic high bone mass (HBM) disorders are characterized by an increased amount of bone in general, or at specific sites in the skeleton. Here, we describe 59 HBM disorders with 50 known disease-causing genes from the literature, and we provide an overview of the signaling pathways and mechanisms involved in the pathogenesis of these disorders. Based on this, we classify the known HBM genes into HBM (sub)groups according to uniform Gene Ontology (GO) terminology. This classification system may aid in hypothesis generation, for both wet lab experimental design and clinical genetic screening strategies. We discuss how functional genomics can shape discovery of novel HBM genes and/or mechanisms in the future, through implementation of omics assessments in existing and future model systems. Finally, we address strategies to improve gene identification in unsolved HBM cases and highlight the importance for cross-laboratory collaborations encompassing multidisciplinary efforts to transfer knowledge generated at the bench to the clinic. © 2022 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Dylan J M Bergen
- School of Physiology, Pharmacology, and Neuroscience, Faculty of Life Sciences, University of Bristol, Bristol, UK.,Musculoskeletal Research Unit, Translational Health Sciences, Bristol Medical School, Faculty of Health Sciences, University of Bristol, Bristol, UK
| | - Antonio Maurizi
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Melissa M Formosa
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, Malta.,Center for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Georgina L K McDonald
- School of Physiology, Pharmacology, and Neuroscience, Faculty of Life Sciences, University of Bristol, Bristol, UK
| | - Ahmed El-Gazzar
- Department of Paediatrics and Adolescent Medicine, Johannes Kepler University Linz, Linz, Austria
| | - Neelam Hassan
- Musculoskeletal Research Unit, Translational Health Sciences, Bristol Medical School, Faculty of Health Sciences, University of Bristol, Bristol, UK
| | | | - José A Riancho
- Department of Internal Medicine, Hospital U M Valdecilla, University of Cantabria, IDIVAL, Santander, Spain
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Evangelia Ntzani
- Department of Hygiene and Epidemiology, Medical School, University of Ioannina, Ioannina, Greece.,Center for Evidence Synthesis in Health, Policy and Practice, Center for Research Synthesis in Health, School of Public Health, Brown University, Providence, RI, USA.,Institute of Biosciences, University Research Center of loannina, University of Ioannina, Ioannina, Greece
| | - Emma L Duncan
- Department of Twin Research & Genetic Epidemiology, School of Life Course Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK.,Department of Endocrinology, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Celia L Gregson
- Musculoskeletal Research Unit, Translational Health Sciences, Bristol Medical School, Faculty of Health Sciences, University of Bristol, Bristol, UK
| | - Douglas P Kiel
- Marcus Institute for Aging Research, Hebrew SeniorLife and Department of Medicine Beth Israel Deaconess Medical Center and Harvard Medical School, Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | - M Carola Zillikens
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Luca Sangiorgi
- Department of Rare Skeletal Diseases, IRCCS Rizzoli Orthopaedic Institute, Bologna, Italy
| | - Wolfgang Högler
- Department of Paediatrics and Adolescent Medicine, Johannes Kepler University Linz, Linz, Austria.,Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
| | | | - Outi Mäkitie
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Folkhälsan Research Centre, Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Wim Van Hul
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
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13
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Tamaki T, Yoshida T, Shibata E, Nishihara H, Ochi H, Kawakami A. Splashed E-box and AP-1 motifs cooperatively drive regeneration response and shape regeneration abilities. Biol Open 2023; 12:286596. [PMID: 36636913 PMCID: PMC9922731 DOI: 10.1242/bio.059810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 01/09/2023] [Indexed: 01/14/2023] Open
Abstract
Injury triggers a genetic program that induces gene expression for regeneration. Recent studies have identified regeneration-response enhancers (RREs); however, it remains unclear whether a common mechanism operates in these RREs. We identified three RREs from the zebrafish fn1b promoter by searching for conserved sequences within the surrounding genomic regions of regeneration-induced genes and performed a transgenic assay for regeneration response. Two regions contained in the transposons displayed RRE activity when combined with the -0.7 kb fn1b promoter. Another non-transposon element functioned as a stand-alone enhancer in combination with a minimum promoter. By searching for transcription factor-binding motifs and validation by transgenic assays, we revealed that the cooperation of E-box and activator protein 1 motifs is necessary and sufficient for regenerative response. Such RREs respond to variety of tissue injuries, including those in the zebrafish heart and Xenopus limb buds. Our findings suggest that the fidelity of regeneration response is ensured by the two signals evoked by tissue injuries. It is speculated that a large pool of potential enhancers in the genome has helped shape the regenerative capacities during evolution.
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Affiliation(s)
- Teruhisa Tamaki
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Takafumi Yoshida
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Eri Shibata
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Hidenori Nishihara
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Haruki Ochi
- Institute for Promotion of Medical Science Research, Faculty of Medicine, Yamagata University, 2-2-2 Iida-Nishi, Yamagata, Yamagata Pref. 990-9585, Japan
| | - Atsushi Kawakami
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan,Author for correspondence ()
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14
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Wnt/β-catenin signalling is required for pole-specific chromatin remodeling during planarian regeneration. Nat Commun 2023; 14:298. [PMID: 36653403 PMCID: PMC9849279 DOI: 10.1038/s41467-023-35937-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 01/09/2023] [Indexed: 01/19/2023] Open
Abstract
For successful regeneration, the identity of the missing tissue must be specified according to the pre-existing tissue. Planarians are ideal for the study of the mechanisms underlying this process; the same field of cells can regrow a head or a tail according to the missing body part. After amputation, the differential activation of the Wnt/β-catenin signal specifies anterior versus posterior identity. Initially, both wnt1 and notum (Wnt inhibitor) are expressed in all wounds, but 48 hours later they are restricted to posterior or anterior facing wounds, respectively, by an unknown mechanism. Here we show that 12 hours after amputation, the chromatin accessibility of cells in the wound region changes according to the polarity of the pre-existing tissue in a Wnt/β-catenin-dependent manner. Genomic analyses suggest that homeobox transcription factors and chromatin-remodeling proteins are direct Wnt/β-catenin targets, which trigger the expression of posterior effectors. Finally, we identify FoxG as a wnt1 up-stream regulator, probably via binding to its first intron enhancer region.
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15
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Yan R, Cigliola V, Oonk KA, Petrover Z, DeLuca S, Wolfson DW, Vekstein A, Mendiola MA, Devlin G, Bishawi M, Gemberling MP, Sinha T, Sargent MA, York AJ, Shakked A, DeBenedittis P, Wendell DC, Ou J, Kang J, Goldman JA, Baht GS, Karra R, Williams AR, Bowles DE, Asokan A, Tzahor E, Gersbach CA, Molkentin JD, Bursac N, Black BL, Poss KD. An enhancer-based gene-therapy strategy for spatiotemporal control of cargoes during tissue repair. Cell Stem Cell 2023; 30:96-111.e6. [PMID: 36516837 PMCID: PMC9830588 DOI: 10.1016/j.stem.2022.11.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 10/06/2022] [Accepted: 11/15/2022] [Indexed: 12/14/2022]
Abstract
The efficacy and safety of gene-therapy strategies for indications like tissue damage hinge on precision; yet, current methods afford little spatial or temporal control of payload delivery. Here, we find that tissue-regeneration enhancer elements (TREEs) isolated from zebrafish can direct targeted, injury-associated gene expression from viral DNA vectors delivered systemically in small and large adult mammalian species. When employed in combination with CRISPR-based epigenome editing tools in mice, zebrafish TREEs stimulated or repressed the expression of endogenous genes after ischemic myocardial infarction. Intravenously delivered recombinant AAV vectors designed with a TREE to direct a constitutively active YAP factor boosted indicators of cardiac regeneration in mice and improved the function of the injured heart. Our findings establish the application of contextual enhancer elements as a potential therapeutic platform for spatiotemporally controlled tissue regeneration in mammals.
