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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 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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2
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Orlova SY, Ruzina MN, Emelianova OR, Sergeev AA, Chikurova EA, Orlov AM, Mugue NS. In Search of a Target Gene for a Desirable Phenotype in Aquaculture: Genome Editing of Cyprinidae and Salmonidae Species. Genes (Basel) 2024; 15:726. [PMID: 38927661 PMCID: PMC11202958 DOI: 10.3390/genes15060726] [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: 04/24/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
Aquaculture supplies the world food market with a significant amount of valuable protein. Highly productive aquaculture fishes can be derived by utilizing genome-editing methods, and the main problem is to choose a target gene to obtain the desirable phenotype. This paper presents a review of the studies of genome editing for genes controlling body development, growth, pigmentation and sex determination in five key aquaculture Salmonidae and Cyprinidae species, such as rainbow trout (Onchorhynchus mykiss), Atlantic salmon (Salmo salar), common carp (Cyprinus carpio), goldfish (Carassius auratus), Gibel carp (Carassius gibelio) and the model fish zebrafish (Danio rerio). Among the genes studied, the most applicable for aquaculture are mstnba, pomc, and acvr2, the knockout of which leads to enhanced muscle growth; runx2b, mutants of which do not form bones in myoseptae; lepr, whose lack of function makes fish fast-growing; fads2, Δ6abc/5Mt, and Δ6bcMt, affecting the composition of fatty acids in fish meat; dnd mettl3, and wnt4a, mutants of which are sterile; and disease-susceptibility genes prmt7, gab3, gcJAM-A, and cxcr3.2. Schemes for obtaining common carp populations consisting of only large females are promising for use in aquaculture. The immobilized and uncolored zebrafish line is of interest for laboratory use.
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Affiliation(s)
- Svetlana Yu. Orlova
- Laboratory of Molecular Genetics, Russian Federal Research Institute of Fisheries and Oceanography, 105187 Moscow, Russia; (S.Y.O.)
| | - Maria N. Ruzina
- Laboratory of Molecular Genetics, Russian Federal Research Institute of Fisheries and Oceanography, 105187 Moscow, Russia; (S.Y.O.)
| | - Olga R. Emelianova
- Laboratory of Molecular Genetics, Russian Federal Research Institute of Fisheries and Oceanography, 105187 Moscow, Russia; (S.Y.O.)
- Department of Biological Evolution, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Alexey A. Sergeev
- Laboratory of Molecular Genetics, Russian Federal Research Institute of Fisheries and Oceanography, 105187 Moscow, Russia; (S.Y.O.)
| | - Evgeniya A. Chikurova
- Laboratory of Molecular Genetics, Russian Federal Research Institute of Fisheries and Oceanography, 105187 Moscow, Russia; (S.Y.O.)
| | - Alexei M. Orlov
- Laboratory of Oceanic Ichthyofauna, Shirshov Institute of Oceanology, Russian Academy of Sciences, 117218 Moscow, Russia
- Laboratory of Behavior of Lower Vertebrates, Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 119071 Moscow, Russia
- Department of Ichthyology, Dagestan State University, 367000 Makhachkala, Russia
| | - Nikolai S. Mugue
- Laboratory of Molecular Genetics, Russian Federal Research Institute of Fisheries and Oceanography, 105187 Moscow, Russia; (S.Y.O.)
