201
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Qiu L, Xu L, Chang G, Guo Q, Liu X, Bi Y, Zhang Y, Wang H, Wang K, Lu W, Ren L, Zhu P, Wu Y, Zhang Y, Xu Q, Chen G. DNA methylation-mediated transcription factors regulate Piwil1 expression during chicken spermatogenesis. J Reprod Dev 2016; 62:367-72. [PMID: 27108736 PMCID: PMC5004792 DOI: 10.1262/jrd.2016-003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The P-element induced wimpy testis (Piwi) protein family is responsible for
initiating spermatogenesis and maintaining the integrity of germ cells and stem
cells, but little is known regarding its transcriptional regulation in poultry. Here,
we characterized the methylation status of the Piwil1 promoter in
five different spermatogenic cell lines using direct bisulfite pyrosequencing and
determined that methylation correlates negatively with germ cell type-specific
expression patterns of piwil1. We demonstrated that methylation of
the −148 CpG site, which is the predicted binding site for the transcription factors
TCF3 and NRF1, was differentially methylated in different spermatogenic cells. This
site was completely methylated in PGCs (primordial germ cells), but was unmethylated
in round spermatids. A similar result was obtained in the region from +121 to +139
CpG sites of the Piwil1 promoter CpG island, which was predicted to
contain SOX2 binding sites. In addition, demethylation assays further demonstrated
that DNA methylation indeed regulates Piwil1 expression during
chicken spermatogenesis. Combined with transcription factor binding site prediction,
we speculate that methylation influences the recruitment of corresponding
transcription factors. Collectively, we show the negative correlation between
promoter methylation and piwil1 expression and that the
spatiotemporal expression of chicken Piwil1 from the PGC stage to
the round spermatid stage is influenced by methylation-mediated transcription factor
regulation.
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Affiliation(s)
- Lingling Qiu
- College of Animal Science & Technology, Yangzhou University, Jiangsu 225009, China
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202
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Xu L, Qiu L, Chang G, Guo Q, Liu X, Bi Y, Zhang Y, Wang H, Li Z, Guo X, Wan F, Zhang Y, Xu Q, Chen G. Discovery of piRNAs Pathway Associated with Early-Stage Spermatogenesis in Chicken. PLoS One 2016; 11:e0151780. [PMID: 27045806 PMCID: PMC4821617 DOI: 10.1371/journal.pone.0151780] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 03/03/2016] [Indexed: 01/10/2023] Open
Abstract
Piwi-interacting RNAs (piRNAs) play a key role in spermatogenesis. Here, we describe the piRNAs profiling of primordial germ cells (PGCs), spermatogonial stem cells (SSCs), and the spermatogonium (Sp) during early-stage spermatogenesis in chicken. We obtained 31,361,989 reads from PGCs, 31,757,666 reads from SSCs, and 46,448,327 reads from Sp cells. The length distribution of piRNAs in the three samples showed peaks at 33 nt. The resulting genes were subsequently annotated against the Gene Ontology (GO) database. Five genes (RPL7A, HSPA8, Pum1, CPXM2, and PRKCA) were found to be involved in cellular processes. Interactive pathway analysis (IPA) further revealed three important pathways in early-stage spermatogenesis including the FGF, Wnt, and EGF receptor signaling pathways. The gene Pum1 was found to promote germline stem cell proliferation, but it also plays a role in spermatogenesis. In conclusion, we revealed characteristics of piRNAs during early spermatogonial development in chicken and provided the basis for future research.
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Affiliation(s)
- Lu Xu
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Lingling Qiu
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Guobin Chang
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
- * E-mail: (GBC); (GHC)
| | - Qixin Guo
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Xiangping Liu
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu, 225003, China
| | - Yulin Bi
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Yu Zhang
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Hongzhi Wang
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu, 225003, China
| | - Zhiteng Li
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Xiaoming Guo
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Fang Wan
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Yang Zhang
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Qi Xu
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Guohong Chen
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
- * E-mail: (GBC); (GHC)
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203
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Czech B, Hannon GJ. One Loop to Rule Them All: The Ping-Pong Cycle and piRNA-Guided Silencing. Trends Biochem Sci 2016; 41:324-337. [PMID: 26810602 PMCID: PMC4819955 DOI: 10.1016/j.tibs.2015.12.008] [Citation(s) in RCA: 300] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 12/17/2015] [Accepted: 12/22/2015] [Indexed: 01/06/2023]
Abstract
The PIWI-interacting RNA (piRNA) pathway is a conserved defense mechanism that protects the genetic information of animal germ cells from the deleterious effects of molecular parasites, such as transposons. Discovered nearly a decade ago, this small RNA silencing system comprises PIWI-clade Argonaute proteins and their associated RNA-binding partners, the piRNAs. In this review, we highlight recent work that has advanced our understanding of how piRNAs preserve genome integrity across generations. We discuss the mechanism of piRNA biogenesis, give an overview of common themes as well as differences in piRNA-mediated silencing between species, and end by highlighting known and emerging functions of piRNAs.
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Affiliation(s)
- Benjamin Czech
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE, UK.
| | - Gregory J Hannon
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE, UK.
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204
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Yang F, Wang PJ. Multiple LINEs of retrotransposon silencing mechanisms in the mammalian germline. Semin Cell Dev Biol 2016; 59:118-125. [PMID: 26957474 DOI: 10.1016/j.semcdb.2016.03.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 02/29/2016] [Accepted: 03/01/2016] [Indexed: 02/07/2023]
Abstract
Retrotransposons play an important role in genome evolution but pose acute challenges to host genome integrity, particularly in early stage germ cells where epigenetic control is relaxed to permit genome-wide reprogramming. In most species, the inability to silence retrotransposons in the germline is usually associated with sterility. LINE1 is the most abundant retrotransposon type in the mammalian genome. Mammalian germ cells employ multiple mechanisms to suppress retrotransposon activity, including small non-coding piRNAs, DNA methylation, and repressive histone modifications. Novel factors contributing to the epigenetic silencing of retrotransposons in the germline continue to be identified. Recent studies have provided insight into how epigenetic changes associated with retrotransposon activation impact on fertility.
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Affiliation(s)
- Fang Yang
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, 3800 Spruce Street, Philadelphia, PA 19104, USA
| | - P Jeremy Wang
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, 3800 Spruce Street, Philadelphia, PA 19104, USA.
