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Sandoval-Velasco M, Dudchenko O, Rodríguez JA, Pérez Estrada C, Dehasque M, Fontsere C, Mak SST, Khan R, Contessoto VG, Oliveira Junior AB, Kalluchi A, Zubillaga Herrera BJ, Jeong J, Roy RP, Christopher I, Weisz D, Omer AD, Batra SS, Shamim MS, Durand NC, O'Connell B, Roca AL, Plikus MV, Kusliy MA, Romanenko SA, Lemskaya NA, Serdyukova NA, Modina SA, Perelman PL, Kizilova EA, Baiborodin SI, Rubtsov NB, Machol G, Rath K, Mahajan R, Kaur P, Gnirke A, Garcia-Treviño I, Coke R, Flanagan JP, Pletch K, Ruiz-Herrera A, Plotnikov V, Pavlov IS, Pavlova NI, Protopopov AV, Di Pierro M, Graphodatsky AS, Lander ES, Rowley MJ, Wolynes PG, Onuchic JN, Dalén L, Marti-Renom MA, Gilbert MTP, Aiden EL. Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample. Cell 2024; 187:3541-3562.e51. [PMID: 38996487 DOI: 10.1016/j.cell.2024.06.002] [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: 06/30/2023] [Revised: 03/07/2024] [Accepted: 06/03/2024] [Indexed: 07/14/2024]
Abstract
Analyses of ancient DNA typically involve sequencing the surviving short oligonucleotides and aligning to genome assemblies from related, modern species. Here, we report that skin from a female woolly mammoth (†Mammuthus primigenius) that died 52,000 years ago retained its ancient genome architecture. We use PaleoHi-C to map chromatin contacts and assemble its genome, yielding 28 chromosome-length scaffolds. Chromosome territories, compartments, loops, Barr bodies, and inactive X chromosome (Xi) superdomains persist. The active and inactive genome compartments in mammoth skin more closely resemble Asian elephant skin than other elephant tissues. Our analyses uncover new biology. Differences in compartmentalization reveal genes whose transcription was potentially altered in mammoths vs. elephants. Mammoth Xi has a tetradic architecture, not bipartite like human and mouse. We hypothesize that, shortly after this mammoth's death, the sample spontaneously freeze-dried in the Siberian cold, leading to a glass transition that preserved subfossils of ancient chromosomes at nanometer scale.
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Affiliation(s)
| | - Olga Dudchenko
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA.
| | - Juan Antonio Rodríguez
- Center for Evolutionary Hologenomics, University of Copenhagen, DK-1353 Copenhagen, Denmark; Centre Nacional d'Anàlisi Genòmica, CNAG, 08028 Barcelona, Spain
| | - Cynthia Pérez Estrada
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Marianne Dehasque
- Centre for Palaeogenetics, SE-106 91 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden; Department of Zoology, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Claudia Fontsere
- Center for Evolutionary Hologenomics, University of Copenhagen, DK-1353 Copenhagen, Denmark
| | - Sarah S T Mak
- Center for Evolutionary Hologenomics, University of Copenhagen, DK-1353 Copenhagen, Denmark
| | - Ruqayya Khan
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | | - Achyuth Kalluchi
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Bernardo J Zubillaga Herrera
- Department of Physics, Northeastern University, Boston, MA 02115, USA; Center for Theoretical Biological Physics, Northeastern University, Boston, MA 02215, USA
| | - Jiyun Jeong
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Renata P Roy
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Departments of Biology and Physics, Texas Southern University, Houston, TX 77004, USA
| | - Ishawnia Christopher
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - David Weisz
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Arina D Omer
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sanjit S Batra
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muhammad S Shamim
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Neva C Durand
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Brendan O'Connell
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Alfred L Roca
- Department of Animal Sciences and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Maksim V Plikus
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Mariya A Kusliy
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia
| | | | - Natalya A Lemskaya
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia
| | | | - Svetlana A Modina
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia
| | - Polina L Perelman
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia
| | - Elena A Kizilova
- Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
| | | | - Nikolai B Rubtsov
- Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
| | - Gur Machol