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Affiliation(s)
- Ruorong Yan
- Duke Regeneration Center, Duke University, Durham, NC, USA; Department of Cell Biology, Duke University Medical School, Durham, NC, USA
| | - Valentina Cigliola
- Duke Regeneration Center, Duke University, Durham, NC, USA; Department of Cell Biology, Duke University Medical School, Durham, NC, USA
| | - Kelsey A Oonk
- Duke Regeneration Center, Duke University, Durham, NC, USA; Department of Cell Biology, Duke University Medical School, Durham, NC, USA
| | - Zachary Petrover
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sophia DeLuca
- Department of Cell Biology, Duke University Medical School, Durham, NC, USA; Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - David W Wolfson
- Duke Regeneration Center, Duke University, Durham, NC, USA; Department of Cell Biology, Duke University Medical School, Durham, NC, USA; Department of Surgery, Duke University School of Medicine, Durham, NC, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Andrew Vekstein
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | | | - Garth Devlin
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Muath Bishawi
- Department of Biomedical Engineering, Duke University, Durham, NC, USA; Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Matthew P Gemberling
- Department of Biomedical Engineering, Duke University, Durham, NC, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Tanvi Sinha
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Michelle A Sargent
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Allen J York
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Avraham Shakked
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | | | - David C Wendell
- Duke Cardiovascular Magnetic Resonance Center, Duke University Medical Center, Durham, NC, USA
| | - Jianhong Ou
- Duke Regeneration Center, Duke University, Durham, NC, USA
| | - Junsu Kang
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Joseph A Goldman
- Department of Biological Chemistry and Pharmacology, Ohio State University, Columbus, OH, USA
| | - Gurpreet S Baht
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA; Department of Orthopaedic Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Ravi Karra
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Adam R Williams
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Dawn E Bowles
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Aravind Asokan
- Duke Regeneration Center, Duke University, Durham, NC, USA; Department of Biomedical Engineering, Duke University, Durham, NC, USA; Department of Surgery, Duke University School of Medicine, Durham, NC, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Eldad Tzahor
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Charles A Gersbach
- Duke Regeneration Center, Duke University, Durham, NC, USA; Department of Cell Biology, Duke University Medical School, Durham, NC, USA; Department of Biomedical Engineering, Duke University, Durham, NC, USA; Department of Surgery, Duke University School of Medicine, Durham, NC, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA; Department of Orthopaedic Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Jeffery D Molkentin
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Nenad Bursac
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Brian L Black
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Kenneth D Poss
- Duke Regeneration Center, Duke University, Durham, NC, USA; Department of Cell Biology, Duke University Medical School, Durham, NC, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA.
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16
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Tanaka EM. Now that We Got There, What Next? Methods Mol Biol 2023; 2562:471-479. [PMID: 36272095 DOI: 10.1007/978-1-0716-2659-7_31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
As seen in the protocols in this book, the opportunities to pursue work at the cellular and molecular work in salamanders have considerably broadened over the last years. The availability of genomic information and genome editing, and the possibility to image tissues live and other methods enhance the spectrum of biological questions accessible to all researchers. Here I provide a personal perspective on what I consider exciting future questions open for investigation.
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Affiliation(s)
- Elly M Tanaka
- Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.
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17
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Erhardt S, Wang J. Cardiac Neural Crest and Cardiac Regeneration. Cells 2022; 12:cells12010111. [PMID: 36611905 PMCID: PMC9818523 DOI: 10.3390/cells12010111] [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] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/23/2022] [Accepted: 12/25/2022] [Indexed: 12/30/2022] Open
Abstract
Neural crest cells (NCCs) are a vertebrate-specific, multipotent stem cell population that have the ability to migrate and differentiate into various cell populations throughout the embryo during embryogenesis. The heart is a muscular and complex organ whose primary function is to pump blood and nutrients throughout the body. Mammalian hearts, such as those of humans, lose their regenerative ability shortly after birth. However, a few vertebrate species, such as zebrafish, have the ability to self-repair/regenerate after cardiac damage. Recent research has discovered the potential functional ability and contribution of cardiac NCCs to cardiac regeneration through the use of various vertebrate species and pluripotent stem cell-derived NCCs. Here, we review the neural crest's regenerative capacity in various tissues and organs, and in particular, we summarize the characteristics of cardiac NCCs between species and their roles in cardiac regeneration. We further discuss emerging and future work to determine the potential contributions of NCCs for disease treatment.
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Affiliation(s)
- Shannon Erhardt
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, The University of Texas, Houston, TX 77030, USA
| | - Jun Wang
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, The University of Texas, Houston, TX 77030, USA
- Correspondence:
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18
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Hu Q, Lian Z, Xia X, Tian H, Li Z. Integrated chromatin accessibility and DNA methylation analysis to reveal the critical epigenetic modification and regulatory mechanism in gonadal differentiation of the sequentially hermaphroditic fish, Monopterus albus. Biol Sex Differ 2022; 13:73. [PMID: 36539889 PMCID: PMC9764712 DOI: 10.1186/s13293-022-00484-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 12/11/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Monopterus albus is a hermaphroditic and economically farmed fish that undergoes sex reversal from ovary to testis via ovotestis during gonadal development. The epigenetic changes that are associated with gonadal development in this species remain unclear. METHODS We produced DNA methylome, transcriptome, and chromatin accessibility maps of the key stages of gonad development: ovary, ovotestis, and testis. The expression of the key candidate genes was detected using qRT-PCR and in situ hybridization and the methylation levels were analysed using bisulphite sequencing PCR. Promoter activity and regulation were assessed using dual-luciferase reporter assays. RESULTS Gonadal development exhibits highly dynamic transcriptomic, DNA methylation, and chromatin accessibility changes. We found that DNA methylation status, especially of the transcription start site, was significantly negatively correlated with gene expression while chromatin accessibility exhibited no correlation with gene expression during gonadal development. The epigenetic signatures revealed many novel regulatory elements and genes involved in sex reversal, which were validated. DNA methylation detection and site mutation of plastin-2 promoter, as a candidate gene, revealed that DNA methylation could impact the binding of transcription factor dmrt1 and foxl2 through methylation and demethylation to regulate plastin-2 expression during gonadal development. CONCLUSIONS These data provide novel insights into epigenetic modification and help elucidate the potential molecular mechanism by which dynamic modification of DNA methylation plays a crucial role in gonadal development.