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205
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206
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Kobayashi H, Tomari Y. RISC assembly: Coordination between small RNAs and Argonaute proteins. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:71-81. [DOI: 10.1016/j.bbagrm.2015.08.007] [Citation(s) in RCA: 194] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 08/11/2015] [Accepted: 08/20/2015] [Indexed: 12/18/2022]
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207
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Papastamoulis P, Martin-Magniette ML, Maugis-Rabusseau C. On the estimation of mixtures of Poisson regression models with large number of components. Comput Stat Data Anal 2016. [DOI: 10.1016/j.csda.2014.07.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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208
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Non-coding RNA in Spermatogenesis and Epididymal Maturation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 886:95-120. [PMID: 26659489 DOI: 10.1007/978-94-017-7417-8_6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Testicular germ and somatic cells express many classes of small ncRNAs, including Dicer-independent PIWI-interacting RNAs, Dicer-dependent miRNAs, and endogenous small interfering RNA. Several studies have identified ncRNAs that are highly, exclusively, or preferentially expressed in the testis and epididymis in specific germ and somatic cell types. Temporal and spatial expression of proteins is a key requirement of successful spermatogenesis and large-scale gene transcription occurs in two key stages, just prior to transcriptional quiescence in meiosis and then during spermiogenesis just prior to nuclear silencing in elongating spermatids. More than 60 % of these transcripts are then stockpiled for subsequent translation. In this capacity ncRNAs may act to interpret and transduce cellular signals to either maintain the undifferentiated stem cell population and/or drive cell differentiation during spermatogenesis and epididymal maturation. The assignation of specific roles to the majority of ncRNA species implicated as having a role in spermatogenesis and epididymal function will underpin fundamental understanding of normal and disease states in humans such as infertility and the development of germ cell tumours.
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209
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Tóth KF, Pezic D, Stuwe E, Webster A. The piRNA Pathway Guards the Germline Genome Against Transposable Elements. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 886:51-77. [PMID: 26659487 DOI: 10.1007/978-94-017-7417-8_4] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Transposable elements (TEs) have the capacity to replicate and insert into new genomic locations. This contributs significantly to evolution of genomes, but can also result in DNA breaks and illegitimate recombination, and therefore poses a significant threat to genomic integrity. Excess damage to the germ cell genome results in sterility. A specific RNA silencing pathway, termed the piRNA pathway operates in germ cells of animals to control TE activity. At the core of the piRNA pathway is a ribonucleoprotein complex consisting of a small RNA, called piRNA, and a protein from the PIWI subfamily of Argonaute nucleases. The piRNA pathway relies on the specificity provided by the piRNA sequence to recognize complementary TE targets, while effector functions are provided by the PIWI protein. PIWI-piRNA complexes silence TEs both at the transcriptional level - by attracting repressive chromatin modifications to genomic targets - and at the posttranscriptional level - by cleaving TE transcripts in the cytoplasm. Impairment of the piRNA pathway leads to overexpression of TEs, significantly compromised genome structure and, invariably, germ cell death and sterility.The piRNA pathway is best understood in the fruit fly, Drosophila melanogaster, and in mouse. This Chapter gives an overview of current knowledge on piRNA biogenesis, and mechanistic details of both transcriptional and posttranscriptional TE silencing by the piRNA pathway. It further focuses on the importance of post-translational modifications and subcellular localization of the piRNA machinery. Finally, it provides a brief description of analogous pathways in other systems.
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Affiliation(s)
- Katalin Fejes Tóth
- Division of Biology and Bioengineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, 91125, USA.
| | - Dubravka Pezic
- Division of Biology and Bioengineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, 91125, USA
| | - Evelyn Stuwe
- Division of Biology and Bioengineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, 91125, USA
| | - Alexandre Webster
- Division of Biology and Bioengineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, 91125, USA
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210
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piRNA biogenesis in the germline: From transcription of piRNA genomic sources to piRNA maturation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:82-92. [DOI: 10.1016/j.bbagrm.2015.09.002] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 08/25/2015] [Accepted: 09/01/2015] [Indexed: 12/22/2022]
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211
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Sharma U, Conine CC, Shea JM, Boskovic A, Derr AG, Bing XY, Belleannee C, Kucukural A, Serra RW, Sun F, Song L, Carone BR, Ricci EP, Li XZ, Fauquier L, Moore MJ, Sullivan R, Mello CC, Garber M, Rando OJ. Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals. Science 2015; 351:391-396. [PMID: 26721685 DOI: 10.1126/science.aad6780] [Citation(s) in RCA: 790] [Impact Index Per Article: 87.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 12/10/2015] [Indexed: 12/13/2022]
Abstract
Several recent studies link parental environments to phenotypes in subsequent generations. In this work, we investigate the mechanism by which paternal diet affects offspring metabolism. Protein restriction in mice affects small RNA (sRNA) levels in mature sperm, with decreased let-7 levels and increased amounts of 5' fragments of glycine transfer RNAs (tRNAs). In testicular sperm, tRNA fragments are scarce but increase in abundance as sperm mature in the epididymis. Epididymosomes (vesicles that fuse with sperm during epididymal transit) carry RNA payloads matching those of mature sperm and can deliver RNAs to immature sperm in vitro. Functionally, tRNA-glycine-GCC fragments repress genes associated with the endogenous retroelement MERVL, in both embryonic stem cells and embryos. Our results shed light on sRNA biogenesis and its dietary regulation during posttesticular sperm maturation, and they also link tRNA fragments to regulation of endogenous retroelements active in the preimplantation embryo.
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Affiliation(s)
- Upasna Sharma
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Colin C Conine
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jeremy M Shea
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ana Boskovic
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Alan G Derr
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.,Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Xin Y Bing
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Clemence Belleannee
- Department of Obstetrics, Gynecology and Reproduction, Université Laval, Centre Hospitalier Universitaire de Québec Research Center,,Quebec City, Canada, G1V 4G2
| | - Alper Kucukural
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.,Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ryan W Serra
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Fengyun Sun
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Lina Song
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Benjamin R Carone
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Emiliano P Ricci
- RNAi Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Xin Z Li
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.,RNAi Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Lucas Fauquier
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Melissa J Moore
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.,RNAi Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA.,Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Robert Sullivan
- Department of Obstetrics, Gynecology and Reproduction, Université Laval, Centre Hospitalier Universitaire de Québec Research Center,,Quebec City, Canada, G1V 4G2
| | - Craig C Mello
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.,RNAi Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA.,Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Manuel Garber
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.,Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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212
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Yang Z, Chen KM, Pandey RR, Homolka D, Reuter M, Janeiro BKR, Sachidanandam R, Fauvarque MO, McCarthy AA, Pillai RS. PIWI Slicing and EXD1 Drive Biogenesis of Nuclear piRNAs from Cytosolic Targets of the Mouse piRNA Pathway. Mol Cell 2015; 61:138-52. [PMID: 26669262 PMCID: PMC4712191 DOI: 10.1016/j.molcel.2015.11.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 10/12/2015] [Accepted: 10/28/2015] [Indexed: 11/19/2022]
Abstract
PIWI-interacting RNAs (piRNAs) guide PIWI proteins to suppress transposons in the cytoplasm and nucleus of animal germ cells, but how silencing in the two compartments is coordinated is not known. Here we demonstrate that endonucleolytic slicing of a transcript by the cytosolic mouse PIWI protein MILI acts as a trigger to initiate its further 5'→3' processing into non-overlapping fragments. These fragments accumulate as new piRNAs within both cytosolic MILI and the nuclear MIWI2. We also identify Exonuclease domain-containing 1 (EXD1) as a partner of the MIWI2 piRNA biogenesis factor TDRD12. EXD1 homodimers are inactive as a nuclease but function as an RNA adaptor within a PET (PIWI-EXD1-Tdrd12) complex. Loss of Exd1 reduces sequences generated by MILI slicing, impacts biogenesis of MIWI2 piRNAs, and de-represses LINE1 retrotransposons. Thus, piRNA biogenesis triggered by PIWI slicing, and promoted by EXD1, ensures that the same guides instruct PIWI proteins in the nucleus and cytoplasm.