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Krisha Rath
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ragini Mahajan
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Department of Biosciences, Rice University, Houston, TX 77005, USA
| | - Parwinder Kaur
- UWA School of Agriculture and Environment, University of Western Australia, Perth, WA 6009, Australia
| | - Andreas Gnirke
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Rob Coke
- San Antonio Zoo, San Antonio, TX 78212, USA
| | | | | | - Aurora Ruiz-Herrera
- Departament de Biologia Cel·lular, Fisiologia i Immunologia and Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | | | | | - Naryya I Pavlova
- Institute of Biological Problems of Cryolitezone SB RAS, Yakutsk 677000, Russia
| | - Albert V Protopopov
- Academy of Sciences of Sakha Republic, Yakutsk 677000, Russia; North-Eastern Federal University, Yakutsk 677027, Russia
| | - Michele Di Pierro
- Department of Physics, Northeastern University, Boston, MA 02115, USA; Center for Theoretical Biological Physics, Northeastern University, Boston, MA 02215, USA
| | | | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - M Jordan Rowley
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Peter G Wolynes
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Department of Biosciences, Rice University, Houston, TX 77005, USA; Departments of Physics, Astronomy, & Chemistry, Rice University, Houston, TX 77005, USA
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Department of Biosciences, Rice University, Houston, TX 77005, USA; Departments of Physics, Astronomy, & Chemistry, Rice University, Houston, TX 77005, USA
| | - Love Dalén
- Centre for Palaeogenetics, SE-106 91 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden; Department of Zoology, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Marc A Marti-Renom
- Centre Nacional d'Anàlisi Genòmica, CNAG, 08028 Barcelona, Spain; Centre for Genomic Regulation, The Barcelona Institute for Science and Technology, 08003 Barcelona, Spain; ICREA, 08010 Barcelona, Spain; Universitat Pompeu Fabra, 08002 Barcelona, Spain.
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, University of Copenhagen, DK-1353 Copenhagen, Denmark; University Museum NTNU, 7012 Trondheim, Norway.
| | - Erez Lieberman Aiden
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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Nguyen TD, Li H, Zhuang Y, Chen B, Kinoshita K, Jamal MA, Xu K, Guo J, Jiao D, Tanabe K, Wei Y, Li Z, Cheng W, Qing Y, Zhao HY, Wei HJ. In vitro and in vivo development of interspecies Asian elephant embryos reconstructed with pig enucleated oocytes. Anim Biotechnol 2023; 34:1909-1918. [PMID: 35404767 DOI: 10.1080/10495398.2022.2058005] [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: 11/01/2022]
Abstract
Interspecies somatic cell nuclear transfer (iSCNT) has an immense potential to rescue endangered animals and extinct species like mammoths. In this study, we successfully established an Asian elephant's fibroblast cell lines from ear tissues, performed iSCNT with porcine oocytes and evaluated the in vitro and in vivo development of reconstructed embryos. A total of 7780 elephant-pig iSCNT embryos were successfully reconstructed and showed in vitro development with cleavage rate, 4-cell, 8-cell and blastocyst rate of 73.01, 30.48, 5.64, and 4.73%, respectively. The total number of elephant-pig blastocyte cells and diameter of hatched blastocyte was 38.67 and 252.75 μm, respectively. Next, we designed species-specific markers targeting EDNRB, AGRP and TYR genes to verify the genome of reconstructed embryos with donor nucleus/species. The results indicated that 53.2, 60.8, and 60.8% of reconstructed embryos (n = 235) contained elephant genome at 1-cell, 2-cell and 4-cell stages, respectively. However, the percentages decreased to 32.3 and 32.7% at 8-cell and blastocyst stages, respectively. Furthermore, we also evaluated the in vivo development of elephant-pig iSCNT cloned embryos and transferred 2260 reconstructed embryos into two surrogate gilts that successfully became pregnant and a total of 11 (1 and 10) fetuses were surgically recovered after 17 and 19 days of gestation, respectively. The crown-rump length and width of elephant-pig cloned fetuses were smaller than the control group. Unfortunately, none of these fetuses contained elephant genomes, which suggested that elephant embryos failed to develop in vivo. In conclusion, we successfully obtained elephant-pig reconstructed embryos for the first time and these embryos are able to develop to blastocyst, but the in vivo developmental failure needs further investigated.
