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Brito T, Julio A, Berni M, de Castro Poncio L, Bernardes ES, Araujo H, Sammeth M, Pane A. Transcriptomic and functional analyses of the piRNA pathway in the Chagas disease vector Rhodnius prolixus. PLoS Negl Trop Dis 2018; 12:e0006760. [PMID: 30303955 PMCID: PMC6179187 DOI: 10.1371/journal.pntd.0006760] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 08/17/2018] [Indexed: 12/18/2022] Open
Abstract
The piRNA pathway is a surveillance system that guarantees oogenesis and adult fertility in a range of animal species. The pathway is centered on PIWI clade Argonaute proteins and the associated small non-coding RNAs termed piRNAs. In this study, we set to investigate the evolutionary conservation of the piRNA pathway in the hemimetabolous insect Rhodnius prolixus. Our transcriptome profiling reveals that core components of the pathway are expressed during previtellogenic stages of oogenesis. Rhodnius’ genome harbors four putative piwi orthologs. We show that Rp-piwi2, Rp-piwi3 and Rp-ago3, but not Rp-piwi1 transcripts are produced in the germline tissues and maternally deposited in the mature eggs. Consistent with a role in Rhodnius oogenesis, parental RNAi against the Rp-piwi2, Rp-piwi3 and Rp-ago3 results in severe egg laying and female adult fertility defects. Furthermore, we show that the reduction of the Rp-piwi2 levels by parental RNAi disrupts oogenesis by causing a dramatic loss of trophocytes, egg chamber degeneration and oogenesis arrest. Intriguingly, the putative Rp-Piwi2 protein features a polyglutamine tract at its N-terminal region, which is conserved in PIWI proteins encoded in the genome of other Triatomine species. Together with R. prolixus, these hematophagous insects are primary vectors of the Chagas disease. Thus, our data shed more light on the evolution of the piRNA pathway and provide a framework for the development of new control strategies for Chagas disease insect vectors. Rhodnius prolixus together with other blood-feeding bugs of the Triatominae family are primary vectors of the protozoan Trypanosoma cruzi, the causative agent of the Chagas disease. It has been estimated that 7–8 million people are affected by this life-threatening illness worldwide, which makes the Chagas disease one of the most neglected tropical diseases. In this study, we describe the transcriptome of previtellogenic stages of Rhodnius oogenesis. Furthermore, by using a combination of molecular biology techniques and functional analyses we show that central components of the piRNA pathway are conserved in this species. The piRNA pathway guarantees genomic stability in the germ cells of organisms as distant as flies and mice. In accordance, we find that the knock-down of the piwi genes, which form the backbone of the pathway, results in partial or complete female adult sterility in Rhodnius. Our data will help improve the annotation of the Rhodnius genome and provide a framework for the development of novel techniques aiming at the eradication of Rhodnius prolixus and other Triatomine species from the infested areas. The achievement of this goal will ultimately prevent the transmission of trypanosomes to humans and reduce or eliminate the diffusion of the Chagas disease.
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Affiliation(s)
- Tarcisio Brito
- Institute of Biomedical Sciences (ICB), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Molecular Entomology (INCT), Rio de Janeiro, Brazil
- Institute of Biophysics Carlos Chagas Filho (IBCCF), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alison Julio
- Institute of Biomedical Sciences (ICB), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Molecular Entomology (INCT), Rio de Janeiro, Brazil
| | - Mateus Berni
- Institute of Biomedical Sciences (ICB), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Molecular Entomology (INCT), Rio de Janeiro, Brazil
| | | | - Emerson Soares Bernardes
- Forrest Brasil Tecnologia Ltda, Araucária, Paraná, Brazil
- Nuclear Energy Research Institute, Radiopharmacy Center, São Paulo, Brazil
| | - Helena Araujo
- Institute of Biomedical Sciences (ICB), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Molecular Entomology (INCT), Rio de Janeiro, Brazil
| | - Michael Sammeth
- Institute of Biophysics Carlos Chagas Filho (IBCCF), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Attilio Pane
- Institute of Biomedical Sciences (ICB), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Molecular Entomology (INCT), Rio de Janeiro, Brazil
- * E-mail:
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102
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Kistler KE, Trcek T, Hurd TR, Chen R, Liang FX, Sall J, Kato M, Lehmann R. Phase transitioned nuclear Oskar promotes cell division of Drosophila primordial germ cells. eLife 2018; 7:37949. [PMID: 30260314 PMCID: PMC6191285 DOI: 10.7554/elife.37949] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 09/09/2018] [Indexed: 12/25/2022] Open
Abstract
Germ granules are non-membranous ribonucleoprotein granules deemed the hubs for post-transcriptional gene regulation and functionally linked to germ cell fate across species. Little is known about the physical properties of germ granules and how these relate to germ cell function. Here we study two types of germ granules in the Drosophila embryo: cytoplasmic germ granules that instruct primordial germ cells (PGCs) formation and nuclear germ granules within early PGCs with unknown function. We show that cytoplasmic and nuclear germ granules are phase transitioned condensates nucleated by Oskar protein that display liquid as well as hydrogel-like properties. Focusing on nuclear granules, we find that Oskar drives their formation in heterologous cell systems. Multiple, independent Oskar protein domains synergize to promote granule phase separation. Deletion of Oskar’s nuclear localization sequence specifically ablates nuclear granules in cell systems. In the embryo, nuclear germ granules promote germ cell divisions thereby increasing PGC number for the next generation.
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Affiliation(s)
- Kathryn E Kistler
- Skirball Institute of Biomolecular Medicine, Howard Hughes Medical Institute, NYU School of Medicine, New York, United States.,Department of Molecular and Cellular Biology, University of Washington, Washington, United States
| | - Tatjana Trcek
- Skirball Institute of Biomolecular Medicine, Howard Hughes Medical Institute, NYU School of Medicine, New York, United States
| | - Thomas R Hurd
- Skirball Institute of Biomolecular Medicine, Howard Hughes Medical Institute, NYU School of Medicine, New York, United States.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Ruoyu Chen
- Skirball Institute of Biomolecular Medicine, Howard Hughes Medical Institute, NYU School of Medicine, New York, United States
| | - Feng-Xia Liang
- Department of Cell Biology, NYU School of Medicine, New York, United States.,DART Microscopy Laboratory, NYU Langone Health, New York, United States
| | - Joseph Sall
- DART Microscopy Laboratory, NYU Langone Health, New York, United States
| | - Masato Kato
- Department of Biochemistry, University of Texas Southwestern Medical Center, Texas, United States
| | - Ruth Lehmann
- Skirball Institute of Biomolecular Medicine, Howard Hughes Medical Institute, NYU School of Medicine, New York, United States.,Department of Cell Biology, NYU School of Medicine, New York, United States
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103
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Belicard T, Jareosettasin P, Sarkies P. The piRNA pathway responds to environmental signals to establish intergenerational adaptation to stress. BMC Biol 2018; 16:103. [PMID: 30227863 PMCID: PMC6145337 DOI: 10.1186/s12915-018-0571-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 08/30/2018] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND piRNAs have a constitutive role in genome defence by silencing transposable elements in the germline. In the nematode Caenorhabditis elegans, piRNAs also induce epigenetic silencing of transgenes, which can be maintained for many generations in the absence of the piRNA pathway. The role of multi-generational epigenetic inheritance in adaptation to the environment is unknown. RESULTS Here, we show that piRNA biogenesis is downregulated in response to a small increase in temperature. Some effects on gene expression persist into subsequent generations and are associated with a negative fitness cost. We show that simultaneous infection with pathogenic bacteria suppresses downregulation of the piRNA pathway in response to increased temperature. This effect is associated with increased fitness of progeny of infected animals in subsequent generations. CONCLUSIONS Our results show that the piRNA pathway integrates inputs from the environment to establish intergenerational responses to environmental conditions, with important consequences for the fitness of the subsequent generation.
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Affiliation(s)
- Tony Belicard
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK.,Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Pree Jareosettasin
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK.,Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Peter Sarkies
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK. .,Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK.
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104
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Rojas-Ríos P, Simonelig M. piRNAs and PIWI proteins: regulators of gene expression in development and stem cells. Development 2018; 145:145/17/dev161786. [PMID: 30194260 DOI: 10.1242/dev.161786] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
PIWI proteins and Piwi-interacting RNAs (piRNAs) have established and conserved roles in repressing transposable elements (TEs) in the germline of animals. However, in several biological contexts, a large proportion of piRNAs are not related to TE sequences and, accordingly, functions for piRNAs and PIWI proteins that are independent of TE regulation have been identified. This aspect of piRNA biology is expanding rapidly. Indeed, recent reports have revealed the role of piRNAs in the regulation of endogenous gene expression programs in germ cells, as well as in somatic tissues, challenging dogma in the piRNA field. In this Review, we focus on recent data addressing the biological and developmental functions of piRNAs, highlighting their roles in embryonic patterning, germ cell specification, stem cell biology, neuronal activity and metabolism.
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Affiliation(s)
- Patricia Rojas-Ríos
- mRNA Regulation and Development, IGH, Univ. Montpellier, CNRS, Montpellier 34396, France
| | - Martine Simonelig
- mRNA Regulation and Development, IGH, Univ. Montpellier, CNRS, Montpellier 34396, France
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105
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Mezquita-Pla J. Gordon H. Dixon's trace in my personal career and the quantic jump experienced in regulatory information. Syst Biol Reprod Med 2018; 64:448-468. [PMID: 30136864 DOI: 10.1080/19396368.2018.1503752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Even before Rosalin Franklin had discovered the DNA double helix, in her impressive X-ray diffraction image pattern, Erwin Schröedinger, described, in his excellent book, What is Life, how the finding of aperiodic crystals in biological systems surprised him (an aperiodic crystal, which, in my opinion is the material carrier of life). In the 21st century and still far from being able to define life, we are attending to a quick acceleration of knowledge on regulatory information. With the discovery of new codes and punctuation marks, we will greatly increase our understanding in front of an impressive avalanche of genomic sequences. Trifonov et al. defined a genetic code as a widespread DNA sequence pattern that carries a message with an impact on biology. These patterns are largely captured in transcribed messages that give meaning and identity to the particular cells. In this review, I will go through my personal career in and after my years of work in the laboratory of Gordon H. Dixon, extending toward the impressive acquisition of new knowledge on regulatory information and genetic codes provided by remarkable scientists in the field. Abbreviations: CA II: carbonic anhydridase II (chicken); Car2: carbonic anhydridase 2 (mouse); CpG islands: short (>0.5 kb) stretches of DNA with a G+C content ≥55%; DNMT1: DNA methyltransferases 1; DNMT3b: DNA methyltransferases 3B; DSB: double-strand DNA breaks; ERT: endogenous retrotransposon; ERV: endogenous retroviruses; ES cells: embryonic stem cells; GAPDH: glyceraldehide phosphate dehydrogenase; H1: histone H1; HATs: histone acetyltransferases; HDACs: histone deacetylases; H3K4me3: histone 3 trimethylated at lys 4; H3K79me2: histone 3 dimethylated at lys 79; HMG: high mobility group proteins; HMT: histone methyltransferase; HP1: heterochromatin protein 1; HR: homologous recombination; HSE: heat-shock element; ICRs: imprinted control regions; IRF: interferon regulatory factor; LDH-A/-B: lactate dehydrogenase A/B; LTR: long terminal repeats; MeCP2: methyl CpG binding protein 2; OCT4: octamer-binding transcription factor 4; PAF1: RNA Polymerase II associated factor 1; piRNA: PIWI-interacting RNA; poly(A) tails: poly-adenine tails; PRC2: polycomb repressive complex 2; PTMs: post-translational modifications; SIRT 1: sirtuin 1, silent information regulator; STAT3: signal transducer and activator of transcription; tRNAs: transfer RNA; tRFs: tRNA-derived fragments; TSS: transcription start site; TE: transposable elements; UB I: polyubiquitin I; UB II: polyubiquitin II; UBE 2N: ubiquitin conjugating enzyme E2N; 5'-UTR: 5'-untranslated sequences; 3'-UTR: 3'-untranslated sequences.
