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Mann JM, Wei C, Chen C. How genetic defects in piRNA trimming contribute to male infertility. Andrology 2023; 11:911-917. [PMID: 36263612 PMCID: PMC10115909 DOI: 10.1111/andr.13324] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/25/2022] [Accepted: 10/10/2022] [Indexed: 11/27/2022]
Abstract
In germ cells, small non-coding PIWI-interacting RNAs (piRNAs) work to silence harmful transposons to maintain genomic stability and regulate gene expression to ensure fertility. However, these piRNAs must undergo a series of steps during biogenesis to be properly loaded onto PIWI proteins and reach the correct nucleotide length. This review is focused on what we are learning about a crucial step in this process, piRNA trimming, in which pre-piRNAs are shortened to final lengths of 21-35 nucleotides. Recently, the 3'-5' exonuclease trimmer has been identified in various models as PNLDC1/PARN-1. Mutations of the piRNA trimmers in vivo lead to increased transposon expression, elevated levels of untrimmed pre-piRNAs, decreased piRNA stability, and male infertility. Here, we will discuss the role of piRNA trimmers in piRNA biogenesis and function, describe consequences of piRNA trimmer mutations using mammalian models and human patients, and examine future avenues of piRNA trimming-related study for clinical advancements for male infertility.
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Affiliation(s)
- Jeffrey M. Mann
- Department of Animal Science, Michigan State University, East Lansing, Michigan, USA
| | - Chao Wei
- Department of Animal Science, Michigan State University, East Lansing, Michigan, USA
| | - Chen Chen
- Department of Animal Science, Michigan State University, East Lansing, Michigan, USA
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan, USA
- Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, Grand Rapids, Michigan, USA
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2
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Izumi N, Shoji K, Kiuchi T, Katsuma S, Tomari Y. The two Gtsf paralogs in silkworms orthogonally activate their partner PIWI proteins for target cleavage. RNA (NEW YORK, N.Y.) 2022; 29:rna.079380.122. [PMID: 36319089 PMCID: PMC9808576 DOI: 10.1261/rna.079380.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
The PIWI-interacting RNA (piRNA) pathway is a protection mechanism against transposons in animal germ cells. Most PIWI proteins possess piRNA-guided endonuclease activity, which is critical for silencing transposons and producing new piRNAs. Gametocyte-specific factor 1 (Gtsf1), an evolutionarily conserved zinc finger protein, promotes catalysis by PIWI proteins. Many animals have multiple Gtsf1 paralogs; however, their respective roles in the piRNA pathway are not fully understood. Here, we dissected the roles of Gtsf1 and its paralog Gtsf1-like (Gtsf1L) in the silkworm piRNA pathway. We found that Gtsf1 and Gtsf1L preferentially bind the two silkworm PIWI paralogs, Siwi and BmAgo3, respectively, and facilitate the endonuclease activity of each PIWI protein. This orthogonal activation effect was further supported by specific reduction of BmAgo3-bound Masculinizer piRNA and Siwi-bound Feminizer piRNA, the unique piRNA pair required for silkworm feminization, upon depletion of Gtsf1 and Gtsf1L, respectively. Our results indicate that the two Gtsf paralogs in silkworms activate their respective PIWI partners, thereby facilitating the amplification of piRNAs.
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3
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Yang Y, Li X, Ye S, Chen X, Wang L, Qian Y, Xin Q, Li L, Gong P. Identification of genes related to sexual differentiation and sterility in embryonic gonads of Mule ducks by transcriptome analysis. Front Genet 2022; 13:1037810. [PMID: 36386800 PMCID: PMC9643717 DOI: 10.3389/fgene.2022.1037810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/10/2022] [Indexed: 12/11/2023] Open
Abstract
The key genes of avian gonadal development are of great significance for sex determination. Transcriptome sequencing analysis of Mule duck gonad as potential sterile model is expected to screen candidate genes related to avian gonad development. In this study, the embryonic gonadal tissues of Mule ducks, Jinding ducks, and Muscovy ducks were collected and identified. Six sample groups including female Mule duck (A), male Mule duck (B), female Jinding duck (C), male Jinding duck (D), female Muscovy duck (E), and male Muscovy duck (F) were subjected to RNA sequencing analysis. A total of 9,471 differential genes (DEGs) and 691 protein-protein interaction pairs were obtained. Totally, 12 genes (Dmrt1, Amh, Sox9, Tex14, Trim71, Slc26a8, Spam1, Tdrp, Tsga10, Boc, Cxcl14, and Hsd17b3) were identified to be specifically related to duck testicular development, and 11 genes (Hsd17b1, Cyp19a1, Cyp17a1, Hhipl2, Tdrp, Uts2r, Cdon, Axin2, Nxph1, Brinp2, and Brinp3) were specifically related to duck ovarian development. Seven genes (Stra8, Dmc1, Terb1, Tex14, Tsga10, Spam1, and Plcd4) were screened to be specifically involved in the female sterility of Mule ducks; eight genes (Gtsf1, Nalcn, Tat, Slc26a8, Kmo, Plcd4, Aldh4a1, and Hgd) were specifically involved in male sterility; and five genes (Terb1, Stra8, Tex14 Tsga10 and Spam1) were involved in both female and male sterility. This study provides an insight into the differential development between male and female gonads of ducks and the sterility mechanism of Mule ducks through function, pathway, and protein interaction analyses. Our findings provide theoretical basis for the further research on sex determination and differentiation of birds and the sterility of Mule ducks.
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Affiliation(s)
- Yu Yang
- Institute of Animal Husbandry and Veterinary Science, Wuhan Academy of Agricultural Science, Wuhan, China
| | - Xuelian Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Shengqiang Ye
- Institute of Animal Husbandry and Veterinary Science, Wuhan Academy of Agricultural Science, Wuhan, China
| | - Xing Chen
- Institute of Animal Husbandry and Veterinary Science, Wuhan Academy of Agricultural Science, Wuhan, China
| | - Lixia Wang
- Institute of Animal Husbandry and Veterinary Science, Wuhan Academy of Agricultural Science, Wuhan, China
| | - Yunguo Qian
- Institute of Animal Husbandry and Veterinary Science, Wuhan Academy of Agricultural Science, Wuhan, China
| | - Qingwu Xin
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Li Li
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Ping Gong
- Institute of Animal Husbandry and Veterinary Science, Wuhan Academy of Agricultural Science, Wuhan, China
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4
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Ipsaro JJ, Joshua‐Tor L. Developmental roles and molecular mechanisms of Asterix/GTSF1. WIRES RNA 2022; 13:e1716. [PMID: 35108755 PMCID: PMC9539491 DOI: 10.1002/wrna.1716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 01/07/2023]
Abstract
Maintenance of germline genomic integrity is critical for the survival of animal species. Consequently, many cellular and molecular processes have evolved to ensure genetic stability during the production of gametes. Here, we describe the discovery, characterization, and emerging molecular mechanisms of the protein Asterix/Gametocyte‐specific factor 1 (GTSF1), an essential gametogenesis factor that is conserved from insects to humans. Beyond its broad importance for healthy germline development, Asterix/GTSF1 has more specific functions in the Piwi‐interacting RNA (piRNA)–RNA interference pathway. There, it contributes to the repression of otherwise deleterious transposons, helping to ensure faithful transmission of genetic information to the next generation. This article is categorized under:Regulatory RNAs/RNAi/Riboswitches > RNAi: Mechanisms of Action Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Interactions with Proteins and Other Molecules > RNA‐Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein‐RNA Interactions: Functional Implications
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Affiliation(s)
- Jonathan J. Ipsaro
- Howard Hughes Medical Institute W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory Cold Spring Harbor New York USA
| | - Leemor Joshua‐Tor
- Howard Hughes Medical Institute W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory Cold Spring Harbor New York USA
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5
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Arif A, Bailey S, Izumi N, Anzelon TA, Ozata DM, Andersson C, Gainetdinov I, MacRae IJ, Tomari Y, Zamore PD. GTSF1 accelerates target RNA cleavage by PIWI-clade Argonaute proteins. Nature 2022; 608:618-625. [PMID: 35772669 PMCID: PMC9385479 DOI: 10.1038/s41586-022-05009-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 06/22/2022] [Indexed: 11/16/2022]
Abstract
Argonaute proteins use nucleic acid guides to find and bind specific DNA or RNA target sequences. Argonaute proteins have diverse biological functions and many retain their ancestral endoribonuclease activity, cleaving the phosphodiester bond between target nucleotides t10 and t11. In animals, the PIWI proteins-a specialized class of Argonaute proteins-use 21-35 nucleotide PIWI-interacting RNAs (piRNAs) to direct transposon silencing, protect the germline genome, and regulate gene expression during gametogenesis1. The piRNA pathway is required for fertility in one or both sexes of nearly all animals. Both piRNA production and function require RNA cleavage catalysed by PIWI proteins. Spermatogenesis in mice and other placental mammals requires three distinct, developmentally regulated PIWI proteins: MIWI (PIWIL1), MILI (PIWIL2) and MIWI22-4 (PIWIL4). The piRNA-guided endoribonuclease activities of MIWI and MILI are essential for the production of functional sperm5,6. piRNA-directed silencing in mice and insects also requires GTSF1, a PIWI-associated protein of unknown function7-12. Here we report that GTSF1 potentiates the weak, intrinsic, piRNA-directed RNA cleavage activities of PIWI proteins, transforming them into efficient endoribonucleases. GTSF1 is thus an example of an auxiliary protein that potentiates the catalytic activity of an Argonaute protein.