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Affiliation(s)
- Zhaolin Yang
- European Molecular Biology Laboratory, Grenoble Outstation, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France; Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France
| | - Kuan-Ming Chen
- European Molecular Biology Laboratory, Grenoble Outstation, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France; Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France
| | - Radha Raman Pandey
- European Molecular Biology Laboratory, Grenoble Outstation, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France; Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France
| | - David Homolka
- European Molecular Biology Laboratory, Grenoble Outstation, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France; Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France
| | - Michael Reuter
- European Molecular Biology Laboratory, Grenoble Outstation, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France; Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France
| | - Bruno Kotska Rodino Janeiro
- European Molecular Biology Laboratory, Grenoble Outstation, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France; Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France
| | - Ravi Sachidanandam
- Department of Oncological Sciences, Icahn School of Medicine at Sinai, One Gustave L. Levy Place, NY 10029, USA
| | | | - Andrew A McCarthy
- European Molecular Biology Laboratory, Grenoble Outstation, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France; Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France
| | - Ramesh S Pillai
- European Molecular Biology Laboratory, Grenoble Outstation, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France; Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France.
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213
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Isbel L, Srivastava R, Oey H, Spurling A, Daxinger L, Puthalakath H, Whitelaw E. Trim33 Binds and Silences a Class of Young Endogenous Retroviruses in the Mouse Testis; a Novel Component of the Arms Race between Retrotransposons and the Host Genome. PLoS Genet 2015; 11:e1005693. [PMID: 26624618 PMCID: PMC4666613 DOI: 10.1371/journal.pgen.1005693] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 10/30/2015] [Indexed: 12/12/2022] Open
Abstract
Transposable elements (TEs) have been active in the mammalian genome for millions of years and the silencing of these elements in the germline is important for the survival of the host. Mice carrying reporter transgenes can be used to model transcriptional silencing. A mutagenesis screen for modifiers of epigenetic gene silencing produced a line with a mutation in Trim33; the mutants displayed increased expression of the reporter transgene. ChIP-seq of Trim33 in testis revealed 9,109 peaks, mostly at promoters. This is the first report of ChIP-seq for Trim33 in any tissue. Comparison with ENCODE datasets showed that regions of high read density for Trim33 had high read density for histone marks associated with transcriptional activity and mapping to TE consensus sequences revealed Trim33 enrichment at RLTR10B, the LTR of one of the youngest retrotransposons in the mouse genome, MMERVK10C. We identified consensus sequences from the 266 regions at which Trim33 ChIP-seq peaks overlapped RLTR10B elements and found a match to the A-Myb DNA-binding site. We found that TRIM33 has E3 ubiquitin ligase activity for A-MYB and regulates its abundance. RNA-seq revealed that mice haploinsufficient for Trim33 had altered expression of a small group of genes in the testis and the gene with the most significant increase was found to be transcribed from an upstream RLTR10B. These studies provide the first evidence that A-Myb has a role in the actions of Trim33 and suggest a role for both A-Myb and Trim33 in the arms race between the transposon and the host. This the first report of any factor specifically regulating RLTR10B and adds to the current literature on the silencing of MMERVK10C retrotransposons. This is also the first report that A-Myb has a role in the transcription of any retrotransposon. Almost half of the genomes of humans and mice are made up of transposable elements. During host evolution, subsets of these elements have periods of transpositional activity during which they spread throughout the genome. This is dependent on the transcriptional activity of these elements in the cells that contribute to the germline. Hosts have evolved pathways to silence their expression. A number of Trim family proteins have been found to have a role in silencing transposable elements, and it was previously shown that Trim33 shared this function in liver. However, the function of Trim33 in other tissues is poorly understood. Here we report a role for Trim33 in silencing a specific subset of retrotransposons that contain RLTR10B LTRs, in the germline. We also show the transcription factor, A-Myb, is responsible for activating transcription of these elements and it is likely that a subset of RLTR10Bs have recently evolved Myb DNA binding sites to capitalise on the critical role that the A-Myb transcription factor has in germ cells. Suppression of A-Myb activity by Trim33 provides a plausible mechanism by which the host keeps transposons in check.
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Affiliation(s)
- Luke Isbel
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Melbourne, Australia
| | - Rahul Srivastava
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Melbourne, Australia
| | - Harald Oey
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Melbourne, Australia
| | - Alex Spurling
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Melbourne, Australia
| | - Lucia Daxinger
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Melbourne, Australia
| | - Hamsa Puthalakath
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Melbourne, Australia
| | - Emma Whitelaw
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Melbourne, Australia
- * E-mail:
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214
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A Small RNA-Based Immune System Defends Germ Cells against Mobile Genetic Elements. Stem Cells Int 2015; 2016:7595791. [PMID: 26681955 PMCID: PMC4670677 DOI: 10.1155/2016/7595791] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 06/11/2015] [Indexed: 11/17/2022] Open
Abstract
Transposons are mobile genetic elements that threaten the survival of species by destabilizing the germline genomes. Limiting the spread of these selfish elements is imperative. Germ cells employ specialized small regulatory RNA pathways to restrain transposon activity. PIWI proteins and Piwi-interacting RNAs (piRNAs) silence transposons at the transcriptional and posttranscriptional level with loss-of-function mutant animals universally exhibiting sterility often associated with germ cell defects. This short review aims to illustrate basic strategies of piRNA-guided defense against transposons. Mechanisms of piRNA silencing are most readily studied in Drosophila melanogaster, which serves as a model to delineate molecular concepts and as a reference for mammalian piRNA systems. PiRNA pathways utilize two major strategies to handle the challenges of transposon control: (1) the hard-wired molecular memory of prior transpositions enables recognition of mobile genetic elements and discriminates transposons from host genes; (2) a feed-forward adaptation mechanism shapes piRNA populations to selectively combat the immediate threat of transposon transcripts. In flies, maternally contributed PIWI-piRNA complexes bolster both of these lines of defense and ensure transgenerational immunity. While recent studies have provided a conceptual framework of what could be viewed as an ancient immune system, we are just beginning to appreciate its many molecular innovations.