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Affiliation(s)
- Jovita Mezquita-Pla
- a Molecular Genetics and Control of Pluripotency Laboratory, Department of Biomedicine, IDIBAPS, Faculty of Medicine , University of Barcelona , Catalonia , Spain
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106
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Steves AN, Turry A, Gill B, Clarkson-Townsend D, Bradner JM, Bachli I, Caudle WM, Miller GW, Chan AWS, Easley CA. Per- and polyfluoroalkyl substances impact human spermatogenesis in a stem-cell-derived model. Syst Biol Reprod Med 2018; 64:225-239. [PMID: 29911897 DOI: 10.1080/19396368.2018.1481465] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Per- and polyfluoroalkyl substances (PFASs) represent a highly ubiquitous group of synthetic chemicals used in products ranging from water and oil repellents and lubricants to firefighting foam. These substances can enter and accumulate in multiple tissue matrices in up to 100% of people assessed. Though animal models strongly identify these compounds as male reproductive toxicants, with exposed rodents experiencing declines in sperm count, alterations in hormones, and DNA damage in spermatids, among other adverse outcomes, human studies report conflicting conclusions as to the reproductive toxicity of these chemicals. Using an innovative, human stem-cell-based model of spermatogenesis, we assessed the effects of the PFASs perfluorooctanesulfonic acid (PFOS), perfluorooctanoic acid (PFOA), perfluorononanoic acid (PFNA), and a mixture of PFOS, PFOA, and PFNA for their impacts on human spermatogenesis in vitro under conditions relevant to the general and occupationally exposed populations. Here, we show that PFOS, PFOA, PFNA, and a mixture of PFOS, PFOA, and PFNA do not decrease in vitro germ cell viability, consistent with reports from human studies. These compounds do not affect mitochondrial membrane potential or increase reactive oxygen species generation, and they do not decrease cell viability of spermatogonia, primary spermatocytes, secondary spermatocytes, or spermatids in vitro under the conditions examined. However, exposure to PFOS, PFOA, and PFNA reduces expression of markers for spermatogonia and primary spermatocytes. While not having direct effects on germ cell viability, these effects suggest the potential for long-term impacts on male fertility through the exhaustion of the spermatogonial stem cell pool and abnormalities in primary spermatocytes. ABBREVIATIONS CDC: Centers for Disease Control; DMSO: dimethyl sulfoxide; GHR: growth hormone receptor; hESCs: human embryonic stem cells; PFASs: per- and polyfluoroalkyl substances; PFCs: perfluorinated compounds; PFNA: perfluorononanoic acid; PFOS: perfluorooctanesulfonic acid; PFOA: perfluorooctanoic acid; PLZF: promyelocytic leukemia zinc finger; ROS: reactive oxygen species; HILI: RNA-mediated gene silencing 2; SSC: spermatogonial stem cell.
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Affiliation(s)
- Alyse N Steves
- a Genetics and Molecular Biology Program , Laney Graduate School, Emory University , Atlanta , GA , USA
| | - Adam Turry
- b College of Public Health , University of Georgia , Athens , GA , USA.,c Regenerative Bioscience Center , University of Georgia , Athens , GA , USA
| | - Brittany Gill
- b College of Public Health , University of Georgia , Athens , GA , USA.,c Regenerative Bioscience Center , University of Georgia , Athens , GA , USA
| | | | - Joshua M Bradner
- d Rollins School of Public Health , Emory University , Atlanta , GA , USA
| | - Ian Bachli
- b College of Public Health , University of Georgia , Athens , GA , USA.,c Regenerative Bioscience Center , University of Georgia , Athens , GA , USA
| | - W Michael Caudle
- d Rollins School of Public Health , Emory University , Atlanta , GA , USA
| | - Gary W Miller
- d Rollins School of Public Health , Emory University , Atlanta , GA , USA
| | - Anthony W S Chan
- e Division of Neuropharmacology and Neurologic Diseases , Yerkes National Primate Research Center , Atlanta , GA , USA.,f Department of Human Genetics , Emory University , Atlanta , GA , USA
| | - Charles A Easley
- b College of Public Health , University of Georgia , Athens , GA , USA.,c Regenerative Bioscience Center , University of Georgia , Athens , GA , USA.,e Division of Neuropharmacology and Neurologic Diseases , Yerkes National Primate Research Center , Atlanta , GA , USA
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107
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Su SC, Reiter RJ, Hsiao HY, Chung WH, Yang SF. Functional Interaction between Melatonin Signaling and Noncoding RNAs. Trends Endocrinol Metab 2018; 29:435-445. [PMID: 29631868 DOI: 10.1016/j.tem.2018.03.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 03/07/2018] [Accepted: 03/12/2018] [Indexed: 12/25/2022]
Abstract
Melatonin was discovered in the pineal gland and first came to be known as a biochemical synchronizer of circadian rhythm. The molecular mechanisms underlying the broad-spectrum actions of melatonin are not restricted to its interaction with proteins but it also has functional effects after influencing RNA species that have no protein-coding potential. In this review we discuss the current understanding of the melatonin-mediated modulation of noncoding RNA (ncRNA) pathways under different physiological and pathological conditions. We also delineate the impact of specific ncRNAs in controlling the synthesis of melatonin. The information compiled herein will serve as a solid foundation to formulate ideas for future mechanistic studies on melatonin and to better explore the emerging functions of the noncoding transcriptome.
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Affiliation(s)
- Shih-Chi Su
- Whole-Genome Research Core Laboratory of Human Diseases, Chang Gung Memorial Hospital, Keelung, Taiwan; Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital, Taipei, Linkou and Keelung, Taiwan
| | - Russel J Reiter
- Department of Cellular and Structural Biology, The University of Texas Health Science Center, San Antonio, TX, USA
| | - Hui-Yi Hsiao
- Center for Tissue Engineering, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Wen-Hung Chung
- Whole-Genome Research Core Laboratory of Human Diseases, Chang Gung Memorial Hospital, Keelung, Taiwan; Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital, Taipei, Linkou and Keelung, Taiwan
| | - Shun-Fa Yang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan; Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan.
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108
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Yashiro R, Murota Y, Nishida KM, Yamashiro H, Fujii K, Ogai A, Yamanaka S, Negishi L, Siomi H, Siomi MC. Piwi Nuclear Localization and Its Regulatory Mechanism in Drosophila Ovarian Somatic Cells. Cell Rep 2018; 23:3647-3657. [DOI: 10.1016/j.celrep.2018.05.051] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/25/2018] [Accepted: 05/16/2018] [Indexed: 10/28/2022] Open
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109
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Chang KW, Tseng YT, Chen YC, Yu CY, Liao HF, Chen YC, Tu YFE, Wu SC, Liu IH, Pinskaya M, Morillon A, Pain B, Lin SP. Stage-dependent piRNAs in chicken implicated roles in modulating male germ cell development. BMC Genomics 2018; 19:425. [PMID: 29859049 PMCID: PMC5984780 DOI: 10.1186/s12864-018-4820-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 05/23/2018] [Indexed: 02/06/2023] Open
Abstract
Background The PIWI/piRNA pathway is a conserved machinery important for germ cell development and fertility. This piRNA-guided molecular machinery is best known for repressing derepressed transposable elements (TE) during epigenomic reprogramming. The extent to which piRNAs are involved in modulating transcripts beyond TEs still need to be clarified, and it may be a stage-dependent event. We chose chicken germline as a study model because of the significantly lower TE complexity in the chicken genome compared to mammalian species. Results We generated high-confidence piRNA candidates in various stages across chicken germline development by 3′-end-methylation-enriched small RNA sequencing and in-house bioinformatics analysis. We observed a significant developmental stage-dependent loss of TE association and a shifting of the ping-pong cycle signatures. Moreover, the stage-dependent reciprocal abundance of LINE retrotransposons, CR1-C, and its associated piRNAs implicated the developmental stage-dependent role of piRNA machinery. The stage dependency of piRNA expression and its potential functions can be better addressed by analyzing the piRNA precursors/clusters. Interestingly, the new piRNA clusters identified from embryonic chicken testes revealed evolutionary conservation between chickens and mammals, which was previously thought to not exist. Conclusions In this report, we provided an original chicken RNA resource and proposed an analytical methodology that can be used to investigate stage-dependent changes in piRNA compositions and their potential roles in TE regulation and beyond, and also revealed possible conserved functions of piRNAs in developing germ cells. Electronic supplementary material The online version of this article (10.1186/s12864-018-4820-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kai-Wei Chang
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, 106, Taiwan.,Present Address: Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Yen-Tzu Tseng
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan.,Department of Animal Science and Technology, National Taiwan University, Taipei, 106, Taiwan
| | - Yi-Chen Chen
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan.,Department of Animal Science and Technology, National Taiwan University, Taipei, 106, Taiwan.,Univ Lyon, Université Lyon 1, INSERM, INRA, Stem Cell and Brain Research Institute, U1208, USC1361, F-69500, Bron, France
| | - Chih-Yun Yu
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Hung-Fu Liao
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Yi-Chun Chen
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Yu-Fan Evan Tu
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Shinn-Chih Wu
- Department of Animal Science and Technology, National Taiwan University, Taipei, 106, Taiwan
| | - I-Hsuan Liu
- Department of Animal Science and Technology, National Taiwan University, Taipei, 106, Taiwan
| | - Marina Pinskaya
- ncRNA, epigenetic and genome fluidity, Institut Curie, Centre de Recherche, CNRS UMR 3244, PSL Research University, Université Pierre et Marie Curie, F-75005, Paris, France
| | - Antonin Morillon
- ncRNA, epigenetic and genome fluidity, Institut Curie, Centre de Recherche, CNRS UMR 3244, PSL Research University, Université Pierre et Marie Curie, F-75005, Paris, France
| | - Bertrand Pain
- Univ Lyon, Université Lyon 1, INSERM, INRA, Stem Cell and Brain Research Institute, U1208, USC1361, F-69500, Bron, France
| | - Shau-Ping Lin
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, 106, Taiwan. .,Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan. .,Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, 106, Taiwan. .,Agricultural Biotechnology Research Centre, Academia Sinica, Taipei, 106, Taiwan. .,Center for Systems Biology, National Taiwan University, Taipei, 106, Taiwan.