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Affiliation(s)
- Amena Arif
- Department of Biochemistry and Molecular Biotechnology Graduate Program, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Howard Hughes Medical Institute and RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Beam Therapeutics, Cambridge, MA, USA
| | - Shannon Bailey
- Howard Hughes Medical Institute and RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Natsuko Izumi
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Todd A Anzelon
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Deniz M Ozata
- Howard Hughes Medical Institute and RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Molecular Biosciences, Stockholm University, Stockholm, Sweden
| | - Cecilia Andersson
- Howard Hughes Medical Institute and RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Ildar Gainetdinov
- Howard Hughes Medical Institute and RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Ian J MacRae
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Yukihide Tomari
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Phillip D Zamore
- Howard Hughes Medical Institute and RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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6
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Mugerwa H, Gautam S, Catto MA, Dutta B, Brown JK, Adkins S, Srinivasan R. Differential Transcriptional Responses in Two Old World Bemisia tabaci Cryptic Species Post Acquisition of Old and New World Begomoviruses. Cells 2022; 11:cells11132060. [PMID: 35805143 PMCID: PMC9265393 DOI: 10.3390/cells11132060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/20/2022] [Accepted: 06/27/2022] [Indexed: 12/13/2022] Open
Abstract
Begomoviruses are transmitted by several cryptic species of the sweetpotato whitefly, Bemisia tabaci (Gennadius), in a persistent and circulative manner. Upon virus acquisition and circulative translocation within the whitefly, a multitude of molecular interactions occur. This study investigated the differentially expressed transcript profiles associated with the acquisition of the Old World monopartite begomovirus, tomato yellow leaf curl virus (TYLCV), and two New World bipartite begomoviruses, sida golden mosaic virus (SiGMV) and cucurbit leaf crumple virus (CuLCrV), in two invasive B. tabaci cryptic species, Middle East-Asia Minor 1 (MEAM1) and Mediterranean (MED). A total of 881 and 559 genes were differentially expressed in viruliferous MEAM1 and MED whiteflies, respectively, compared with their non-viruliferous counterparts, of which 146 genes were common between the two cryptic species. For both cryptic species, the number of differentially expressed genes (DEGs) associated with TYLCV and SiGMV acquisition were higher compared with DEGs associated with CuLCrV acquisition. Pathway analysis indicated that the acquisition of begomoviruses induced differential changes in pathways associated with metabolism and organismal systems. Contrasting expression patterns of major genes associated with virus infection and immune systems were observed. These genes were generally overexpressed and underexpressed in B. tabaci MEAM1 and MED adults, respectively. Further, no specific expression pattern was observed among genes associated with fitness (egg production, spermatogenesis, and aging) in viruliferous whiteflies. The weighted gene correlation network analysis of viruliferous B. tabaci MEAM1 and MED adults identified different hub genes potentially implicated in the vector competence and circulative tropism of viruses. Taken together, the results indicate that both vector cryptic species and the acquired virus species could differentially affect gene expression.
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Affiliation(s)
- Habibu Mugerwa
- Department of Entomology, University of Georgia, 1109 Experiment Street, Griffin, GA 30223, USA; (H.M.); (S.G.); (M.A.C.)
| | - Saurabh Gautam
- Department of Entomology, University of Georgia, 1109 Experiment Street, Griffin, GA 30223, USA; (H.M.); (S.G.); (M.A.C.)
| | - Michael A. Catto
- Department of Entomology, University of Georgia, 1109 Experiment Street, Griffin, GA 30223, USA; (H.M.); (S.G.); (M.A.C.)
| | - Bhabesh Dutta
- Department of Plant Pathology, University of Georgia, 3250 Rainwater Road, Tifton, GA 31793, USA;
| | - Judith K. Brown
- School of Plant Sciences, University of Arizona, Tuscon, AZ 85721, USA;
| | - Scott Adkins
- USDA-ARS, U.S. Horticultural Research Laboratory, Fort Pierce, FL 34945, USA;
| | - Rajagopalbabu Srinivasan
- Department of Entomology, University of Georgia, 1109 Experiment Street, Griffin, GA 30223, USA; (H.M.); (S.G.); (M.A.C.)
- Correspondence: ; Tel.: +1-770-229-3099
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7
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Garstka K, Hecel A, Kozłowski H, Rowińska-Żyrek M. Specific Zn(II)-binding site in the C-terminus of Aspf2, a zincophore from Aspergillus fumigatus. Metallomics 2022; 14:6608364. [PMID: 35700143 PMCID: PMC9780748 DOI: 10.1093/mtomcs/mfac042] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/23/2022] [Indexed: 12/27/2022]
Abstract
Aspergillus fumigatus, one of the most widespread opportunistic human fungal pathogens, adapts to zinc limitation by secreting a 310 amino acid Aspf2 zincophore, able to specifically bind Zn(II) and deliver it to a transmembrane zinc transporter, ZrfC. In this work, we focus on the thermodynamics of Zn(II) complexes with unstructured regions of Aspf2; basing on a variety of spectrometric and potentiometric data, we show that the C-terminal part has the highest Zn(II)-binding affinity among the potential binding sites, and Ni(II) does not compete with Zn(II) binding to this region. The 14 amino acid Aspf2 C-terminus coordinates Zn(II) via two Cys thiolates and two His imidazoles and it could be considered as a promising A. fumigatus targeting molecule.
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Affiliation(s)
- Kinga Garstka
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Aleksandra Hecel
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Henryk Kozłowski
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland,Institute of Health Sciences, University of Opole, Katowicka 68 St, 45-060 Opole, Poland
| | - Magdalena Rowińska-Żyrek
- Correspondence: Magdalena Rowińska-Żyrek, Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland. E-mail:
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8
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Zhou S, Sakashita A, Yuan S, Namekawa SH. Retrotransposons in the Mammalian Male Germline. Sex Dev 2022:1-19. [PMID: 35231923 DOI: 10.1159/000520683] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 10/25/2021] [Indexed: 11/19/2022] Open
Abstract
Retrotransposons are a subset of DNA sequences that constitute a large part of the mammalian genome. They can translocate autonomously or non-autonomously, potentially jeopardizing the heritable germline genome. Retrotransposons coevolved with the host genome, and the germline is the prominent battlefield between retrotransposons and the host genome to maximize their mutual fitness. Host genomes have developed various mechanisms to suppress and control retrotransposons, including DNA methylation, histone modifications, and Piwi-interacting RNA (piRNA), for their own benefit. Thus, rapidly evolved retrotransposons often acquire positive functions, including gene regulation within the germline, conferring reproductive fitness in a species over the course of evolution. The male germline serves as an ideal model to examine the regulation and evolution of retrotransposons, resulting in genomic co-evolution with the host genome. In this review, we summarize and discuss the regulatory mechanisms of retrotransposons, stage-by-stage, during male germ cell development, with a particular focus on mice as an extensively studied mammalian model, highlighting suppression mechanisms and emerging functions of retrotransposons in the male germline.
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Affiliation(s)
- Shumin Zhou
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Akihiko Sakashita
- Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan
| | - Shuiqiao Yuan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, China
| | - Satoshi H Namekawa
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, USA
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9
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Almeida MV, Vernaz G, Putman AL, Miska EA. Taming transposable elements in vertebrates: from epigenetic silencing to domestication. Trends Genet 2022; 38:529-553. [DOI: 10.1016/j.tig.2022.02.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 12/20/2022]
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10
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Omolaoye TS, Hachim MY, du Plessis SS. Using publicly available transcriptomic data to identify mechanistic and diagnostic biomarkers in azoospermia and overall male infertility. Sci Rep 2022; 12:2584. [PMID: 35173218 PMCID: PMC8850557 DOI: 10.1038/s41598-022-06476-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 01/28/2022] [Indexed: 12/23/2022] Open
Abstract
Azoospermia, which is the absence of spermatozoa in an ejaculate occurring due to defects in sperm production, or the obstruction of the reproductive tract, affects about 1% of all men and is prevalent in up to 10–15% of infertile males. Conventional semen analysis remains the gold standard for diagnosing and treating male infertility; however, advances in molecular biology and bioinformatics now highlight the insufficiency thereof. Hence, the need to widen the scope of investigating the aetiology of male infertility stands pertinent. The current study aimed to identify common differentially expressed genes (DEGs) that might serve as potential biomarkers for non-obstructive azoospermia (NOA) and overall male infertility. DEGs across different datasets of transcriptomic profiling of testis from human patients with different causes of infertility/ impaired spermatogenesis and/or azoospermia were explored using the gene expression omnibus (GEO) database. Following the search using the GEOquery, 30 datasets were available, with 5 meeting the inclusion criteria. The DEGs for datasets were identified using limma R packages through the GEO2R tool. The annotated genes of the probes in each dataset were intersected with DEGs from all other datasets. Enriched Ontology Clustering for the identified genes was performed using Metascape to explore the possible connection or interaction between the genes. Twenty-five DEGs were shared between most of the datasets, which might indicate their role in the pathogenesis of male infertility. Of the 25 DEGs, eight genes (THEG, SPATA20, ROPN1L, GSTF1, TSSK1B, CABS1, ADAD1, RIMBP3) are either involved in the overall spermatogenic processes or at specific phases of spermatogenesis. We hypothesize that alteration in the expression of these genes leads to impaired spermatogenesis and, ultimately, male infertility. Thus, these genes can be used as potential biomarkers for the early detection of NOA.
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Affiliation(s)
- Temidayo S Omolaoye
- Department of Basic Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Mahmood Yaseen Hachim
- Department of Basic Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE.
| | - Stefan S du Plessis
- Department of Basic Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE.,Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
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11
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Gainetdinov I, Colpan C, Cecchini K, Arif A, Jouravleva K, Albosta P, Vega-Badillo J, Lee Y, Özata DM, Zamore PD. Terminal modification, sequence, length, and PIWI-protein identity determine piRNA stability. Mol Cell 2021; 81:4826-4842.e8. [PMID: 34626567 DOI: 10.1016/j.molcel.2021.09.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 12/15/2022]
Abstract
In animals, PIWI-interacting RNAs (piRNAs) silence transposons, fight viral infections, and regulate gene expression. piRNA biogenesis concludes with 3' terminal trimming and 2'-O-methylation. Both trimming and methylation influence piRNA stability. Our biochemical data show that multiple mechanisms destabilize unmethylated mouse piRNAs, depending on whether the piRNA 5' or 3' sequence is complementary to a trigger RNA. Unlike target-directed degradation of microRNAs, complementarity-dependent destabilization of piRNAs in mice and flies is blocked by 3' terminal 2'-O-methylation and does not require base pairing to both the piRNA seed and the 3' sequence. In flies, 2'-O-methylation also protects small interfering RNAs (siRNAs) from complementarity-dependent destruction. By contrast, pre-piRNA trimming protects mouse piRNAs from a degradation pathway unaffected by trigger complementarity. In testis lysate and in vivo, internal or 3' terminal uridine- or guanine-rich tracts accelerate pre-piRNA decay. Loss of both trimming and 2'-O-methylation causes the mouse piRNA pathway to collapse, demonstrating that these modifications collaborate to stabilize piRNAs.
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Affiliation(s)
- Ildar Gainetdinov
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
| | - Cansu Colpan
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Katharine Cecchini
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Amena Arif
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Karina Jouravleva
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Paul Albosta
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Joel Vega-Badillo
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Yongjin Lee
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Deniz M Özata
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Phillip D Zamore
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
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12
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The birth of piRNAs: how mammalian piRNAs are produced, originated, and evolved. Mamm Genome 2021; 33:293-311. [PMID: 34724117 PMCID: PMC9114089 DOI: 10.1007/s00335-021-09927-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 10/15/2021] [Indexed: 11/24/2022]
Abstract
PIWI-interacting RNAs (piRNAs), small noncoding RNAs 24–35 nucleotides long, are essential for animal fertility. They play critical roles in a range of functions, including transposable element suppression, gene expression regulation, imprinting, and viral defense. In mammals, piRNAs are the most abundant small RNAs in adult testes and the only small RNAs that direct epigenetic modification of chromatin in the nucleus. The production of piRNAs is a complex process from transcription to post-transcription, requiring unique machinery often distinct from the biogenesis of other RNAs. In mice, piRNA biogenesis occurs in specialized subcellular locations, involves dynamic developmental regulation, and displays sexual dimorphism. Furthermore, the genomic loci and sequences of piRNAs evolve much more rapidly than most of the genomic regions. Understanding piRNA biogenesis should reveal novel RNA regulations recognizing and processing piRNA precursors and the forces driving the gain and loss of piRNAs during animal evolution. Such findings may provide the basis for the development of engineered piRNAs capable of modulating epigenetic regulation, thereby offering possible single-dose RNA therapy without changing the genomic DNA. In this review, we focus on the biogenesis of piRNAs in mammalian adult testes that are derived from long non-coding RNAs. Although piRNA biogenesis is believed to be evolutionarily conserved from fruit flies to humans, recent studies argue for the existence of diverse, mammalian-specific RNA-processing pathways that convert precursor RNAs into piRNAs, perhaps associated with the unique features of mammalian piRNAs or germ cell development. We end with the discussion of major questions in the field, including substrate recognition and the birth of new piRNAs.