- Laboratory of Genome Evolution and Speciation, Institute of Developmental Biology Russian Academy of Sciences, 117808 Moscow, Russia
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Bongiovanni C, Bueno-Levy H, Posadas Pena D, Del Bono I, Miano C, Boriati S, Da Pra S, Sacchi F, Redaelli S, Bergen M, Romaniello D, Pontis F, Tassinari R, Kellerer L, Petraroia I, Mazzeschi M, Lauriola M, Ventura C, Heermann S, Weidinger G, Tzahor E, D'Uva G. BMP7 promotes cardiomyocyte regeneration in zebrafish and adult mice. Cell Rep 2024; 43:114162. [PMID: 38678558 DOI: 10.1016/j.celrep.2024.114162] [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: 11/08/2023] [Revised: 03/06/2024] [Accepted: 04/11/2024] [Indexed: 05/01/2024] Open
Abstract
Zebrafish have a lifelong cardiac regenerative ability after damage, whereas mammals lose this capacity during early postnatal development. This study investigated whether the declining expression of growth factors during postnatal mammalian development contributes to the decrease of cardiomyocyte regenerative potential. Besides confirming the proliferative ability of neuregulin 1 (NRG1), interleukin (IL)1b, receptor activator of nuclear factor kappa-Β ligand (RANKL), insulin growth factor (IGF)2, and IL6, we identified other potential pro-regenerative factors, with BMP7 exhibiting the most pronounced efficacy. Bmp7 knockdown in neonatal mouse cardiomyocytes and loss-of-function in adult zebrafish during cardiac regeneration reduced cardiomyocyte proliferation, indicating that Bmp7 is crucial in the regenerative stages of mouse and zebrafish hearts. Conversely, bmp7 overexpression in regenerating zebrafish or administration at post-mitotic juvenile and adult mouse stages, in vitro and in vivo following myocardial infarction, enhanced cardiomyocyte cycling. Mechanistically, BMP7 stimulated proliferation through BMPR1A/ACVR1 and ACVR2A/BMPR2 receptors and downstream SMAD5, ERK, and AKT signaling. Overall, BMP7 administration is a promising strategy for heart regeneration.
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Affiliation(s)
- Chiara Bongiovanni
- Department of Medical and Surgical Sciences, University of Bologna, via Massarenti 9, 40138 Bologna, Italy; Centre for Applied Biomedical Research (CRBA), University of Bologna, via Massarenti 9, 40138 Bologna, Italy; National Laboratory of Molecular Biology and Stem Cell Engineering, National Institute of Biostructures and Biosystems (INBB), via di Corticella 183, 40128 Bologna, Italy
| | - Hanna Bueno-Levy
- Department of Molecular Cell Biology, Weizmann Institute of Science, Herzl St. 234, Rehovot 76100, Israel
| | - Denise Posadas Pena
- Institute of Biochemistry and Molecular Biology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Irene Del Bono
- Department of Medical and Surgical Sciences, University of Bologna, via Massarenti 9, 40138 Bologna, Italy; Centre for Applied Biomedical Research (CRBA), University of Bologna, via Massarenti 9, 40138 Bologna, Italy
| | - Carmen Miano
- Department of Medical and Surgical Sciences, University of Bologna, via Massarenti 9, 40138 Bologna, Italy; Centre for Applied Biomedical Research (CRBA), University of Bologna, via Massarenti 9, 40138 Bologna, Italy; National Laboratory of Molecular Biology and Stem Cell Engineering, National Institute of Biostructures and Biosystems (INBB), via di Corticella 183, 40128 Bologna, Italy
| | - Stefano Boriati
- Department of Medical and Surgical Sciences, University of Bologna, via Massarenti 9, 40138 Bologna, Italy; Centre for Applied Biomedical Research (CRBA), University of Bologna, via Massarenti 9, 40138 Bologna, Italy
| | - Silvia Da Pra
- Department of Medical and Surgical Sciences, University of Bologna, via Massarenti 9, 40138 Bologna, Italy; Centre for Applied Biomedical Research (CRBA), University of Bologna, via Massarenti 9, 40138 Bologna, Italy
| | - Francesca Sacchi
- Department of Medical and Surgical Sciences, University of Bologna, via Massarenti 9, 40138 Bologna, Italy; Centre for Applied Biomedical Research (CRBA), University of Bologna, via Massarenti 9, 40138 Bologna, Italy; National Laboratory of Molecular Biology and Stem Cell Engineering, National Institute of Biostructures and Biosystems (INBB), via di Corticella 183, 40128 Bologna, Italy
| | - Simone Redaelli
- Institute of Biochemistry and Molecular Biology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Max Bergen
- Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, Albertstrasse 17, 79104 Freiburg, Germany