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Affiliation(s)
- Tien Dat Nguyen
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- Xenotransplantation Engineering Research Center in Yunnan Province, Kunming, China
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Honghui Li
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- Xenotransplantation Engineering Research Center in Yunnan Province, Kunming, China
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Yiquan Zhuang
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- Xenotransplantation Engineering Research Center in Yunnan Province, Kunming, China
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Bowei Chen
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- Xenotransplantation Engineering Research Center in Yunnan Province, Kunming, China
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Keiji Kinoshita
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- Xenotransplantation Engineering Research Center in Yunnan Province, Kunming, China
| | - Muhammad Ameen Jamal
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- Xenotransplantation Engineering Research Center in Yunnan Province, Kunming, China
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Kaixiang Xu
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- Xenotransplantation Engineering Research Center in Yunnan Province, Kunming, China
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Jianxiong Guo
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- Xenotransplantation Engineering Research Center in Yunnan Province, Kunming, China
| | - Deling Jiao
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- Xenotransplantation Engineering Research Center in Yunnan Province, Kunming, China
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Kumiko Tanabe
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- Xenotransplantation Engineering Research Center in Yunnan Province, Kunming, China
| | - Yunfang Wei
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- Xenotransplantation Engineering Research Center in Yunnan Province, Kunming, China
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Zhuo Li
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- Xenotransplantation Engineering Research Center in Yunnan Province, Kunming, China
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Wenming Cheng
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- Xenotransplantation Engineering Research Center in Yunnan Province, Kunming, China
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Yubo Qing
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- Xenotransplantation Engineering Research Center in Yunnan Province, Kunming, China
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Hong-Ye Zhao
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- Xenotransplantation Engineering Research Center in Yunnan Province, Kunming, China
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Hong-Jiang Wei
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- Xenotransplantation Engineering Research Center in Yunnan Province, Kunming, China
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
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3
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Gambini A, Briski O, Canel NG. State of the art of nuclear transfer technologies for assisting mammalian reproduction. Mol Reprod Dev 2022; 89:230-242. [PMID: 35642677 DOI: 10.1002/mrd.23615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/14/2022] [Accepted: 05/22/2022] [Indexed: 12/27/2022]
Abstract
The transfer of nuclear genomic DNA from a cell to a previously enucleated oocyte or zygote constitutes one of the main tools for studying epigenetic reprogramming, nucleus-cytoplasm compatibility, pluripotency state, and for genetic preservation or edition in animals. More than 50 years ago, the first experiences in nuclear transfer began to reveal that factors stored in the cytoplasm of oocytes could reprogram the nucleus of another cell and support the development of an embryo with new genetic information. Furthermore, when the nuclear donor cell is an oocyte, egg, or a zygote, the implementation of these technologies acquires clinical relevance for patients with repeated failures in ART associated with poor oocyte quality or mitochondrial dysfunctions. This review describes the current state, scope, and future perspectives of nuclear transfer techniques currently available for assisting mammal reproduction.