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13
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Li Y, Zhang Y, Liu M. Knockout Gene-Based Evidence for PIWI-Interacting RNA Pathway in Mammals. Front Cell Dev Biol 2021; 9:681188. [PMID: 34336834 PMCID: PMC8317503 DOI: 10.3389/fcell.2021.681188] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 06/08/2021] [Indexed: 01/05/2023] Open
Abstract
The PIWI-interacting RNA (piRNA) pathway mainly consists of evolutionarily conserved protein factors. Intriguingly, many mutations of piRNA pathway factors lead to meiotic arrest during spermatogenesis. The majority of piRNA factor-knockout animals show arrested meiosis in spermatogenesis, and only a few show post-meiosis male germ cell arrest. It is still unclear whether the majority of piRNA factors expressed in spermatids are involved in long interspersed nuclear element-1 repression after meiosis, but future conditional knockout research is expected to resolve this. In addition, recent hamster knockout studies showed that a piRNA factor is necessary for oocytes-in complete contrast to the findings in mice. This species discrepancy allows researchers to reexamine the function of piRNA in female germ cells. This mini-review focuses on the current knowledge of protein factors derived from mammalian knockout studies and summarizes their roles in the biogenesis and function of piRNAs.
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Affiliation(s)
- Yinuo Li
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Yue Zhang
- State Key Laboratory of Reproductive Medicine, Clinical Center of Reproductive Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Mingxi Liu
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
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14
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Xia Q, Cui G, Fan Y, Wang X, Hu G, Wang L, Luo X, Yang L, Cai Q, Xu K, Guo W, Gao M, Li Y, Wu J, Li W, Chen J, Qi H, Peng G, Yao H. RNA helicase DDX5 acts as a critical regulator for survival of neonatal mouse gonocytes. Cell Prolif 2021; 54:e13000. [PMID: 33666296 PMCID: PMC8088469 DOI: 10.1111/cpr.13000] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/11/2021] [Accepted: 01/14/2021] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES Mammalian spermatogenesis is a biological process of male gamete formation. Gonocytes are the only precursors of spermatogonial stem cells (SSCs) which develop into mature spermatozoa. DDX5 is one of DEAD-box RNA helicases and expresses in male germ cells, suggesting that Ddx5 plays important functions during spermatogenesis. Here, we explore the functions of Ddx5 in regulating the specification of gonocytes. MATERIALS AND METHODS Germ cell-specific Ddx5 knockout (Ddx5-/- ) mice were generated. The morphology of testes and epididymides and fertility in both wild-type and Ddx5-/- mice were analysed. Single-cell RNA sequencing (scRNA-seq) was used to profile the transcriptome in testes from wild-type and Ddx5-/- mice at postnatal day (P) 2. Dysregulated genes were validated by single-cell qRT-PCR and immunofluorescent staining. RESULTS In male mice, Ddx5 was expressed in germ cells at different stages of development. Germ cell-specific Ddx5 knockout adult male mice were sterile due to completely devoid of germ cells. Male germ cells gradually disappeared in Ddx5-/- mice from E18.5 to P6. Single-cell transcriptome analysis showed that genes involved in cell cycle and glial cell line-derived neurotrophic factor (GDNF) pathway were significantly decreased in Ddx5-deficient gonocytes. Notably, Ddx5 ablation impeded the proliferation of gonocytes. CONCLUSIONS Our study reveals the critical roles of Ddx5 in fate determination of gonocytes, offering a novel insight into the pathogenesis of male sterility.
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15
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Ipsaro JJ, O'Brien PA, Bhattacharya S, Palmer AG, Joshua-Tor L. Asterix/Gtsf1 links tRNAs and piRNA silencing of retrotransposons. Cell Rep 2021; 34:108914. [PMID: 33789107 DOI: 10.1016/j.celrep.2021.108914] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/15/2021] [Accepted: 03/05/2021] [Indexed: 02/05/2023] Open
Abstract
The Piwi-interacting RNA (piRNA) pathway safeguards genomic integrity by silencing transposable elements (transposons) in the germline. While Piwi is the central piRNA factor, others including Asterix/Gtsf1 have also been demonstrated to be critical for effective silencing. Here, using enhanced crosslinking and immunoprecipitation (eCLIP) with a custom informatic pipeline, we show that Asterix/Gtsf1 specifically binds tRNAs in cellular contexts. We determined the structure of mouse Gtsf1 by NMR spectroscopy and identified the RNA-binding interface on the protein's first zinc finger, which was corroborated by biochemical analysis as well as cryo-EM structures of Gtsf1 in complex with co-purifying tRNA. Consistent with the known dependence of long terminal repeat (LTR) retrotransposons on tRNA primers, we demonstrate that LTR retrotransposons are, in fact, preferentially de-repressed in Asterix mutants. Together, these findings link Asterix/Gtsf1, tRNAs, and LTR retrotransposon silencing and suggest that Asterix exploits tRNA dependence to identify transposon transcripts and promote piRNA silencing.
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Affiliation(s)
- Jonathan J Ipsaro
- Howard Hughes Medical Institute, W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Paul A O'Brien
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, 650 West 168th Street, New York, NY 10032, USA
| | | | - Arthur G Palmer
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, 650 West 168th Street, New York, NY 10032, USA
| | - Leemor Joshua-Tor
- Howard Hughes Medical Institute, W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
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16
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Kirchmeyer M, Servais F, Ginolhac A, Nazarov PV, Margue C, Philippidou D, Nicot N, Behrmann I, Haan C, Kreis S. Systematic Transcriptional Profiling of Responses to STAT1- and STAT3-Activating Cytokines in Different Cancer Types. J Mol Biol 2020; 432:5902-5919. [PMID: 32950480 DOI: 10.1016/j.jmb.2020.09.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/14/2020] [Accepted: 09/14/2020] [Indexed: 02/06/2023]
Abstract
Cytokines orchestrate responses to pathogens and in inflammatory processes, but they also play an important role in cancer by shaping the expression levels of cytokine response genes. Here, we conducted a large profiling study comparing miRNome and mRNA transcriptome data generated following different cytokine stimulations. Transcriptomic responses to STAT1- (IFNγ, IL-27) and STAT3-activating cytokines (IL6, OSM) were systematically compared in nine cancerous and non-neoplastic cell lines of different tissue origins (skin, liver and colon). The largest variation in our datasets was seen between cell lines of the three different tissues rather than stimuli. Notably, the variability in miRNome datasets was a lot more pronounced than in mRNA data. Our data also revealed that cells of skin, liver and colon tissues respond very differently to cytokines and that the cell signaling networks activated or silenced in response to STAT1- or STAT3-activating cytokines are specific to the tissue and the type of cytokine. However, globally, STAT1-activating cytokines had stronger effects than STAT3-inducing cytokines with most significant responses in liver cells, showing more genes upregulated and with higher fold change. A more detailed analysis of gene regulations upon cytokine stimulation in these cells provided insights into STAT1- versus STAT3-driven processes in hepatocarcinogenesis. Finally, independent component analysis revealed interconnected transcriptional networks distinct between cancer cells and their healthy counterparts.
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Affiliation(s)
- Mélanie Kirchmeyer
- Signal Transduction Laboratory, Department of Life Sciences and Medicine, University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Florence Servais
- Signal Transduction Laboratory, Department of Life Sciences and Medicine, University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Aurélien Ginolhac
- Signal Transduction Laboratory, Department of Life Sciences and Medicine, University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Petr V Nazarov
- Quantitative Biology Unit, Luxembourg Institute of Health, 1AB rue Thomas Edison, L-1445 Strassen, Luxembourg
| | - Christiane Margue
- Signal Transduction Laboratory, Department of Life Sciences and Medicine, University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Demetra Philippidou
- Signal Transduction Laboratory, Department of Life Sciences and Medicine, University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Nathalie Nicot
- Quantitative Biology Unit, Luxembourg Institute of Health, 1AB rue Thomas Edison, L-1445 Strassen, Luxembourg
| | - Iris Behrmann
- Signal Transduction Laboratory, Department of Life Sciences and Medicine, University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Claude Haan
- Signal Transduction Laboratory, Department of Life Sciences and Medicine, University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Stephanie Kreis
- Signal Transduction Laboratory, Department of Life Sciences and Medicine, University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg.
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17
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Mitochondria Associated Germinal Structures in Spermatogenesis: piRNA Pathway Regulation and Beyond. Cells 2020; 9:cells9020399. [PMID: 32050598 PMCID: PMC7072634 DOI: 10.3390/cells9020399] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 01/31/2020] [Accepted: 02/05/2020] [Indexed: 12/24/2022] Open
Abstract
Multiple specific granular structures are present in the cytoplasm of germ cells, termed nuage, which are electron-dense, non-membranous, close to mitochondria and/or nuclei, variant size yielding to different compartments harboring different components, including intermitochondrial cement (IMC), piP-body, and chromatoid body (CB). Since mitochondria exhibit different morphology and topographical arrangements to accommodate specific needs during spermatogenesis, the distribution of mitochondria-associated nuage is also dynamic. The most relevant nuage structure with mitochondria is IMC, also called pi-body, present in prospermatogonia, spermatogonia, and spermatocytes. IMC is primarily enriched with various Piwi-interacting RNA (piRNA) proteins and mainly functions as piRNA biogenesis, transposon silencing, mRNA translation, and mitochondria fusion. Importantly, our previous work reported that mitochondria-associated ER membranes (MAMs) are abundant in spermatogenic cells and contain many crucial proteins associated with the piRNA pathway. Provocatively, IMC functionally communicates with other nuage structures, such as piP-body, to perform its complex functions in spermatogenesis. Although little is known about the formation of both IMC and MAMs, its distinctive characters have attracted considerable attention. Here, we review the insights gained from studying the structural components of mitochondria-associated germinal structures, including IMC, CB, and MAMs, which are pivotal structures to ensure genome integrity and male fertility. We discuss the roles of the structural components in spermatogenesis and piRNA biogenesis, which provide new insights into mitochondria-associated germinal structures in germ cell development and male reproduction.