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215
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Chirn GW, Rahman R, Sytnikova YA, Matts JA, Zeng M, Gerlach D, Yu M, Berger B, Naramura M, Kile BT, Lau NC. Conserved piRNA Expression from a Distinct Set of piRNA Cluster Loci in Eutherian Mammals. PLoS Genet 2015; 11:e1005652. [PMID: 26588211 PMCID: PMC4654475 DOI: 10.1371/journal.pgen.1005652] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/15/2015] [Indexed: 12/18/2022] Open
Abstract
The Piwi pathway is deeply conserved amongst animals because one of its essential functions is to repress transposons. However, many Piwi-interacting RNAs (piRNAs) do not base-pair to transposons and remain mysterious in their targeting function. The sheer number of piRNA cluster (piC) loci in animal genomes and infrequent piRNA sequence conservation also present challenges in determining which piC loci are most important for development. To address this question, we determined the piRNA expression patterns of piC loci across a wide phylogenetic spectrum of animals, and reveal that most genic and intergenic piC loci evolve rapidly in their capacity to generate piRNAs, regardless of known transposon silencing function. Surprisingly, we also uncovered a distinct set of piC loci with piRNA expression conserved deeply in Eutherian mammals. We name these loci Eutherian-Conserved piRNA cluster (ECpiC) loci. Supporting the hypothesis that conservation of piRNA expression across ~100 million years of Eutherian evolution implies function, we determined that one ECpiC locus generates abundant piRNAs antisense to the STOX1 transcript, a gene clinically associated with preeclampsia. Furthermore, we confirmed reduced piRNAs in existing mouse mutations at ECpiC-Asb1 and -Cbl, which also display spermatogenic defects. The Asb1 mutant testes with strongly reduced Asb1 piRNAs also exhibit up-regulated gene expression profiles. These data indicate ECpiC loci may be specially adapted to support Eutherian reproduction. Animal genomes from flies to humans contain many hundreds of non-coding elements called Piwi-interacting RNAs (piRNAs) cluster loci (piC loci). Some of these elements generate piRNAs that direct the silencing of transposable elements, which are pervasive genetic parasites. However, we lack an understanding of the targeting function for the remaining bulk of piRNAs because their loci are not complementarity to transposable elements. In addition, the field does not know if all piC loci are quickly evolving, or if some piC loci might be deeply conserved in piRNA expression, an indication of its potentially functional importance. Our study confirms the highly rapid evolution in piRNA expression capacity for the majority of piC loci in flies and mammals, with many clade- and species-specific piC loci expression patterns. In spite of this, we also discover a cohort of piC loci that are deeply conserved in piRNA expression from the human to the dog, a significantly broad phylogenetic spectrum of eutherian mammals. However, this conservation in piRNA expression ends at non-eutherian mammals like marsupials and monotremes. Existing mutations in two of these Eutherian-Conserved piC (ECpiC) loci impair mouse reproduction and abrogate piRNA production. Therefore, we suggest these ECpiC loci are conserved for piRNA expression due to their important function in eutherian reproduction and stand out as prime candidates for future genetic studies.
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Affiliation(s)
- Gung-wei Chirn
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Reazur Rahman
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Yuliya A. Sytnikova
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Jessica A. Matts
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Mei Zeng
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Daniel Gerlach
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Michael Yu
- Mathematics Department and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Bonnie Berger
- Mathematics Department and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Mayumi Naramura
- Eppley Institute, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Benjamin T. Kile
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Nelson C. Lau
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, United States of America
- * E-mail:
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216
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Rosenkranz D. piRNA cluster database: a web resource for piRNA producing loci. Nucleic Acids Res 2015; 44:D223-30. [PMID: 26582915 PMCID: PMC4702893 DOI: 10.1093/nar/gkv1265] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 11/03/2015] [Indexed: 12/14/2022] Open
Abstract
Piwi proteins and their guiding small RNAs, termed Piwi-interacting (pi-) RNAs, are essential for silencing of transposons in the germline of animals. A substantial fraction of piRNAs originates from genomic loci termed piRNA clusters and sequences encoded in these piRNA clusters determine putative targets for the Piwi/piRNA system. In the past decade, studies of piRNA transcriptomes in different species revealed additional roles for piRNAs beyond transposon silencing, reflecting the astonishing plasticity of the Piwi/piRNA system along different phylogenetic branches. Moreover, piRNA transcriptomes can change drastically during development and vary across different tissues. Since piRNA clusters crucially shape piRNA profiles, analysis of these loci is imperative for a thorough understanding of functional and evolutionary aspects of the piRNA pathway. But despite the ever-growing amount of available piRNA sequence data, we know little about the factors that determine differential regulation of piRNA clusters, nor the evolutionary events that cause their gain or loss. In order to facilitate addressing these subjects, we established a user-friendly piRNA cluster database (http://www.smallrnagroup-mainz.de/piRNAclusterDB.html) that provides comprehensive data on piRNA clusters in multiple species, tissues and developmental stages based on small RNA sequence data deposited at NCBI's Sequence Read Archive (SRA).
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Affiliation(s)
- David Rosenkranz
- Institute of Anthropology, Johannes Gutenberg University, Mainz 55099, Germany
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217
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Lim RSM, Kai T. A piece of the pi(e): The diverse roles of animal piRNAs and their PIWI partners. Semin Cell Dev Biol 2015; 47-48:17-31. [PMID: 26582251 DOI: 10.1016/j.semcdb.2015.10.025] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Small non-coding RNAs are indispensable to many biological processes. A class of endogenous small RNAs, termed PIWI-interacting RNAs (piRNAs) because of their association with PIWI proteins, has known roles in safeguarding the genome against inordinate transposon mobilization, embryonic development, and stem cell regulation, among others. This review discusses the biogenesis of animal piRNAs and their diverse functions together with their PIWI protein partners, both in the germline and in somatic cells, and highlights the evolutionarily conserved aspects of these molecular players in animal biology.
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Affiliation(s)
- Robyn S M Lim
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.
| | - Toshie Kai
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.