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Affiliation(s)
- Qiaomu Hu
- grid.43308.3c0000 0000 9413 3760Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wudayuan First Road 8, Wuhan, 430223 China
| | - Zitong Lian
- grid.43308.3c0000 0000 9413 3760Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wudayuan First Road 8, Wuhan, 430223 China
| | - Xueping Xia
- grid.43308.3c0000 0000 9413 3760Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wudayuan First Road 8, Wuhan, 430223 China
| | - Haifeng Tian
- grid.43308.3c0000 0000 9413 3760Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wudayuan First Road 8, Wuhan, 430223 China
| | - Zhong Li
- grid.43308.3c0000 0000 9413 3760Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wudayuan First Road 8, Wuhan, 430223 China
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19
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Vernaz G, Hudson AG, Santos ME, Fischer B, Carruthers M, Shechonge AH, Gabagambi NP, Tyers AM, Ngatunga BP, Malinsky M, Durbin R, Turner GF, Genner MJ, Miska EA. Epigenetic divergence during early stages of speciation in an African crater lake cichlid fish. Nat Ecol Evol 2022; 6:1940-1951. [PMID: 36266459 PMCID: PMC9715432 DOI: 10.1038/s41559-022-01894-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 08/26/2022] [Indexed: 12/15/2022]
Abstract
Epigenetic variation can alter transcription and promote phenotypic divergence between populations facing different environmental challenges. Here, we assess the epigenetic basis of diversification during the early stages of speciation. Specifically, we focus on the extent and functional relevance of DNA methylome divergence in the very young radiation of Astatotilapia calliptera in crater Lake Masoko, southern Tanzania. Our study focuses on two lake ecomorphs that diverged approximately 1,000 years ago and a population in the nearby river from which they separated approximately 10,000 years ago. The two lake ecomorphs show no fixed genetic differentiation, yet are characterized by different morphologies, depth preferences and diets. We report extensive genome-wide methylome divergence between the two lake ecomorphs, and between the lake and river populations, linked to key biological processes and associated with altered transcriptional activity of ecologically relevant genes. Such genes differing between lake ecomorphs include those involved in steroid metabolism, hemoglobin composition and erythropoiesis, consistent with their divergent habitat occupancy. Using a common-garden experiment, we found that global methylation profiles are often rapidly remodeled across generations but ecomorph-specific differences can be inherited. Collectively, our study suggests an epigenetic contribution to the early stages of vertebrate speciation.
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Affiliation(s)
- Grégoire Vernaz
- Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK.
- Department of Genetics, University of Cambridge, Cambridge, UK.
- Wellcome Sanger Institute, Hinxton, UK.
| | - Alan G Hudson
- School of Biological Sciences, University of Bristol, Bristol, UK
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - M Emília Santos
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Bettina Fischer
- Department of Genetics, University of Cambridge, Cambridge, UK
| | | | | | | | - Alexandra M Tyers
- School of Natural Sciences, Bangor University, Bangor, UK
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | - Milan Malinsky
- Wellcome Sanger Institute, Hinxton, UK
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | | | - Martin J Genner
- School of Biological Sciences, University of Bristol, Bristol, UK.
| | - Eric A Miska
- Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK.
- Department of Genetics, University of Cambridge, Cambridge, UK.
- Wellcome Sanger Institute, Hinxton, UK.
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20
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Begeman IJ, Emery B, Kurth A, Kang J. Regeneration and developmental enhancers are differentially compatible with minimal promoters. Dev Biol 2022; 492:47-58. [PMID: 36167150 PMCID: PMC10211259 DOI: 10.1016/j.ydbio.2022.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 12/01/2022]
Abstract
Enhancers and promoters are cis-regulatory elements that control gene expression. Enhancers are activated in a cell type-, tissue-, and condition-specific manner to stimulate promoter function and transcription. Zebrafish have emerged as a powerful animal model for examining the activities of enhancers derived from various species through transgenic enhancer assays, in which an enhancer is coupled with a minimal promoter. However, the efficiency of minimal promoters and their compatibility with multiple developmental and regeneration enhancers have not been systematically tested in zebrafish. Thus, we assessed the efficiency of six minimal promoters and comprehensively interrogated the compatibility of the promoters with developmental and regeneration enhancers. We found that the fos minimal promoter and Drosophila synthetic core promoter (DSCP) yielded high rates of leaky expression that may complicate the interpretation of enhancer assays. Notably, the adenovirus E1b promoter, the zebrafish lepb 0.8-kb (P0.8) and lepb 2-kb (P2) promoters, and a new zebrafish synthetic promoter (ZSP) that combines elements of the E1b and P0.8 promoters drove little or no ectopic expression, making them suitable for transgenic assays. We also found significant differences in compatibility among specific combinations of promoters and enhancers, indicating the importance of promoters as key regulatory elements determining the specificity of gene expression. Our study provides guidelines for transgenic enhancer assays in zebrafish to aid in the discovery of functional enhancers regulating development and regeneration.
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Affiliation(s)
- Ian J Begeman
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Benjamin Emery
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Andrew Kurth
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Junsu Kang
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA; UW Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA.
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21
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Jimenez E, Slevin CC, Song W, Chen Z, Frederickson SC, Gildea D, Wu W, Elkahloun AG, Ovcharenko I, Burgess SM. A regulatory network of Sox and Six transcription factors initiate a cell fate transformation during hearing regeneration in adult zebrafish. CELL GENOMICS 2022; 2. [PMID: 36212030 PMCID: PMC9540346 DOI: 10.1016/j.xgen.2022.100170] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Using adult zebrafish inner ears as a model for sensorineural regeneration, we ablated the mechanosensory receptors and characterized the single-cell epigenome and transcriptome at consecutive time points during hair cell regeneration. We utilized deep learning on the regeneration-induced open chromatin sequences and identified cell-specific transcription factor (TF) motif patterns. Enhancer activity correlated with gene expression and identified potential gene regulatory networks. A pattern of overlapping Sox- and Six-family TF gene expression and binding motifs was detected, suggesting a combinatorial program of TFs driving regeneration and cell identity. Pseudotime analysis of single-cell transcriptomic data suggested that support cells within the sensory epithelium changed cell identity to a “progenitor” cell population that could differentiate into hair cells. We identified a 2.6 kb DNA enhancer upstream of the sox2 promoter that, when deleted, showed a dominant phenotype that resulted in a hair-cell-regeneration-specific deficit in both the lateral line and adult inner ear. Jimenez et al. interrogate the epigenomic and transcriptomic landscape of regenerating adult zebrafish inner-ear sensory epithelia. They show that the support-cell population transitions to an intermediate “progenitor” cell state that becomes new hair cells, and they demonstrate that the cell fate decisions may be driven by the coordinate regulation and spatial co-binding of Sox and Six transcription factors. By functionally validating a predicted regeneration-responsive enhancer upstream of sox2, they show that precise timing of sox2 expression is critical for hearing regeneration in zebrafish.