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18
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Drucker E, Holzer K, Pusch S, Winkler J, Calvisi DF, Eiteneuer E, Herpel E, Goeppert B, Roessler S, Ori A, Schirmacher P, Breuhahn K, Singer S. Karyopherin α2-dependent import of E2F1 and TFDP1 maintains protumorigenic stathmin expression in liver cancer. Cell Commun Signal 2019; 17:159. [PMID: 31783876 PMCID: PMC6883611 DOI: 10.1186/s12964-019-0456-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 10/10/2019] [Indexed: 12/14/2022] Open
Abstract
Background Members of the karyopherin superfamily serve as nuclear transport receptors/adaptor proteins and provide exchange of macromolecules between the nucleo- and cytoplasm. Emerging evidence suggests a subset of karyopherins to be dysregulated in hepatocarcinogenesis including karyopherin-α2 (KPNA2). However, the functional and regulatory role of KPNA2 in liver cancer remains incompletely understood. Methods Quantitative proteomics (LC-MS/MS, ~ 1750 proteins in total) was used to study changes in global protein abundance upon siRNA-mediated KPNA2 knockdown in HCC cells. Functional and mechanistic analyses included colony formation and 2D migration assays, co-immunoprecipitation (CoIP), chromatin immunoprecipitation (ChIP), qRT-PCR, immmunblotting, and subcellular fractionation. In vitro results were correlated with data derived from a murine HCC model and HCC patient samples (3 cohorts, n > 600 in total). Results The proteomic approach revealed the pro-tumorigenic, microtubule (MT) interacting protein stathmin (STMN1) among the most downregulated proteins upon KPNA2 depletion in HCC cells. We further observed that KPNA2 knockdown leads to reduced tumor cell migration and colony formation of HCC cells, which could be phenocopied by direct knockdown of stathmin. As the underlying regulatory mechanism, we uncovered E2F1 and TFDP1 as transport substrates of KPNA2 being retained in the cytoplasm upon KPNA2 ablation, thereby resulting in reduced STMN1 expression. Finally, murine and human HCC data indicate significant correlations of STMN1 expression with E2F1/TFPD1 and with KPNA2 expression and their association with poor prognosis in HCC patients. Conclusion Our data suggest that KPNA2 regulates STMN1 by import of E2F1/TFDP1 and thereby provide a novel link between nuclear transport and MT-interacting proteins in HCC with functional and prognostic significance.
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Affiliation(s)
- Elisabeth Drucker
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany.,Institute of Pathology, University Medicine Greifswald, Friedrich-Loeffler-Straße 23e, 17475, Greifswald, Germany
| | - Kerstin Holzer
- Institute of Pathology, University Medicine Greifswald, Friedrich-Loeffler-Straße 23e, 17475, Greifswald, Germany
| | - Stefan Pusch
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany.,German Consortium of Translational Cancer Research (DKTK), Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Juliane Winkler
- Department of Anatomy, University of California, 513 Parnassus Avenue, San Francisco, CA, 94143, USA
| | - Diego F Calvisi
- Institute of Pathology, University Regensburg, Franz-Josef-Strauß-Allee 11, 93053, Regensburg, Germany
| | - Eva Eiteneuer
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Esther Herpel
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Benjamin Goeppert
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Stephanie Roessler
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Alessandro Ori
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117, Heidelberg, Germany.,Leibniz-Institute on Aging, Fritz-Lipmann-Institute (FLI), Beutenbergstraße 11, 07745, Jena, Germany
| | - Peter Schirmacher
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Kai Breuhahn
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Stephan Singer
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany. .,Institute of Pathology, University Medicine Greifswald, Friedrich-Loeffler-Straße 23e, 17475, Greifswald, Germany.
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19
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Ozata DM, Gainetdinov I, Zoch A, O'Carroll D, Zamore PD. PIWI-interacting RNAs: small RNAs with big functions. Nat Rev Genet 2019; 20:89-108. [PMID: 30446728 DOI: 10.1038/s41576-018-0073-3] [Citation(s) in RCA: 641] [Impact Index Per Article: 128.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In animals, PIWI-interacting RNAs (piRNAs) of 21-35 nucleotides in length silence transposable elements, regulate gene expression and fight viral infection. piRNAs guide PIWI proteins to cleave target RNA, promote heterochromatin assembly and methylate DNA. The architecture of the piRNA pathway allows it both to provide adaptive, sequence-based immunity to rapidly evolving viruses and transposons and to regulate conserved host genes. piRNAs silence transposons in the germ line of most animals, whereas somatic piRNA functions have been lost, gained and lost again across evolution. Moreover, most piRNA pathway proteins are deeply conserved, but different animals employ remarkably divergent strategies to produce piRNA precursor transcripts. Here, we discuss how a common piRNA pathway allows animals to recognize diverse targets, ranging from selfish genetic elements to genes essential for gametogenesis.
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Affiliation(s)
- Deniz M Ozata
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ildar Gainetdinov
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ansgar Zoch
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Dónal O'Carroll
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Phillip D Zamore
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA, USA.
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20
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Singh R, Junghare V, Hazra S, Singh U, Sengar GS, Raja TV, Kumar S, Tyagi S, Das AK, Kumar A, Koringa P, Jakhesara S, Joshi CJ, Deb R. Database on spermatozoa transcriptogram of catagorised Frieswal crossbred (Holstein Friesian X Sahiwal) bulls. Theriogenology 2019; 129:130-145. [PMID: 30844654 DOI: 10.1016/j.theriogenology.2019.01.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 01/11/2019] [Accepted: 01/31/2019] [Indexed: 12/22/2022]
Abstract
Bull spermatozoa contain different functional genes and many of them plays important roles in different stages of spermatogenesis, spermatozoa kinetics, fertilization as well as embryonic development. RNA deep sequencing is one of the preferred tools for absolute quantification of messenger RNA. The intention of the current study was to investigate the abundance of spermatozoal transcripts in categorized Frieswal (Holstein-Friesian X Sahiwal) crossbred bull semen through RNA deep sequencing. A total 1546561 and 1019308 numbers of reads were identified among good and poor quality bull spermatozoa based on their conception rate. Post mapping with Bos taurus reference genome identified 1,321,236 and 842,022 number of transcripts among good and poor quality RNA libraries, respectively. However, a total number of 3510 and 6759 functional transcripts were identified among good and poor quality bull spermatozoa, respectively. Most of the identified transcripts were related to spermatozoa functions, embryonic development and other functional aspects of fertilization. Wet laboratory validation of the top five selected transcripts (AKAP4, PRM1, ATP2B4, TRIM71 and SLC9B2) illustrated the significant (p < 0.01) level of expression in the good quality crossbred bull semen than the poor quality counterparts. The present study with comprehensive profiling of spermatozoal transcripts provides a useful non-invasive tool to understand the causes of as well as an effective way to predict male infertility in crossbred bulls.
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Affiliation(s)
- Rani Singh
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Meerut, 250001, Uttar Pradesh, India.
| | - Vivek Junghare
- Department of Biotechnology, Center of Nanotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, India
| | - Saugata Hazra
- Department of Biotechnology, Center of Nanotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, India
| | - Umesh Singh
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Meerut, 250001, Uttar Pradesh, India
| | - Gyanendra Singh Sengar
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Meerut, 250001, Uttar Pradesh, India
| | - T V Raja
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Meerut, 250001, Uttar Pradesh, India
| | - Sushil Kumar
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Meerut, 250001, Uttar Pradesh, India
| | - Shrikant Tyagi
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Meerut, 250001, Uttar Pradesh, India
| | - A K Das
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Meerut, 250001, Uttar Pradesh, India
| | - Ashish Kumar
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Meerut, 250001, Uttar Pradesh, India
| | - Prakash Koringa
- Ome Research Laboratory, Anand Agricultural University, Anand, Gujarat, India
| | - Subhash Jakhesara
- Ome Research Laboratory, Anand Agricultural University, Anand, Gujarat, India
| | - C J Joshi
- Ome Research Laboratory, Anand Agricultural University, Anand, Gujarat, India
| | - Rajib Deb
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Meerut, 250001, Uttar Pradesh, India.
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21
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Almeida MV, Dietz S, Redl S, Karaulanov E, Hildebrandt A, Renz C, Ulrich HD, König J, Butter F, Ketting RF. GTSF-1 is required for formation of a functional RNA-dependent RNA Polymerase complex in Caenorhabditis elegans. EMBO J 2018; 37:embj.201899325. [PMID: 29769402 DOI: 10.15252/embj.201899325] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 03/22/2018] [Accepted: 03/24/2018] [Indexed: 11/09/2022] Open
Abstract
Argonaute proteins and their associated small RNAs (sRNAs) are evolutionarily conserved regulators of gene expression. Gametocyte-specific factor 1 (Gtsf1) proteins, characterized by two tandem CHHC zinc fingers and an unstructured C-terminal tail, are conserved in animals and have been shown to interact with Piwi clade Argonautes, thereby assisting their activity. We identified the Caenorhabditis elegans Gtsf1 homolog, named it gtsf-1 and characterized it in the context of the sRNA pathways of C. elegans We report that GTSF-1 is not required for Piwi-mediated gene silencing. Instead, gtsf-1 mutants show a striking depletion of 26G-RNAs, a class of endogenous sRNAs, fully phenocopying rrf-3 mutants. We show, both in vivo and in vitro, that GTSF-1 interacts with RRF-3 via its CHHC zinc fingers. Furthermore, we demonstrate that GTSF-1 is required for the assembly of a larger RRF-3 and DCR-1-containing complex (ERIC), thereby allowing for 26G-RNA generation. We propose that GTSF-1 homologs may act to drive the assembly of larger complexes that act in sRNA production and/or in imposing sRNA-mediated silencing activities.