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218
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FOXO regulates RNA interference in Drosophila and protects from RNA virus infection. Proc Natl Acad Sci U S A 2015; 112:14587-92. [PMID: 26553999 DOI: 10.1073/pnas.1517124112] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Small RNA pathways are important players in posttranscriptional regulation of gene expression. These pathways play important roles in all aspects of cellular physiology from development to fertility to innate immunity. However, almost nothing is known about the regulation of the central genes in these pathways. The forkhead box O (FOXO) family of transcription factors is a conserved family of DNA-binding proteins that responds to a diverse set of cellular signals. FOXOs are crucial regulators of cellular homeostasis that have a conserved role in modulating organismal aging and fitness. Here, we show that Drosophila FOXO (dFOXO) regulates the expression of core small RNA pathway genes. In addition, we find increased dFOXO activity results in an increase in RNA interference (RNAi) efficacy, establishing a direct link between cellular physiology and RNAi. Consistent with these findings, dFOXO activity is stimulated by viral infection and is required for effective innate immune response to RNA virus infection. Our study reveals an unanticipated connection among dFOXO, stress responses, and the efficacy of small RNA-mediated gene silencing and suggests that organisms can tune their gene silencing in response to environmental and metabolic conditions.
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219
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Zhou X, Battistoni G, El Demerdash O, Gurtowski J, Wunderer J, Falciatori I, Ladurner P, Schatz MC, Hannon GJ, Wasik KA. Dual functions of Macpiwi1 in transposon silencing and stem cell maintenance in the flatworm Macrostomum lignano. RNA (NEW YORK, N.Y.) 2015; 21:1885-97. [PMID: 26323280 PMCID: PMC4604429 DOI: 10.1261/rna.052456.115] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 06/29/2015] [Indexed: 06/04/2023]
Abstract
PIWI proteins and piRNA pathways are essential for transposon silencing and some aspects of gene regulation during animal germline development. In contrast to most animal species, some flatworms also express PIWIs and piRNAs in somatic stem cells, where they are required for tissue renewal and regeneration. Here, we have identified and characterized piRNAs and PIWI proteins in the emerging model flatworm Macrostomum lignano. We found that M. lignano encodes at least three PIWI proteins. One of these, Macpiwi1, acts as a key component of the canonical piRNA pathway in the germline and in somatic stem cells. Knockdown of Macpiwi1 dramatically reduces piRNA levels, derepresses transposons, and severely impacts stem cell maintenance. Knockdown of the piRNA biogenesis factor Macvasa caused an even greater reduction in piRNA levels with a corresponding increase in transposons. Yet, in Macvasa knockdown animals, we detected no major impact on stem cell self-renewal. These results may suggest stem cell maintenance functions of PIWI proteins in flatworms that are distinguishable from their impact on transposons and that might function independently of what are considered canonical piRNA populations.
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Affiliation(s)
- Xin Zhou
- Cold Spring Harbor Laboratory and Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA Molecular and Cellular Biology Graduate Program, Stony Brook University, Stony Brook, New York 11794, USA
| | - Giorgia Battistoni
- Cold Spring Harbor Laboratory and Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA
| | - Osama El Demerdash
- Cold Spring Harbor Laboratory and Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA
| | - James Gurtowski
- Cold Spring Harbor Laboratory and Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA
| | - Julia Wunderer
- University of Innsbruck, Institute of Zoology and CMBI, A-6020 Innsbruck, Austria
| | - Ilaria Falciatori
- Cold Spring Harbor Laboratory and Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA
| | - Peter Ladurner
- University of Innsbruck, Institute of Zoology and CMBI, A-6020 Innsbruck, Austria
| | - Michael C Schatz
- Cold Spring Harbor Laboratory and Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA
| | - Gregory J Hannon
- Cold Spring Harbor Laboratory and Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Kaja A Wasik
- Cold Spring Harbor Laboratory and Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA
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220
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Campanini EB, Vandewege MW, Pillai NE, Tay BH, Jones JL, Venkatesh B, Hoffmann FG. Early Evolution of Vertebrate Mybs: An Integrative Perspective Combining Synteny, Phylogenetic, and Gene Expression Analyses. Genome Biol Evol 2015; 7:3009-21. [PMID: 26475318 PMCID: PMC5635590 DOI: 10.1093/gbe/evv197] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The genes in the Myb superfamily encode for three related transcription factors in most vertebrates, A-, B-, and c-Myb, with functionally distinct roles, whereas most invertebrates have a single Myb. B-Myb plays an essential role in cell division and cell cycle progression, c-Myb is involved in hematopoiesis, and A-Myb is involved in spermatogenesis and regulating expression of pachytene PIWI interacting RNAs, a class of small RNAs involved in posttranscriptional gene regulation and the maintenance of reproductive tissues. Comparisons between teleost fish and tetrapods suggest that the emergence and functional divergence of the Myb genes were linked to the two rounds of whole-genome duplication early in vertebrate evolution. We combined phylogenetic, synteny, structural, and gene expression analyses of the Myb paralogs from elephant shark and lampreys with data from 12 bony vertebrates to reconstruct the early evolution of vertebrate Mybs. Phylogenetic and synteny analyses suggest that the elephant shark and Japanese lamprey have copies of the A-, B-, and c-Myb genes, implying their origin could be traced back to the common ancestor of lampreys and gnathostomes. However, structural and gene expression analyses suggest that their functional roles diverged between gnathostomes and cyclostomes. In particular, we did not detect A-Myb expression in testis suggesting that the involvement of A-Myb in the pachytene PIWI interacting RNA pathway is probably a gnathostome-specific innovation. We speculate that the secondary loss of a central domain in lamprey A-Myb underlies the functional differences between the cyclostome and gnathostome A-Myb proteins.