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110
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Steves AN, Bradner JM, Fowler KL, Clarkson-Townsend D, Gill BJ, Turry AC, Caudle WM, Miller GW, Chan AWS, Easley CA. Ubiquitous Flame-Retardant Toxicants Impair Spermatogenesis in a Human Stem Cell Model. iScience 2018; 3:161-176. [PMID: 29901031 PMCID: PMC5994764 DOI: 10.1016/j.isci.2018.04.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 03/27/2018] [Accepted: 04/05/2018] [Indexed: 01/08/2023] Open
Abstract
Sperm counts have rapidly declined in Western males over the past four decades. This rapid decline remains largely unexplained, but exposure to environmental toxicants provides one potential explanation for this decline. Flame retardants are highly prevalent and persistent in the environment, but many have not been assessed for their effects on human spermatogenesis. Using a human stem cell-based model of spermatogenesis, we evaluated two major flame retardants, hexabromocyclododecane (HBCDD) and tetrabromobisphenol A (TBBPA), under acute conditions simulating occupational-level exposures. Here we show that HBCDD and TBBPA are human male reproductive toxicants in vitro. Although these toxicants do not specifically affect the survival of haploid spermatids, they affect spermatogonia and primary spermatocytes through mitochondrial membrane potential perturbation and reactive oxygen species generation, ultimately causing apoptosis. Taken together, these results show that HBCDD and TBBPA affect human spermatogenesis in vitro and potentially implicate this highly prevalent class of toxicants in the decline of Western males' sperm counts.
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Affiliation(s)
- Alyse N Steves
- Genetics and Molecular Biology Program, Laney Graduate School, Emory University, Atlanta, GA 30322, USA
| | - Joshua M Bradner
- Department of Environmental Health Science, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Kristen L Fowler
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA 30602, USA; Regenerative Bioscience Center, University of Georgia, Athens, GA 30602, USA
| | - Danielle Clarkson-Townsend
- Department of Environmental Health Science, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Brittany J Gill
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA 30602, USA; Regenerative Bioscience Center, University of Georgia, Athens, GA 30602, USA
| | - Adam C Turry
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA 30602, USA; Regenerative Bioscience Center, University of Georgia, Athens, GA 30602, USA
| | - W Michael Caudle
- Department of Environmental Health Science, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Gary W Miller
- Department of Environmental Health Science, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Anthony W S Chan
- Genetics and Molecular Biology Program, Laney Graduate School, Emory University, Atlanta, GA 30322, USA; Division of Neuropharmacology and Neurologic Diseases, Yerkes National Primate Research Center, GA 30322, USA; Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Charles A Easley
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA 30602, USA; Regenerative Bioscience Center, University of Georgia, Athens, GA 30602, USA; Division of Neuropharmacology and Neurologic Diseases, Yerkes National Primate Research Center, GA 30322, USA.
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111
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Kashima M, Agata K, Shibata N. Searching for non-transposable targets of planarian nuclear PIWI in pluripotent stem cells and differentiated cells. Dev Growth Differ 2018; 60:260-277. [DOI: 10.1111/dgd.12536] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 04/07/2018] [Accepted: 04/09/2018] [Indexed: 12/27/2022]
Affiliation(s)
- Makoto Kashima
- Department of Biophysics; Graduate School of Science; Kyoto University; Kyoto Japan
| | - Kiyokazu Agata
- Department of Biophysics; Graduate School of Science; Kyoto University; Kyoto Japan
| | - Norito Shibata
- Department of Biophysics; Graduate School of Science; Kyoto University; Kyoto Japan
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112
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Sousa-Victor P, Ayyaz A, Hayashi R, Qi Y, Madden DT, Lunyak VV, Jasper H. Piwi Is Required to Limit Exhaustion of Aging Somatic Stem Cells. Cell Rep 2018; 20:2527-2537. [PMID: 28903034 DOI: 10.1016/j.celrep.2017.08.059] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 06/14/2017] [Accepted: 08/17/2017] [Indexed: 12/29/2022] Open
Abstract
Sophisticated mechanisms that preserve genome integrity are critical to ensure the maintenance of regenerative capacity while preventing transformation of somatic stem cells (SCs), yet little is known about mechanisms regulating genome maintenance in these cells. Here, we show that intestinal stem cells (ISCs) induce the Argonaute family protein Piwi in response to JAK/STAT signaling during acute proliferative episodes. Piwi function is critical to ensure heterochromatin maintenance, suppress retrotransposon activation, and prevent DNA damage in homeostasis and under regenerative pressure. Accordingly, loss of Piwi results in the loss of actively dividing ISCs and their progenies by apoptosis. We further show that Piwi expression is sufficient to allay age-related retrotransposon expression, DNA damage, apoptosis, and mis-differentiation phenotypes in the ISC lineage, improving epithelial homeostasis. Our data identify a role for Piwi in the regulation of somatic SC function, and they highlight the importance of retrotransposon control in somatic SC maintenance.
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Affiliation(s)
- Pedro Sousa-Victor
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945-1400, USA
| | - Arshad Ayyaz
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945-1400, USA
| | | | - Yanyan Qi
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945-1400, USA
| | - David T Madden
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945-1400, USA; College of Pharmacy, Touro University California, 1310 Club Drive, Vallejo, CA 94592, USA
| | - Victoria V Lunyak
- Aelan Cell Technologies, 665/280 Third Street, San Francisco, CA 94107, USA
| | - Heinrich Jasper
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945-1400, USA; Immunology Discovery, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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113
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Parikh RY, Lin H, Gangaraju VK. A critical role for nucleoporin 358 (Nup358) in transposon silencing and piRNA biogenesis in Drosophila. J Biol Chem 2018; 293:9140-9147. [PMID: 29735528 DOI: 10.1074/jbc.ac118.003264] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 04/27/2018] [Indexed: 01/10/2023] Open
Abstract
Piwi-interacting RNAs (piRNAs) are a class of small noncoding RNAs that bind Piwi proteins to silence transposons and to regulate gene expression. In Drosophila germ cells, the Aubergine (Aub)-Argonaute 3 (Ago3)-dependent ping-pong cycle generates most germline piRNAs. Loading of antisense piRNAs amplified by this cycle enables Piwi to enter the nucleus and silence transposons. Nuclear localization is crucial for Piwi function in transposon silencing, but how this process is regulated remains unknown. It is also not known whether any of the components of the nuclear pore complex (NPC) directly function in the piRNA pathway. Here, we show that nucleoporin 358 (Nup358) and Piwi interact with each other and that a germline knockdown (GLKD) of Nup358 with short hairpin RNA prevents Piwi entry into the nucleus. The Nup358 GLKD also activated transposons, increased genomic instability, and derailed piRNA biogenesis because of a combination of decreased piRNA precursor transcription and a collapse of the ping-pong cycle. Our results point to a critical role for Nup358 in the piRNA pathway, laying the foundation for future studies to fully elucidate the mechanisms by which Nup358 contributes to piRNA biogenesis and transposon silencing.
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Affiliation(s)
- Rasesh Y Parikh
- From the Department of Biochemistry and Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425 and
| | - Haifan Lin
- Yale Stem Cell Center and Department of Cell Biology, Yale University, New Haven, Connecticut 06510
| | - Vamsi K Gangaraju
- From the Department of Biochemistry and Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425 and
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114
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Dattani A, Sridhar D, Aziz Aboobaker A. Planarian flatworms as a new model system for understanding the epigenetic regulation of stem cell pluripotency and differentiation. Semin Cell Dev Biol 2018; 87:79-94. [PMID: 29694837 DOI: 10.1016/j.semcdb.2018.04.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 04/21/2018] [Indexed: 12/11/2022]
Abstract
Planarian flatworms possess pluripotent stem cells (neoblasts) that are able to differentiate into all cell types that constitute the adult body plan. Consequently, planarians possess remarkable regenerative capabilities. Transcriptomic studies have revealed that gene expression is coordinated to maintain neoblast pluripotency, and ensure correct lineage specification during differentiation. But as yet they have not revealed how this regulation of expression is controlled. In this review, we propose that planarians represent a unique and effective system to study the epigenetic regulation of these processes in an in vivo context. We consolidate evidence suggesting that although DNA methylation is likely present in some flatworm lineages, it does not regulate neoblast function in Schmidtea mediterranea. A number of phenotypic studies have documented the role of histone modification and chromatin remodelling complexes in regulating distinct neoblast processes, and we focus on four important examples of planarian epigenetic regulators: Nucleosome Remodeling Deacetylase (NuRD) complex, Polycomb Repressive Complex (PRC), the SET1/MLL methyltransferases, and the nuclear PIWI/piRNA complex. Given the recent advent of ChIP-seq in planarians, we propose future avenues of research that will identify the genomic targets of these complexes allowing for a clearer picture of how neoblast processes are coordinated at the epigenetic level. These insights into neoblast biology may be directly relevant to mammalian stem cells and disease. The unique biology of planarians will also allow us to investigate how extracellular signals feed into epigenetic regulatory networks to govern concerted neoblast responses during regenerative polarity, tissue patterning, and remodelling.
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Affiliation(s)
- Anish Dattani
- Department of Zoology, South Parks Road, University of Oxford, OX1 3PS, UK.
| | - Divya Sridhar
- Department of Zoology, South Parks Road, University of Oxford, OX1 3PS, UK
| | - A Aziz Aboobaker
- Department of Zoology, South Parks Road, University of Oxford, OX1 3PS, UK.
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115
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Wu Y, Xu K, Qi H. Domain-functional analyses of PIWIL1 and PABPC1 indicate their synergistic roles in protein translation via 3′-UTRs of meiotic mRNAs†. Biol Reprod 2018; 99:773-788. [DOI: 10.1093/biolre/ioy100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 04/24/2018] [Indexed: 12/12/2022] Open
Affiliation(s)
- Yaoyao Wu
- School of Life Science, University of Science and Technology of China, Hefei, China
- Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Kaibiao Xu
- Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Huayu Qi
- Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
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116
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Tang W, Seth M, Tu S, Shen EZ, Li Q, Shirayama M, Weng Z, Mello CC. A Sex Chromosome piRNA Promotes Robust Dosage Compensation and Sex Determination in C. elegans. Dev Cell 2018; 44:762-770.e3. [PMID: 29456136 DOI: 10.1016/j.devcel.2018.01.025] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 01/22/2018] [Accepted: 01/28/2018] [Indexed: 01/25/2023]
Abstract
In metazoans, Piwi-related Argonaute proteins engage piRNAs (Piwi-interacting small RNAs) to defend the genome against invasive nucleic acids, such as transposable elements. Yet many organisms-including worms and humans-express thousands of piRNAs that do not target transposons, suggesting that piRNA function extends beyond genome defense. Here, we show that the X chromosome-derived piRNA 21ux-1 downregulates XOL-1 (XO Lethal), a master regulator of X chromosome dosage compensation and sex determination in Caenorhabditis elegans. Mutations in 21ux-1 and several Piwi-pathway components sensitize hermaphrodites to dosage compensation and sex determination defects. We show that the piRNA pathway also targets xol-1 in C. briggsae, a nematode species related to C. elegans. Our findings reveal physiologically important piRNA-mRNA interactions, raising the possibility that piRNAs function broadly to ensure robust gene expression and germline development.