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Affiliation(s)
| | - Sabrina Dietz
- Quantitative Proteomics Group, Institute of Molecular Biology, Mainz, Germany
| | - Stefan Redl
- Biology of Non-coding RNA Group, Institute of Molecular Biology, Mainz, Germany
| | - Emil Karaulanov
- Bioinformatics Core Facility, Institute of Molecular Biology, Mainz, Germany
| | - Andrea Hildebrandt
- Genomic Views of Splicing Regulation Group, Institute of Molecular Biology, Mainz, Germany
| | - Christian Renz
- Maintenance of Genome Stability Group, Institute of Molecular Biology, Mainz, Germany
| | - Helle D Ulrich
- Maintenance of Genome Stability Group, Institute of Molecular Biology, Mainz, Germany
| | - Julian König
- Genomic Views of Splicing Regulation Group, Institute of Molecular Biology, Mainz, Germany
| | - Falk Butter
- Quantitative Proteomics Group, Institute of Molecular Biology, Mainz, Germany
| | - René F Ketting
- Biology of Non-coding RNA Group, Institute of Molecular Biology, Mainz, Germany
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22
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Yoshimura T, Watanabe T, Kuramochi-Miyagawa S, Takemoto N, Shiromoto Y, Kudo A, Kanai-Azuma M, Tashiro F, Miyazaki S, Katanaya A, Chuma S, Miyazaki JI. Mouse GTSF1 is an essential factor for secondary piRNA biogenesis. EMBO Rep 2018; 19:embr.201642054. [PMID: 29437694 DOI: 10.15252/embr.201642054] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 01/11/2018] [Accepted: 01/17/2018] [Indexed: 11/09/2022] Open
Abstract
The piRNA pathway is a piRNA-guided retrotransposon silencing system which includes processing of retrotransposon transcripts by PIWI-piRNAs in secondary piRNA biogenesis. Although several proteins participate in the piRNA pathway, the ones crucial for the cleavage of target RNAs by PIWI-piRNAs have not been identified. Here, we show that GTSF1, an essential factor for retrotransposon silencing in male germ cells in mice, associates with both MILI and MIWI2, mouse PIWI proteins that function in prospermatogonia. GTSF1 deficiency leads to a severe defect in the production of secondary piRNAs, which are generated from target RNAs of PIWI-piRNAs. Furthermore, in Gtsf1 mutants, a known target RNA of PIWI-piRNAs is left unsliced at the cleavage site, and the generation of secondary piRNAs from this transcript is defective. Our findings indicate that GTSF1 is a crucial factor for the slicing of target RNAs by PIWI-piRNAs and thus affects secondary piRNA biogenesis in prospermatogonia.
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Affiliation(s)
- Takuji Yoshimura
- Laboratory of Reproductive Engineering, The Institute of Experimental Animal Sciences, Osaka University Medical School, Suita, Osaka, Japan.,Division of Stem Cell Regulation Research, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Toshiaki Watanabe
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA.,Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA.,Central Institute for Experimental Animals, Kawasaki-ku, Kawasaki, Kanagawa, Japan
| | - Satomi Kuramochi-Miyagawa
- Department of Pathology, Graduate School of Medicine and Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Noriaki Takemoto
- Division of Stem Cell Regulation Research, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Yusuke Shiromoto
- Department of Pathology, Graduate School of Medicine and Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Akihiko Kudo
- Department of Anatomy, Kyorin University School of Medicine Shinkawa, Mitaka, Tokyo, Japan
| | - Masami Kanai-Azuma
- Center for Experimental Animal, Tokyo Medical and Dental University, Bunkyo-ku Tokyo, Japan
| | - Fumi Tashiro
- Division of Stem Cell Regulation Research, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Satsuki Miyazaki
- Division of Stem Cell Regulation Research, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Ami Katanaya
- Institute for Frontier Medical Sciences, Kyoto University, Kyoto, Japan
| | - Shinichiro Chuma
- Institute for Frontier Medical Sciences, Kyoto University, Kyoto, Japan
| | - Jun-Ichi Miyazaki
- Division of Stem Cell Regulation Research, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
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23
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Gao DY, Ling Y, Lou XL, Wang YY, Liu LM. GTSF1 gene may serve as a novel potential diagnostic biomarker for liver cancer. Oncol Lett 2017; 15:3133-3140. [PMID: 29435047 DOI: 10.3892/ol.2017.7695] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 10/26/2017] [Indexed: 12/16/2022] Open
Abstract
The gametocyte-specific factor 1 (GTSF1) gene participates in DNA methylation and retrotransposon activation in germ cells, particularly during cell proliferation. The present study aimed to assess the level of GTSF1 gene expression in liver cancer tumor tissues, and its role in human hepatoma cell lines in vitro and in a nude mouse model in vivo. GTSF1 gene expression was detected in liver cancer tumor tissues, compared with in healthy controls, via reverse transcription quantitative polymerase chain reaction. An adeno-associated virus vector was used to study tumor stem cell proliferation in vivo. A plasmid expressing GTSF1 was constructed and transfected into various human hepatoma cell lines, in order to analyze the cellular proliferation and apoptosis of liver cancer cells using small interfering (si)RNAs in vitro. In the present study, GTSF1 gene expression was detected in 18/24 (75.0%) liver cancer tumor tissues from patients with hepatocellular carcinoma (HCC), and elevated GTSF1 expression was identified in the tissue of one of 32 healthy control samples (3.13%; P<0.05). Notably, the GTSF1 gene was expressed at a higher frequency in AFP-positive HCC samples (14/16, 87.50%) compared with in AFP-negative HCC samples (4/8, 50.0%; P=0.129). In addition, there was no statistical significance between GTSF1 expression in non-HBV-infected (71.42%) and HBV-infected HCC specimens (76.47%), as determined by a χ2 test (P=0.921). It was demonstrated that GTSF1 significantly increased the tumorigenicity of Ad-shNC-transfected (GTSF1-positive) HepG2 cells in the nude mouse xenograft model, whereas the sizes and weights of the tumors in the GTSF1-negative group were dercreased in comparison with the GTSF1-positive group (P<0.05). Reduced levels of GTSF1 mRNA, along with fewer and smaller colonies, were identified in two groups of human liver cancer cells treated with with GTSF1-targeting siRNA, when compared with cells without GTSF1 mRNA interference (P<0.05). In summary, the present study elucidated the GTSF1 mRNA expression pattern in liver cancer, and investigated the potential role of GTSF1 in tumorigenesis. The data suggest an important role for the GTSF1 gene in the molecular etiology of hepatocarcinogenesis, and indicate a potential application of GTSF1 mRNA expression in liver cancer diagnosis and therapy.
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Affiliation(s)
- De-Yong Gao
- Department of Infectious Diseases, Songjiang Hospital Affiliated to Shanghai First People's Hospital, Shanghai Jiaotong University, Shanghai 201600, P.R. China
| | - Yun Ling
- Department of Infectious Diseases, Shanghai Public Health Clinical Center Affiliated to Fudan University, Shanghai 200083, P.R. China
| | - Xiao-Li Lou
- Department of Infectious Diseases, Songjiang Hospital Affiliated to Shanghai First People's Hospital, Shanghai Jiaotong University, Shanghai 201600, P.R. China
| | - Ying-Ying Wang
- Department of Infectious Diseases, Songjiang Hospital Affiliated to Shanghai First People's Hospital, Shanghai Jiaotong University, Shanghai 201600, P.R. China
| | - Liang-Ming Liu
- Department of Infectious Diseases, Songjiang Hospital Affiliated to Shanghai First People's Hospital, Shanghai Jiaotong University, Shanghai 201600, P.R. China
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Card CJ, Krieger KE, Kaproth M, Sartini BL. Oligo-dT selected spermatozoal transcript profiles differ among higher and lower fertility dairy sires. Anim Reprod Sci 2017; 177:105-123. [PMID: 28081858 DOI: 10.1016/j.anireprosci.2016.12.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 11/30/2016] [Accepted: 12/22/2016] [Indexed: 01/12/2023]
Abstract
Spermatozoal messenger RNA (mRNA) has the potential as a molecular marker for sire fertility because this population can reflect gene expression that occurred during spermatogenesis and may have a functional role in early embryonic development. The goal of this study was to compare the oligo-dT selected spermatozoal transcript profiles of higher fertility (Conception Rate (CR) 1.8-3.5) and lower fertility (CR -2.9 to -0.4) sires using Ribonucleic Acid Sequencing (RNA-Seq). A total of 3227 transcripts and 5366 transcripts were identified in the higher and lower fertility populations, respectively. While common transcripts between the two populations were identified (2422 transcripts), several transcripts were also unique to the fertility populations including 805 transcripts that were unique to the higher fertility population and 2944 transcripts that were unique to the lower fertility population. From gene ontological analysis, the transcripts unique to each fertility population differed in Biological Processes (BP), including enrichment of regulatory transcripts for growth and protein kinase activity in the higher fertility bulls. Biological variation in transcript presence among individual sires was also found. Of the candidate fertility spermatozoal transcripts chosen from the RNA-Seq population analysis reported here and previous publications, COX7C was negatively correlated with sire fertility. Using high-throughput sequencing, candidate spermatozoal transcripts were identified for further study as potential markers for sire fertility.
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Affiliation(s)
- C J Card
- Department of Fisheries, Animal and Veterinary Science, University of Rhode Island, Kingston 02881, United States
| | - K E Krieger
- Genex Cooperative Inc., Shawano, WI 54166, United States
| | - M Kaproth
- Genex Cooperative Inc., Shawano, WI 54166, United States
| | - B L Sartini
- Department of Fisheries, Animal and Veterinary Science, University of Rhode Island, Kingston 02881, United States.
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25
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Huntriss J, Lu J, Hemmings K, Bayne R, Anderson R, Rutherford A, Balen A, Elder K, Picton HM. Isolation and expression of the human gametocyte-specific factor 1 gene (GTSF1) in fetal ovary, oocytes, and preimplantation embryos. J Assist Reprod Genet 2016; 34:23-31. [PMID: 27646122 PMCID: PMC5330970 DOI: 10.1007/s10815-016-0795-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 08/16/2016] [Indexed: 01/23/2023] Open
Abstract
Purpose Gametocyte-specific factor 1 has been shown in other species to be required for the silencing of retrotransposons via the Piwi-interacting RNA (piRNA) pathway. In this study, we aimed to isolate and assess expression of transcripts of the gametocyte-specific factor 1 (GTSF1) gene in the human female germline and in preimplantation embryos. Methods Complementary DNA (cDNA) libraries from human fetal ovaries and testes, human oocytes and preimplantation embryos and ovarian follicles isolated from an adult ovarian cortex biopsy were used to as templates for PCR, cloning and sequencing, and real time PCR experiments of GTSF1 expression. Results GTSF1 cDNA clones that covered the entire coding region were isolated from human oocytes and preimplantation embryos. GTSF1 mRNA expression was detected in archived cDNAs from staged human ovarian follicles, germinal vesicle (GV) stage oocytes, metaphase II oocytes, and morula and blastocyst stage preimplantation embryos. Within the adult female germline, expression was highest in GV oocytes. GTSF1 mRNA expression was also assessed in human fetal ovary and was observed to increase during gestation, from 8 to 21 weeks, during which time oogonia enter meiosis and primordial follicle formation first occurs. In human fetal testis, GTSF1 expression also increased from 8 to 19 weeks. Conclusions To our knowledge, this report is the first to describe the expression of the human GTSF1 gene in human gametes and preimplantation embryos. Electronic supplementary material The online version of this article (doi:10.1007/s10815-016-0795-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- John Huntriss
- Division of Reproduction and Early Development, Leeds Institute of Cardiovascular and Metabolic Medicine, Clarendon Way, University of Leeds, Leeds, LS2 9JT, UK.
