1
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Hirano T, Wright D, Suzuki A, Saga Y. A cooperative mechanism of target RNA selection via germ-cell-specific RNA-binding proteins NANOS2 and DND1. Cell Rep 2022; 39:110894. [PMID: 35705038 DOI: 10.1016/j.celrep.2022.110894] [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: 03/06/2021] [Revised: 12/09/2021] [Accepted: 05/06/2022] [Indexed: 11/03/2022] Open
Abstract
The germ-cell-specific RNA-binding protein (RBP) NANOS2 plays a pivotal role in male gonocyte differentiation and spermatogonial stem cell maintenance. Although NANOS2 interacts with the CNOT deadenylation complex and Dead end 1 (DND1) to repress target RNAs, the molecular mechanisms underlying target mRNA selection remain unclear because of the limited cell resource in vivo. Here, we demonstrate that exogenous NANOS2-DND1 suppresses target mRNAs in somatic cells. Using this somatic cell system, we find that NANOS2 interacts with RNA-bound DND1 and recruits the CNOT complex to the mRNAs. However, a fusion construct composed of the CNOT1-binding site of NANOS2 (NIM) and DND1 fails to repress the target gene expression. Therefore, NANOS2 is required not only for recruitment of the CNOT complex but also for selecting the target mRNA with DND1. This study reveals that NANOS2 functions as a second-layer RBP for the target recognition and functional adaptation of DND1.
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Affiliation(s)
- Takamasa Hirano
- Mammalian Development Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, 1111 Mishima, Shizuoka 411-8582, Japan
| | - Danelle Wright
- Mammalian Development Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, 1111 Mishima, Shizuoka 411-8582, Japan; Department of Genetics, SOKENDAI, 1111 Mishima, Shizuoka 411-8582, Japan
| | - Atsushi Suzuki
- Division of Materials Science and Chemical Engineering, Graduate School of Engineering, Yokohama National University, Yokohama, Kanagawa 240-8501 Japan
| | - Yumiko Saga
- Mammalian Development Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, 1111 Mishima, Shizuoka 411-8582, Japan; Department of Genetics, SOKENDAI, 1111 Mishima, Shizuoka 411-8582, Japan; Division for Development of Genetic-Engineered Mouse Resource, Genetic Resource Center, National Institute of Genetics, 1111 Mishima, Shizuoka 411-8582, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.
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2
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Zhang Y, Li Y, Chachad D, Liu B, Godavarthi JD, Williams-Villalobo A, Lasisi L, Xiong S, Matin A. In silico analysis of DND1 and its co-expressed genes in human cancers. Biochem Biophys Rep 2022; 29:101206. [PMID: 35059511 PMCID: PMC8760529 DOI: 10.1016/j.bbrep.2022.101206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 10/31/2022] Open
Abstract
Dead-End (DND1) is an RNA-binding protein involved in translational regulation. Defects in DND1 gene causes germ cell tumors and sterility in rodents. Experimental studies with human somatic cancer cells indicate that DND1 has anti-proliferative and pro-apoptotic function in some while oncogenic function in other cells. We examined The Cancer Genome Atlas data for gene alterations and gene expression changes in DND1 in a variety of human cancers. We found that DND1 is amplified, deleted or mutated in multiple human cancers. In different cancers, DND1 alteration correlates with increased diagnosis age of patients, shift in tumor spectrum or change of tumor sites and in some cases is significantly associated with worse survival for cancer patients. For 15 cancers, we retrieved expression data of thousands of genes that co-expressed with DND1. We found that these cancers contain different percentage of genes that are positively or negatively co-expressed with DND1. Ingenuity Pathway Analysis was performed to explore the biological implications of these genes. More than 10 canonical pathways were identified and each cancer type exhibits unique pathway profiles. Comparison analysis across all 15 cancer types showed that some cancers exhibit strikingly similar profiles of DND1-correlated signaling pathway activation or suppression. Our data reinforce the notion that the biological role of DND1 is cell-type specific and suggest that DND1 may play opposing role by exerting anti-proliferative effects in some cancer cells while being pro-proliferative in others. Our study provides valuable insights to direct experimental investigations of DND1 function in somatic cancers. DND1 is altered with different frequencies in multiple human cancers. DND1 changes in cancers correlate with clinical outcomes including worse prognosis. DND1 is co-expressed with a large number of genes across multiple cancer types. DND1 correlates with activation or suppression of canonical biological pathways.