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Affiliation(s)
- Emeline B Campanini
- Departament of Genetics and Evolution, Federal University of São Carlos, Brazil
| | - Michael W Vandewege
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University
| | - Nisha E Pillai
- Institute of Molecular and Cell Biology, Comparative and Medical Genomics Laboratory, Agency for Science, Technology and Research, Biopolis, Singapore
| | - Boon-Hui Tay
- Institute of Molecular and Cell Biology, Comparative and Medical Genomics Laboratory, Agency for Science, Technology and Research, Biopolis, Singapore
| | - Justin L Jones
- Department of Biological & Physical Sciences, Saint Augustine's University
| | - Byrappa Venkatesh
- Institute of Molecular and Cell Biology, Comparative and Medical Genomics Laboratory, Agency for Science, Technology and Research, Biopolis, Singapore Departments of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University
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221
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Gebert D, Rosenkranz D. RNA-based regulation of transposon expression. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:687-708. [DOI: 10.1002/wrna.1310] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 09/08/2015] [Accepted: 09/13/2015] [Indexed: 11/12/2022]
Affiliation(s)
- Daniel Gebert
- Institute of Anthropology; Johannes Gutenberg University; Mainz Germany
| | - David Rosenkranz
- Institute of Anthropology; Johannes Gutenberg University; Mainz Germany
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222
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Williams Z, Morozov P, Mihailovic A, Lin C, Puvvula P, Juranek S, Rosenwaks Z, Tuschl T. Discovery and Characterization of piRNAs in the Human Fetal Ovary. Cell Rep 2015; 13:854-863. [DOI: 10.1016/j.celrep.2015.09.030] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Revised: 07/10/2015] [Accepted: 09/10/2015] [Indexed: 11/28/2022] Open
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223
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Parrish NF, Fujino K, Shiromoto Y, Iwasaki YW, Ha H, Xing J, Makino A, Kuramochi-Miyagawa S, Nakano T, Siomi H, Honda T, Tomonaga K. piRNAs derived from ancient viral processed pseudogenes as transgenerational sequence-specific immune memory in mammals. RNA (NEW YORK, N.Y.) 2015; 21:1691-1703. [PMID: 26283688 PMCID: PMC4574747 DOI: 10.1261/rna.052092.115] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 07/08/2015] [Indexed: 06/04/2023]
Abstract
Endogenous bornavirus-like nucleoprotein elements (EBLNs) are sequences within vertebrate genomes derived from reverse transcription and integration of ancient bornaviral nucleoprotein mRNA via the host retrotransposon machinery. While species with EBLNs appear relatively resistant to bornaviral disease, the nature of this association is unclear. We hypothesized that EBLNs could give rise to antiviral interfering RNA in the form of PIWI-interacting RNAs (piRNAs), a class of small RNA known to silence transposons but not exogenous viruses. We found that in both rodents and primates, which acquired their EBLNs independently some 25-40 million years ago, EBLNs are present within piRNA-generating regions of the genome far more often than expected by chance alone (ℙ = 8 × 10(-3)-6 × 10(-8)). Three of the seven human EBLNs fall within annotated piRNA clusters and two marmoset EBLNs give rise to bona fide piRNAs. In both rats and mice, at least two of the five EBLNs give rise to abundant piRNAs in the male gonad. While no EBLNs are syntenic between rodent and primate, some of the piRNA clusters containing EBLNs are; thus we deduce that EBLNs were integrated into existing piRNA clusters. All true piRNAs derived from EBLNs are antisense relative to the proposed ancient bornaviral nucleoprotein mRNA. These observations are consistent with a role for EBLN-derived piRNA-like RNAs in interfering with ancient bornaviral infection. They raise the hypothesis that retrotransposon-dependent virus-to-host gene flow could engender RNA-mediated, sequence-specific antiviral immune memory in metazoans analogous to the CRISPR/Cas system in prokaryotes.
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Affiliation(s)
- Nicholas F Parrish
- Department of Viral Oncology, Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan
| | - Kan Fujino
- Department of Viral Oncology, Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan
| | - Yusuke Shiromoto
- Department of Pathology, Medical School and Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
| | - Yuka W Iwasaki
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Hongseok Ha
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Jinchuan Xing
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Akiko Makino
- Department of Viral Oncology, Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan Center for Emerging Virus Research, Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan
| | - Satomi Kuramochi-Miyagawa
- Department of Pathology, Medical School and Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
| | - Toru Nakano
- Department of Pathology, Medical School and Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
| | - Haruhiko Siomi
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Tomoyuki Honda
- Department of Viral Oncology, Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan Department of Tumor Viruses, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Keizo Tomonaga
- Department of Viral Oncology, Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan Department of Tumor Viruses, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto 606-8507, Japan
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224
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Luangpraseuth-Prosper A, Lesueur E, Jouneau L, Pailhoux E, Cotinot C, Mandon-Pépin B. TOPAZ1, a germ cell specific factor, is essential for male meiotic progression. Dev Biol 2015; 406:158-71. [PMID: 26358182 DOI: 10.1016/j.ydbio.2015.09.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 09/01/2015] [Accepted: 09/04/2015] [Indexed: 11/19/2022]
Abstract
Topaz1 (Testis and Ovary-specific PAZ domain gene 1) is a germ cell specific gene highly conserved in vertebrates. The putative protein TOPAZ1 contains a PAZ domain, specifically found in PIWI, Argonaute and Zwille proteins. Consequently, Topaz1 is supposed to have a role during gametogenesis and may be involved in the piRNA pathway and contribute to silencing of transposable elements and maintenance of genome integrity. Here we report Topaz1 inactivation in mouse. Female fertility was not affected, but male sterility appeared exclusively in homozygous mutants in accordance with the high expression of Topaz1 in male germ cells. Pachytene Topaz1--deficient spermatocytes progress through meiosis without either derepression of retrotransposons or MSCI dysfunction, but become arrested before the post-meiotic round spermatid stage with extensive apoptosis. Consequently, an absence of spermatids and spermatozoa was observed in Topaz1(-/-) testis. Histological analysis also revealed that disturbances of spermatogenesis take place between post natal days 15 and 20, during the first wave of male meiosis and before the generation of haploid germ cells. Transcriptomic analysis at these two stages showed that TOPAZ1 influences the expression of one hundred transcripts, most of which are up-regulated in mutant testis at post natal day 20. Our results also showed that 10% of these transcripts are long non-coding RNA. This suggests that a highly regulated balance of lncRNAs seems to be essential during spermatogenesis for induction of appropriate male gamete production.
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Affiliation(s)
| | - Elodie Lesueur
- INRA, UMR 1198 Biologie du Développement et Reproduction, F-78350 Jouy-en-Josas, France.
| | - Luc Jouneau
- INRA, UMR 1198 Biologie du Développement et Reproduction, F-78350 Jouy-en-Josas, France.
| | - Eric Pailhoux
- INRA, UMR 1198 Biologie du Développement et Reproduction, F-78350 Jouy-en-Josas, France.
| | - Corinne Cotinot
- INRA, UMR 1198 Biologie du Développement et Reproduction, F-78350 Jouy-en-Josas, France.
| | - Béatrice Mandon-Pépin
- INRA, UMR 1198 Biologie du Développement et Reproduction, F-78350 Jouy-en-Josas, France.