| | - Jianping Lu
- Division of Reproduction and Early Development, Leeds Institute of Cardiovascular and Metabolic Medicine, Clarendon Way, University of Leeds, Leeds, LS2 9JT, UK
| | - Karen Hemmings
- Division of Reproduction and Early Development, Leeds Institute of Cardiovascular and Metabolic Medicine, Clarendon Way, University of Leeds, Leeds, LS2 9JT, UK
| | - Rosemary Bayne
- MRC Centre for Reproductive Health, University of Edinburgh, Queen's Medical Research Institute, Edinburgh, EH16 4TJ, UK
| | - Richard Anderson
- MRC Centre for Reproductive Health, University of Edinburgh, Queen's Medical Research Institute, Edinburgh, EH16 4TJ, UK
| | - Anthony Rutherford
- Leeds Centre for Reproductive Medicine, Leeds Teaching Hospital NHS Trust, Seacroft Hospital, York Road, Leeds, LS14 6UH, UK
| | - Adam Balen
- Leeds Centre for Reproductive Medicine, Leeds Teaching Hospital NHS Trust, Seacroft Hospital, York Road, Leeds, LS14 6UH, UK
| | - Kay Elder
- Bourn Hall Clinic, Cambridge, CB23 2TN, UK
| | - Helen M Picton
- Division of Reproduction and Early Development, Leeds Institute of Cardiovascular and Metabolic Medicine, Clarendon Way, University of Leeds, Leeds, LS2 9JT, UK
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Abstract
Retrotransposons have generated about 40 % of the human genome. This review examines the strategies the cell has evolved to coexist with these genomic "parasites", focussing on the non-long terminal repeat retrotransposons of humans and mice. Some of the restriction factors for retrotransposition, including the APOBECs, MOV10, RNASEL, SAMHD1, TREX1, and ZAP, also limit replication of retroviruses, including HIV, and are part of the intrinsic immune system of the cell. Many of these proteins act in the cytoplasm to degrade retroelement RNA or inhibit its translation. Some factors act in the nucleus and involve DNA repair enzymes or epigenetic processes of DNA methylation and histone modification. RISC and piRNA pathway proteins protect the germline. Retrotransposon control is relaxed in some cell types, such as neurons in the brain, stem cells, and in certain types of disease and cancer, with implications for human health and disease. This review also considers potential pitfalls in interpreting retrotransposon-related data, as well as issues to consider for future research.
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Affiliation(s)
- John L. Goodier
- McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA 212051
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27
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Ishizuka M, Ohtsuka E, Inoue A, Odaka M, Ohshima H, Tamura N, Yoshida K, Sako N, Baba T, Kashiwabara SI, Okabe M, Noguchi J, Hagiwara H. Abnormal spermatogenesis and male infertility in testicular zinc finger protein Zfp318-knockout mice. Dev Growth Differ 2016; 58:600-8. [PMID: 27385512 DOI: 10.1111/dgd.12301] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Revised: 05/07/2016] [Accepted: 05/23/2016] [Indexed: 11/30/2022]
Abstract
Zfp318, a mouse gene with a Cys2/His2 zinc finger motif, is mainly expressed in germ cells in the testis. It encodes two alternative transcripts, which regulate androgen receptor-mediated transcriptional activation or repression by overexpression of them. However, the role of Zfp318 is still obscure in vivo, especially in spermatogenesis. To elucidate the role of Zfp318 during gamete production, we established a knockout mouse line. Zfp318-null male mice exhibited infertility, whereas Zfp318-null female mice displayed normal fertility. ZFP318 was expressed during multiple stages of spermatogenesis, from spermatocytes to round spermatids. The nuclei of secondary spermatocytes showed high levels of expression. Histological analysis and quantitative analysis of DNA content showed decreased numbers of both spermatids in the seminiferous tubules and mature spermatozoa in the epididymides of Zfp318-null mice. These results suggest that Zfp318 is expressed as a functional protein in testicular germ cells and plays an important role in meiosis during spermatogenesis.
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Affiliation(s)
- Masamichi Ishizuka
- Department of Biological Sciences, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Eri Ohtsuka
- Department of Biological Sciences, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Atsuto Inoue
- Department of Biological Sciences, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Mirei Odaka
- Department of Biological Sciences, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Hirotaka Ohshima
- Department of Biological Sciences, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Norihisa Tamura
- Department of Biological Sciences, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Kaoru Yoshida
- Biomedical Engineering Center, Toin University of Yokohama, Yokohama, 225-8503, Japan
| | - Norihisa Sako
- Department of Biomedical Engineering, Toin University of Yokohama, Yokohama, 225-8503, Japan
| | - Tadashi Baba
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, 305-8572, Japan
| | - Shin-Ichi Kashiwabara
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, 305-8572, Japan
| | - Masaru Okabe
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan
| | - Junko Noguchi
- Germ Cell Conservation Laboratory, National Institute of Agrobiological Sciences, Ibaraki, 305-8602, Japan
| | - Hiromi Hagiwara
- Department of Biological Sciences, Tokyo Institute of Technology, Yokohama, 226-8501, Japan. .,Department of Biomedical Engineering, Toin University of Yokohama, Yokohama, 225-8503, Japan.
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28
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Jiang Y, Shi Y, He J, Zhang Z, Zhou G, Zhang W, Cao Y, Liu W. Enhanced tenogenic differentiation and tendon-like tissue formation by tenomodulin overexpression in murine mesenchymal stem cells. J Tissue Eng Regen Med 2016; 11:2525-2536. [PMID: 27098985 DOI: 10.1002/term.2150] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 11/12/2015] [Accepted: 12/22/2015] [Indexed: 01/22/2023]
Affiliation(s)
- Yongkang Jiang
- Department of Plastic and Reconstructive Surgery shanghai 9th People's Hospital; People's Republic of China
| | - Yuan Shi
- Department of Plastic and Reconstructive Surgery shanghai 9th People's Hospital; People's Republic of China
| | - Jing He
- Department of Anatomy and Neurobiology; Tongji University School of Medicine; Shanghai People's Republic of China
| | - Zhiyong Zhang
- Department of Plastic and Reconstructive Surgery shanghai 9th People's Hospital; People's Republic of China
- National Tissue Engineering Centre of China; Shanghai People's Republic of China
| | - Guangdong Zhou
- Department of Plastic and Reconstructive Surgery shanghai 9th People's Hospital; People's Republic of China
- National Tissue Engineering Centre of China; Shanghai People's Republic of China
| | - Wenjie Zhang
- Department of Plastic and Reconstructive Surgery shanghai 9th People's Hospital; People's Republic of China
- National Tissue Engineering Centre of China; Shanghai People's Republic of China
| | - Yilin Cao
- Department of Plastic and Reconstructive Surgery shanghai 9th People's Hospital; People's Republic of China
- National Tissue Engineering Centre of China; Shanghai People's Republic of China
| | - Wei Liu
- Department of Plastic and Reconstructive Surgery shanghai 9th People's Hospital; People's Republic of China
- National Tissue Engineering Centre of China; Shanghai People's Republic of China
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29
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Yang F, Wang PJ. Multiple LINEs of retrotransposon silencing mechanisms in the mammalian germline. Semin Cell Dev Biol 2016; 59:118-125. [PMID: 26957474 DOI: 10.1016/j.semcdb.2016.03.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 02/29/2016] [Accepted: 03/01/2016] [Indexed: 02/07/2023]
Abstract
Retrotransposons play an important role in genome evolution but pose acute challenges to host genome integrity, particularly in early stage germ cells where epigenetic control is relaxed to permit genome-wide reprogramming. In most species, the inability to silence retrotransposons in the germline is usually associated with sterility. LINE1 is the most abundant retrotransposon type in the mammalian genome. Mammalian germ cells employ multiple mechanisms to suppress retrotransposon activity, including small non-coding piRNAs, DNA methylation, and repressive histone modifications. Novel factors contributing to the epigenetic silencing of retrotransposons in the germline continue to be identified. Recent studies have provided insight into how epigenetic changes associated with retrotransposon activation impact on fertility.
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Affiliation(s)
- Fang Yang
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, 3800 Spruce Street, Philadelphia, PA 19104, USA
| | - P Jeremy Wang
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, 3800 Spruce Street, Philadelphia, PA 19104, USA.
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30
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Takemoto N, Yoshimura T, Miyazaki S, Tashiro F, Miyazaki JI. Gtsf1l and Gtsf2 Are Specifically Expressed in Gonocytes and Spermatids but Are Not Essential for Spermatogenesis. PLoS One 2016; 11:e0150390. [PMID: 26930067 PMCID: PMC4773171 DOI: 10.1371/journal.pone.0150390] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 02/12/2016] [Indexed: 12/31/2022] Open
Abstract
The unknown protein family 0224 (UPF0224) includes three members that are expressed in germ-line cells in mice: Gtsf1, Gtsf1l, and BC048502 (Gtsf2). These genes produce proteins with two repeats of the CHHC Zn-finger domain, a predicted RNA-binding motif, in the N terminus. We previously reported that Gtsf1 is essential for spermatogenesis and retrotransposon suppression. In this study, we investigated the expression patterns and functions of Gtsf1l and Gtsf2. Interestingly, Gtsf1l and Gtsf2 were found to be sequentially but not simultaneously expressed in gonocytes and spermatids. Pull-down experiments showed that both GTSF1L and GTSF2 can interact with PIWI-protein complexes. Nevertheless, knocking out Gtsf1, Gtsf2, or both did not cause defects in spermatogenesis or retrotransposon suppression in mice.