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Affiliation(s)
- Erin Jimenez
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Claire C. Slevin
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Wei Song
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Zelin Chen
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Stephen C. Frederickson
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Derek Gildea
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Weiwei Wu
- Vaccine Immunology Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Abdel G. Elkahloun
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Ivan Ovcharenko
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Shawn M. Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
- Corresponding author
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22
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Osorio-Méndez D, Miller A, Begeman IJ, Kurth A, Hagle R, Rolph D, Dickson AL, Chen CH, Halloran M, Poss KD, Kang J. Voltage-gated sodium channel scn8a is required for innervation and regeneration of amputated adult zebrafish fins. Proc Natl Acad Sci U S A 2022; 119:e2200342119. [PMID: 35867745 PMCID: PMC9282381 DOI: 10.1073/pnas.2200342119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 05/10/2022] [Indexed: 01/09/2023] Open
Abstract
Teleost fishes and urodele amphibians can regenerate amputated appendages, whereas this ability is restricted to digit tips in adult mammals. One key component of appendage regeneration is reinnervation of the wound area. However, how innervation is regulated in injured appendages of adult vertebrates has seen limited research attention. From a forward genetics screen for temperature-sensitive defects in zebrafish fin regeneration, we identified a mutation that disrupted regeneration while also inducing paralysis at the restrictive temperature. Genetic mapping and complementation tests identify a mutation in the major neuronal voltage-gated sodium channel (VGSC) gene scn8ab. Conditional disruption of scn8ab impairs early regenerative events, including blastema formation, but does not affect morphogenesis of established regenerates. Whereas scn8ab mutations reduced neural activity as expected, they also disrupted axon regrowth and patterning in fin regenerates, resulting in hypoinnervation. Our findings indicate that the activity of VGSCs plays a proregenerative role by promoting innervation of appendage stumps.
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Affiliation(s)
- Daniel Osorio-Méndez
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI 53705
| | - Andrew Miller
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53705
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705
| | - Ian J. Begeman
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI 53705
| | - Andrew Kurth
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI 53705
| | - Ryan Hagle
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI 53705
| | - Daniela Rolph
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI 53705
| | - Amy L. Dickson
- Duke Regeneration Center, Department of Cell Biology, Duke University Medical Center, Durham, NC 27710
| | - Chen-Hui Chen
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Mary Halloran
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53705
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705
| | - Kenneth D. Poss
- Duke Regeneration Center, Department of Cell Biology, Duke University Medical Center, Durham, NC 27710
| | - Junsu Kang
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI 53705
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23
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Sehring I, Weidinger G. Zebrafish Fin: Complex Molecular Interactions and Cellular Mechanisms Guiding Regeneration. Cold Spring Harb Perspect Biol 2022; 14:a040758. [PMID: 34649924 PMCID: PMC9248819 DOI: 10.1101/cshperspect.a040758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The zebrafish caudal fin has become a popular model to study cellular and molecular mechanisms of regeneration due to its high regenerative capacity, accessibility for experimental manipulations, and relatively simple anatomy. The formation of a regenerative epidermis and blastema are crucial initial events and tightly regulated. Both the regenerative epidermis and the blastema are highly organized structures containing distinct domains, and several signaling pathways regulate the formation and interaction of these domains. Bone is the major tissue regenerated from the progenitor cells of the blastema. Several cellular mechanisms can provide source cells for blastemal (pre-)osteoblasts, including dedifferentiation of differentiated osteoblasts and de novo formation from other cell types, providing intriguing examples of cellular plasticity. In recent years, omics analyses and single-cell approaches have elucidated genetic and epigenetic regulation, increasing our knowledge of the surprisingly complex coordination of various mechanisms to achieve successful restoration of a seemingly simple structure.
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Affiliation(s)
- Ivonne Sehring
- Institute of Biochemistry and Molecular Biology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Gilbert Weidinger
- Institute of Biochemistry and Molecular Biology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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24
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Lee HJ, Hou Y, Maeng JH, Shah NM, Chen Y, Lawson HA, Yang H, Yue F, Wang T. Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish. Genome Res 2022; 32:1424-1436. [PMID: 35649578 PMCID: PMC9341505 DOI: 10.1101/gr.276052.121] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 05/27/2022] [Indexed: 12/04/2022]
Abstract
Transposable elements (TEs) encode regulatory elements that impact gene expression in multiple species, yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here, we systematically investigate the epigenomic and transcriptomic landscape of TEs across 11 adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE-derived transcriptional units expressed across tissues. Finally, we show that novel TE-derived promoters can initiate tissue-specific transcription of alternate gene isoforms. This work provides a comprehensive profile of TE activity across normal zebrafish tissues, shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.
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Affiliation(s)
- Hyung Joo Lee
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Yiran Hou
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Ju Heon Maeng
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Nakul M Shah
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Yujie Chen
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Heather A Lawson
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Hongbo Yang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois 60611, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
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25
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Sehring IM, Mohammadi HF, Haffner-Luntzer M, Ignatius A, Huber-Lang M, Weidinger G. Zebrafish fin regeneration involves generic and regeneration-specific osteoblast injury responses. eLife 2022; 11:77614. [PMID: 35748539 PMCID: PMC9259016 DOI: 10.7554/elife.77614] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 06/23/2022] [Indexed: 11/13/2022] Open
Abstract
Successful regeneration requires the coordinated execution of multiple cellular responses to injury. In amputated zebrafish fins, mature osteoblasts dedifferentiate, migrate towards the injury and form proliferative osteogenic blastema cells. We show that osteoblast migration is preceded by cell elongation and alignment along the proximodistal axis, which require actomyosin, but not microtubule turnover. Surprisingly, osteoblast dedifferentiation and migration can be uncoupled. Using pharmacological and genetic interventions, we found that NF-ĸB and retinoic acid signalling regulate dedifferentiation without affecting migration, while the complement system and actomyosin dynamics affect migration but not dedifferentiation. Furthermore, by removing bone at two locations within a fin ray, we established an injury model containing two injury sites. We found that osteoblasts dedifferentiate at and migrate towards both sites, while accumulation of osteogenic progenitor cells and regenerative bone formation only occur at the distal-facing injury. Together, these data indicate that osteoblast dedifferentiation and migration represent generic injury responses that are differentially regulated and can occur independently of each other and of regenerative growth. We conclude that successful fin bone regeneration appears to involve the coordinated execution of generic and regeneration-specific responses of osteoblasts to injury.
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Affiliation(s)
| | | | | | - Anita Ignatius
- Institute of Orthopaedic Research and Biomechanics, University Hospital Ulm, Ulm, Germany
| | - Markus Huber-Lang
- Institute of Clinical and Experimental Trauma-Immunology (ITI), University Hospital Ulm, Ulm, Germany
| | - Gilbert Weidinger
- Institute of Biochemistry and Molecular Biology, University of Ulm, Ulm, Germany
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26
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Xu H, Tong G, Yan T, Dong L, Yang X, Dou D, Sun Z, Liu T, Zheng X, Yang J, Sun X, Zhou Y, Kuang Y. Transcriptomic Analysis Provides Insights to Reveal the bmp6 Function Related to the Development of Intermuscular Bones in Zebrafish. Front Cell Dev Biol 2022; 10:821471. [PMID: 35646941 PMCID: PMC9135397 DOI: 10.3389/fcell.2022.821471] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/24/2022] [Indexed: 12/13/2022] Open
Abstract
Intermuscular bones (IBs) are small, hard-boned spicules located in the muscle tissue that mainly exist in the myosepta of lower teleosts, which hurt the edibleness and economic value of fish. The study of the development of IBs is very important for freshwater aquaculture fish, but the molecular mechanism of its formation and the key regulatory genes remain unclear. In this study, we first constructed two types of zebrafish mutants (the mutants losing IBs and the mutants with partial deletion of IBs) by knocking out bmp6. We then carried out a transcriptomic analysis to reveal the role of bmp6 in the developmental mechanism of IBs; we used the caudal musculoskeletal tissues of these mutants and wild-type zebrafish at three development stages (20, 45, and 60 dph) to perform transcriptomic analysis. The results showed that the deficiency of bmp6 upregulated sik1 and activated the TNF-A signaling via the NF-KB pathway, which inhibited the development of osteoblasts and promoted osteoclast formation, thereby inhibiting the formation of IBs. These results provided insights to understand the role of bmp6 in the development of IBs in zebrafish and are useful for selective breeding of IBs in cyprinids.