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225
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Barckmann B, Pierson S, Dufourt J, Papin C, Armenise C, Port F, Grentzinger T, Chambeyron S, Baronian G, Desvignes JP, Curk T, Simonelig M. Aubergine iCLIP Reveals piRNA-Dependent Decay of mRNAs Involved in Germ Cell Development in the Early Embryo. Cell Rep 2015; 12:1205-16. [PMID: 26257181 PMCID: PMC4626872 DOI: 10.1016/j.celrep.2015.07.030] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 06/17/2015] [Accepted: 07/14/2015] [Indexed: 11/25/2022] Open
Abstract
The Piwi-interacting RNA (piRNA) pathway plays an essential role in the repression of transposons in the germline. Other functions of piRNAs such as post-transcriptional regulation of mRNAs are now emerging. Here, we perform iCLIP with the PIWI protein Aubergine (Aub) and identify hundreds of maternal mRNAs interacting with Aub in the early Drosophila embryo. Gene expression profiling reveals that a proportion of these mRNAs undergo Aub-dependent destabilization during the maternal-to-zygotic transition. Strikingly, Aub-dependent unstable mRNAs encode germ cell determinants. iCLIP with an Aub mutant that is unable to bind piRNAs confirms piRNA-dependent binding of Aub to mRNAs. Base pairing between piRNAs and mRNAs can induce mRNA cleavage and decay that are essential for embryonic development. These results suggest general regulation of maternal mRNAs by Aub and piRNAs, which plays a key developmental role in the embryo through decay and localization of mRNAs encoding germ cell determinants. Aub binds to maternal mRNAs in early Drosophila embryos Interaction between Aub and maternal mRNAs depends on piRNAs aub mutants are defective in mRNA decay during the MZT Aub-dependent unstable mRNAs encode germ cell determinants
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Affiliation(s)
- Bridlin Barckmann
- mRNA Regulation and Development, Institut de Génétique Humaine, CNRS, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
| | - Stéphanie Pierson
- mRNA Regulation and Development, Institut de Génétique Humaine, CNRS, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
| | - Jérémy Dufourt
- mRNA Regulation and Development, Institut de Génétique Humaine, CNRS, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
| | - Catherine Papin
- mRNA Regulation and Development, Institut de Génétique Humaine, CNRS, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
| | - Claudia Armenise
- RNA Silencing and Control of Transposition, Institut de Génétique Humaine, CNRS, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
| | - Fillip Port
- Division of Cell Biology, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Thomas Grentzinger
- RNA Silencing and Control of Transposition, Institut de Génétique Humaine, CNRS, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
| | - Séverine Chambeyron
- RNA Silencing and Control of Transposition, Institut de Génétique Humaine, CNRS, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
| | - Grégory Baronian
- MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, 141 rue de la cardonille, 34094 Montpellier Cedex 5, France
| | - Jean-Pierre Desvignes
- MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, 141 rue de la cardonille, 34094 Montpellier Cedex 5, France
| | - Tomaz Curk
- Faculty of Computer and Information Science, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Martine Simonelig
- mRNA Regulation and Development, Institut de Génétique Humaine, CNRS, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France.
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226
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Kistler WS, Baas D, Lemeille S, Paschaki M, Seguin-Estevez Q, Barras E, Ma W, Duteyrat JL, Morlé L, Durand B, Reith W. RFX2 Is a Major Transcriptional Regulator of Spermiogenesis. PLoS Genet 2015; 11:e1005368. [PMID: 26162102 PMCID: PMC4498915 DOI: 10.1371/journal.pgen.1005368] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 06/17/2015] [Indexed: 11/21/2022] Open
Abstract
Spermatogenesis consists broadly of three phases: proliferation of diploid germ cells, meiosis, and finally extensive differentiation of the haploid cells into effective delivery vehicles for the paternal genome. Despite detailed characterization of many haploid developmental steps leading to sperm, only fragmentary information exists on the control of gene expression underlying these processes. Here we report that the RFX2 transcription factor is a master regulator of genes required for the haploid phase. A targeted mutation of Rfx2 was created in mice. Rfx2-/- mice are perfectly viable but show complete male sterility. Spermatogenesis appears to progress unperturbed through meiosis. However, haploid cells undergo a complete arrest in spermatid development just prior to spermatid elongation. Arrested cells show altered Golgi apparatus organization, leading to a deficit in the generation of a spreading acrosomal cap from proacrosomal vesicles. Arrested cells ultimately merge to form giant multinucleated cells released to the epididymis. Spermatids also completely fail to form the flagellar axoneme. RNA-Seq analysis and ChIP-Seq analysis identified 139 genes directly controlled by RFX2 during spermiogenesis. Gene ontology analysis revealed that genes required for cilium function are specifically enriched in down- and upregulated genes showing that RFX2 allows precise temporal expression of ciliary genes. Several genes required for cell adhesion and cytoskeleton remodeling are also downregulated. Comparison of RFX2-regulated genes with those controlled by other major transcriptional regulators of spermiogenesis showed that each controls independent gene sets. Altogether, these observations show that RFX2 plays a major and specific function in spermiogenesis. Failure of spermatogenesis, which is presumed to often result from genetic defects, is a common cause of male sterility. Although numerous genes associated with defects in male spermatogenesis have been identified, numerous cases of genetic male infertility remain unelucidated. We report here that the transcription factor RFX2 is a master regulator of gene expression programs required for progression through the haploid phase of spermatogenesis. Male RFX2-deficient mice are completely sterile. Spermatogenesis progresses through meiosis, but haploid cells undergo a complete block in development just prior to spermatid elongation. Gene expression profiling and ChIP-Seq analysis revealed that RFX2 controls key pathways implicated in cilium/flagellum formation, as well as genes implicated in microtubule and vesicle associated transport. The set of genes activated by RFX2 in spermatids exhibits virtually no overlap with those controlled by other known transcriptional regulators of spermiogenesis, establishing RFX2 as an essential new player in this developmental process. RFX2-deficient mice should therefore represent a valuable new model for deciphering the regulatory networks that direct sperm formation, and thereby contribute to the identification of causes of human male infertility.