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Affiliation(s)
- Andrés Gambini
- Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina.,School of Agriculture and Food Sciences, The University of Queensland, Gatton, Queensland, Australia
| | - Olinda Briski
- Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Natalia Gabriela Canel
- Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina.,Hospital de Clínicas "José de San Martín," Instituto Universitario de Fertilidad y Reproducción Humana, Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
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4
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Technical, Biological and Molecular Aspects of Somatic Cell Nuclear Transfer – A Review. ANNALS OF ANIMAL SCIENCE 2022. [DOI: 10.2478/aoas-2021-0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Abstract
Since the announcement of the birth of the first cloned mammal in 1997, Dolly the sheep, 24 animal species including laboratory, farm, and wild animals have been cloned. The technique for somatic cloning involves transfer of the donor nucleus of a somatic cell into an enucleated oocyte at the metaphase II (MII) stage for the generation of a new individual, genetically identical to the somatic cell donor. There is increasing interest in animal cloning for different purposes such as rescue of endangered animals, replication of superior farm animals, production of genetically engineered animals, creation of biomedical models, and basic research. However, the efficiency of cloning remains relatively low. High abortion, embryonic, and fetal mortality rates are frequently observed. Moreover, aberrant developmental patterns during or after birth are reported. Researchers attribute these abnormal phenotypes mainly to incomplete nuclear remodeling, resulting in incomplete reprogramming. Nevertheless, multiple factors influence the success of each step of the somatic cloning process. Various strategies have been used to improve the efficiency of nuclear transfer and most of the phenotypically normal born clones can survive, grow, and reproduce. This paper will present some technical, biological, and molecular aspects of somatic cloning, along with remarkable achievements and current improvements.
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5
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Effect of bFGF on fibroblasts derived from the golden snub-nosed monkey. Primates 2020; 62:369-378. [PMID: 33211213 DOI: 10.1007/s10329-020-00875-6] [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: 01/26/2020] [Accepted: 10/31/2020] [Indexed: 10/22/2022]
Abstract
Golden snub-nosed monkeys are endangered animals in China, and their cells have been demonstrated to be important as genetic resources and in applications for advancing biological research. Moreover, in primary research, basic fibroblast growth factor (bFGF) is used to promote the proliferation of fibroblasts to create abundant cells for cryopreservation. To further investigate the effect of bFGF on the efficiency of preservation of fibroblasts obtained from an endangered species, a fibroblast cell line was isolated from a dead golden snub-nosed monkey. Cell viability and mitochondrial membrane potential were assessed using CCK8 and JC-1 assay kits. The karyotype was analyzed by chromosomal microarray analysis, while RNA sequencing and gene expression analyses were performed to assess molecular changes in response to bFGF. Flow cytometry was used to characterize changes in cell surface markers in response to bFGF treatment. The results showed that cells maintained typical fibroblast morphology, while cell viability and mitochondrial membrane potential were not significantly affected between three and eight passages (p > 0.05). We also observed that the addition of bFGF promoted fibroblast proliferation and increased mitochondrial membrane potential. In addition, the bFGF treatment did not alter the normal karyotype of cells, downregulating fibroblast-associated genes and upregulating those associated with cell regulation, including those of the WNT, PI3K and MAPK pathways. The addition of bFGF also increased CD29, CD90, CD105, CD34 and CD44 expression while decreasing that of CD14 and HLA-DR at the protein level. Taken together, these results demonstrate that bFGF may upregulate the WNT, PI3K and MAPK pathways to promote cell proliferation while also increasing the expression of genes and surface markers associated with mesenchymal and hematopoietic cell linages.
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6
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Potential role of intraspecific and interspecific cloning in the conservation of wild mammals. ZYGOTE 2019; 27:111-117. [DOI: 10.1017/s0967199419000170] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
SummaryIntraspecific and interspecific cloning via somatic cell nuclear transfer (iSCNT) is a biotechnique with great possibilities for wild mammals because it allows the maintenance of biodiversity by recovering species, nuclear reprogramming for the production of pluripotency-induced cells, and studies related to embryonic development. Nevertheless, many areas in cloning, especially those associated with wild mammals, are still in question because of the difficulty in obtaining cytoplasmic donor cells (or cytoplasts). Conversely, donor cell nuclei (or karyoplasts) are widely obtained from the skin of living or post-mortem individuals and often maintained in somatic cell banks. Moreover, the creation of karyoplast–cytoplast complexes by fusion followed by activation and embryo development is one of the most difficult steps that requires further clarification to avoid genetic failures. Although difficult, cloning different species, such as wild carnivores and ungulates, can be successful via iSCNT with embryo development and the birth of offspring. Thus, novel research in the area that contributes to the conservation of biodiversity and knowledge of the physiology of species continues. The present review presents the failures and successes that occurred with the application of the technique in wild mammals, with the goal of helping future work on cloning via iSCNT.