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Affiliation(s)
- Noriaki Takemoto
- Division of Stem Cell Regulation Research, Osaka University Graduate School of Medicine, 2–2 Yamadaoka, Suita, Osaka, 565–0871, Japan
| | - Takuji Yoshimura
- Division of Stem Cell Regulation Research, Osaka University Graduate School of Medicine, 2–2 Yamadaoka, Suita, Osaka, 565–0871, Japan
- Laboratory of Reproductive Engineering, Institute of Experimental Animal Sciences, Osaka University Medical School, 2–2 Yamadaoka, Suita, Osaka, 565–0871, Japan
| | - Satsuki Miyazaki
- Division of Stem Cell Regulation Research, Osaka University Graduate School of Medicine, 2–2 Yamadaoka, Suita, Osaka, 565–0871, Japan
| | - Fumi Tashiro
- Division of Stem Cell Regulation Research, Osaka University Graduate School of Medicine, 2–2 Yamadaoka, Suita, Osaka, 565–0871, Japan
| | - Jun-ichi Miyazaki
- Division of Stem Cell Regulation Research, Osaka University Graduate School of Medicine, 2–2 Yamadaoka, Suita, Osaka, 565–0871, Japan
- * E-mail:
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31
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Luangpraseuth-Prosper A, Lesueur E, Jouneau L, Pailhoux E, Cotinot C, Mandon-Pépin B. TOPAZ1, a germ cell specific factor, is essential for male meiotic progression. Dev Biol 2015; 406:158-71. [PMID: 26358182 DOI: 10.1016/j.ydbio.2015.09.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 09/01/2015] [Accepted: 09/04/2015] [Indexed: 11/19/2022]
Abstract
Topaz1 (Testis and Ovary-specific PAZ domain gene 1) is a germ cell specific gene highly conserved in vertebrates. The putative protein TOPAZ1 contains a PAZ domain, specifically found in PIWI, Argonaute and Zwille proteins. Consequently, Topaz1 is supposed to have a role during gametogenesis and may be involved in the piRNA pathway and contribute to silencing of transposable elements and maintenance of genome integrity. Here we report Topaz1 inactivation in mouse. Female fertility was not affected, but male sterility appeared exclusively in homozygous mutants in accordance with the high expression of Topaz1 in male germ cells. Pachytene Topaz1--deficient spermatocytes progress through meiosis without either derepression of retrotransposons or MSCI dysfunction, but become arrested before the post-meiotic round spermatid stage with extensive apoptosis. Consequently, an absence of spermatids and spermatozoa was observed in Topaz1(-/-) testis. Histological analysis also revealed that disturbances of spermatogenesis take place between post natal days 15 and 20, during the first wave of male meiosis and before the generation of haploid germ cells. Transcriptomic analysis at these two stages showed that TOPAZ1 influences the expression of one hundred transcripts, most of which are up-regulated in mutant testis at post natal day 20. Our results also showed that 10% of these transcripts are long non-coding RNA. This suggests that a highly regulated balance of lncRNAs seems to be essential during spermatogenesis for induction of appropriate male gamete production.
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Affiliation(s)
| | - Elodie Lesueur
- INRA, UMR 1198 Biologie du Développement et Reproduction, F-78350 Jouy-en-Josas, France.
| | - Luc Jouneau
- INRA, UMR 1198 Biologie du Développement et Reproduction, F-78350 Jouy-en-Josas, France.
| | - Eric Pailhoux
- INRA, UMR 1198 Biologie du Développement et Reproduction, F-78350 Jouy-en-Josas, France.
| | - Corinne Cotinot
- INRA, UMR 1198 Biologie du Développement et Reproduction, F-78350 Jouy-en-Josas, France.
| | - Béatrice Mandon-Pépin
- INRA, UMR 1198 Biologie du Développement et Reproduction, F-78350 Jouy-en-Josas, France.
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32
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Transcriptome analysis of chicken ES, blastodermal and germ cells reveals that chick ES cells are equivalent to mouse ES cells rather than EpiSC. Stem Cell Res 2014; 14:54-67. [PMID: 25514344 PMCID: PMC4305369 DOI: 10.1016/j.scr.2014.11.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 11/19/2014] [Accepted: 11/24/2014] [Indexed: 12/21/2022] Open
Abstract
Pluripotent Embryonic Stem cell (ESC) lines can be derived from a variety of sources. Mouse lines derived from the early blastocyst and from primordial germ cells (PGCs) can contribute to all somatic lineages and to the germ line, whereas cells from slightly later embryos (EpiSC) no longer contribute to the germ line. In chick, pluripotent ESCs can be obtained from PGCs and from early blastoderms. Established PGC lines and freshly isolated blastodermal cells (cBC) can contribute to both germinal and somatic lineages but established lines from the former (cESC) can only produce somatic cell types. For this reason, cESCs are often considered to be equivalent to mouse EpiSC. To define these cell types more rigorously, we have performed comparative microarray analysis to describe a transcriptomic profile specific for each cell type. This is validated by real time RT-PCR and in situ hybridisation. We find that both cES and cBC cells express classic pluripotency-related genes (including cPOUV/OCT4, NANOG, SOX2/3, KLF2 and SALL4), whereas expression of DAZL, DND1, DDX4 and PIWIL1 defines a molecular signature for germ cells. Surprisingly, contrary to the prevailing view, our results also suggest that cES cells resemble mouse ES cells more closely than mouse EpiSC.
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33
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Gou LT, Dai P, Liu MF. Small noncoding RNAs and male infertility. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 5:733-45. [PMID: 25044449 DOI: 10.1002/wrna.1252] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 05/29/2014] [Accepted: 06/03/2014] [Indexed: 11/07/2022]
Abstract
Small noncoding RNAs (ncRNAs) are a novel class of gene regulators that modulate gene expression at transcriptional, post-transcriptional, and epigenetic levels, and they play crucial roles in almost all cellular processes in eukaryotes. Recent studies have indicated that several types of small noncoding RNAs, including microRNAs (miRNAs), endo-small interference RNAs (endo-siRNAs), and Piwi-interacting RNAs (piRNAs), are expressed in the male germline and are required for spermatogenesis in animals. In this review, we summarize the recent knowledge of these small noncoding RNAs in male germ cells and their biological functions and mechanisms of action in animal spermatogenesis.
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Affiliation(s)
- Lan-Tao Gou
- Center for RNA Research, State Key Laboratory of Molecular Biology-University of Chinese Academy of Sciences, Shanghai, China; Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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34
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Chambeyron S, Seitz H. Insect small non-coding RNA involved in epigenetic regulations. CURRENT OPINION IN INSECT SCIENCE 2014; 1:1-9. [PMID: 32846724 DOI: 10.1016/j.cois.2014.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Revised: 05/01/2014] [Accepted: 05/01/2014] [Indexed: 06/11/2023]
Abstract
Small regulatory RNAs can not only guide post-transcriptional repression of target genes, but some of them can also direct heterochromatin formation of specific genomic loci. Here we review the published literature on small RNA-guided epigenetic regulation in insects. The recent development of novel analytical technologies (deep sequencing and RNAi screens) has led to the identification of some of the factors involved in these processes, as well as their molecular mechanism and subcellular localization. Other findings uncovered an additional mode of epigenetic control, where maternally inherited small RNAs can affect phenotypes in a stable, transgenerational manner. The evolutive history of small RNA effector proteins in insects suggests that these two modes of regulation are variably conserved among species.
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Affiliation(s)
- Séverine Chambeyron
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique (CNRS), UPR 1142, 141, rue de la Cardonille, 34396 Montpellier Cedex 5, France
| | - Hervé Seitz
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique (CNRS), UPR 1142, 141, rue de la Cardonille, 34396 Montpellier Cedex 5, France.
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35
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Fu Q, Wang PJ. Mammalian piRNAs: Biogenesis, function, and mysteries. SPERMATOGENESIS 2014; 4:e27889. [PMID: 25077039 DOI: 10.4161/spmg.27889] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Revised: 12/23/2013] [Accepted: 01/16/2014] [Indexed: 12/20/2022]
Abstract
Piwi-interacting RNAs (piRNAs) are a distinct class of small non-coding RNAs specifically expressed in the germline of many species. They are most notably required for transposon silencing. Loss of piRNAs results in defects in germ cell development, and thus, infertility. Most studies of piRNAs have been done in Drosophila, but much progress has also been made on piRNAs in the germline of mammals and other species in the past few years. This review provides a summary of our current knowledge of the biogenesis and functions of piRNAs during mouse spermatogenesis and discusses challenges in the mammalian piRNA field.
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Affiliation(s)
- Qi Fu
- Department of Animal Biology; University of Pennsylvania School of Veterinary Medicine; Philadelphia, PA USA
| | - P Jeremy Wang
- Department of Animal Biology; University of Pennsylvania School of Veterinary Medicine; Philadelphia, PA USA
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36
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Dönertas D, Sienski G, Brennecke J. Drosophila Gtsf1 is an essential component of the Piwi-mediated transcriptional silencing complex. Genes Dev 2013; 27:1693-705. [PMID: 23913922 DOI: 10.1101/gad.221150.113] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The PIWI-interacting RNA (piRNA) pathway is a small RNA silencing system that keeps selfish genetic elements such as transposons under control in animal gonads. Several lines of evidence indicate that nuclear PIWI family proteins guide transcriptional silencing of their targets, yet the composition of the underlying silencing complex is unknown. Here we demonstrate that the double CHHC zinc finger protein gametocyte-specific factor 1 (Gtsf1) is an essential factor for Piwi-mediated transcriptional repression in Drosophila. Cells lacking Gtsf1 contain nuclear Piwi loaded with piRNAs, yet Piwi's silencing capacity is ablated. Gtsf1 interacts directly with a small subpool of nuclear Piwi, and loss of Gtsf1 phenocopies loss of Piwi in terms of deregulation of transposons, loss of H3K9 trimethylation (H3K9me3) marks at euchromatic transposon insertions, and deregulation of genes in proximity to repressed transposons. We propose that only a small fraction of nuclear Piwi is actively engaged in target silencing and that Gtsf1 is an essential component of the underlying Piwi-centered silencing complex.
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Affiliation(s)
- Derya Dönertas
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences IMBA, 1030 Vienna, Austria
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Ohtani H, Iwasaki YW, Shibuya A, Siomi H, Siomi MC, Saito K. DmGTSF1 is necessary for Piwi-piRISC-mediated transcriptional transposon silencing in the Drosophila ovary. Genes Dev 2013; 27:1656-61. [PMID: 23913921 DOI: 10.1101/gad.221515.113] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The Piwi-piRNA (PIWI-interacting RNA) complex (Piwi-piRISC) in Drosophila ovarian somatic cells represses transposons transcriptionally to maintain genome integrity; however, the underlying mechanisms remain obscure. Here, we reveal that DmGTSF1, a Drosophila homolog of gametocyte-specific factor 1 (GTSF1) (which is required for transposon silencing in mouse testes), is necessary for Piwi-piRISC to repress target transposons and neighboring genes. DmGTSF1 depletion affected neither piRNA biogenesis nor nuclear import of Piwi-piRISC. DmGTSF1 mutations caused derepression of transposons and loss of ovary follicle layers, resulting in female infertility. We suggest that DmGTSF1, a nuclear Piwi interactor, is an integral factor in Piwi-piRISC-mediated transcriptional silencing.
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Affiliation(s)
- Hitoshi Ohtani
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
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Muerdter F, Guzzardo PM, Gillis J, Luo Y, Yu Y, Chen C, Fekete R, Hannon GJ. A genome-wide RNAi screen draws a genetic framework for transposon control and primary piRNA biogenesis in Drosophila. Mol Cell 2013; 50:736-48. [PMID: 23665228 DOI: 10.1016/j.molcel.2013.04.006] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 04/04/2013] [Accepted: 04/05/2013] [Indexed: 01/19/2023]
Abstract
A large fraction of our genome consists of mobile genetic elements. Governing transposons in germ cells is critically important, and failure to do so compromises genome integrity, leading to sterility. In animals, the piRNA pathway is the key to transposon constraint, yet the precise molecular details of how piRNAs are formed and how the pathway represses mobile elements remain poorly understood. In an effort to identify general requirements for transposon control and components of the piRNA pathway, we carried out a genome-wide RNAi screen in Drosophila ovarian somatic sheet cells. We identified and validated 87 genes necessary for transposon silencing. Among these were several piRNA biogenesis factors. We also found CG3893 (asterix) to be essential for transposon silencing, most likely by contributing to the effector step of transcriptional repression. Asterix loss leads to decreases in H3K9me3 marks on certain transposons but has no effect on piRNA levels.