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3
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Zhang Y, Godavarthi JD, Williams-Villalobo A, Polk S, Matin A. The Role of DND1 in Cancers. Cancers (Basel) 2021; 13:cancers13153679. [PMID: 34359581 PMCID: PMC8345090 DOI: 10.3390/cancers13153679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 11/16/2022] Open
Abstract
The Ter mutation in Dead-End 1 (Dnd1), Dnd1Ter, which leads to a premature stop codon, has been determined to be the cause for primordial germ cell deficiency, accompanied with a high incidence of congenital testicular germ cell tumors (TGCTs) or teratomas in the 129/Sv-Ter mice. As an RNA-binding protein, DND1 can bind the 3'-untranslated region (3'-UTR) of mRNAs and function in translational regulation. DND1 can block microRNA (miRNA) access to the 3'-UTR of target mRNAs, thus inhibiting miRNA-mediated mRNA degradation and up-regulating translation or can also function to degrade or repress mRNAs. Other mechanisms of DND1 activity include promoting translation initiation and modifying target protein activity. Although Dnd1Ter mutation causes spontaneous TGCT only in male 129 mice, it can also cause ovarian teratomas in mice when combined with other genetic defects or cause germ cell teratomas in both genders in the WKY/Ztm rat strain. Furthermore, studies on human cell lines, patient cancer tissues, and the use of human cancer genome analysis indicate that DND1 may possess either tumor-suppressive or -promoting functions in a variety of somatic cancers. Here we review the involvement of DND1 in cancers, including what appears to be its emerging role in somatic cancers.
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Affiliation(s)
- Yun Zhang
- Correspondence: (Y.Z.); (A.M.); Tel.: +1-713-313-7557 (Y.Z.); +1-713-313-7160 (A.M.)
| | | | | | | | - Angabin Matin
- Correspondence: (Y.Z.); (A.M.); Tel.: +1-713-313-7557 (Y.Z.); +1-713-313-7160 (A.M.)
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4
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Baloch AR, Franěk R, Saito T, Pšenička M. Dead-end (dnd) protein in fish-a review. FISH PHYSIOLOGY AND BIOCHEMISTRY 2021; 47:777-784. [PMID: 30671782 DOI: 10.1007/s10695-018-0606-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 12/28/2018] [Indexed: 06/09/2023]
Abstract
Dead end (dnd) is a germ plasm-specific maternal RNA discovered in zebrafish and then in other vertebrates. Dnd protein is essential for migration and motility of primordial germ cells (PGCs), only cells destined to transfer genetic information to offspring. PGCs arise far from somatic cells of developing gonads and they must migrate to their site of function. Migration of PGCs follows complex path by various developing tissues as their disruption impacts on the fertility. Recently, it has been found that dnd is not required for survival of PGCs and dnd-deficient zebrafish PGCs transdifferentiate into the somatic cells. In fish, targeting dnd causes removal of PGCs that ultimately affects sex differentiation. Sterility in various fish species can be achieved by knockdown or knockout of dnd. In our review, we have discussed dnd as a germ cell-specific molecular marker in fish, its interaction with miRNAs, and its use in aquaculture and fish conservation.