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Affiliation(s)
- Wen Tang
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Meetu Seth
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Shikui Tu
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - En-Zhi Shen
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Qian Li
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Masaki Shirayama
- RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Craig C Mello
- RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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117
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Investigation of piwi-interacting RNA pathway genes role in idiopathic non-obstructive azoospermia. Sci Rep 2018; 8:142. [PMID: 29317647 PMCID: PMC5760646 DOI: 10.1038/s41598-017-17518-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 11/27/2017] [Indexed: 01/17/2023] Open
Abstract
Genes involved in piwi-interacting RNAs (piRNAs) pathway have an essential role in spermatogenesis. HIWI and TDRD proteins are critical for piRNA biogenesis and function. Therefore, Mutations and polymorphisms in HIWI and TDRD genes may play role in male infertility. The aim of the present study was to investigate the role of HIWI2 rs508485 (T>C) and HIWI3 rs11703684 (C>T) polymorphisms and mutational analysis of TDRD5 gene in idiopathic non-obstructive azoospermia in a case-control study including 226 non-obstructive azoospermia patients and 200 fertile males. Genotyping for both polymorphisms was performed using Tetra-Primer ARMS PCR. Mutation analysis of TDRD5 gene was done using multi-temperature single strand conformation polymorphism technique (MSSCP). The frequency of rs508485TC genotype was significantly different in the studied groups (P = 0.0032; OR = 2.12; 95% CI, 1.29-3.48). In addition, the genotype frequencies showed a significant difference under dominant model (P = 0.005; OR = 2.79; 95% CI, 1.22-3.13). No mutation was detected in the Tudor domain of the TDRD5 in the studied patients. In conclusion, we provide evidence for association between genetic variation in the HIWI2 gene and idiopathic non-obstructive azoospermia in Iranian patients. Therefore, piRNA pathway genes variants can be considered as risk factors for male infertility.
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118
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TDRD5 binds piRNA precursors and selectively enhances pachytene piRNA processing in mice. Nat Commun 2018; 9:127. [PMID: 29317670 PMCID: PMC5760656 DOI: 10.1038/s41467-017-02622-w] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 12/11/2017] [Indexed: 11/08/2022] Open
Abstract
Pachytene piRNAs are the most abundant piRNAs in mammalian adult testes. They are generated from long precursor transcripts by the primary piRNA biogenesis pathway but the factors involved in pachytene piRNA precursors processing are poorly understood. Here we show that the Tudor domain-containing 5 (TDRD5) protein is essential for pachytene piRNA biogenesis in mice. Conditional inactivation of TDRD5 in mouse postnatal germ cells reveals that TDRD5 selectively regulates the production of pachytene piRNAs from abundant piRNA-producing precursors, with little effect on low-abundant piRNAs. Unexpectedly, TDRD5 is not required for the 5′ end processing of the precursors, but is crucial for promoting production of piRNAs from the other regions of the transcript. Furthermore, we show that TDRD5 is an RNA-binding protein directly associating with piRNA precursors. These observations establish TDRD5 as a piRNA biogenesis factor and reveal two genetically separable steps at the start of pachytene piRNA processing. Pachytene piRNAs are abundant piRNAs in mammalian adult testes but their biogenesis pathway is not fully understood. Here, the authors identify TDRD5 as a piRNA biogenesis factor in mice, showing that it binds piRNA precursors and promotes pachytene piRNA production from specific transcript regions.
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119
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Xiao Z, Shen J, Zhang L, Li M, Hu W, Cho C. Therapeutic targeting of noncoding RNAs in hepatocellular carcinoma: Recent progress and future prospects. Oncol Lett 2018; 15:3395-3402. [PMID: 29467864 PMCID: PMC5796293 DOI: 10.3892/ol.2018.7758] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 10/18/2017] [Indexed: 12/12/2022] Open
Abstract
Due to the high mortality rate and unsatisfactory treatment options available, hepatocellular carcinoma (HCC) remains one of the most common malignancies and a leading cause of cancer-associated mortality. Novel therapeutic targets for HCC are urgently required. Advanced RNA sequencing technology enables the identification of considerable amounts of noncoding RNAs (ncRNAs), including small noncoding RNAs and long noncoding RNAs, which exhibit no protein-coding activities. In this respect, ncRNAs and their regulatory processes are important factors in liver tumorigenesis. The present review focuses on the characteristics and biological roles of ncRNAs in HCC. Potential therapeutic applications of ncRNAs in HCC are also evaluated.
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Affiliation(s)
- Zhangang Xiao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Jing Shen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Lin Zhang
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, P.R. China
| | - Mingxing Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Wei Hu
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, P.R. China
| | - Chihin Cho
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan 646000, P.R. China.,School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, P.R. China
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120
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Leaf wax trait in crops for drought and biotic stress tolerance: regulators of epicuticular wax synthesis and role of small RNAs. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/s40502-017-0333-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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121
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Praher D, Zimmermann B, Genikhovich G, Columbus-Shenkar Y, Modepalli V, Aharoni R, Moran Y, Technau U. Characterization of the piRNA pathway during development of the sea anemone Nematostella vectensis. RNA Biol 2017; 14:1727-1741. [PMID: 28783426 PMCID: PMC5731801 DOI: 10.1080/15476286.2017.1349048] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 06/22/2017] [Accepted: 06/27/2017] [Indexed: 12/11/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) and associated proteins comprise a conserved pathway for silencing transposons in metazoan germlines. piRNA pathway components are also expressed in multipotent somatic stem cells in various organisms. piRNA functions have been extensively explored in bilaterian model systems, however, comprehensive studies in non-bilaterian phyla remain limited. Here we investigate the piRNA pathway during the development of Nematostella vectensis, a well-established model system belonging to Cnidaria, the sister group to Bilateria. To date, no population of somatic stem cells has been identified in this organism, despite its long life-span and regenerative capacities that require a constant cell-renewal. We show that Nematostella piRNA pathway components are broadly expressed in early developmental stages, while piRNAs themselves show differential expression, suggesting specific developmental roles of distinct piRNA families. In adults, piRNA associated proteins are enriched in the germline but also expressed in somatic cells, indicating putative stem cell properties. Furthermore, we provide experimental evidence that Nematostella piRNAs cleave transposable elements as well as protein-coding genes. Our results demonstrate that somatic expression of piRNA associated proteins as well as the roles of piRNAs in transposon repression and gene regulation are likely ancestral features that evolved before the split between Cnidaria and Bilateria.
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Affiliation(s)
- Daniela Praher
- Department of Molecular Evolution and Development; Centre of Organismal Systems Biology, Faculty of Life Sciences, University of Vienna; Althanstrasse 14, Wien, Austria
| | - Bob Zimmermann
- Department of Molecular Evolution and Development; Centre of Organismal Systems Biology, Faculty of Life Sciences, University of Vienna; Althanstrasse 14, Wien, Austria
| | - Grigory Genikhovich
- Department of Molecular Evolution and Development; Centre of Organismal Systems Biology, Faculty of Life Sciences, University of Vienna; Althanstrasse 14, Wien, Austria
| | - Yaara Columbus-Shenkar
- Department of Ecology, Evolution and Behavior; Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem; Givat Ram, Jerusalem, Israel
| | - Vengamanaidu Modepalli
- Department of Ecology, Evolution and Behavior; Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem; Givat Ram, Jerusalem, Israel
| | - Reuven Aharoni
- Department of Ecology, Evolution and Behavior; Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem; Givat Ram, Jerusalem, Israel
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior; Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem; Givat Ram, Jerusalem, Israel
| | - Ulrich Technau
- Department of Molecular Evolution and Development; Centre of Organismal Systems Biology, Faculty of Life Sciences, University of Vienna; Althanstrasse 14, Wien, Austria
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122
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Sakakibara K, Siomi MC. The PIWI-Interacting RNA Molecular Pathway: Insights From Cultured Silkworm Germline Cells. Bioessays 2017; 40. [DOI: 10.1002/bies.201700068] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 09/26/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Kazuhiro Sakakibara
- Department of Biological Sciences; Graduate School of Science; The University of Tokyo; Tokyo 113-0032 Japan
| | - Mikiko C. Siomi
- Department of Biological Sciences; Graduate School of Science; The University of Tokyo; Tokyo 113-0032 Japan
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123
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A Functional Role for the Epigenetic Regulator ING1 in Activity-induced Gene Expression in Primary Cortical Neurons. Neuroscience 2017; 369:248-260. [PMID: 29158107 DOI: 10.1016/j.neuroscience.2017.11.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 11/09/2017] [Accepted: 11/11/2017] [Indexed: 12/19/2022]
Abstract
Epigenetic regulation of activity-induced gene expression involves multiple levels of molecular interaction, including histone and DNA modifications, as well as mechanisms of DNA repair. Here we demonstrate that the genome-wide deposition of inhibitor of growth family member 1 (ING1), which is a central epigenetic regulatory protein, is dynamically regulated in response to activity in primary cortical neurons. ING1 knockdown leads to decreased expression of genes related to synaptic plasticity, including the regulatory subunit of calcineurin, Ppp3r1. In addition, ING1 binding at a site upstream of the transcription start site (TSS) of Ppp3r1 depends on yet another group of neuroepigenetic regulatory proteins, the Piwi-like family, which are also involved in DNA repair. These findings provide new insight into a novel mode of activity-induced gene expression, which involves the interaction between different epigenetic regulatory mechanisms traditionally associated with gene repression and DNA repair.
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124
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Gong J, Zhang Q, Wang Q, Ma Y, Du J, Zhang Y, Zhao X. Identification and verification of potential piRNAs from domesticated yak testis. Reproduction 2017; 155:117-127. [PMID: 29101267 PMCID: PMC5763474 DOI: 10.1530/rep-17-0592] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 10/24/2017] [Accepted: 11/03/2017] [Indexed: 01/02/2023]
Abstract
PIWI-interacting RNAs (piRNA) are small non-coding RNA molecules expressed in animal germ cells that interact with PIWI family proteins to form RNA–protein complexes involved in epigenetic and post-transcriptional gene silencing of retrotransposons and other genetic elements in germ line cells, including reproductive stem cell self-sustainment, differentiation, meiosis and spermatogenesis. In the present study, we performed high-throughput sequencing of piRNAs in testis samples from yaks in different stages of sexual maturity. Deep sequencing of the small RNAs (18–40 nt in length) yielded 4,900,538 unique reads from a total of 53,035,635 reads. We identified yak small RNAs (18–30 nt) and performed functional characterization. Yak small RNAs showed a bimodal length distribution, with two peaks at 22 nt and >28 nt. More than 80% of the 3,106,033 putative piRNAs were mapped to 4637 piRNA-producing genomic clusters using RPKM. 6388 candidate piRNAs were identified from clean reads and the annotations were compared with the yak reference genome repeat region. Integrated network analysis suggested that some differentially expressed genes were involved in spermatogenesis through ECM–receptor interaction and PI3K-Akt signaling pathways. Our data provide novel insights into the molecular expression and regulation similarities and diversities in spermatogenesis and testicular development in yaks at different stages of sexual maturity.