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Affiliation(s)
- Felix Muerdter
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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Sharif J, Shinkai Y, Koseki H. Is there a role for endogenous retroviruses to mediate long-term adaptive phenotypic response upon environmental inputs? Philos Trans R Soc Lond B Biol Sci 2013; 368:20110340. [PMID: 23166400 DOI: 10.1098/rstb.2011.0340] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Endogenous retroviruses (ERVs) are long terminal repeat-containing virus-like elements that have colonized approximately 10 per cent of the present day mammalian genomes. The intracisternal A particles (IAPs) are a class of ERVs that is currently highly active in the rodents. IAP elements can influence the transcription profile of nearby genes by providing functional promoter elements and modulating local epigenetic landscape through changes in DNA methylation and histone (H3K9) modifications. Despite the potential role for IAPs in gene regulation, the precise genomic locations where these elements are integrated are not well understood. To address this issue, we have identified more than 400 novel IAP insertion sites within/near annotated genes by searching the murine genome, which suggests that the impact of IAP elements on local and/or global gene regulation could be more profound than was previously expected. On the basis of our independent analyses and already published reports, here we argue that IAPs and ERV elements in general could have an evolutionary role for modulating phenotypic plasticity upon environmental inputs, and that this could be mediated through specific stages of embryonic development such as placentation during which the epigenetic constraints on IAP elements are partially relaxed.
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Affiliation(s)
- Jafar Sharif
- Developmental Genetics Group, RIKEN Research Center for Allergy & Immunology, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Kanagawa, Japan.
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Card CJ, Anderson EJ, Zamberlan S, Krieger KE, Kaproth M, Sartini BL. Cryopreserved Bovine Spermatozoal Transcript Profile as Revealed by High-Throughput Ribonucleic Acid Sequencing1. Biol Reprod 2013; 88:49. [DOI: 10.1095/biolreprod.112.103788] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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Gaspar JA, Doss MX, Winkler J, Wagh V, Hescheler J, Kolde R, Vilo J, Schulz H, Sachinidis A. Gene expression signatures defining fundamental biological processes in pluripotent, early, and late differentiated embryonic stem cells. Stem Cells Dev 2012; 21:2471-84. [PMID: 22420508 DOI: 10.1089/scd.2011.0637] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Investigating the molecular mechanisms controlling the in vivo developmental program postembryogenesis is challenging and time consuming. However, the developmental program can be partly recapitulated in vitro by the use of cultured embryonic stem cells (ESCs). Similar to the totipotent cells of the inner cell mass, gene expression and morphological changes in cultured ESCs occur hierarchically during their differentiation, with epiblast cells developing first, followed by germ layers and finally somatic cells. Combination of high throughput -omics technologies with murine ESCs offers an alternative approach for studying developmental processes toward organ-specific cell phenotypes. We have made an attempt to understand differentiation networks controlling embryogenesis in vivo using a time kinetic, by identifying molecules defining fundamental biological processes in the pluripotent state as well as in early and the late differentiation stages of ESCs. Our microarray data of the differentiation of the ESCs clearly demonstrate that the most critical early differentiation processes occur at days 2 and 3 of differentiation. Besides monitoring well-annotated markers pertinent to both self-renewal and potency (capacity to differentiate to different cell lineage), we have identified candidate molecules for relevant signaling pathways. These molecules can be further investigated in gain and loss-of-function studies to elucidate their role for pluripotency and differentiation. As an example, siRNA knockdown of MageB16, a gene highly expressed in the pluripotent state, has proven its influence in inducing differentiation when its function is repressed.
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Affiliation(s)
- John Antonydas Gaspar
- Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne, Germany
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Pillai RS, Chuma S. piRNAs and their involvement in male germline development in mice. Dev Growth Differ 2012; 54:78-92. [PMID: 22221002 DOI: 10.1111/j.1440-169x.2011.01320.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Piwi-interacting RNAs (piRNAs) are a class of small non-coding RNAs expressed in the animal gonads. They are implicated in silencing the genome instability threat posed by mobile genetic elements called transposons. Unlike other small RNAs, which use double-stranded precursors, piRNAs seem to arise from long single-stranded precursor transcripts expressed from discrete genomic regions. In mice, the Piwi pathway is essential for male fertility, and its loss-of-function mutations affect several distinct stages of spermatogenesis. While this small RNA pathway primarily operates post-transcriptionally, it also impacts DNA methylation of target retrotransposon loci, representing an intriguing model of RNA-directed epigenetic control in mammals. Remarkably the Piwi pathway components are specifically localized at germinal granule/nuage, an evolutionarily conserved but still enigmatic ribonucleoprotein compartment in the germline. The inaccessibility of the germline for easy experimental manipulation has meant that this class of RNAs has remained enigmatic. However, recent advances in the use of cell culture models and cell-free systems have greatly advanced our understanding. In this review, we briefly summarize our current understanding of the Piwi pathway, focusing on its developmental regulation, piRNA biogenesis and key function in male germline development from fetal spermatogonial stem cell stage to postnatal haploid spermiogenesis in mice.
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Affiliation(s)
- Ramesh S Pillai
- European Molecular Biology Laboratory, 6 Rue Jules Horowitz, BP 181 CNRS-UJF-EMBL International Unit (UMI 3265) for Virus Host Cell Interactions (UVHCI), 38042 Grenoble, France.
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Rosser JM, An W. L1 expression and regulation in humans and rodents. Front Biosci (Elite Ed) 2012; 4:2203-25. [PMID: 22202032 DOI: 10.2741/537] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Long interspersed elements type 1 (LINE-1s, or L1s) have impacted mammalian genomes at multiple levels. L1 transcription is mainly controlled by its 5' untranslated region (5'UTR), which differs significantly among active human and rodent L1 families. In this review, L1 expression and its regulation are examined in the context of human and rodent development. First, endogenous L1 expression patterns in three different species-human, rat, and mouse-are compared and contrasted. A detailed account of relevant experimental evidence is presented according to the source material, such as cell lines, tumors, and normal somatic and germline tissues from different developmental stages. Second, factors involved in the regulation of L1 expression at both transcriptional and posttranscriptional levels are discussed. These include transcription factors, DNA methylation, PIWI-interacting RNAs (piRNAs), RNA interference (RNAi), and posttranscriptional host factors. Similarities and differences between human and rodent L1s are highlighted. Third, recent findings from transgenic mouse models of L1 are summarized and contrasted with those from endogenous L1 studies. Finally, the challenges and opportunities for L1 mouse models are discussed.
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Affiliation(s)
- James M Rosser
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA 99164, USA
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Rowe HM, Trono D. Dynamic control of endogenous retroviruses during development. Virology 2011; 411:273-87. [PMID: 21251689 DOI: 10.1016/j.virol.2010.12.007] [Citation(s) in RCA: 200] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Accepted: 12/06/2010] [Indexed: 02/07/2023]
Abstract
Close to half of the human genome encompasses mobile genetic elements, most of which are retrotransposons. These genetic invaders are formidable evolutionary forces that have shaped the architecture of the genomes of higher organisms, with some conserving the ability to induce new integrants within their hosts' genome. Expectedly, the control of endogenous retroviruses is tight and multi-pronged. It is most crucially established in the germ line and during the first steps of embryogenesis, primarily through transcriptional mechanisms that have likely evolved under their very pressure, but are now engaged in controlling gene expression at large, notably during early development.
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Affiliation(s)
- Helen M Rowe
- National Program, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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van der Heijden GW, Castañeda J, Bortvin A. Bodies of evidence - compartmentalization of the piRNA pathway in mouse fetal prospermatogonia. Curr Opin Cell Biol 2010; 22:752-7. [PMID: 20822889 DOI: 10.1016/j.ceb.2010.08.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Accepted: 08/10/2010] [Indexed: 10/19/2022]
Abstract
Epigenetic reprogramming of embryonic mouse germ cells involves DNA demethylation of the genome that is accompanied by derepression of transposable elements (TEs). Threatening the genome's integrity, TE activation is efficiently countered by the concerted action of de novo DNA methylation and PIWI-interacting small RNAs (piRNAs). Recent studies have closely examined the subcellular localization of various piRNA pathway proteins in fetal prospermatogonia of wild-type and piRNA pathway mutant mice. Our survey highlights hierarchies and partnerships between the members of this ancient defensive mechanism. Overall, the elaborate cytoplasmic compartmentalization of the piRNA pathway in fetal prospermatogonia provides a highly informative context to aid our understanding of the mouse piRNA pathway.
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Tashiro F, Kanai-Azuma M, Miyazaki S, Kato M, Tanaka T, Toyoda S, Yamato E, Kawakami H, Miyazaki T, Miyazaki JI. Maternal-effect gene Ces5/Ooep/Moep19/Floped is essential for oocyte cytoplasmic lattice formation and embryonic development at the maternal-zygotic stage transition. Genes Cells 2010; 15:813-28. [DOI: 10.1111/j.1365-2443.2010.01420.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Mutations of the Wilms tumor 1 gene (WT1) in older patients with primary cytogenetically normal acute myeloid leukemia: a Cancer and Leukemia Group B study. Blood 2010; 116:788-92. [PMID: 20442368 DOI: 10.1182/blood-2010-01-262543] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
We previously reported the adverse prognostic impact of Wilms tumor 1 gene (WT1) mutations in younger adult cytogenetically normal acute myeloid leukemia (CN-AML). Here, we investigated 243 older (> or = 60 years) primary CN-AML patients. WT1 mutated (WT1mut) patients (7%) had FLT3-ITD more frequently (P < .001), lower hemoglobin (P = .01), higher white blood cell count (P = .03) and percentage blood blasts (P = .03), and a shorter overall survival (P = .08) than WT1 wild-type (WT1wt) patients. Comparing older and younger WT1mut patients, they had similar pretreatment characteristics and outcome. By contrast, among WT1wt CN-AML, younger patients had a significantly better outcome. A WT1 mutation-associated gene-expression signature, reported here for the first time, included CD96, a leukemia stem cell-specific marker, and genes involved in gene regulation (eg, MLL, PML, and SNRPN) and in proliferative and metabolic processes (eg, INSR, IRS2, and PRKAA1), supporting the role of mutated WT1 in deregulating multiple homeostatic processes. Our results indicate that WT1mut CN-AML represents a distinct entity with poor treatment response across age groups. This study has been registered at www.clinicaltrials.gov as #NCT00900224.
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