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Affiliation(s)
- Abdul Rasheed Baloch
- South Bohemian Research Center for Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice, Zatisi 728/II, 389 25, Vodnany, Czech Republic.
| | - Roman Franěk
- South Bohemian Research Center for Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice, Zatisi 728/II, 389 25, Vodnany, Czech Republic
| | - Taiju Saito
- South Bohemian Research Center for Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice, Zatisi 728/II, 389 25, Vodnany, Czech Republic
- Nishiura Station, South Ehime Fisheries Research Center, Ehime University, Uchidomari, Ainan, Ehime, 798-4206, Japan
| | - Martin Pšenička
- South Bohemian Research Center for Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice, Zatisi 728/II, 389 25, Vodnany, Czech Republic
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5
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Kumari P, Bhavesh NS. Human DND1-RRM2 forms a non-canonical domain swapped dimer. Protein Sci 2021; 30:1184-1195. [PMID: 33860980 PMCID: PMC8138521 DOI: 10.1002/pro.4083] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 11/09/2022]
Abstract
RNA recognition motif (RRM) being the most abundant RNA binding domain in eukaryotes, is a major player in cellular regulation. Several variations in the canonical βαββαβ topology have been observed. We have determined the 2.3 Å crystal structure of the human DND1-RRM2 domain. The structure revealed an interesting non-canonical RRM fold, which is maintained by the formation of a 3D domain swapped dimer between β1 and β4 strands across protomers. We have delineated the structural basis of the stable domain swapped dimer formation using the residue level dynamics of protein explored by NMR spectroscopy and MD simulations. Our structural and dynamics studies substantiate major determinants and molecular basis for domain swapped dimerization observed in the RRM domain.
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Affiliation(s)
- Pooja Kumari
- Transcription Regulation GroupInternational Centre for Genetic Engineering and Biotechnology (ICGEB)New DelhiIndia
| | - Neel Sarovar Bhavesh
- Transcription Regulation GroupInternational Centre for Genetic Engineering and Biotechnology (ICGEB)New DelhiIndia
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6
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Ruthig VA, Yokonishi T, Friedersdorf MB, Batchvarova S, Hardy J, Garness JA, Keene JD, Capel B. A transgenic DND1GFP fusion allele reports in vivo expression and RNA-binding targets in undifferentiated mouse germ cells†. Biol Reprod 2021; 104:861-874. [PMID: 33394034 PMCID: PMC8324984 DOI: 10.1093/biolre/ioaa233] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 11/23/2020] [Accepted: 12/30/2020] [Indexed: 01/20/2023] Open
Abstract
In vertebrates, the RNA-binding protein (RBP) dead end 1 (DND1) is essential for primordial germ cell (PGC) survival and maintenance of cell identity. In multiple species, Dnd1 loss or mutation leads to severe PGC loss soon after specification or, in some species, germ cell transformation to somatic lineages. Our investigations into the role of DND1 in PGC specification and differentiation have been limited by the absence of an available antibody. To address this problem, we used CRISPR/Cas9 gene editing to establish a transgenic mouse line carrying a DND1GFP fusion allele. We present imaging analysis of DND1GFP expression showing that DND1GFP expression is heterogeneous among male germ cells (MGCs) and female germ cells (FGCs). DND1GFP was detected in MGCs throughout fetal life but lost from FGCs at meiotic entry. In postnatal and adult testes, DND1GFP expression correlated with classic markers for the premeiotic spermatogonial population. Utilizing the GFP tag for RNA immunoprecipitation (RIP) analysis in MGCs validated this transgenic as a tool for identifying in vivo transcript targets of DND1. The DND1GFP mouse line is a novel tool for isolation and analysis of embryonic and fetal germ cells, and the spermatogonial population of the postnatal and adult testis.
