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Woo SW, Kim M, Kang D, Choe YH, Oh SJ, You AS, Lee SL, Kim J. Genome-Wide Characterization of Somatic Mutation Patterns in Cloned Dogs Reveals Implications for Neuronal Function, Tumorigenesis, and Aging. Genes (Basel) 2024; 15:801. [PMID: 38927737 PMCID: PMC11202621 DOI: 10.3390/genes15060801] [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: 04/25/2024] [Revised: 05/27/2024] [Accepted: 06/15/2024] [Indexed: 06/28/2024] Open
Abstract
Studies on somatic mutations in cloned animals have revealed slight genetic variances between clones and their originals, but have yet to identify the precise effects of these differences within the organism. Somatic mutations contribute to aging and are implicated in tumor development and other age-related diseases. Thus, we compared whole genome sequencing data from an original dog with that of cloned dogs, identifying candidate somatic mutations that were disproportionately located within genes previously implicated in aging. The substitutional signature of cloning-specific somatic mutations mirrored the uniform distribution characteristic of the signature associated with human aging. Further analysis of genes revealed significant enrichment of traits associated with body size as well as the molecular mechanisms underlying neuronal function and tumorigenesis. Overall, the somatic mutations found in cloned dogs may indicate a conserved mechanism driving aging across species and a broad spectrum of pathway alterations.
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Affiliation(s)
- Seung-Wan Woo
- Division of Applied Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea; (S.-W.W.); (D.K.)
- Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea;
| | - Miju Kim
- Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea;
| | - Dayeon Kang
- Division of Applied Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea; (S.-W.W.); (D.K.)
- Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea;
| | - Yong-ho Choe
- College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea; (Y.-h.C.); (S.-J.O.); (S.-L.L.)
| | - Seong-Ju Oh
- College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea; (Y.-h.C.); (S.-J.O.); (S.-L.L.)
| | - Are-Sun You
- Division of Animal Diseases & Health, National Institute of Animal Science, RDA, Wanju 55365, Republic of Korea;
| | - Sung-Lim Lee
- College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea; (Y.-h.C.); (S.-J.O.); (S.-L.L.)
| | - Jaemin Kim
- Division of Applied Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea; (S.-W.W.); (D.K.)
- Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea;
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Han Y, Lin Q. [Research Progress of PR Domain Zinc Finger Protein 14]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2016; 19:93-7. [PMID: 26903163 PMCID: PMC6015138 DOI: 10.3779/j.issn.1009-3419.2016.02.06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
正性调节区锌指蛋白14(PR domain zinc finger protein 14, PRDM14)是PRDM家族中的重要成员,PRDM14基因对维持细胞的完整性和控制细胞的分化、生长及凋亡起着关键作用,在原始生殖细胞的形成、干细胞全能性的维持和其他组织器官的形成中都发挥了重要作用。PRDM14具有1个PR结构域和6个锌指结构,PRDM14参与了组蛋白的去乙酰化及甲基化过程,通过启动子区甲基化水平的改变参与肿瘤的形成。PRDM14异常甲基化能够引起染色质结构、DNA构象及DNA与蛋白质作用方式的改变,使基因的转录和表达受抑制,这些改变引起了肿瘤的发生、发展及转移。本文根据国内外发表的相关文献对PRDM14的研究现状进行综述。
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Affiliation(s)
- Yudong Han
- Department of Thoracic Surgery, Shanghai General Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200080, China
| | - Qiang Lin
- Department of Thoracic Surgery, Shanghai General Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200080, China
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Hrossova D, Sikorsky T, Potesil D, Bartosovic M, Pasulka J, Zdrahal Z, Stefl R, Vanacova S. RBM7 subunit of the NEXT complex binds U-rich sequences and targets 3'-end extended forms of snRNAs. Nucleic Acids Res 2015; 43:4236-48. [PMID: 25852104 PMCID: PMC4417160 DOI: 10.1093/nar/gkv240] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 03/06/2015] [Indexed: 01/09/2023] Open
Abstract
The Nuclear Exosome Targeting (NEXT) complex is a key cofactor of the mammalian nuclear exosome in the removal of Promoter Upstream Transcripts (PROMPTs) and potentially aberrant forms of other noncoding RNAs, such as snRNAs. NEXT is composed of three subunits SKIV2L2, ZCCHC8 and RBM7. We have recently identified the NEXT complex in our screen for oligo(U) RNA-binding factors. Here, we demonstrate that NEXT displays preference for U-rich pyrimidine sequences and this RNA binding is mediated by the RNA recognition motif (RRM) of the RBM7 subunit. We solved the structure of RBM7 RRM and identified two phenylalanine residues that are critical for interaction with RNA. Furthermore, we showed that these residues are required for the NEXT interaction with snRNAs in vivo. Finally, we show that depletion of components of the NEXT complex alone or together with exosome nucleases resulted in the accumulation of mature as well as extended forms of snRNAs. Thus, our data suggest a new scenario in which the NEXT complex is involved in the surveillance of snRNAs and/or biogenesis of snRNPs.