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Affiliation(s)
- Jishang Gong
- Gansu Agricultural UniversityLanzhou, People's Republic of China
| | - Quanwei Zhang
- Gansu Agricultural UniversityLanzhou, People's Republic of China
| | - Qi Wang
- Gansu Agricultural UniversityLanzhou, People's Republic of China
| | - Youji Ma
- Gansu Agricultural UniversityLanzhou, People's Republic of China
| | - Jiaxiang Du
- Gansu Agricultural UniversityLanzhou, People's Republic of China
| | - Yong Zhang
- Gansu Agricultural UniversityLanzhou, People's Republic of China
| | - Xingxu Zhao
- Gansu Agricultural UniversityLanzhou, People's Republic of China
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125
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Fierro-Constaín L, Schenkelaars Q, Gazave E, Haguenauer A, Rocher C, Ereskovsky A, Borchiellini C, Renard E. The Conservation of the Germline Multipotency Program, from Sponges to Vertebrates: A Stepping Stone to Understanding the Somatic and Germline Origins. Genome Biol Evol 2017; 9:474-488. [PMID: 28082608 PMCID: PMC5381599 DOI: 10.1093/gbe/evw289] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2016] [Indexed: 12/13/2022] Open
Abstract
The germline definition in metazoans was first based on few bilaterian models. As a result, gene function interpretations were often based on phenotypes observed in those models and led to the definition of a set of genes, considered as specific of the germline, named the “germline core”. However, some of these genes were shown to also be involved in somatic stem cells, thus leading to the notion of germline multipotency program (GMP). Because Porifera and Ctenophora are currently the best candidates to be the sister-group to all other animals, the comparative analysis of gene contents and functions between these phyla, Cnidaria and Bilateria is expected to provide clues on early animal evolution and on the links between somatic and germ lineages. Our present bioinformatic analyses at the metazoan scale show that a set of 18 GMP genes was already present in the last common ancestor of metazoans and indicate more precisely the evolution of some of them in the animal lineage. The expression patterns and levels of 11 of these genes in the homoscleromorph sponge Oscarella lobularis show that they are expressed throughout their life cycle, in pluri/multipotent progenitors, during gametogenesis, embryogenesis and during wound healing. This new study in a nonbilaterian species reinforces the hypothesis of an ancestral multipotency program.
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Affiliation(s)
- Laura Fierro-Constaín
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, UMR 7263, Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale IMBE, Station Marine d’Endoume, Rue de la Batterie des Lions, Marseille, France
- Corresponding authors: E-mails: ;
| | - Quentin Schenkelaars
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, UMR 7263, Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale IMBE, Station Marine d’Endoume, Rue de la Batterie des Lions, Marseille, France
- Department of Genetics and Evolution, Faculty of Sciences, Institute of Genetics and Genomics in Geneva (IGe3), University of Geneva
| | - Eve Gazave
- Institut Jacques Monod, CNRS, UMR 7592, Univ Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Anne Haguenauer
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, UMR 7263, Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale IMBE, Station Marine d’Endoume, Rue de la Batterie des Lions, Marseille, France
| | - Caroline Rocher
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, UMR 7263, Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale IMBE, Station Marine d’Endoume, Rue de la Batterie des Lions, Marseille, France
| | - Alexander Ereskovsky
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, UMR 7263, Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale IMBE, Station Marine d’Endoume, Rue de la Batterie des Lions, Marseille, France
- Department of Embryology, Faculty of Biology, St. Petersburg State University, St. Petersburg, Russia
| | - Carole Borchiellini
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, UMR 7263, Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale IMBE, Station Marine d’Endoume, Rue de la Batterie des Lions, Marseille, France
| | - Emmanuelle Renard
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, UMR 7263, Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale IMBE, Station Marine d’Endoume, Rue de la Batterie des Lions, Marseille, France
- Corresponding authors: E-mails: ;
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126
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Rojas-Ríos P, Chartier A, Pierson S, Simonelig M. Aubergine and piRNAs promote germline stem cell self-renewal by repressing the proto-oncogene Cbl. EMBO J 2017; 36:3194-3211. [PMID: 29030484 PMCID: PMC5666619 DOI: 10.15252/embj.201797259] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 08/30/2017] [Accepted: 09/04/2017] [Indexed: 12/19/2022] Open
Abstract
PIWI proteins play essential roles in germ cells and stem cell lineages. In Drosophila, Piwi is required in somatic niche cells and germline stem cells (GSCs) to support GSC self‐renewal and differentiation. Whether and how other PIWI proteins are involved in GSC biology remains unknown. Here, we show that Aubergine (Aub), another PIWI protein, is intrinsically required in GSCs for their self‐renewal and differentiation. Aub needs to be loaded with piRNAs to control GSC self‐renewal and acts through direct mRNA regulation. We identify the Cbl proto‐oncogene, a regulator of mammalian hematopoietic stem cells, as a novel GSC differentiation factor. Aub stimulates GSC self‐renewal by repressing Cbl mRNA translation and does so in part through recruitment of the CCR4‐NOT complex. This study reveals the role of piRNAs and PIWI proteins in controlling stem cell homeostasis via translational repression and highlights piRNAs as major post‐transcriptional regulators in key developmental decisions.
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Affiliation(s)
- Patricia Rojas-Ríos
- mRNA Regulation and Development, Institute of Human Genetics, UMR9002 CNRS-Université de Montpellier, Montpellier Cedex 5, France
| | - Aymeric Chartier
- mRNA Regulation and Development, Institute of Human Genetics, UMR9002 CNRS-Université de Montpellier, Montpellier Cedex 5, France
| | - Stéphanie Pierson
- mRNA Regulation and Development, Institute of Human Genetics, UMR9002 CNRS-Université de Montpellier, Montpellier Cedex 5, France
| | - Martine Simonelig
- mRNA Regulation and Development, Institute of Human Genetics, UMR9002 CNRS-Université de Montpellier, Montpellier Cedex 5, France
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127
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Ding D, Liu J, Dong K, Midic U, Hess RA, Xie H, Demireva EY, Chen C. PNLDC1 is essential for piRNA 3' end trimming and transposon silencing during spermatogenesis in mice. Nat Commun 2017; 8:819. [PMID: 29018194 PMCID: PMC5635004 DOI: 10.1038/s41467-017-00854-4] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 07/28/2017] [Indexed: 12/04/2022] Open
Abstract
Piwi-interacting RNAs are small regulatory RNAs with key roles in transposon silencing and regulation of gametogenesis. The production of mature piwi-interacting RNAs requires a critical step of trimming piwi-interacting RNA intermediates to achieve optimally sized piwi-interacting RNAs. The poly(A)-specific ribonuclease family deadenylase PNLDC1 is implicated in piwi-interacting RNA trimming in silkworms. The physiological function of PNLDC1 in mammals remains unknown. Using Pnldc1-deficient mice, here we show that PNLDC1 is required for piwi-interacting RNA biogenesis, transposon silencing, and spermatogenesis. Pnldc1 mutation in mice inhibits piwi-interacting RNA trimming and causes accumulation of untrimmed piwi-interacting RNA intermediates with 3′ end extension, leading to severe reduction of mature piwi-interacting RNAs in the testis. Pnldc1 mutant mice exhibit disrupted LINE1 retrotransposon silencing and defect in spermiogenesis. Together, these results define PNLDC1 as a mammalian piwi-interacting RNA biogenesis factor that protects the germline genome and ensures normal sperm production in mice. piRNAs are regulatory RNAs that play a critical role in transposon silencing and gametogenesis. Here, the authors provide evidence that mammalian PNLDC1 is a regulator of piRNA biogenesis, transposon silencing and spermatogenesis, protecting the germline genome in mice.
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Affiliation(s)
- Deqiang Ding
- Department of Animal Science, Michigan State University, East Lansing, MI, 48824, USA
| | - Jiali Liu
- Department of Animal Science, Michigan State University, East Lansing, MI, 48824, USA.,State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Kunzhe Dong
- USDA, Agricultural Research Service, Avian Disease and Oncology Laboratory, East Lansing, MI, 48823, USA
| | - Uros Midic
- Department of Animal Science, Michigan State University, East Lansing, MI, 48824, USA
| | - Rex A Hess
- Department of Comparative Biosciences, University of Illinois, Urbana, IL, 61801, USA
| | - Huirong Xie
- Transgenic and Genome Editing Facility, Michigan State University, East Lansing, MI, 48824, USA
| | - Elena Y Demireva
- Transgenic and Genome Editing Facility, Michigan State University, East Lansing, MI, 48824, USA
| | - Chen Chen
- Department of Animal Science, Michigan State University, East Lansing, MI, 48824, USA. .,Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, 48824, USA. .,Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, Grand Rapids, MI, 49503, USA.
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128
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Wu S, Li Y, Chen S, Liang S, Ren X, Guo W, Sun Q, Yang X. Effect of dietary Astragalus Polysaccharide supplements on testicular piRNA expression profiles of breeding cocks. Int J Biol Macromol 2017; 103:957-964. [DOI: 10.1016/j.ijbiomac.2017.05.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 05/08/2017] [Accepted: 05/19/2017] [Indexed: 01/04/2023]
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129
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Molecular characterization of mitochondrial Zucchini and its relation to nuage-piRNA pathway components in Bombyx mori ovary-derived BmN4 cells. Biochem Biophys Res Commun 2017; 493:971-978. [PMID: 28942151 DOI: 10.1016/j.bbrc.2017.09.107] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 09/19/2017] [Indexed: 11/23/2022]
Abstract
Piwi-interacting RNAs (piRNAs) are a class of small non-coding RNAs that associate with PIWI subfamily proteins, which play an important role in transposon silencing in animal germ cell. The piRNAs biogenesis is divided into two major pathways: primary and secondary, and both pathways are independent of double-stranded RNA-processing enzyme Dicer, which processes the single-stranded RNA transcripts in microRNA (miRNA) and siRNA (small interfering RNA) pathway. Primary piRNAs are processed from long non-coding RNA precursors transcribed from piRNA clusters. Zucchini (Zuc), a mitochondrial phospholipase D (PLD) superfamily protein is conserved among the animals and involved in piRNA biogenesis. Recent studies showed that the Zucchini is an endoribonuclease essential for primary piRNA maturation and production of phased piRNA in secondary piRNA biogenesis of drosophila germ cell. Based on these reports, here we identified and studied the silkworm Zucchini (BmZuc) at subcellular level in ovary-derived BmN4 cell. The silkworm Zuc specifically expressed in germ-related tissues and localized on mitochondria and partially co-localized with perinuclear nuage-piRNA pathway components and nuage marker protein BmVasa. Molecular dissection analyses revealed that the conserved mitochondrial localization sequence, RGV motif, PLDc 2 domain and HKD motif are important for the BmZuc mitochondrial localization. Moreover, the knockdown analyses showed that the piRNA pathway components are independent on BmZuc for their nuage localization, whereas BmZuc depend on piRNA pathway components for the proper localization. Our data provides vital information on mitochondrial BmZuc and its relationship to "nuage" in ovary-derived BmN4 cell.