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Affiliation(s)
- Victor A Ruthig
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
| | | | - Matthew B Friedersdorf
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Sofia Batchvarova
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
| | - Josiah Hardy
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
| | - Jason A Garness
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
| | - Jack D Keene
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Blanche Capel
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
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7
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Rescue of germ cells in dnd crispant embryos opens the possibility to produce inherited sterility in Atlantic salmon. Sci Rep 2020; 10:18042. [PMID: 33093479 PMCID: PMC7581530 DOI: 10.1038/s41598-020-74876-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 10/07/2020] [Indexed: 11/12/2022] Open
Abstract
Genetic introgression of escaped farmed Atlantic salmon (Salmo salar) into wild populations is a major environmental concern for the salmon aquaculture industry. Using sterile fish in commercial aquaculture operations is, therefore, a sustainable strategy for bio-containment. So far, the only commercially used methodology for producing sterile fish is triploidization. However, triploid fish are less robust. A novel approach in which to achieve sterility is to produce germ cell-free salmon, which can be accomplished by knocking out the dead-end (dnd) gene using CRISPR-Cas9. The lack of germ cells in the resulting dnd crispants, thus, prevents reproduction and inhibits subsequent large-scale production of sterile fish. Here, we report a rescue approach for producing germ cells in Atlantic salmon dnd crispants. To achieve this, we co-injected the wild-type (wt) variant of salmon dnd mRNA together with CRISPR-Cas9 constructs targeting dnd into 1-cell stage embryos. We found that rescued one-year-old fish contained germ cells, type A spermatogonia in males and previtellogenic primary oocytes in females. The method presented here opens a possibility for large-scale production of germ-cell free Atlantic salmon offspring through the genetically sterile broodstock which can pass the sterility trait on the next generation.
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8
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Imai A, Hagiwara Y, Niimi Y, Tokumoto T, Saga Y, Suzuki A. Mouse dead end1 acts with Nanos2 and Nanos3 to regulate testicular teratoma incidence. PLoS One 2020; 15:e0232047. [PMID: 32339196 PMCID: PMC7185693 DOI: 10.1371/journal.pone.0232047] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 04/06/2020] [Indexed: 11/19/2022] Open
Abstract
Spontaneous testicular teratomas (STTs) derived from primordial germ cells (PGCs) in the mouse embryonic testes predominantly develop in the 129 family inbred strain. Ter (spontaneous mutation) is a single nucleotide polymorphism that generates a premature stop codon of Dead end1 (Dnd1) and increases the incidence of STTs in the 129 genetic background. We previously found that DND1 interacts with NANOS2 or NANOS3 and that these complexes play a vital role in male embryonic germ cells and adult spermatogonia. However, the following are unclear: (a) whether DND1 works with NANOS2 or NANOS3 to regulate teratoma incidence, and (b) whether Ter simply causes Dnd1 loss or produces a short mutant DND1 protein. In the current study, we newly established a conventional Dnd1-knockout mouse line and found that these mice showed phenotypes similar to those of Ter mutant mice in spermatogenesis, oogenesis, and teratoma incidence, with a slight difference in spermiogenesis. In addition, we found that the amount of DND1 in Dnd1+/Ter embryos decreased to half of that in wild-type embryos, while the expression of the short mutant DND1 was not detected. We also found that double mutants for Dnd1 and Nanos2 or Nanos3 showed synergistic increase in the incidence of STTs. These data support the idea that Ter causes Dnd1 loss, leading to an increase in STT incidence, and that DND1 acts with NANOS2 and NANOS3 to regulate the development of teratoma from PGCs in the 129 genetic background. Thus, our results clarify the role of Dnd1 in the development of STTs and provide a novel insight into its pathogenic mechanism.