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7
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Yamagata K, Nagai K, Miyamoto H, Anzai M, Kato H, Miyamoto K, Kurosaka S, Azuma R, Kolodeznikov II, Protopopov AV, Plotnikov VV, Kobayashi H, Kawahara-Miki R, Kono T, Uchida M, Shibata Y, Handa T, Kimura H, Hosoi Y, Mitani T, Matsumoto K, Iritani A. Signs of biological activities of 28,000-year-old mammoth nuclei in mouse oocytes visualized by live-cell imaging. Sci Rep 2019; 9:4050. [PMID: 30858410 PMCID: PMC6411884 DOI: 10.1038/s41598-019-40546-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 02/19/2019] [Indexed: 12/12/2022] Open
Abstract
The 28,000-year-old remains of a woolly mammoth, named ‘Yuka’, were found in Siberian permafrost. Here we recovered the less-damaged nucleus-like structures from the remains and visualised their dynamics in living mouse oocytes after nuclear transfer. Proteomic analyses demonstrated the presence of nuclear components in the remains. Nucleus-like structures found in the tissue homogenate were histone- and lamin-positive by immunostaining. In the reconstructed oocytes, the mammoth nuclei showed the spindle assembly, histone incorporation and partial nuclear formation; however, the full activation of nuclei for cleavage was not confirmed. DNA damage levels, which varied among the nuclei, were comparable to those of frozen-thawed mouse sperm and were reduced in some reconstructed oocytes. Our work provides a platform to evaluate the biological activities of nuclei in extinct animal species.
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Affiliation(s)
- Kazuo Yamagata
- Graduate School of Biology-Oriented Science and Technology, Kindai University, Wakayama, 649-6493, Japan
| | - Kouhei Nagai
- Graduate School of Biology-Oriented Science and Technology, Kindai University, Wakayama, 649-6493, Japan
| | - Hiroshi Miyamoto
- Graduate School of Biology-Oriented Science and Technology, Kindai University, Wakayama, 649-6493, Japan
| | - Masayuki Anzai
- Institute of Advanced Technology, Kindai University, Wakayama, 642-0017, Japan
| | - Hiromi Kato
- Institute of Advanced Technology, Kindai University, Wakayama, 642-0017, Japan
| | - Kei Miyamoto
- Graduate School of Biology-Oriented Science and Technology, Kindai University, Wakayama, 649-6493, Japan
| | - Satoshi Kurosaka
- Institute of Advanced Technology, Kindai University, Wakayama, 642-0017, Japan
| | - Rika Azuma
- Graduate School of Biology-Oriented Science and Technology, Kindai University, Wakayama, 649-6493, Japan
| | - Igor I Kolodeznikov
- Department of Mammoth Faunal Studies, Sakha (Yakutia) Republic Academy of the Sciences, Yakutsk, 677077, Russia
| | - Albert V Protopopov
- Department of Mammoth Faunal Studies, Sakha (Yakutia) Republic Academy of the Sciences, Yakutsk, 677077, Russia
| | - Valerii V Plotnikov
- Department of Mammoth Faunal Studies, Sakha (Yakutia) Republic Academy of the Sciences, Yakutsk, 677077, Russia
| | - Hisato Kobayashi
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, 156-8502, Japan
| | - Ryouka Kawahara-Miki
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, 156-8502, Japan
| | - Tomohiro Kono
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, 156-8502, Japan.,Department of Bioscience, Tokyo University of Agriculture, Tokyo, 156-8502, Japan
| | - Masao Uchida
- National Institute for Environmental Studies, Ibaraki, 305-8506, Japan
| | - Yasuyuki Shibata
- National Institute for Environmental Studies, Ibaraki, 305-8506, Japan
| | - Tetsuya Handa
- Institute of Innovative Research, Tokyo Institute of Technology, Kanagawa, 226-8503, Japan
| | - Hiroshi Kimura
- Institute of Innovative Research, Tokyo Institute of Technology, Kanagawa, 226-8503, Japan
| | - Yoshihiko Hosoi
- Graduate School of Biology-Oriented Science and Technology, Kindai University, Wakayama, 649-6493, Japan
| | - Tasuku Mitani
- Graduate School of Biology-Oriented Science and Technology, Kindai University, Wakayama, 649-6493, Japan
| | - Kazuya Matsumoto
- Graduate School of Biology-Oriented Science and Technology, Kindai University, Wakayama, 649-6493, Japan
| | - Akira Iritani
- Institute of Advanced Technology, Kindai University, Wakayama, 642-0017, Japan.
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8