| | - Donatella Romaniello
- Department of Medical and Surgical Sciences, University of Bologna, via Massarenti 9, 40138 Bologna, Italy; Centre for Applied Biomedical Research (CRBA), University of Bologna, via Massarenti 9, 40138 Bologna, Italy
| | - Francesca Pontis
- Scientific and Technological Pole, IRCCS MultiMedica, via Fantoli 16/15, 20138 Milan, Italy
| | | | - Laura Kellerer
- Institute of Biochemistry and Molecular Biology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Ilaria Petraroia
- Scientific and Technological Pole, IRCCS MultiMedica, via Fantoli 16/15, 20138 Milan, Italy
| | - Martina Mazzeschi
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, via Massarenti 9, 40138 Bologna, Italy
| | - Mattia Lauriola
- Department of Medical and Surgical Sciences, University of Bologna, via Massarenti 9, 40138 Bologna, Italy; Centre for Applied Biomedical Research (CRBA), University of Bologna, via Massarenti 9, 40138 Bologna, Italy
| | - Carlo Ventura
- Department of Medical and Surgical Sciences, University of Bologna, via Massarenti 9, 40138 Bologna, Italy; National Laboratory of Molecular Biology and Stem Cell Engineering, National Institute of Biostructures and Biosystems (INBB), via di Corticella 183, 40128 Bologna, Italy
| | - Stephan Heermann
- Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, Albertstrasse 17, 79104 Freiburg, Germany
| | - Gilbert Weidinger
- Institute of Biochemistry and Molecular Biology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Eldad Tzahor
- Department of Molecular Cell Biology, Weizmann Institute of Science, Herzl St. 234, Rehovot 76100, Israel
| | - Gabriele D'Uva
- Department of Medical and Surgical Sciences, University of Bologna, via Massarenti 9, 40138 Bologna, Italy; IRCCS Azienda Ospedaliero-Universitaria di Bologna, via Massarenti 9, 40138 Bologna, Italy.
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Wang H, Xu W, Li L. Tefluthrin induced toxicities in zebrafish: Focusing on enantioselectivity. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2023; 195:105572. [PMID: 37666624 DOI: 10.1016/j.pestbp.2023.105572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/25/2023] [Accepted: 08/07/2023] [Indexed: 09/06/2023]
Abstract
Tefluthrin is one of widely used chiral pyrethroid pesticides. The potential enantioselective risk posed by tefluthrin to the aquatic ecosystem is still unclear. In this study, the toxicity differences and corresponding mechanism of tefluthrin on zebrafish were investigated at the enantiomeric level. The results indicated that two tefluthrin enantiomers showed different acute toxicity, developmental toxicity and oxidative stress to zebrafish. The acute toxicity of (1R,3R)-tefluthrin was 130-176 fold as that of (1S,3S)-tefluthrin on zebrafish embryos, larvae and adults. (1R,3R)-Tefluthrin presented approximately 10, 3 and 2 times inhibition effect on the deformity rate, hatching rate and spontaneous movements on embryos as that of (1S,3S)-tefluthrin. Meanwhile, (1R,3R)-tefluthrin caused stronger oxidative stress on zebrafish embryo than (1S,3S)-tefluthrin. The molecular docking results revealed that there were stereospecific binding affinities between tefluthrin enantimers and sodium channel protein (Nav1.6), which may lead to acute toxicity differences. Transcriptome analysis showed that the two tefluthrin enantiomers markedly disturbed differential embryonic genes expression, thereby potentially causing the chronic enantioselective toxicity. The findings of the study reveal the toxicity differences and potential mechanism of tefluthrin enantiomers on zebrafish. These results also provides a foundation for a systematic evaluation of tefluthrin at enantiomer level.
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Affiliation(s)
- Hongjie Wang
- Hebei Key Laboratory of Close-to-Nature Restoration Technology of Wetlands, School of Eco-Environment, Hebei University, Baoding 071002, China; Institute of Xiong'an New Area, Hebei university, Baoding 071002, China; College of Life Science, Hebei University, Baoding 071002, China
| | - Weiye Xu
- Hebei Key Laboratory of Close-to-Nature Restoration Technology of Wetlands, School of Eco-Environment, Hebei University, Baoding 071002, China
| | - Lianshan Li
- Hebei Key Laboratory of Close-to-Nature Restoration Technology of Wetlands, School of Eco-Environment, Hebei University, Baoding 071002, China; Institute of Xiong'an New Area, Hebei university, Baoding 071002, China.