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Affiliation(s)
- Atsuki Imai
- Division of Materials Science and Chemical Engineering, Graduate School of Engineering, Yokohama National University, Yokohama, Kanagawa, Japan
| | - Yoshihiko Hagiwara
- Division of Materials Science and Chemical Engineering, Graduate School of Engineering, Yokohama National University, Yokohama, Kanagawa, Japan
| | - Yuki Niimi
- Division of Materials Science and Chemical Engineering, Graduate School of Engineering, Yokohama National University, Yokohama, Kanagawa, Japan
| | - Toshinobu Tokumoto
- Biological Science Course, Graduate School of Science, National University Corporation Shizuoka University, Suruga, Shizuoka, Japan
| | - Yumiko Saga
- Division of Mammalian Development, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Atsushi Suzuki
- Division of Materials Science and Chemical Engineering, Graduate School of Engineering, Yokohama National University, Yokohama, Kanagawa, Japan
- Division of Materials Science and Chemical Engineering, Faculty of Engineering, Yokohama National University, Yokohama, Kanagawa, Japan
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9
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Gross-Thebing T, Raz E. Dead end and Detour: The function of the RNA-binding protein Dnd in posttranscriptional regulation in the germline. Curr Top Dev Biol 2020; 140:181-208. [DOI: 10.1016/bs.ctdb.2019.12.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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10
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Nunez L, Mokkapati S, Yu C, Deng JM, Behringer RR, Matin A. Generation of a novel mouse strain with conditional, cell-type specific, expression of DND1. Genesis 2019; 57:e23335. [PMID: 31513344 DOI: 10.1002/dvg.23335] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 08/28/2019] [Accepted: 08/29/2019] [Indexed: 01/26/2023]
Abstract
Dead-End 1 (DND1) encodes an RNA binding protein critical for viable primordial germ cells in vertebrates. When introduced into cancer cell lines, DND1 suppresses cell proliferation and enhances apoptosis. However, the molecular function of mammalian wild-type DND1 has mostly been studied in cell lines and not verified in the organism. To facilitate study of wild-type DND1 function in mammalian systems, we generated a novel transgenic mouse line, LSL-FM-DND1 flox/+ , which conditionally expresses genetically engineered, FLAG-tagged and myc-tagged DND1 in a cell type-specific manner. We report that FLAG-myc-DND1 is indeed expressed in specific tissues of the mouse when LSL-FM-DND1 flox/+ is combined with mouse strains expressing Cre-recombinase. LSL-FM-DND1 flox/+ mice are fertile with no overt health effects. We expressed FLAG-myc-DND1 in the pancreas and found that chronic, ectopic expression of FLAG-myc-DND1 led to increase in fasting glucose levels in older mice. Thus, this novel LSL-FM-DND1 flox/+ mouse strain will facilitate studies on the biological and molecular function of wild-type DND1.
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Affiliation(s)
- Lisa Nunez
- Department of Pharmaceutical Sciences, Texas Southern University, Houston, Texas
| | - Sharada Mokkapati
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chengtai Yu
- Department of Biology and Biochemistry, University of Houston, Houston, Texas
| | - Jian M Deng
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Richard R Behringer
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Angabin Matin
- Department of Pharmaceutical Sciences, Texas Southern University, Houston, Texas
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11
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Ruthig VA, Friedersdorf MB, Garness JA, Munger SC, Bunce C, Keene JD, Capel B. The RNA-binding protein DND1 acts sequentially as a negative regulator of pluripotency and a positive regulator of epigenetic modifiers required for germ cell reprogramming. Development 2019; 146:dev175950. [PMID: 31253634 PMCID: PMC6803376 DOI: 10.1242/dev.175950] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 06/20/2019] [Indexed: 12/18/2022]
Abstract
The adult spermatogonial stem cell population arises from pluripotent primordial germ cells (PGCs) that enter the fetal testis around embryonic day (E)10.5. PGCs undergo rapid mitotic proliferation, then enter prolonged cell cycle arrest (G1/G0), during which they transition to pro-spermatogonia. In mice homozygous for the Ter mutation in the RNA-binding protein Dnd1 (Dnd1Ter/Ter ), many male germ cells (MGCs) fail to enter G1/G0 and instead form teratomas: tumors containing many embryonic cell types. To investigate the origin of these tumors, we sequenced the MGC transcriptome in Dnd1Ter/Ter mutants at E12.5, E13.5 and E14.5, immediately prior to teratoma formation, and correlated this information with DO-RIP-Seq-identified DND1 direct targets. Consistent with previous results, we found DND1 controls downregulation of many genes associated with pluripotency and active cell cycle, including mTor, Hippo and Bmp/Nodal signaling pathway elements. However, DND1 targets also include genes associated with male differentiation, including a large group of chromatin regulators activated in wild-type but not mutant MGCs during the E13.5 and E14.5 transition. Results suggest multiple DND1 functions and link DND1 to initiation of epigenetic modifications in MGCs.