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130
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Wasserman GA, Szymaniak AD, Hinds AC, Yamamoto K, Kamata H, Smith NM, Hilliard KL, Carrieri C, Labadorf AT, Quinton LJ, Ai X, Varelas X, Chen F, Mizgerd JP, Fine A, O'Carroll D, Jones MR. Expression of Piwi protein MIWI2 defines a distinct population of multiciliated cells. J Clin Invest 2017; 127:3866-3876. [PMID: 28920925 PMCID: PMC5617666 DOI: 10.1172/jci94639] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 07/27/2017] [Indexed: 12/31/2022] Open
Abstract
P-element-induced wimpy testes (Piwi) proteins are known for suppressing retrotransposon activation in the mammalian germline. However, whether Piwi protein or Piwi-dependent functions occur in the mammalian soma is unclear. Contrary to germline-restricted expression, we observed that Piwi-like Miwi2 mRNA is indeed expressed in epithelial cells of the lung in adult mice and that it is induced during pneumonia. Further investigation revealed that MIWI2 protein localized to the cytoplasm of a discrete population of multiciliated airway epithelial cells. Isolation and next-generation sequencing of MIWI2-positive multiciliated cells revealed that they are phenotypically distinct from neighboring MIWI2-negative multiciliated cells. Mice lacking MIWI2 exhibited an altered balance of airway epithelial cells, demonstrating fewer multiciliated cells and an increase in club cells. During pneumococcal pneumonia, Miwi2-deficient mice exhibited increased expression of inflammatory mediators and increased immune cell recruitment, leading to enhanced bacterial clearance. Taken together, our data delineate MIWI2-dependent functions outside of the germline and demonstrate the presence of distinct subsets of airway multiciliated cells that can be discriminated by MIWI2 expression. By demonstrating roles for MIWI2 in airway cell identity and pulmonary innate immunity, these studies elucidate unanticipated physiological functions for Piwi proteins in somatic tissues.
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Affiliation(s)
| | | | | | | | | | - Nicole Ms Smith
- The Pulmonary Center.,Department of Medicine.,Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Kristie L Hilliard
- The Pulmonary Center.,Department of Medicine.,Department of Microbiology
| | - Claudia Carrieri
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Adam T Labadorf
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Lee J Quinton
- The Pulmonary Center.,Department of Medicine.,Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Xingbin Ai
- Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | | | | | - Joseph P Mizgerd
- The Pulmonary Center.,Department of Medicine.,Department of Microbiology.,Department of Biochemistry, and
| | - Alan Fine
- The Pulmonary Center.,Department of Medicine
| | - Dónal O'Carroll
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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131
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Abstract
Piwi-interacting RNAs (piRNAs) are the non-coding RNAs with 24-32 nucleotides (nt). They exhibit stark differences in length, expression pattern, abundance, and genomic organization when compared to micro-RNAs (miRNAs). There are hundreds of thousands unique piRNA sequences in each species. Numerous piRNAs have been identified and deposited in public databases. Since the piRNAs were originally discovered and well-studied in the germline, a few other studies have reported the presence of piRNAs in somatic cells including neurons. This paper reviewed the common features, biogenesis, functions, and distributions of piRNAs and summarized their specific functions in the brain. This review may provide new insights and research direction for brain disorders.
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Affiliation(s)
- Lingjun Zuo
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Zhiren Wang
- Biological Psychiatry Research Center, Beijing Huilongguan Hospital, Beijing, China
| | - Yunlong Tan
- Biological Psychiatry Research Center, Beijing Huilongguan Hospital, Beijing, China
| | - Xiangning Chen
- Nevada Institute of Personalized Medicine and Department of Psychology, University of Nevada, Las Vegas, NV, USA
| | - Xingguang Luo
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA; Biological Psychiatry Research Center, Beijing Huilongguan Hospital, Beijing, China
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132
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Chen C. A novel reporter mouse to monitor in vivo retrotransposition in the germline. Biol Reprod 2017; 97:335-336. [PMID: 29024952 DOI: 10.1093/biolre/iox111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 08/29/2017] [Indexed: 01/16/2023] Open
Affiliation(s)
- 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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133
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Sivagurunathan S, Arunachalam JP, Chidambaram S. PIWI-like protein, HIWI2 is aberrantly expressed in retinoblastoma cells and affects cell-cycle potentially through OTX2. Cell Mol Biol Lett 2017; 22:17. [PMID: 28861107 PMCID: PMC5576095 DOI: 10.1186/s11658-017-0048-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/22/2017] [Indexed: 12/30/2022] Open
Abstract
Retinoblastoma (RB), a childhood cancer, is caused by biallelic mutation of the RB1 gene, but its development is not clearly understood. Furthermore, the presence of a cancer stem cell subpopulation in RB might impact its treatment. PIWI protein, known for its role in stem cell self-renewal, is aberrantly expressed in cancers. We examined the role of the PIWI-like protein HIWI2 in RB and its effect on the stem cell markers in cells of the RB line, Y79. The expression of HIWI2 is significantly increased in Y79 compared with its level in HeLa and ARPE19 cells. The stem cell markers Oct-3/4, Nanog and Sox-2 were not altered upon HIWI2 knockdown in Y79 cells. Interestingly, OTX2 was significantly downregulated in the absence of HIWI2. Otx2 transcripts also decreased in HIWI2-silenced Y79 and ARPE19 cells. Moreover, silencing HIWI2 in Y79 accumulated the cells at G2–M phase and reduced the levels of proliferating cell nuclear antigen (PCNA) and the tumor suppressor, p16. Our results demonstrate that HIWI2 is aberrantly expressed in Y79 cells and silencing of HIWI2 downregulates OTX2, suggesting that HIWI2 might play a role in the progression of RB.
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Affiliation(s)
- Suganya Sivagurunathan
- RS Mehta Jain Department of Biochemistry and Cell Biology, Vision Research Foundation, Chennai, India.,School of Chemical and Biotechnology, SASTRA University, Thanjavur, India
| | - Jayamuruga Pandian Arunachalam
- SN ONGC Department of Genetics and Molecular Biology, Vision Research Foundation, Chennai, India.,Central Inter-Disciplinary Research Facility (CIDRF), Sri Balaji Vidyapeeth University, Mahatma Gandhi Medical College and Research Institute Campus, Pondicherry, India
| | - Subbulakshmi Chidambaram
- RS Mehta Jain Department of Biochemistry and Cell Biology, Vision Research Foundation, Chennai, India.,Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry, India
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134
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LTR-Retrotransposon Control by tRNA-Derived Small RNAs. Cell 2017; 170:61-71.e11. [PMID: 28666125 DOI: 10.1016/j.cell.2017.06.013] [Citation(s) in RCA: 256] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Revised: 04/13/2017] [Accepted: 05/09/2017] [Indexed: 12/31/2022]
Abstract
Transposon reactivation is an inherent danger in cells that lose epigenetic silencing during developmental reprogramming. In the mouse, long terminal repeat (LTR)-retrotransposons, or endogenous retroviruses (ERV), account for most novel insertions and are expressed in the absence of histone H3 lysine 9 trimethylation in preimplantation stem cells. We found abundant 18 nt tRNA-derived small RNA (tRF) in these cells and ubiquitously expressed 22 nt tRFs that include the 3' terminal CCA of mature tRNAs and target the tRNA primer binding site (PBS) essential for ERV reverse transcription. We show that the two most active ERV families, IAP and MusD/ETn, are major targets and are strongly inhibited by tRFs in retrotransposition assays. 22 nt tRFs post-transcriptionally silence coding-competent ERVs, while 18 nt tRFs specifically interfere with reverse transcription and retrotransposon mobility. The PBS offers a unique target to specifically inhibit LTR-retrotransposons, and tRF-targeting is a potentially highly conserved mechanism of small RNA-mediated transposon control.
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135
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Ishizu H, Sumiyoshi T, Siomi MC. Use of the CRISPR-Cas9 system for genome editing in cultured Drosophila ovarian somatic cells. Methods 2017; 126:186-192. [DOI: 10.1016/j.ymeth.2017.05.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 05/08/2017] [Accepted: 05/24/2017] [Indexed: 11/27/2022] Open
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136
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Silencing of Transposable Elements by piRNAs in Drosophila: An Evolutionary Perspective. GENOMICS PROTEOMICS & BIOINFORMATICS 2017; 15:164-176. [PMID: 28602845 PMCID: PMC5487533 DOI: 10.1016/j.gpb.2017.01.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 01/02/2017] [Accepted: 01/12/2017] [Indexed: 11/28/2022]
Abstract
Transposable elements (TEs) are DNA sequences that can move within the genome. TEs have greatly shaped the genomes, transcriptomes, and proteomes of the host organisms through a variety of mechanisms. However, TEs generally disrupt genes and destabilize the host genomes, which substantially reduce fitness of the host organisms. Understanding the genomic distribution and evolutionary dynamics of TEs will greatly deepen our understanding of the TE-mediated biological processes. Most TE insertions are highly polymorphic in Drosophila melanogaster, providing us a good system to investigate the evolution of TEs at the population level. Decades of theoretical and experimental studies have well established “transposition-selection” population genetics model, which assumes that the equilibrium between TE replication and purifying selection determines the copy number of TEs in the genome. In the last decade, P-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs) were demonstrated to be master repressors of TE activities in Drosophila. The discovery of piRNAs revolutionized our understanding of TE repression, because it reveals that the host organisms have evolved an adaptive mechanism to defend against TE invasion. Tremendous progress has been made to understand the molecular mechanisms by which piRNAs repress active TEs, although many details in this process remain to be further explored. The interaction between piRNAs and TEs well explains the molecular mechanisms underlying hybrid dysgenesis for the I-R and P-M systems in Drosophila, which have puzzled evolutionary biologists for decades. The piRNA repression pathway provides us an unparalleled system to study the co-evolutionary process between parasites and host organisms.
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137
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Single-Cell RNA-Seq Analysis Maps Development of Human Germline Cells and Gonadal Niche Interactions. Cell Stem Cell 2017; 20:858-873.e4. [DOI: 10.1016/j.stem.2017.03.007] [Citation(s) in RCA: 237] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 11/30/2016] [Accepted: 03/15/2017] [Indexed: 11/15/2022]
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138
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Gou LT, Kang JY, Dai P, Wang X, Li F, Zhao S, Zhang M, Hua MM, Lu Y, Zhu Y, Li Z, Chen H, Wu LG, Li D, Fu XD, Li J, Shi HJ, Liu MF. Ubiquitination-Deficient Mutations in Human Piwi Cause Male Infertility by Impairing Histone-to-Protamine Exchange during Spermiogenesis. Cell 2017; 169:1090-1104.e13. [PMID: 28552346 DOI: 10.1016/j.cell.2017.04.034] [Citation(s) in RCA: 176] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 06/07/2016] [Accepted: 04/03/2017] [Indexed: 11/25/2022]
Abstract
Genetic studies have elucidated critical roles of Piwi proteins in germline development in animals, but whether Piwi is an actual disease gene in human infertility remains unknown. We report germline mutations in human Piwi (Hiwi) in patients with azoospermia that prevent its ubiquitination and degradation. By modeling such mutations in Piwi (Miwi) knockin mice, we demonstrate that the genetic defects are directly responsible for male infertility. Mechanistically, we show that MIWI binds the histone ubiquitin ligase RNF8 in a Piwi-interacting RNA (piRNA)-independent manner, and MIWI stabilization sequesters RNF8 in the cytoplasm of late spermatids. The resulting aberrant sperm show histone retention, abnormal morphology, and severely compromised activity, which can be functionally rescued via blocking RNF8-MIWI interaction in spermatids with an RNF8-N peptide. Collectively, our findings identify Piwi as a factor in human infertility and reveal its role in regulating the histone-to-protamine exchange during spermiogenesis.