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Moulavi F, Hosseini S, Tanhaie-Vash N, Ostadhosseini S, Hosseini S, Hajinasrollah M, Asghari M, Gourabi H, Shahverdi A, Vosough A, Nasr-Esfahani M. Interspecies somatic cell nuclear transfer in Asiatic cheetah using nuclei derived from post-mortem frozen tissue in absence of cryo-protectant and in vitro matured domestic cat oocytes. Theriogenology 2017; 90:197-203. [DOI: 10.1016/j.theriogenology.2016.11.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 11/25/2016] [Accepted: 11/26/2016] [Indexed: 11/28/2022]
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9
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Abstract
The convergence of several disparate research programmes raises the possibility that the long-term evolutionary processes of innovation and radiation may become amenable to laboratory experimentation. Ancestors might be resurrected directly from naturally stored propagules or tissues, or indirectly from the expression of ancestral genes in contemporary genomes. New kinds of organisms might be evolved through artificial selection of major developmental genes. Adaptive radiation can be studied by mimicking major ecological transitions in the laboratory. All of these possibilities are subject to severe quantitative and qualitative limitations. In some cases, however, laboratory experiments may be capable of illuminating the processes responsible for the evolution of new kinds of organisms.
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Affiliation(s)
- Graham Bell
- Biology Department, McGill University, 1205 avenue docteur Penfield, Montreal, Quebec, Canada H3A 1B1
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10
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Affiliation(s)
- Douglas J. Richmond
- Section for Evolutionary Genomics Natural History Museum of Denmark University of Copenhagen Øster Voldgade 5–7 1350 Copenhagen Denmark
| | - Mikkel‐Holger S. Sinding
- Section for Evolutionary Genomics Natural History Museum of Denmark University of Copenhagen Øster Voldgade 5–7 1350 Copenhagen Denmark
- Natural History Museum University of Oslo P.O. Box 1172 Blindern NO‐0318 Oslo Norway
| | - M. Thomas P. Gilbert
- Section for Evolutionary Genomics Natural History Museum of Denmark University of Copenhagen Øster Voldgade 5–7 1350 Copenhagen Denmark
- Trace and Environmental DNA Laboratory Department of Environment and Agriculture Curtin University Perth WA 6102 Australia
- NTNU University Museum NO‐7491 Trondheim Norway
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Wisely SM, Ryder OA, Santymire RM, Engelhardt JF, Novak BJ. A Road Map for 21st Century Genetic Restoration: Gene Pool Enrichment of the Black-Footed Ferret. J Hered 2015; 106:581-92. [PMID: 26304983 PMCID: PMC4567841 DOI: 10.1093/jhered/esv041] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 06/07/2015] [Indexed: 12/15/2022] Open
Abstract
Interspecies somatic cell nuclear transfer (iSCNT) could benefit recovery programs of critically endangered species but must be weighed with the risks of failure. To weigh the risks and benefits, a decision-making process that evaluates progress is needed. Experiments that evaluate the efficiency and efficacy of blastocyst, fetal, and post-parturition development are necessary to determine the success or failure or species-specific iSCNT programs. Here, we use the black-footed ferret (Mustela nigripes) as a case study for evaluating this emerging biomedical technology as a tool for genetic restoration. The black-footed ferret has depleted genetic variation yet genome resource banks contain genetic material of individuals not currently represented in the extant lineage. Thus, genetic restoration of the species is in theory possible and could help reduce the persistent erosion of genetic diversity from drift. Extensive genetic, genomic, and reproductive science tools have previously been developed in black-footed ferrets and would aid in the process of developing an iSCNT protocol for this species. Nonetheless, developing reproductive cloning will require years of experiments and a coordinated effort among recovery partners. The information gained from a well-planned research effort with the goal of genetic restoration via reproductive cloning could establish a 21st century model for evaluating and implementing conservation breeding that would be applicable to other genetically impoverished species.