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Affiliation(s)
- Victor A Ruthig
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Matthew B Friedersdorf
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Jason A Garness
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | | | - Corey Bunce
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Jack D Keene
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Blanche Capel
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
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12
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Aguero T, Jin Z, Owens D, Malhotra A, Newman K, Yang J, King ML. Combined functions of two RRMs in Dead-end1 mimic helicase activity to promote nanos1 translation in the germline. Mol Reprod Dev 2018; 85:896-908. [PMID: 30230100 DOI: 10.1002/mrd.23062] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 09/14/2018] [Indexed: 12/31/2022]
Abstract
Dead-end1 (Dnd1) expression is restricted to the vertebrate germline where it is believed to activate translation of messenger RNAs (mRNAs) required to protect and promote that unique lineage. Nanos1 is one such germline mRNA whose translation is blocked by a secondary mRNA structure within the open reading frame (ORF). Dnd1 contains a canonical RNA recognition motif (RRM1) in its N-terminus but also contains a less conserved RRM2. Here we provide a mechanistic picture of the nanos1 mRNA-Dnd1 interaction in the Xenopus germline. We show that RRM1, but not RRM2, is required for binding nanos1. Similar to the zebrafish homolog, Xenopus Dnd1 possesses ATPase activity. Surprisingly, this activity appears to be within the RRM2, different from the C-terminal region where it is found in zebrafish. More importantly, we show that RRM2 is required for nanos1 translation and germline survival. Further, Dnd1 functions as a homodimer and binds nanos1 mRNA just downstream of the secondary structure required for nanos1 repression. We propose a model in which the RRM1 is required to bind nanos1 mRNA while the RRM2 is required to promote translation through the action of ATPase. Dnd1 appears to use RRMs to mimic the function of helicases.
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Affiliation(s)
- Tristan Aguero
- Department of Cell Biology University of Miami, Miller School of Medicine, Miami, Florida
| | - Zhigang Jin
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Dawn Owens
- Department of Cell Biology University of Miami, Miller School of Medicine, Miami, Florida
| | - Arun Malhotra
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida
| | - Karen Newman
- Department of Cell Biology University of Miami, Miller School of Medicine, Miami, Florida
| | - Jing Yang
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Mary Lou King
- Department of Cell Biology University of Miami, Miller School of Medicine, Miami, Florida
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13
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Do Gametes Woo? Evidence for Their Nonrandom Union at Fertilization. Genetics 2018; 207:369-387. [PMID: 28978771 DOI: 10.1534/genetics.117.300109] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/10/2017] [Indexed: 12/18/2022] Open
Abstract
A fundamental tenet of inheritance in sexually reproducing organisms such as humans and laboratory mice is that gametes combine randomly at fertilization, thereby ensuring a balanced and statistically predictable representation of inherited variants in each generation. This principle is encapsulated in Mendel's First Law. But exceptions are known. With transmission ratio distortion, particular alleles are preferentially transmitted to offspring. Preferential transmission usually occurs in one sex but not both, and is not known to require interactions between gametes at fertilization. A reanalysis of our published work in mice and of data in other published reports revealed instances where any of 12 mutant genes biases fertilization, with either too many or too few heterozygotes and homozygotes, depending on the mutant gene and on dietary conditions. Although such deviations are usually attributed to embryonic lethality of the underrepresented genotypes, the evidence is more consistent with genetically-determined preferences for specific combinations of egg and sperm at fertilization that result in genotype bias without embryo loss. This unexpected discovery of genetically-biased fertilization could yield insights about the molecular and cellular interactions between sperm and egg at fertilization, with implications for our understanding of inheritance, reproduction, population genetics, and medical genetics.