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Affiliation(s)
- Dominika Hrossova
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, 62500, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
| | - Tomas Sikorsky
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, 62500, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
| | - David Potesil
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, 62500, Czech Republic
| | - Marek Bartosovic
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, 62500, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
| | - Josef Pasulka
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, 62500, Czech Republic
| | - Zbynek Zdrahal
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, 62500, Czech Republic
| | - Richard Stefl
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, 62500, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
| | - Stepanka Vanacova
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, 62500, Czech Republic
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Abstract
The PR-domain (PRDM) family of genes encodes transcriptional regulators, several of which are deregulated in cancer. By using a functional screening approach, we sought to identify novel tumor suppressors among the PRDMs. Here we demonstrate oncogenic collaboration between depletion of the previously uncharacterized PR-domain family member Prdm11 and overexpression of MYC. Overexpression of PRDM11 inhibits proliferation and induces apoptosis. Prdm11 knockout mice are viable, and loss of Prdm11 accelerates MYC-driven lymphomagenesis in the Eµ-Myc mouse model. Moreover, we show that patients with PRDM11-deficient diffuse large B-cell lymphomas (DLBCLs) have poorer overall survival and belong to the nongerminal center B-cell-like subtype. Mechanistically, genome-wide mapping of PRDM11 binding sites coupled with transcriptome sequencing in human DLBCL cells evidenced that PRDM11 associates with transcriptional start sites of target genes and regulates important oncogenes such as FOS and JUN. Hence, we characterize PRDM11 as a putative novel tumor suppressor that controls the expression of key oncogenes, and we add new mechanistic insight into B-cell lymphomagenesis.
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Baudat F, Imai Y, de Massy B. Meiotic recombination in mammals: localization and regulation. Nat Rev Genet 2013; 14:794-806. [PMID: 24136506 DOI: 10.1038/nrg3573] [Citation(s) in RCA: 390] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
During meiosis, a programmed induction of DNA double-strand breaks (DSBs) leads to the exchange of genetic material between homologous chromosomes. These exchanges increase genome diversity and are essential for proper chromosome segregation at the first meiotic division. Recent findings have highlighted an unexpected molecular control of the distribution of meiotic DSBs in mammals by a rapidly evolving gene, PR domain-containing 9 (PRDM9), and genome-wide analyses have facilitated the characterization of meiotic DSB sites at unprecedented resolution. In addition, the identification of new players in DSB repair processes has allowed the delineation of recombination pathways that have two major outcomes, crossovers and non-crossovers, which have distinct mechanistic roles and consequences for genome evolution.
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Affiliation(s)
- Frédéric Baudat
- Institute of Human Genetics, Unité Propre de Recherche 1142, Centre National de la Recherche Scientifique, 141 rue de la Cardonille, 34396 Montpellier, France
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Thoren LA, Fog CK, Jensen KT, Buza-Vidas N, Côme C, Lund AH, Porse BT. PRDM11 is dispensable for the maintenance and function of hematopoietic stem and progenitor cells. Stem Cell Res 2013; 11:1129-36. [DOI: 10.1016/j.scr.2013.07.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 06/17/2013] [Accepted: 07/30/2013] [Indexed: 12/13/2022] Open
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The PR/SET domain zinc finger protein Prdm4 regulates gene expression in embryonic stem cells but plays a nonessential role in the developing mouse embryo. Mol Cell Biol 2013; 33:3936-50. [PMID: 23918801 PMCID: PMC3811882 DOI: 10.1128/mcb.00498-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Prdm4 is a highly conserved member of the Prdm family of PR/SET domain zinc finger proteins. Many well-studied Prdm family members play critical roles in development and display striking loss-of-function phenotypes. Prdm4 functional contributions have yet to be characterized. Here, we describe its widespread expression in the early embryo and adult tissues. We demonstrate that DNA binding is exclusively mediated by the Prdm4 zinc finger domain, and we characterize its tripartite consensus sequence via SELEX (systematic evolution of ligands by exponential enrichment) and ChIP-seq (chromatin immunoprecipitation-sequencing) experiments. In embryonic stem cells (ESCs), Prdm4 regulates key pluripotency and differentiation pathways. Two independent strategies, namely, targeted deletion of the zinc finger domain and generation of a EUCOMM LacZ reporter allele, resulted in functional null alleles. However, homozygous mutant embryos develop normally and adults are healthy and fertile. Collectively, these results strongly suggest that Prdm4 functions redundantly with other transcriptional partners to cooperatively regulate gene expression in the embryo and adult animal.
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Fog CK, Galli GG, Lund AH. PRDM proteins: important players in differentiation and disease. Bioessays 2011; 34:50-60. [PMID: 22028065 DOI: 10.1002/bies.201100107] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The PRDM family has recently spawned considerable interest as it has been implicated in fundamental aspects of cellular differentiation and exhibits expanding ties to human diseases. The PRDMs belong to the SET domain family of histone methyltransferases, however, enzymatic activity has been determined for only few PRDMs suggesting that they act by recruiting co-factors or, more speculatively, confer methylation of non-histone targets. Several PRDM family members are deregulated in human diseases, most prominently in hematological malignancies and solid cancers, where they can act as both tumor suppressors or drivers of oncogenic processes. The molecular mechanisms have been delineated for only few PRDMs and little is known about functional redundancy within the family. Future studies should identify target genes of PRDM proteins and the protein complexes in which PRDM proteins reside to provide a more comprehensive understanding of the biological and biochemical functions of this important protein family.
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Affiliation(s)
- Cathrine K Fog
- Biotech Research and Innovation Centre and Centre for Epigenetics, University of Copenhagen, Denmark
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