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Affiliation(s)
- Lan-Tao Gou
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Jun-Yan Kang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Peng Dai
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Xin Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Feng Li
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Shuang Zhao
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Man Zhang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Min-Min Hua
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China; Key Lab of Reproduction Regulation of NPFPC-Shanghai Institute of Planned Parenthood Research, Fudan University Reproduction and Development Institution, Shanghai 200032, China
| | - Yi Lu
- Key Lab of Reproduction Regulation of NPFPC-Shanghai Institute of Planned Parenthood Research, Fudan University Reproduction and Development Institution, Shanghai 200032, China
| | - Yong Zhu
- Department of Andrology and PFD, Center for Men's Health, Department of ART, Institute of Urology, Urologic Medical Center Shanghai General Hospital, Shanghai Key Lab of Reproductive Medicine Shanghai Jiao Tong University, Shanghai, 200080, China
| | - Zheng Li
- Department of Andrology and PFD, Center for Men's Health, Department of ART, Institute of Urology, Urologic Medical Center Shanghai General Hospital, Shanghai Key Lab of Reproductive Medicine Shanghai Jiao Tong University, Shanghai, 200080, China
| | - Hong Chen
- Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Li-Gang Wu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Dangsheng Li
- Shanghai Information Center for Life Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Jinsong Li
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China; School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
| | - Hui-Juan Shi
- Key Lab of Reproduction Regulation of NPFPC-Shanghai Institute of Planned Parenthood Research, Fudan University Reproduction and Development Institution, Shanghai 200032, China.
| | - Mo-Fang Liu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China; School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China; Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200438, China.
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139
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Discovery of microRNAs during early spermatogenesis in chicken. PLoS One 2017; 12:e0177098. [PMID: 28531200 PMCID: PMC5439670 DOI: 10.1371/journal.pone.0177098] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 04/21/2017] [Indexed: 12/01/2022] Open
Abstract
Spermatogenesis is a complex process that involves many elements. However, until now, little is known at the molecular level about spermatogenesis in poultry. Here we investigated microRNAs and their target genes that may be involved in germ cell development and spermatogonial in chicken. We used next-generation sequencing to analyze miRNA expression profiles in three types of germline cells: primordial germ cells (PGCs), spermatogonial stem cells (SSCs), and spermatogonia (Sp) during early stage of spermatogenesis. After validated the candidate miRNAs and corresponding genes’ expression in three types of cells, we found 15 miRNAs that were enriched 21 target genes that may be involved in spermatogenesis. Among the enriched miRNAs, miR-202-5p/3p were up-regulated in the Sp library and down-regulated in the PGCs library. Through RT-qPCR and Dual-Luciferase reporter assay, we confirmed that miR-202-5p bind to LIMK2 and involved in germ cell development. Collectively, we firstly discover the novel miRNAs, like miR-202-5p, and its related genes and pathways, expressed during the early spermatogonial stage in chicken, which will provide new clues for deciphering the molecular mechanism of the miRNAs regulating germline stem cell differentiation and spermatogenesis in chicken.
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140
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Hili Inhibits HIV Replication in Activated T Cells. J Virol 2017; 91:JVI.00237-17. [PMID: 28331090 DOI: 10.1128/jvi.00237-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 03/02/2017] [Indexed: 02/06/2023] Open
Abstract
P-element-induced wimpy-like (Piwil) proteins restrict the replication of mobile genetic elements in the germ line. They are also expressed in many transformed cell lines. In this study, we discovered that the human Piwil 2 (Hili) protein can also inhibit HIV replication, especially in activated CD4+ T cells that are the preferred target cells for this virus in the infected host. Although resting cells did not express Hili, its expression was rapidly induced following T cell activation. In these cells and transformed cell lines, depletion of Hili increased levels of viral proteins and new viral particles. Further studies revealed that Hili binds to tRNA. Some of the tRNAs represent rare tRNA species, whose codons are overrepresented in the viral genome. Targeting tRNAArg(UCU) with an antisense oligonucleotide replicated effects of Hili and also inhibited HIV replication. Finally, Hili also inhibited the retrotransposition of the endogenous intracysternal A particle (IAP) by a similar mechanism. Thus, Hili joins a list of host proteins that inhibit the replication of HIV and other mobile genetic elements.IMPORTANCE Piwil proteins inhibit the movement of mobile genetic elements in the germ line. In their absence, sperm does not form and male mice are sterile. This inhibition is thought to occur via small Piwi-interacting RNAs (piRNAs). However, in some species and in human somatic cells, Piwil proteins bind primarily to tRNA. In this report, we demonstrate that human Piwil proteins, especially Hili, not only bind to select tRNA species, including rare tRNAs, but also inhibit HIV replication. Importantly, T cell activation induces the expression of Hili in CD4+ T cells. Since Hili also inhibited the movement of an endogenous retrovirus (IAP), our finding shed new light on this intracellular resistance to exogenous and endogenous retroviruses as well as other mobile genetic elements.
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141
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Sumiyoshi T, Sato K, Yamamoto H, Iwasaki YW, Siomi H, Siomi MC. Loss of l(3)mbt leads to acquisition of the ping-pong cycle in Drosophila ovarian somatic cells. Genes Dev 2017; 30:1617-22. [PMID: 27474440 PMCID: PMC4973291 DOI: 10.1101/gad.283929.116] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 06/15/2016] [Indexed: 11/24/2022]
Abstract
Sumiyoshi et al. show that CRISPR-mediated loss of function of lethal (3) malignant brain tumor [l(3)mbt] leads to ectopic activation of the germ-specific ping-pong cycle in ovarian somatic cells. Perinuclear foci resembling nuage, the ping-pong center, appeared following l(3)mbt mutation. In Drosophila germ cells, PIWI-interacting RNAs (piRNAs) are amplified through a PIWI slicer-dependent feed-forward loop termed the ping-pong cycle, yielding secondary piRNAs. However, the detailed mechanism remains poorly understood, largely because an ex vivo model system amenable to biochemical analyses has not been available. Here, we show that CRISPR-mediated loss of function of lethal (3) malignant brain tumor [l(3)mbt] leads to ectopic activation of the germ-specific ping-pong cycle in ovarian somatic cells. Perinuclear foci resembling nuage, the ping-pong center, appeared following l(3)mbt mutation. This activation of the ping-pong machinery in cultured cells will greatly facilitate elucidation of the mechanism underlying secondary piRNA biogenesis in Drosophila.
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Affiliation(s)
- Tetsutaro Sumiyoshi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
| | - Kaoru Sato
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
| | - Hitomi Yamamoto
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
| | - Yuka W Iwasaki
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 162-8582, Japan
| | - Haruhiko Siomi
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 162-8582, Japan
| | - Mikiko C Siomi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
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142
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Spina EJ, Guzman E, Zhou H, Kosik KS, Smith WC. A microRNA-mRNA expression network during oral siphon regeneration in Ciona. Development 2017; 144:1787-1797. [PMID: 28432214 DOI: 10.1242/dev.144097] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 04/10/2017] [Indexed: 12/14/2022]
Abstract
Here we present a parallel study of mRNA and microRNA expression during oral siphon (OS) regeneration in Ciona robusta, and the derived network of their interactions. In the process of identifying 248 mRNAs and 15 microRNAs as differentially expressed, we also identified 57 novel microRNAs, several of which are among the most highly differentially expressed. Analysis of functional categories identified enriched transcripts related to stress responses and apoptosis at the wound healing stage, signaling pathways including Wnt and TGFβ during early regrowth, and negative regulation of extracellular proteases in late stage regeneration. Consistent with the expression results, we found that inhibition of TGFβ signaling blocked OS regeneration. A correlation network was subsequently inferred for all predicted microRNA-mRNA target pairs expressed during regeneration. Network-based clustering associated transcripts into 22 non-overlapping groups, the functional analysis of which showed enrichment of stress response, signaling pathway and extracellular protease categories that could be related to specific microRNAs. Predicted targets of the miR-9 cluster suggest a role in regulating differentiation and the proliferative state of neural progenitors through regulation of the cytoskeleton and cell cycle.
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Affiliation(s)
- Elijah J Spina
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Elmer Guzman
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Hongjun Zhou
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Kenneth S Kosik
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.,Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - William C Smith
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA .,Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
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143
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Kamaliyan Z, Pouriamanesh S, Amin-beidokhti M, Rezagholizadeh A, Mirfakhraie R. HIWI2 rs508485 Polymorphism Is Associated with Non-obstructive Azoospermia in Iranian Patients. Rep Biochem Mol Biol 2017; 5:108-111. [PMID: 28367472 PMCID: PMC5346278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 05/22/2016] [Indexed: 06/07/2023]
Abstract
BACKGROUND The PIWI-interacting RNA (piRNA) pathway has an essential role in transposon silencing, meiosis progression, spermatogenesis, and germline maintenance. HIWI genes are critical for piRNA biogenesis and function. Therefore, polymorphisms in HIWI genes contribute to spermatogenesis defects and can be considered as risk factors for male infertility. The aim of the present study was to investigate the association between the HIWI2 gene rs508485 polymorphism and non-obstructive azoospermia. METHODS A total of 121 Iranian men with idiopathic azoospermia and 100 fertile controls were genotyped for HIWI2 rs508485 (T>C) polymorphism using Tetra-ARMS PCR. The presence of eight sequence-tagged site (STS) markers from the Y chromosome AZF region was also investigated by Multiplex PCR (M-PCR). RESULTS Thirteen (10.74%) patients showed Y chromosome microdeletions and therefore were excluded from the study. rs508485 in the 3'UTR of HIWI2 was associated with increased risk of azoospermia in our studied population with a P-value of 0.035 and odds ratio of 2.00 (CI 95%: 1.04-3.86). CONCLUSIONS We provide evidence for an association between genetic variation in the HIWI2 gene involved in the piRNA pathway and idiopathic non-obstructive azoospermia in Iranian patients. Therefore, piRNA pathway gene variants can be considered as risk factors for male infertility.