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14
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The Vertebrate Protein Dead End Maintains Primordial Germ Cell Fate by Inhibiting Somatic Differentiation. Dev Cell 2017; 43:704-715.e5. [DOI: 10.1016/j.devcel.2017.11.019] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 09/14/2017] [Accepted: 11/20/2017] [Indexed: 12/14/2022]
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15
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Parent-of-origin effects of A1CF and AGO2 on testicular germ-cell tumors, testicular abnormalities, and fertilization bias. Proc Natl Acad Sci U S A 2016; 113:E5425-33. [PMID: 27582469 DOI: 10.1073/pnas.1604773113] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Testicular tumors, the most common cancer in young men, arise from abnormalities in germ cells during fetal development. Unconventional inheritance for testicular germ cell tumor (TGCT) risk both in humans and mice implicates epigenetic mechanisms. Apolipoprotein B mRNA-editing enzyme complex 1 (APOBEC1) cytidine deaminase and Deadend-1, which are involved in C-to-U RNA editing and microRNA-dependent mRNA silencing, respectively, are potent epigenetic modifiers of TGCT susceptibility in the genetically predisposed 129/Sv inbred mouse strain. Here, we show that partial loss of either APOBEC1 complementation factor (A1CF), the RNA-binding cofactor of APOBEC1 in RNA editing, or Argonaute 2 (AGO2), a key factor in the biogenesis of certain noncoding RNAs, modulates risk for TGCTs and testicular abnormalities in both parent-of-origin and conventional genetic manners. In addition, non-Mendelian inheritance was found among progeny of A1cf and Ago2 mutant intercrosses but not in backcrosses and without fetal loss. Together these findings suggest nonrandom union of gametes rather than meiotic drive or preferential lethality. Finally, this survey also suggested that A1CF contributes to long-term reproductive performance. These results directly implicate the RNA-binding proteins A1CF and AGO2 in the epigenetic control of germ-cell fate, urogenital development, and gamete functions.
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Bustamante-Marin XM, Cook MS, Gooding J, Newgard C, Capel B. Left-Biased Spermatogenic Failure in 129/SvJ Dnd1Ter/+ Mice Correlates with Differences in Vascular Architecture, Oxygen Availability, and Metabolites. Biol Reprod 2015; 93:78. [PMID: 26224005 PMCID: PMC6322448 DOI: 10.1095/biolreprod.115.128850] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Revised: 03/06/2015] [Accepted: 07/06/2015] [Indexed: 01/19/2023] Open
Abstract
Homozygosity for the Ter mutation in the RNA-binding protein Dead end 1 (Dnd1(Ter/Ter)) sensitizes germ cells to degeneration in all mouse strains. In 129/SvJ mice, approximately 10% of Dnd1(Ter/+) heterozygotes develop spermatogenic failure, and 95% of unilateral cases occur in the left testis. The first differences between right and left testes were detected at Postnatal Day 15 when many more spermatogonial stem cells (SSCs) were undergoing apoptosis in the left testis compared to the right. As we detected no significant left/right differences in the molecular pathway associated with body axis asymmetry or in the expression of signals known to promote proliferation, differentiation, and survival of germ cells, we investigated whether physiological differences might account for asymmetry of the degeneration phenotype. We show that left/right differences in vascular architecture are associated with a decrease in hemoglobin saturation and increased levels of HIF-1alpha in the left testis compared to the right. In Dnd1 heterozygotes, lower oxygen availability was associated with metabolic differences, including lower levels of ATP and NADH in the left testis. These experiments suggest a dependence on oxygen availability and metabolic substrates for SSC survival and suggest that Dnd1(Ter/+) SSCs may act as efficient sensors to detect subtle environmental changes that alter SSC fate.