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Affiliation(s)
- Huan Xu
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
- National and Local Joint Engineering Laboratory for Freshwater Fish Breeding, Harbin, China
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China
- Heilongjiang Provincial Key Laboratory of Hard Tissue Development and Regeneration, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Guangxiang Tong
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
- National and Local Joint Engineering Laboratory for Freshwater Fish Breeding, Harbin, China
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Ting Yan
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
- National and Local Joint Engineering Laboratory for Freshwater Fish Breeding, Harbin, China
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Le Dong
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Xiaoxing Yang
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Dongyu Dou
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
| | - Zhipeng Sun
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
- National and Local Joint Engineering Laboratory for Freshwater Fish Breeding, Harbin, China
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Tianqi Liu
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
- National and Local Joint Engineering Laboratory for Freshwater Fish Breeding, Harbin, China
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Xianhu Zheng
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
- National and Local Joint Engineering Laboratory for Freshwater Fish Breeding, Harbin, China
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Jian Yang
- Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo, China
| | - Xiaowen Sun
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
- National and Local Joint Engineering Laboratory for Freshwater Fish Breeding, Harbin, China
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Yi Zhou
- Stem Cell Program of Boston Children’s Hospital, Division of Hematology/Oncology, Boston Children’s Hospital and Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, United States
| | - Youyi Kuang
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
- National and Local Joint Engineering Laboratory for Freshwater Fish Breeding, Harbin, China
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China
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27
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Sun F, Ou J, Shoffner AR, Luan Y, Yang H, Song L, Safi A, Cao J, Yue F, Crawford GE, Poss KD. Enhancer selection dictates gene expression responses in remote organs during tissue regeneration. Nat Cell Biol 2022; 24:685-696. [PMID: 35513710 DOI: 10.1038/s41556-022-00906-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 03/23/2022] [Indexed: 12/14/2022]
Abstract
Acute trauma stimulates local repair mechanisms but can also impact structures distant from the injury, for example through the activity of circulating factors. To study the responses of remote tissues during tissue regeneration, we profiled transcriptomes of zebrafish brains after experimental cardiac damage. We found that the transcription factor gene cebpd was upregulated remotely in brain ependymal cells as well as kidney tubular cells, in addition to its local induction in epicardial cells. cebpd mutations altered both local and distant cardiac injury responses, altering the cycling of epicardial cells as well as exchange between distant fluid compartments. Genome-wide profiling and transgenesis identified a hormone-responsive enhancer near cebpd that exists in a permissive state, enabling rapid gene expression in heart, brain and kidney after cardiac injury. Deletion of this sequence selectively abolished cebpd induction in remote tissues and disrupted fluid regulation after injury, without affecting its local cardiac expression response. Our findings suggest a model to broaden gene function during regeneration in which enhancer regulatory elements define short- and long-range expression responses to injury.
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Affiliation(s)
- Fei Sun
- Duke Regeneration Center, Duke University, Durham, NC, USA.,Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
| | - Jianhong Ou
- Duke Regeneration Center, Duke University, Durham, NC, USA
| | - Adam R Shoffner
- Duke Regeneration Center, Duke University, Durham, NC, USA.,Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
| | - Yu Luan
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Hongbo Yang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.,Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Lingyun Song
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA.,Division of Medical Genetics, Department of Pediatrics, Duke University, Durham, NC, USA
| | - Alexias Safi
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA.,Division of Medical Genetics, Department of Pediatrics, Duke University, Durham, NC, USA
| | - Jingli Cao
- Cardiovascular Research Institute, Weill Cornell Medical College, New York, NY, USA.,Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, NY, USA
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Gregory E Crawford
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA.,Division of Medical Genetics, Department of Pediatrics, Duke University, Durham, NC, USA
| | - Kenneth D Poss
- Duke Regeneration Center, Duke University, Durham, NC, USA. .,Department of Cell Biology, Duke University Medical Center, Durham, NC, USA.
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28
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Tang WJ, Watson CJ, Olmstead T, Allan CH, Kwon RY. Single-cell resolution of MET- and EMT-like programs in osteoblasts during zebrafish fin regeneration. iScience 2022; 25:103784. [PMID: 35169687 PMCID: PMC8829776 DOI: 10.1016/j.isci.2022.103784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 10/15/2021] [Accepted: 01/14/2022] [Indexed: 12/04/2022] Open
Abstract
Zebrafish regenerate fin rays following amputation through epimorphic regeneration, a process that has been proposed to involve the epithelial-to-mesenchymal transition (EMT). We performed single-cell RNA sequencing (scRNA-seq) to elucidate osteoblastic transcriptional programs during zebrafish caudal fin regeneration. We show that osteoprogenitors are enriched with components associated with EMT and its reverse, mesenchymal-to-epithelial transition (MET), and provide evidence that the EMT markers cdh11 and twist2 are co-expressed in dedifferentiating cells at the amputation stump at 1 dpa, and in differentiating osteoblastic cells in the regenerate, the latter of which are enriched in EMT signatures. We also show that esrp1, a regulator of alternative splicing in epithelial cells that is associated with MET, is expressed in a subset of osteoprogenitors during outgrowth. This study provides a single cell resource for the study of osteoblastic cells during zebrafish fin regeneration, and supports the contribution of MET- and EMT-associated components to this process. Osteoblasts express EMT/MET signatures during zebrafish fin regeneration De/re-differentiating osteoblasts express cdh11, an EMT marker A subset of osteoprogenitors express the MET marker esrp1 Our scRNA-seq data can be explored online
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Affiliation(s)
- W Joyce Tang
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, WA 98105, USA.,Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Claire J Watson
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, WA 98105, USA.,Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Theresa Olmstead
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, WA 98105, USA.,Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Christopher H Allan
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, WA 98105, USA.,Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Ronald Y Kwon
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, WA 98105, USA.,Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
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29
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Cao Y, Xia Y, Balowski JJ, Ou J, Song L, Safi A, Curtis T, Crawford GE, Poss KD, Cao J. Identification of enhancer regulatory elements that direct epicardial gene expression during zebrafish heart regeneration. Development 2022; 149:dev200133. [PMID: 35179181 PMCID: PMC8918790 DOI: 10.1242/dev.200133] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/11/2022] [Indexed: 12/17/2022]
Abstract
The epicardium is a mesothelial tissue layer that envelops the heart. Cardiac injury activates dynamic gene expression programs in epicardial tissue, which in zebrafish enables subsequent regeneration through paracrine and vascularizing effects. To identify tissue regeneration enhancer elements (TREEs) that control injury-induced epicardial gene expression during heart regeneration, we profiled transcriptomes and chromatin accessibility in epicardial cells purified from regenerating zebrafish hearts. We identified hundreds of candidate TREEs, which are defined by increased chromatin accessibility of non-coding elements near genes with increased expression during regeneration. Several of these candidate TREEs were incorporated into stable transgenic lines, with five out of six elements directing injury-induced epicardial expression but not ontogenetic epicardial expression in larval hearts. Whereas two independent TREEs linked to the gene gnai3 showed similar functional features of gene regulation in transgenic lines, two independent ncam1a-linked TREEs directed distinct spatiotemporal domains of epicardial gene expression. Thus, multiple TREEs linked to a regeneration gene can possess either matching or complementary regulatory controls. Our study provides a new resource and principles for understanding the regulation of epicardial genetic programs during heart regeneration. This article has an associated 'The people behind the papers' interview.