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Affiliation(s)
- Zeeba Kamaliyan
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Sara Pouriamanesh
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mona Amin-beidokhti
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Amir Rezagholizadeh
- Biology Department, Islamic Azad University, East Tehran Branch, Tehran, Iran.
| | - Reza Mirfakhraie
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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144
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Ma X, Zhu X, Han Y, Story B, Do T, Song X, Wang S, Zhang Y, Blanchette M, Gogol M, Hall K, Peak A, Anoja P, Xie T. Aubergine Controls Germline Stem Cell Self-Renewal and Progeny Differentiation via Distinct Mechanisms. Dev Cell 2017; 41:157-169.e5. [DOI: 10.1016/j.devcel.2017.03.023] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Revised: 02/10/2017] [Accepted: 03/29/2017] [Indexed: 01/09/2023]
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145
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Toombs JA, Sytnikova YA, Chirn GW, Ang I, Lau NC, Blower MD. Xenopus Piwi proteins interact with a broad proportion of the oocyte transcriptome. RNA (NEW YORK, N.Y.) 2017; 23:504-520. [PMID: 28031481 PMCID: PMC5340914 DOI: 10.1261/rna.058859.116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 12/21/2016] [Indexed: 06/06/2023]
Abstract
Piwi proteins utilize small RNAs (piRNAs) to recognize target transcripts such as transposable elements (TE). However, extensive piRNA sequence diversity also suggests that Piwi/piRNA complexes interact with many transcripts beyond TEs. To determine Piwi target RNAs, we used ribonucleoprotein-immunoprecipitation (RIP) and cross-linking and immunoprecipitation (CLIP) to identify thousands of transcripts associated with the Piwi proteins XIWI and XILI (Piwi-protein-associated transcripts, PATs) from early stage oocytes of X. laevis and X. tropicalis Most PATs associate with both XIWI and XILI and include transcripts of developmentally important proteins in oogenesis and embryogenesis. Only a minor fraction of PATs in both frog species displayed near perfect matches to piRNAs. Since predicting imperfect pairing between all piRNAs and target RNAs remains intractable, we instead determined that PAT read counts correlate well with the lengths and expression levels of transcripts, features that have also been observed for oocyte mRNAs associated with Drosophila Piwi proteins. We used an in vitro assay with exogenous RNA to confirm that XIWI associates with RNAs in a length- and concentration-dependent manner. In this assay, noncoding transcripts with many perfectly matched antisense piRNAs were unstable, whereas coding transcripts with matching piRNAs were stable, consistent with emerging evidence that Piwi proteins both promote the turnover of TEs and other RNAs, and may also regulate mRNA localization and translation. Our study suggests that Piwi proteins play multiple roles in germ cells and establishes a tractable vertebrate system to study the role of Piwi proteins in transcript regulation.
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Affiliation(s)
- James A Toombs
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yuliya A Sytnikova
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Gung-Wei Chirn
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Ignatius Ang
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Nelson C Lau
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Michael D Blower
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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146
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Litwin M, Szczepańska-Buda A, Piotrowska A, Dzięgiel P, Witkiewicz W. The meaning of PIWI proteins in cancer development. Oncol Lett 2017; 13:3354-3362. [PMID: 28529570 PMCID: PMC5431467 DOI: 10.3892/ol.2017.5932] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 02/01/2017] [Indexed: 12/13/2022] Open
Abstract
Cancer is a histologically and genetically heterogeneous population of tumor cells that exhibits distinct molecular profiles determined by epigenetic alterations. P-element-induced wimpy testis (PIWI) proteins in complex with PIWI-interacting RNA (piRNA) have been previously demonstrated to be involved in epigenetic regulation in germline cells. Recently, reactivation of PIWI expression, primarily PIWI-like protein 1 and 2, through aberrant DNA methylation resulting in genomic silencing has been identified in various types of tumors. It has been suggested that the PIWI-piRNA complex contributes to cancer development and progression by promoting a stem-like state of cancer cells, or cancer stem cells (CSCs). It has been identified that CSCs represent the cells that have undergone epithelial-mesenchymal transition (EMT) and acquired metastatic capacities. However, the molecular association between the EMT process and the stem-cell state remains unclear. Further extensive characterization of CSCs in individual types of tumors is required to identify specific markers for the heterogeneous population of CSCs and therefore selectively target CSCs. Previous studies indicate a reciprocal regulation between PIWI proteins and a complex signaling network linking markers characterized for CSCs and transcription factors involved in EMT. In the present review, studies of PIWI function are summarized, and the potential involvement of PIWI proteins in cancer development and progression is discussed.
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Affiliation(s)
- Monika Litwin
- Research and Development Centre, Regional Specialist Hospital in Wrocław, Poland.,Research and Development Centre Novasome Sp. z o.o., 51-423 Wrocław, Poland
| | - Anna Szczepańska-Buda
- Research and Development Centre, Regional Specialist Hospital in Wrocław, Poland.,Research and Development Centre Novasome Sp. z o.o., 51-423 Wrocław, Poland
| | - Aleksandra Piotrowska
- Department of Histology and Embryology, Wrocław Medical University, 50-368 Wrocław, Poland
| | - Piotr Dzięgiel
- Department of Histology and Embryology, Wrocław Medical University, 50-368 Wrocław, Poland.,Department of Physiotherapy and Occupational Therapy in Conservative and Interventional Medicine, 51-612 Wrocław, Poland
| | - Wojciech Witkiewicz
- Research and Development Centre, Regional Specialist Hospital in Wrocław, Poland
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147
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Karam JA, Parikh RY, Nayak D, Rosenkranz D, Gangaraju VK. Co-chaperone Hsp70/Hsp90-organizing protein (Hop) is required for transposon silencing and Piwi-interacting RNA (piRNA) biogenesis. J Biol Chem 2017; 292:6039-6046. [PMID: 28193840 DOI: 10.1074/jbc.c117.777730] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 02/08/2017] [Indexed: 11/06/2022] Open
Abstract
Piwi-interacting RNAs (piRNAs) are 26-30-nucleotide germ line-specific small non-coding RNAs that have evolutionarily conserved function in mobile genetic element (transposons) silencing and maintenance of genome integrity. Drosophila Hsp70/90-organizing protein homolog (Hop), a co-chaperone, interacts with piRNA-binding protein Piwi and mediates silencing of phenotypic variations. However, it is not known whether Hop has a direct role in piRNA biogenesis and transposon silencing. Here, we show that knockdown of Hop in the germ line nurse cells (GLKD) of Drosophila ovaries leads to activation of transposons. Hop GLKD females can lay eggs at the same rate as wild-type counterparts, but the eggs do not hatch into larvae. Hop GLKD leads to the accumulation of γ-H2Av foci in the germ line, indicating increased DNA damage in the ovary. We also show that Hop GLKD-induced transposon up-regulation is due to inefficient piRNA biogenesis. Based on these results, we conclude that Hop is a critical component of the piRNA pathway and that it maintains genome integrity by silencing transposons.
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Affiliation(s)
- Joseph A Karam
- From the Department of Biochemistry and Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425 and
| | - Rasesh Y Parikh
- From the Department of Biochemistry and Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425 and
| | - Dhananjaya Nayak
- From the Department of Biochemistry and Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425 and
| | - David Rosenkranz
- the Institute of Organismic and Molecular Evolutionary Biology, Johannes Gutenberg-Universität Mainz, 55122 Mainz, Germany
| | - Vamsi K Gangaraju
- From the Department of Biochemistry and Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425 and
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148
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Localization in Oogenesis of Maternal Regulators of Embryonic Development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 953:173-207. [DOI: 10.1007/978-3-319-46095-6_5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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149
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Phay M, Kim HH, Yoo S. Analysis of piRNA-Like Small Non-coding RNAs Present in Axons of Adult Sensory Neurons. Mol Neurobiol 2016; 55:483-494. [PMID: 27966078 DOI: 10.1007/s12035-016-0340-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 12/02/2016] [Indexed: 10/20/2022]
Abstract
Small non-coding RNAs (sncRNAs) have been shown to play pivotal roles in spatiotemporal-specific gene regulation that is linked to many different biological functions. PIWI-interacting RNAs (piRNAs), typically 25-34-nucleotide long, are originally identified and thought to be restricted in germline cells. However, recent studies suggest that piRNAs associate with neuronal PIWI proteins, contributing to neuronal development and function. Here, we identify a cohort of piRNA-like sncRNAs (piLRNAs) in rat sciatic nerve axoplasm and directly contrast temporal changes of piLRNA levels in the nerve following injury, as compared with those in an uninjured nerve using deep sequencing. We find that 32 of a total of 53 annotated piLRNAs show significant changes in their levels in the regenerating nerve, suggesting that individual axonal piLRNAs may play important regulatory roles in local messenger RNA (mRNA) translation during regeneration. Bioinformatics and biochemical analyses show that these piLRNAs carry characteristic features of mammalian piRNAs, including sizes, a sequence bias for uracil at the 5'-end and a 2'-O-methylation at the 3'-end. Their axonal expression is directly visualized by fluorescence in situ hybridization in cultured dorsal root ganglion neurons as well as immunoprecipitation with MIWI. Further, depletion of MIWI protein using RNAi from cultured sensory neurons increases axon growth rates, decreases axon retraction after injury, and increases axon regrowth after injury. All these data suggest more general roles for MIWI/piLRNA pathway that could confer a unique advantage for coordinately altering the population of proteins generated in growth cones and axons of neurons by targeting mRNA cohorts.
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Affiliation(s)
- Monichan Phay
- Nemours Biomedical Research, Alfred I duPont Hospital for Children, Wilmington, DE, 19803, USA.,Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Hak Hee Kim
- Nemours Biomedical Research, Alfred I duPont Hospital for Children, Wilmington, DE, 19803, USA
| | - Soonmoon Yoo
- Nemours Biomedical Research, Alfred I duPont Hospital for Children, Wilmington, DE, 19803, USA. .,Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA.
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150
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Abstract
Stem cells are critical to maintaining steady-state organ homeostasis and regenerating injured tissues. Recent intriguing reports implicate extracellular vesicles (EVs) as carriers for the distribution of morphogens and growth and differentiation factors from tissue parenchymal cells to stem cells, and conversely, stem cell-derived EVs carrying certain proteins and nucleic acids can support healing of injured tissues. We describe approaches to make use of engineered EVs as technology platforms in therapeutics and diagnostics in the context of stem cells. For some regenerative therapies, natural and engineered EVs from stem cells may be superior to single-molecule drugs, biologics, whole cells, and synthetic liposome or nanoparticle formulations because of the ease of bioengineering with multiple factors while retaining superior biocompatibility and biostability and posing fewer risks for abnormal differentiation or neoplastic transformation. Finally, we provide an overview of current challenges and future directions of EVs as potential therapeutic alternatives to cells for clinical applications.
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Affiliation(s)
- Milad Riazifar
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697; .,Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, California 92697.,Chao Family Comprehensive Cancer Center, University of California, Irvine, Orange, California 92868.,Edwards Lifesciences Center for Advanced Cardiovascular Technology, University of California, Irvine, California 92697.,Department of Biomedical Engineering, University of California, Irvine, California 92697.,Department of Biological Chemistry, University of California, Irvine, California 92697
| | - Egest J Pone
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697; .,Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, California 92697.,Chao Family Comprehensive Cancer Center, University of California, Irvine, Orange, California 92868.,Edwards Lifesciences Center for Advanced Cardiovascular Technology, University of California, Irvine, California 92697.,Department of Biomedical Engineering, University of California, Irvine, California 92697.,Department of Biological Chemistry, University of California, Irvine, California 92697
| | - Jan Lötvall
- Krefting Research Centre, Institute of Medicine, The Sahlgrenska Academy, Göteborg University, SE-405 30 Göteborg, Sweden.,Codiak BioSciences Inc., Woburn, Massachusetts 01801
| | - Weian Zhao
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697; .,Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, California 92697.,Chao Family Comprehensive Cancer Center, University of California, Irvine, Orange, California 92868.,Edwards Lifesciences Center for Advanced Cardiovascular Technology, University of California, Irvine, California 92697.,Department of Biomedical Engineering, University of California, Irvine, California 92697.,Department of Biological Chemistry, University of California, Irvine, California 92697
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