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Affiliation(s)
- Ximena M Bustamante-Marin
- Department of Cell Biology, Duke University, Durham, North Carolina Departmento Biomédico, Facultad de Ciencias de la Salud, Universidad de Antofagasta, Antofagasta, Chile
| | - Matthew S Cook
- Department of Cell Biology, Duke University, Durham, North Carolina Department of Anatomy, University of California, San Francisco, California
| | - Jessica Gooding
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Departments of Pharmacology and Cancer Biology & Medicine, Duke University Medical Center, Durham, North Carolina
| | - Christopher Newgard
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Departments of Pharmacology and Cancer Biology & Medicine, Duke University Medical Center, Durham, North Carolina
| | - Blanche Capel
- Department of Cell Biology, Duke University, Durham, North Carolina
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Lim CY, Solter D, Knowles BB, Damjanov I. Development of Teratocarcinomas and Teratomas in Severely Immunodeficient NOD.Cg-Prkdcscid Il2rgtm1Wjl/Szj (NSG) Mice. Stem Cells Dev 2015; 24:1515-20. [DOI: 10.1089/scd.2015.0033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Chin Yan Lim
- Epithelial Epigenetics and Development Lab, Institute of Medical Biology, A*STAR, Singapore, Singapore
| | - Davor Solter
- Epithelial Epigenetics and Development Lab, Institute of Medical Biology, A*STAR, Singapore, Singapore
| | - Barbara B. Knowles
- Epithelial Epigenetics and Development Lab, Institute of Medical Biology, A*STAR, Singapore, Singapore
| | - Ivan Damjanov
- Department of Pathology, The University of Kansas School of Medicine, Kansas City, Kansas
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18
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Blanc V, Park E, Schaefer S, Miller M, Lin Y, Kennedy S, Billing AM, Hamidane HB, Graumann J, Mortazavi A, Nadeau JH, Davidson NO. Genome-wide identification and functional analysis of Apobec-1-mediated C-to-U RNA editing in mouse small intestine and liver. Genome Biol 2014; 15:R79. [PMID: 24946870 PMCID: PMC4197816 DOI: 10.1186/gb-2014-15-6-r79] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 06/19/2014] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND RNA editing encompasses a post-transcriptional process in which the genomically templated sequence is enzymatically altered and introduces a modified base into the edited transcript. Mammalian C-to-U RNA editing represents a distinct subtype of base modification, whose prototype is intestinal apolipoprotein B mRNA, mediated by the catalytic deaminase Apobec-1. However, the genome-wide identification, tissue-specificity and functional implications of Apobec-1-mediated C-to-U RNA editing remain incompletely explored. RESULTS Deep sequencing, data filtering and Sanger-sequence validation of intestinal and hepatic RNA from wild-type and Apobec-1-deficient mice revealed 56 novel editing sites in 54 intestinal mRNAs and 22 novel sites in 17 liver mRNAs, all within 3' untranslated regions. Eleven of 17 liver RNAs shared editing sites with intestinal RNAs, while 6 sites are unique to liver. Changes in RNA editing lead to corresponding changes in intestinal mRNA and protein levels for 11 genes. Analysis of RNA editing in vivo following tissue-specific Apobec-1 adenoviral or transgenic Apobec-1 overexpression reveals that a subset of targets identified in wild-type mice are restored in Apobec-1-deficient mouse intestine and liver following Apobec-1 rescue. We find distinctive polysome profiles for several RNA editing targets and demonstrate novel exonic editing sites in nuclear preparations from intestine but not hepatic apolipoprotein B RNA. RNA editing is validated using cell-free extracts from wild-type but not Apobec-1-deficient mice, demonstrating that Apobec-1 is required. CONCLUSIONS These studies define selective, tissue-specific targets of Apobec-1-dependent RNA editing and show the functional consequences of editing are both transcript- and tissue-specific.
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Affiliation(s)
- Valerie Blanc
- Department of Medicine, Washington University St Louis, St Louis, MO 63110, USA
| | - Eddie Park
- Department of Developmental and Cell Biology and Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, USA
| | - Sabine Schaefer
- Pacific Northwest Research Institute, Seattle, WA 98122, USA
| | - Melanie Miller
- Department of Medicine, Washington University St Louis, St Louis, MO 63110, USA
| | - Yiing Lin
- Departments of Surgery, Washington University St Louis, St Louis, MO 63110, USA
| | - Susan Kennedy
- Department of Medicine, Washington University St Louis, St Louis, MO 63110, USA
| | - Anja M Billing
- Proteomics Core, Weill Cornell Medical College in Qatar, Doha, Qatar
| | | | - Johannes Graumann
- Proteomics Core, Weill Cornell Medical College in Qatar, Doha, Qatar
| | - Ali Mortazavi
- Department of Developmental and Cell Biology and Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, USA
| | - Joseph H Nadeau
- Pacific Northwest Research Institute, Seattle, WA 98122, USA
| | - Nicholas O Davidson
- Department of Medicine, Washington University St Louis, St Louis, MO 63110, USA
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