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Affiliation(s)
- Yingxi Cao
- Cardiovascular Research Institute, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10021, USA
- Department of Cell and Developmental Biology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10021, USA
| | - Yu Xia
- Cardiovascular Research Institute, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10021, USA
- Department of Cell and Developmental Biology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10021, USA
| | - Joseph J. Balowski
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
- Duke Regeneration Center, Duke University, Durham, NC 27710, USA
| | - Jianhong Ou
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
- Duke Regeneration Center, Duke University, Durham, NC 27710, USA
| | - Lingyun Song
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27710, USA
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, NC 27710, USA
| | - Alexias Safi
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27710, USA
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, NC 27710, USA
| | - Timothy Curtis
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
- Duke Regeneration Center, Duke University, Durham, NC 27710, USA
| | - Gregory E. Crawford
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27710, USA
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, NC 27710, USA
| | - Kenneth D. Poss
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
- Duke Regeneration Center, Duke University, Durham, NC 27710, USA
| | - Jingli Cao
- Cardiovascular Research Institute, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10021, USA
- Department of Cell and Developmental Biology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10021, USA
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30
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Bergen DJM, Tong Q, Shukla A, Newham E, Zethof J, Lundberg M, Ryan R, Youlten SE, Frysz M, Croucher PI, Flik G, Richardson RJ, Kemp JP, Hammond CL, Metz JR. Regenerating zebrafish scales express a subset of evolutionary conserved genes involved in human skeletal disease. BMC Biol 2022; 20:21. [PMID: 35057801 PMCID: PMC8780716 DOI: 10.1186/s12915-021-01209-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 12/07/2021] [Indexed: 12/23/2022] Open
Abstract
Background Scales are mineralised exoskeletal structures that are part of the dermal skeleton. Scales have been mostly lost during evolution of terrestrial vertebrates whilst bony fish have retained a mineralised dermal skeleton in the form of fin rays and scales. Each scale is a mineralised collagen plate that is decorated with both matrix-building and resorbing cells. When removed, an ontogenetic scale is quickly replaced following differentiation of the scale pocket-lining cells that regenerate a scale. Processes promoting de novo matrix formation and mineralisation initiated during scale regeneration are poorly understood. Therefore, we performed transcriptomic analysis to determine gene networks and their pathways involved in dermal scale regeneration. Results We defined the transcriptomic profiles of ontogenetic and regenerating scales of zebrafish and identified 604 differentially expressed genes (DEGs). These were enriched for extracellular matrix, ossification, and cell adhesion pathways, but not in enamel or dentin formation processes indicating that scales are reminiscent to bone. Hypergeometric tests involving monogenetic skeletal disorders showed that DEGs were strongly enriched for human orthologues that are mutated in low bone mass and abnormal bone mineralisation diseases (P< 2× 10−3). The DEGs were also enriched for human orthologues associated with polygenetic skeletal traits, including height (P< 6× 10−4), and estimated bone mineral density (eBMD, P< 2× 10−5). Zebrafish mutants of two human orthologues that were robustly associated with height (COL11A2, P=6× 10−24) or eBMD (SPP1, P=6× 10−20) showed both exo- and endo- skeletal abnormalities as predicted by our genetic association analyses; col11a2Y228X/Y228X mutants showed exoskeletal and endoskeletal features consistent with abnormal growth, whereas spp1P160X/P160X mutants predominantly showed mineralisation defects. Conclusion We show that scales have a strong osteogenic expression profile comparable to other elements of the dermal skeleton, enriched in genes that favour collagen matrix growth. Despite the many differences between scale and endoskeletal developmental processes, we also show that zebrafish scales express an evolutionarily conserved sub-population of genes that are relevant to human skeletal disease. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01209-8.
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31
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Kaliya-Perumal AK, Ingham PW. Musculoskeletal regeneration: A zebrafish perspective. Biochimie 2021; 196:171-181. [PMID: 34715269 DOI: 10.1016/j.biochi.2021.10.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/17/2021] [Accepted: 10/22/2021] [Indexed: 12/18/2022]
Abstract
Musculoskeletal injuries are common in humans. The cascade of cellular and molecular events following such injuries results either in healing with functional recovery or scar formation. While fibrotic scar tissue serves to bridge between injured planes, it undermines functional integrity. Hence, faithful regeneration is the most desired outcome; however, the potential to regenerate is limited in humans. In contrast, various non-mammalian vertebrates have fascinating capabilities of regenerating even an entire appendage following amputation. Among them, zebrafish is an important and accessible laboratory model organism, sharing striking similarities with mammalian embryonic musculoskeletal development. Moreover, clinically relevant muscle and skeletal injury zebrafish models recapitulate mammalian regeneration. Upon muscle injury, quiescent stem cells - known as satellite cells - become activated, proliferate, differentiate and fuse to form new myofibres, while bone fracture results in a phased response involving hematoma formation, inflammation, fibrocartilaginous callus formation, bony callus formation and remodelling. These models are well suited to testing gene- or pharmaco-therapy for the benefit of conditions like muscle tears and fractures. Insights from further studies on whole body part regeneration, a hallmark of the zebrafish model, have the potential to complement regenerative strategies to achieve faster and desired healing following injuries without any scar formation and, in the longer run, drive progress towards the realisation of large-scale regeneration in mammals. Here, we provide an overview of the basic mechanisms of musculoskeletal regeneration, highlight the key features of zebrafish as a regenerative model and outline the relevant studies that have contributed to the advancement of this field.
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Affiliation(s)
- Arun-Kumar Kaliya-Perumal
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, 59 Nanyang Drive, Singapore 636921, Singapore.
| | - Philip W Ingham
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, 59 Nanyang Drive, Singapore 636921, Singapore.
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32
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Choe CP, Choi SY, Kee Y, Kim MJ, Kim SH, Lee Y, Park HC, Ro H. Transgenic fluorescent zebrafish lines that have revolutionized biomedical research. Lab Anim Res 2021; 37:26. [PMID: 34496973 PMCID: PMC8424172 DOI: 10.1186/s42826-021-00103-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/26/2021] [Indexed: 12/22/2022] Open
Abstract
Since its debut in the biomedical research fields in 1981, zebrafish have been used as a vertebrate model organism in more than 40,000 biomedical research studies. Especially useful are zebrafish lines expressing fluorescent proteins in a molecule, intracellular organelle, cell or tissue specific manner because they allow the visualization and tracking of molecules, intracellular organelles, cells or tissues of interest in real time and in vivo. In this review, we summarize representative transgenic fluorescent zebrafish lines that have revolutionized biomedical research on signal transduction, the craniofacial skeletal system, the hematopoietic system, the nervous system, the urogenital system, the digestive system and intracellular organelles.