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Affiliation(s)
- Samantha M Wisely
- From the Department of Wildlife Ecology and Conservation, University of Florida, 110 Newins-Ziegler Hall, Gainesville, Florida, 32611 USA (Wisely); San Diego Zoo Institute for Conservation Research, 15600 San Pasqual Valley Road, San Diego Zoo Global, Escondido, California, 92027 USA (Ryder); Davee Center for Epidemiology and Endocrinology, 2001 North Clark Street, Lincoln Park Zoo, Chicago, Illinois, 60614 USA (Santymire); Department of Anatomy and Cell Biology, 51 Newton Road, University of Iowa, Iowa City, Iowa, 52242 USA (Engelhardt); and Revive & Restore, The Long Now Foundation, 2 Marina Boulevard Building A, San Francisco, California, 94123 USA (Novak).
| | - Oliver A Ryder
- From the Department of Wildlife Ecology and Conservation, University of Florida, 110 Newins-Ziegler Hall, Gainesville, Florida, 32611 USA (Wisely); San Diego Zoo Institute for Conservation Research, 15600 San Pasqual Valley Road, San Diego Zoo Global, Escondido, California, 92027 USA (Ryder); Davee Center for Epidemiology and Endocrinology, 2001 North Clark Street, Lincoln Park Zoo, Chicago, Illinois, 60614 USA (Santymire); Department of Anatomy and Cell Biology, 51 Newton Road, University of Iowa, Iowa City, Iowa, 52242 USA (Engelhardt); and Revive & Restore, The Long Now Foundation, 2 Marina Boulevard Building A, San Francisco, California, 94123 USA (Novak)
| | - Rachel M Santymire
- From the Department of Wildlife Ecology and Conservation, University of Florida, 110 Newins-Ziegler Hall, Gainesville, Florida, 32611 USA (Wisely); San Diego Zoo Institute for Conservation Research, 15600 San Pasqual Valley Road, San Diego Zoo Global, Escondido, California, 92027 USA (Ryder); Davee Center for Epidemiology and Endocrinology, 2001 North Clark Street, Lincoln Park Zoo, Chicago, Illinois, 60614 USA (Santymire); Department of Anatomy and Cell Biology, 51 Newton Road, University of Iowa, Iowa City, Iowa, 52242 USA (Engelhardt); and Revive & Restore, The Long Now Foundation, 2 Marina Boulevard Building A, San Francisco, California, 94123 USA (Novak)
| | - John F Engelhardt
- From the Department of Wildlife Ecology and Conservation, University of Florida, 110 Newins-Ziegler Hall, Gainesville, Florida, 32611 USA (Wisely); San Diego Zoo Institute for Conservation Research, 15600 San Pasqual Valley Road, San Diego Zoo Global, Escondido, California, 92027 USA (Ryder); Davee Center for Epidemiology and Endocrinology, 2001 North Clark Street, Lincoln Park Zoo, Chicago, Illinois, 60614 USA (Santymire); Department of Anatomy and Cell Biology, 51 Newton Road, University of Iowa, Iowa City, Iowa, 52242 USA (Engelhardt); and Revive & Restore, The Long Now Foundation, 2 Marina Boulevard Building A, San Francisco, California, 94123 USA (Novak)
| | - Ben J Novak
- From the Department of Wildlife Ecology and Conservation, University of Florida, 110 Newins-Ziegler Hall, Gainesville, Florida, 32611 USA (Wisely); San Diego Zoo Institute for Conservation Research, 15600 San Pasqual Valley Road, San Diego Zoo Global, Escondido, California, 92027 USA (Ryder); Davee Center for Epidemiology and Endocrinology, 2001 North Clark Street, Lincoln Park Zoo, Chicago, Illinois, 60614 USA (Santymire); Department of Anatomy and Cell Biology, 51 Newton Road, University of Iowa, Iowa City, Iowa, 52242 USA (Engelhardt); and Revive & Restore, The Long Now Foundation, 2 Marina Boulevard Building A, San Francisco, California, 94123 USA (Novak)