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Mansuri A, Kansara K, Raiyani D, Mazmudar D, Kumar A. New insight into long-term effects of phthalates microplastics in developing zebrafish: Evidence from genomic alteration and organ development. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2023; 99:104087. [PMID: 36841272 DOI: 10.1016/j.etap.2023.104087] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/19/2023] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
The plasticizer leaches from the microplastics are one of the significant concerns related to plastic pollution. These plasticizers are known to be endocrine disrupters; however, little is known about their long-term effect on the development of aquatic vertebrates. Hence, the present study has been conducted to provide a holistic understanding of the effect of the three most common plasticizers, dibutyl phthalate (DBP), diethyl phthalate (DEP), and di-ethylhexyl phthalate (DEHP) leaching out from the microplastics in zebrafish development. Zebrafish larvae were exposed to different phthalates at different concentrations. The phthalates have shown significantly higher mortality and morphological changes in the larva upon exposure compared to the control. A significant change in the genes related to cardiovascular development (krit1, fbn2b), dorsoventral axis development (chrd, smad5), tail formation (pkd2, wnt3a, wnt8a), and floorplate development (foxa2) were also observed under the effects of the phthalates in comparison to control.
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Affiliation(s)
- Abdulkhalik Mansuri
- Biological and Life Sciences, School of Arts & Sciences, Ahmedabad University, Central Campus, Navrangpura, Ahmedabad 380009, Gujarat, India.
| | - Krupa Kansara
- Biological and Engineering Discipline, Indian Institute of Technology - Gandhinagar (IITGN), Palaj 382355, Gujarat, India.
| | - Dixit Raiyani
- Biological and Life Sciences, School of Arts & Sciences, Ahmedabad University, Central Campus, Navrangpura, Ahmedabad 380009, Gujarat, India.
| | - Dhairya Mazmudar
- Biological and Life Sciences, School of Arts & Sciences, Ahmedabad University, Central Campus, Navrangpura, Ahmedabad 380009, Gujarat, India.
| | - Ashutosh Kumar
- Biological and Life Sciences, School of Arts & Sciences, Ahmedabad University, Central Campus, Navrangpura, Ahmedabad 380009, Gujarat, India.
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Wu Y, Sun A, Nie C, Gao ZX, Wan SM. Functional differentiation of bmp2a and bmp2b genes in zebrafish. Gene Expr Patterns 2022; 46:119288. [PMID: 36332886 DOI: 10.1016/j.gep.2022.119288] [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: 08/21/2022] [Revised: 09/25/2022] [Accepted: 10/29/2022] [Indexed: 11/06/2022]
Abstract
Bone morphogenetic protein 2 plays an important role in the regulation of osteoblast proliferation and differentiation. Phylogenetic analysis showed that the bmp2 ortholog evolved from the same ancestral gene family in vertebrates and was duplicated in teleost, which were named bmp2a and bmp2b. The results of whole-mount in situ hybridization showed that the expression locations of bmp2a and bmp2b in zebrafish were different in different periods (24 hpf, 48 hpf, 72 hpf), which revealed potential functional differentiation between bmp2a and bmp2b. Phenotypic analysis showed that bmp2a mutations caused partial rib and vertebral deformities in zebrafish, while bmp2b-/- embryos died massively after 12 hpf due to abnormal somite formation. We further explored the expression pattern changes of genes (bmp2a, bmp2b, smad1, fgf4, runx2b, alp) related to skeletal development at different developmental stages (20 dpf, 60 dpf, 90 dpf) in wild-type and bmp2a-/- zebrafish. The results showed that the expression of runx2b in bmp2a-/- was significantly downregulated at three stages and the expression of other genes were significantly downregulated at 90 dpf compared with wild-type zebrafish. The study revealed functional differentiation of bmp2a and bmp2b in zebrafish embryonic and skeletal development.
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Affiliation(s)
- Yaming Wu
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Aili Sun
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chunhong Nie
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ze-Xia Gao
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Shi-Ming Wan
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.
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