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Affiliation(s)
- Chong Pyo Choe
- Division of Life Science, Gyeongsang National University, Jinju, 52828, Republic of Korea.,Division of Applied Life Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Seok-Yong Choi
- Department of Biomedical Sciences, Chonnam National University Medical School, Hwasun, 58128, Republic of Korea
| | - Yun Kee
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.
| | - Min Jung Kim
- Department of Biological Sciences, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Seok-Hyung Kim
- Department of Marine Life Sciences and Fish Vaccine Research Center, Jeju National University, Jeju, 63243, Republic of Korea
| | - Yoonsung Lee
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea
| | - Hae-Chul Park
- Department of Biomedical Sciences, College of Medicine, Korea University, Ansan, 15355, Republic of Korea
| | - Hyunju Ro
- Department of Biological Sciences, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
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33
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Zhang C, Macchi F, Magnani E, Sadler KC. Chromatin states shaped by an epigenetic code confer regenerative potential to the mouse liver. Nat Commun 2021; 12:4110. [PMID: 34226551 PMCID: PMC8257577 DOI: 10.1038/s41467-021-24466-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 06/10/2021] [Indexed: 02/06/2023] Open
Abstract
We hypothesized that the highly controlled pattern of gene expression that is essential for liver regeneration is encoded by an epigenetic code set in quiescent hepatocytes. Here we report that epigenetic and transcriptomic profiling of quiescent and regenerating mouse livers define chromatin states that dictate gene expression and transposon repression. We integrate ATACseq and DNA methylation profiling with ChIPseq for the histone marks H3K4me3, H3K27me3 and H3K9me3 and the histone variant H2AZ to identify 6 chromatin states with distinct functional characteristics. We show that genes involved in proliferation reside in active states, but are marked with H3K27me3 and silenced in quiescent livers. We find that during regeneration, H3K27me3 is depleted from their promoters, facilitating their dynamic expression. These findings demonstrate that hepatic chromatin states in quiescent livers predict gene expression and that pro-regenerative genes are maintained in active chromatin states, but are restrained by H3K27me3, permitting a rapid and synchronized response during regeneration.
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Affiliation(s)
- Chi Zhang
- grid.440573.1Biology Program, NYU Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Filippo Macchi
- grid.440573.1Biology Program, NYU Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Elena Magnani
- grid.440573.1Biology Program, NYU Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Kirsten C. Sadler
- grid.440573.1Biology Program, NYU Abu Dhabi, Abu Dhabi, United Arab Emirates
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34
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Bergo V, Trompouki E. New tools for 'ZEBRA-FISHING'. Brief Funct Genomics 2021:elab001. [PMID: 33605988 DOI: 10.1093/bfgp/elab001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/14/2020] [Accepted: 01/04/2021] [Indexed: 11/14/2022] Open
Abstract
Zebrafish has been established as a classical model for developmental studies, yet in the past years, with the explosion of novel technological methods, the use of zebrafish as a model has expanded. One of the prominent fields that took advantage of zebrafish as a model organism early on is hematopoiesis, the process of blood cell generation from hematopoietic stem and progenitor cells (HSPCs). In zebrafish, HSPCs are born early during development in the aorta-gonad-mesonephros region and then translocate to the caudal hematopoietic tissue, where they expand and finally take residence in the kidney marrow. This journey is tightly regulated at multiple levels from extracellular signals to chromatin. In order to delineate the mechanistic underpinnings of this process, next-generation sequencing techniques could be an important ally. Here, we describe genome-wide approaches that have been undertaken to delineate zebrafish hematopoiesis.
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35
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Begeman IJ, Shin K, Osorio-Méndez D, Kurth A, Lee N, Chamberlain TJ, Pelegri FJ, Kang J. Decoding an organ regeneration switch by dissecting cardiac regeneration enhancers. Development 2020; 147:226055. [PMID: 33246928 DOI: 10.1242/dev.194019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 11/13/2020] [Indexed: 12/16/2022]
Abstract
Heart regeneration in regeneration-competent organisms can be accomplished through the remodeling of gene expression in response to cardiac injury. This dynamic transcriptional response relies on the activities of tissue regeneration enhancer elements (TREEs); however, the mechanisms underlying TREEs are poorly understood. We dissected a cardiac regeneration enhancer in zebrafish to elucidate the mechanisms governing spatiotemporal gene expression during heart regeneration. Cardiac lepb regeneration enhancer (cLEN) exhibits dynamic, regeneration-dependent activity in the heart. We found that multiple injury-activated regulatory elements are distributed throughout the enhancer region. This analysis also revealed that cardiac regeneration enhancers are not only activated by injury, but surprisingly, they are also actively repressed in the absence of injury. Our data identified a short (22 bp) DNA element containing a key repressive element. Comparative analysis across Danio species indicated that the repressive element is conserved in closely related species. The repression mechanism is not operational during embryogenesis and emerges when the heart begins to mature. Incorporating both activation and repression components into the mechanism of tissue regeneration constitutes a new paradigm that might be extrapolated to other regeneration scenarios.
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Affiliation(s)
- Ian J Begeman
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Kwangdeok Shin
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Daniel Osorio-Méndez
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Andrew Kurth
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Nutishia Lee
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | | | - Francisco J Pelegri
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Junsu Kang
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA.,UW Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
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36
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Yang H, Luan Y, Liu T, Lee HJ, Fang L, Wang Y, Wang X, Zhang B, Jin Q, Ang KC, Xing X, Wang J, Xu J, Song F, Sriranga I, Khunsriraksakul C, Salameh T, Li D, Choudhary MNK, Topczewski J, Wang K, Gerhard GS, Hardison RC, Wang T, Cheng KC, Yue F. A map of cis-regulatory elements and 3D genome structures in zebrafish. Nature 2020; 588:337-343. [PMID: 33239788 DOI: 10.1038/s41586-020-2962-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 09/17/2020] [Indexed: 01/08/2023]
Abstract
The zebrafish (Danio rerio) has been widely used in the study of human disease and development, and about 70% of the protein-coding genes are conserved between the two species1. However, studies in zebrafish remain constrained by the sparse annotation of functional control elements in the zebrafish genome. Here we performed RNA sequencing, assay for transposase-accessible chromatin using sequencing (ATAC-seq), chromatin immunoprecipitation with sequencing, whole-genome bisulfite sequencing, and chromosome conformation capture (Hi-C) experiments in up to eleven adult and two embryonic tissues to generate a comprehensive map of transcriptomes, cis-regulatory elements, heterochromatin, methylomes and 3D genome organization in the zebrafish Tübingen reference strain. A comparison of zebrafish, human and mouse regulatory elements enabled the identification of both evolutionarily conserved and species-specific regulatory sequences and networks. We observed enrichment of evolutionary breakpoints at topologically associating domain boundaries, which were correlated with strong histone H3 lysine 4 trimethylation (H3K4me3) and CCCTC-binding factor (CTCF) signals. We performed single-cell ATAC-seq in zebrafish brain, which delineated 25 different clusters of cell types. By combining long-read DNA sequencing and Hi-C, we assembled the sex-determining chromosome 4 de novo. Overall, our work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionarily conserved elements of 3D genome organization.