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Loi P, Saragusty J, Ptak G. Cloning the mammoth: a complicated task or just a dream? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 753:489-502. [PMID: 25091921 DOI: 10.1007/978-1-4939-0820-2_19] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Recently there has been growing interest in applying the most advanced embryological tools, particularly cloning, to bring extinct species back to life, with a particular focus on the woolly mammoth (Mammuthus primigenius). Mammoth's bodies found in the permafrost are relatively well preserved, with identifiable nuclei in their tissues. The purpose of this chapter is to review the literature published on the topic, and to present the strategies potentially suitable for a mammoth cloning project, with a frank assessment of their feasibility and the ethical issues involved.
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Affiliation(s)
- Pasqualino Loi
- Department of Comparative Biomedical Sciences, University of Teramo, Piazza Aldo Moro 45, Teramo, 64100, Italy,
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Loi P, Fulka J, Hildebrand T, Ptak G. Genome of non-living cells: trash or recycle? Reproduction 2011; 142:497-503. [PMID: 21778214 DOI: 10.1530/rep-11-0063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Reproductive technologies have been often used as a tool in research not strictly connected with developmental biology. In this study, we retrace the experimental routes that have led to the adoption of two reproductive technologies, ICSI and somatic cell nuclear transfer (SCNT), as biological assays to probe the 'functionality' of the genome from dead cells. The structural peculiarities of the spermatozoa nucleus, namely its lower water content and its compact chromatin structure, have made it the preferred cell for these experiments. The studies, primarily focused on mice, have demonstrated an unexpected stability of the spermatozoa nuclei, which retained the capacity to form pronuclei once injected into the oocytes even after severe denaturing agents like acid treatment and high-temperature exposure. These findings inspired further research culminating in the production of mice after ICSI of lyophilized spermatozoa. The demonstrated non-equivalence between cell vitality and nuclear vitality in spermatozoa prompted analogous studies on somatic cells. Somatic cells were treated with the same physical stress applied to spermatozoa and were injected into enucleated sheep oocytes. Despite the presumptive fragile nuclear structure, nuclei from non-viable cells (heat treated) directed early and post-implantation embryonic development on nuclear transfer, resulting in normal offspring. Recently, lyophilized somatic cells used for nuclear transfer have developed into normal embryos. In summary, ICSI and SCNT have been useful tools to prove that alternative strategies for storing banks of non-viable cells are realistic. Finally, the potential application of freeze-dried spermatozoa and cells is also discussed.
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Affiliation(s)
- Pasqualino Loi
- Department of Comparative Biomedical Sciences, University of Teramo, Piazza Aldo Moro 45, 64100 Teramo, Italy.
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