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Affiliation(s)
- Hongbo Yang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Yu Luan
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Tingting Liu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Hyung Joo Lee
- Department of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Li Fang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yanli Wang
- Bioinformatics and Genomics Program, The Pennsylvania State University, State College, PA, USA
| | - Xiaotao Wang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Bo Zhang
- Bioinformatics and Genomics Program, The Pennsylvania State University, State College, PA, USA
| | - Qiushi Jin
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Khai Chung Ang
- Department of Pathology and Penn State Zebrafish Functional Genomics Core, College of Medicine, The Pennsylvania State University, Hershey, PA, USA
| | - Xiaoyun Xing
- Department of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Juan Wang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Jie Xu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Fan Song
- Bioinformatics and Genomics Program, The Pennsylvania State University, State College, PA, USA
| | - Iyyanki Sriranga
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | | | - Tarik Salameh
- Bioinformatics and Genomics Program, The Pennsylvania State University, State College, PA, USA
| | - Daofeng Li
- Department of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Mayank N K Choudhary
- Department of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Jacek Topczewski
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Glenn S Gerhard
- Department of Medical Genetics and Molecular Biochemistry, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Ting Wang
- Department of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Keith C Cheng
- Department of Pathology and Penn State Zebrafish Functional Genomics Core, College of Medicine, The Pennsylvania State University, Hershey, PA, USA
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA. .,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA.
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37
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Ferrario C, Sugni M, Somorjai IML, Ballarin L. Beyond Adult Stem Cells: Dedifferentiation as a Unifying Mechanism Underlying Regeneration in Invertebrate Deuterostomes. Front Cell Dev Biol 2020; 8:587320. [PMID: 33195242 PMCID: PMC7606891 DOI: 10.3389/fcell.2020.587320] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 09/25/2020] [Indexed: 12/15/2022] Open
Abstract
The diversity of regenerative phenomena seen in adult metazoans, as well as their underlying mechanistic bases, are still far from being comprehensively understood. Reviewing both ultrastructural and molecular data, the present work aims to showcase the increasing relevance of invertebrate deuterostomes, i.e., echinoderms, hemichordates, cephalochordates and tunicates, as invaluable models to study cellular aspects of adult regeneration. Our comparative approach suggests a fundamental contribution of local dedifferentiation -rather than mobilization of resident undifferentiated stem cells- as an important cellular mechanism contributing to regeneration in these groups. Thus, elucidating the cellular origins, recruitment and fate of cells, as well as the molecular signals underpinning tissue regrowth in regeneration-competent deuterostomes, will provide the foundation for future research in tackling the relatively limited regenerative abilities of vertebrates, with clear applications in regenerative medicine.
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Affiliation(s)
- Cinzia Ferrario
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
- Center for Complexity and Biosystems, Department of Physics, University of Milan, Milan, Italy
| | - Michela Sugni
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
- Center for Complexity and Biosystems, Department of Physics, University of Milan, Milan, Italy
- GAIA 2050 Center, Department of Environmental Science and Policy, University of Milan, Milan, Italy
| | - Ildiko M. L. Somorjai
- The Willie Russel Laboratories, Biomedical Sciences Research Complex, North Haugh, University of St Andrews, St Andrews, United Kingdom
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38
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Thompson JD, Ou J, Lee N, Shin K, Cigliola V, Song L, Crawford GE, Kang J, Poss KD. Identification and requirements of enhancers that direct gene expression during zebrafish fin regeneration. Development 2020; 147:dev.191262. [PMID: 32665240 DOI: 10.1242/dev.191262] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/01/2020] [Indexed: 12/13/2022]
Abstract
To identify candidate tissue regeneration enhancer elements (TREEs) important for zebrafish fin regeneration, we performed ATAC-seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins. We identified tens of thousands of DNA regions from each sample type with dynamic accessibility during regeneration, and assigned these regions to proximal genes with corresponding expression changes by RNA-seq. To determine whether these profiles reveal bona fide TREEs, we tested the sufficiency and requirements of several sequences in stable transgenic lines and mutant lines with homozygous deletions. These experiments validated new non-coding regulatory sequences near induced and/or essential genes during fin regeneration, including fgf20a, mdka and cx43, identifying distinct domains of directed expression for each confirmed TREE. Whereas deletion of the previously identified LEN enhancer abolished detectable induction of the nearby leptin b gene during regeneration, deletions of enhancers linked to fgf20a, mdka and cx43 had no effect or partially reduced gene expression. Our study generates a new resource for dissecting the regulatory mechanisms of appendage generation and reveals a range of requirements for individual TREEs in control of regeneration programs.
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Affiliation(s)
- John D Thompson
- Regeneration Next, Duke University, Durham, NC 27710, USA.,Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Jianhong Ou
- Regeneration Next, Duke University, Durham, NC 27710, USA
| | - Nutishia Lee
- Regeneration Next, Duke University, Durham, NC 27710, USA.,Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Kwangdeok Shin
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Valentina Cigliola
- Regeneration Next, Duke University, Durham, NC 27710, USA.,Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Lingyun Song
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center; Center for Genomic and Computational Biology; Center for Advanced Genomic Technologies, Durham, NC 27710, USA
| | - Gregory E Crawford
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center; Center for Genomic and Computational Biology; Center for Advanced Genomic Technologies, Durham, NC 27710, USA
| | - Junsu Kang
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Kenneth D Poss
- Regeneration Next, Duke University, Durham, NC 27710, USA .,Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
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Lee HJ, Hou Y, Chen Y, Dailey ZZ, Riddihough A, Jang HS, Wang T, Johnson SL. Regenerating zebrafish fin epigenome is characterized by stable lineage-specific DNA methylation and dynamic chromatin accessibility. Genome Biol 2020; 21:52. [PMID: 32106888 PMCID: PMC7047409 DOI: 10.1186/s13059-020-1948-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 01/28/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Zebrafish can faithfully regenerate injured fins through the formation of a blastema, a mass of proliferative cells that can grow and develop into the lost body part. After amputation, various cell types contribute to blastema formation, where each cell type retains fate restriction and exclusively contributes to regeneration of its own lineage. Epigenetic changes that are associated with lineage restriction during regeneration remain underexplored. RESULTS We produce epigenome maps, including DNA methylation and chromatin accessibility, as well as transcriptomes, of osteoblasts and other cells in uninjured and regenerating fins. This effort reveals regeneration as a process of highly dynamic and orchestrated transcriptomic and chromatin accessibility changes, coupled with stably maintained lineage-specific DNA methylation. The epigenetic signatures also reveal many novel regeneration-specific enhancers, which are experimentally validated. Regulatory networks important for regeneration are constructed through integrative analysis of the epigenome map, and a knockout of a predicted upstream regulator disrupts normal regeneration, validating our prediction. CONCLUSION Our study shows that lineage-specific DNA methylation signatures are stably maintained during regeneration, and regeneration enhancers are preset as hypomethylated before injury. In contrast, chromatin accessibility is dynamically changed during regeneration. Many enhancers driving regeneration gene expression as well as upstream regulators of regeneration are identified and validated through integrative epigenome analysis.
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Affiliation(s)
- Hyung Joo Lee
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| | - Yiran Hou
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Yujie Chen
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Zea Z Dailey
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Aiyana Riddihough
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Hyo Sik Jang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA.
| | - Stephen L Johnson
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
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