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Affiliation(s)
- W. Stephen Kistler
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, United States of America
- * E-mail: (WSK); (BD)
| | - Dominique Baas
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire, CNRS UMR 5534, Université Claude Bernard Lyon-1, Villeurbanne, Lyon, France
| | - Sylvain Lemeille
- Department of Pathology and Immunology, University of Geneva Medical School, CMU, Geneva, Switzerland
| | - Marie Paschaki
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire, CNRS UMR 5534, Université Claude Bernard Lyon-1, Villeurbanne, Lyon, France
| | - Queralt Seguin-Estevez
- Department of Pathology and Immunology, University of Geneva Medical School, CMU, Geneva, Switzerland
| | - Emmanuèle Barras
- Department of Pathology and Immunology, University of Geneva Medical School, CMU, Geneva, Switzerland
| | - Wenli Ma
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, United States of America
| | - Jean-Luc Duteyrat
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire, CNRS UMR 5534, Université Claude Bernard Lyon-1, Villeurbanne, Lyon, France
| | - Laurette Morlé
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire, CNRS UMR 5534, Université Claude Bernard Lyon-1, Villeurbanne, Lyon, France
| | - Bénédicte Durand
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire, CNRS UMR 5534, Université Claude Bernard Lyon-1, Villeurbanne, Lyon, France
- * E-mail: (WSK); (BD)
| | - Walter Reith
- Department of Pathology and Immunology, University of Geneva Medical School, CMU, Geneva, Switzerland
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227
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PIWI Slicing and RNA Elements in Precursors Instruct Directional Primary piRNA Biogenesis. Cell Rep 2015; 12:418-28. [DOI: 10.1016/j.celrep.2015.06.030] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 05/12/2015] [Accepted: 06/05/2015] [Indexed: 01/14/2023] Open
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228
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Wasik KA, Tam OH, Knott SR, Falciatori I, Hammell M, Vagin VV, Hannon GJ. RNF17 blocks promiscuous activity of PIWI proteins in mouse testes. Genes Dev 2015; 29:1403-15. [PMID: 26115953 PMCID: PMC4511215 DOI: 10.1101/gad.265215.115] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 06/03/2015] [Indexed: 01/21/2023]
Abstract
PIWI proteins and their associated piRNAs protect germ cells from the activity of mobile genetic elements. Two classes of piRNAs—primary and secondary—are defined by their mechanisms of biogenesis. Primary piRNAs are processed directly from transcripts of piRNA cluster loci, whereas secondary piRNAs are generated in an adaptive amplification loop, termed the ping-pong cycle. In mammals, piRNA populations are dynamic, shifting as male germ cells develop. Embryonic piRNAs consist of both primary and secondary species and are mainly directed toward transposons. In meiotic cells, the piRNA population is transposon-poor and largely restricted to primary piRNAs derived from pachytene piRNA clusters. The transition from the embryonic to the adult piRNA pathway is not well understood. Here we show that RNF17 shapes adult meiotic piRNA content by suppressing the production of secondary piRNAs. In the absence of RNF17, ping-pong occurs inappropriately in meiotic cells. Ping-pong initiates piRNA responses against not only transposons but also protein-coding genes and long noncoding RNAs, including genes essential for germ cell development. Thus, the sterility of Rnf17 mutants may be a manifestation of a small RNA-based autoimmune reaction.
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Affiliation(s)
- Kaja A Wasik
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, New York 11724, USA; Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, New York 11724, USA
| | - Oliver H Tam
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, New York 11724, USA
| | - Simon R Knott
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, New York 11724, USA; Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, New York 11724, USA
| | - Ilaria Falciatori
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, New York 11724, USA; Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, New York 11724, USA
| | - Molly Hammell
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, New York 11724, USA
| | - Vasily V Vagin
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, New York 11724, USA; Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, New York 11724, USA
| | - Gregory J Hannon
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, New York 11724, USA; Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, New York 11724, USA; Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
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229
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Yamtich J, Heo SJ, Dhahbi J, Martin DIK, Boffelli D. piRNA-like small RNAs mark extended 3'UTRs present in germ and somatic cells. BMC Genomics 2015; 16:462. [PMID: 26076733 PMCID: PMC4469462 DOI: 10.1186/s12864-015-1662-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 05/29/2015] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Piwi-interacting RNAs (piRNAs) are a class of small RNAs; distinct types of piRNAs are expressed in the mammalian testis at different stages of development. The function of piRNAs expressed in the adult testis is not well established. We conducted a detailed characterization of piRNAs aligning at or near the 3' UTRs of protein-coding genes in a deep dataset of small RNAs from adult mouse testis. RESULTS We identified 2710 piRNA clusters associated with 3' UTRs, including 1600 that overlapped genes not previously associated with piRNAs. 35% of the clusters extend beyond the annotated transcript; we find that these clusters correspond to, and are likely derived from, novel polyadenylated mRNA isoforms that contain previously unannotated extended 3'UTRs. Extended 3' UTRs, and small RNAs derived from them, are also present in somatic tissues; a subset of these somatic 3'UTR small RNA clusters are absent in mice lacking MIWI2, indicating a role for MIWI2 in the metabolism of somatic small RNAs. CONCLUSIONS The finding that piRNAs are processed from extended 3' UTRs suggests a role for piRNAs in the remodeling of 3' UTRs. The presence of both clusters and extended 3'UTRs in somatic cells, with evidence for involvement of MIWI2, indicates that this pathway is more broadly distributed than currently appreciated.
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Affiliation(s)
- Jennifer Yamtich
- Children's Hospital Oakland Research Institute, Oakland, CA, 94609, USA.
| | - Seok-Jin Heo
- Children's Hospital Oakland Research Institute, Oakland, CA, 94609, USA.
| | - Joseph Dhahbi
- Children's Hospital Oakland Research Institute, Oakland, CA, 94609, USA.
| | - David I K Martin
- Children's Hospital Oakland Research Institute, Oakland, CA, 94609, USA.
| | - Dario Boffelli
- Children's Hospital Oakland Research Institute, Oakland, CA, 94609, USA.
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230
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Goh WSS, Falciatori I, Tam OH, Burgess R, Meikar O, Kotaja N, Hammell M, Hannon GJ. piRNA-directed cleavage of meiotic transcripts regulates spermatogenesis. Genes Dev 2015; 29:1032-44. [PMID: 25995188 PMCID: PMC4441051 DOI: 10.1101/gad.260455.115] [Citation(s) in RCA: 177] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 04/28/2015] [Indexed: 11/25/2022]
Abstract
MIWI catalytic activity is required for spermatogenesis, indicating that piRNA-guided cleavage is critical for germ cell development. To identify meiotic piRNA targets, we augmented the mouse piRNA repertoire by introducing a human meiotic piRNA cluster. This triggered a spermatogenesis defect by inappropriately targeting the piRNA machinery to mouse mRNAs essential for germ cell development. Analysis of such de novo targets revealed a signature for pachytene piRNA target recognition. This enabled identification of both transposable elements and meiotically expressed protein-coding genes as targets of native piRNAs. Cleavage of genic targets began at the pachytene stage and resulted in progressive repression through meiosis, driven at least in part via the ping-pong cycle. Our data support the idea that meiotic piRNA populations must be strongly selected to enable successful spermatogenesis, both driving the response away from essential genes and directing the pathway toward mRNA targets that are regulated by small RNAs in meiotic cells.
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Affiliation(s)
- Wee Siong Sho Goh
- Howard Hughes Medical Institute, Cold Spring Harbor, New York 11724, USA; Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA
| | - Ilaria Falciatori
- Howard Hughes Medical Institute, Cold Spring Harbor, New York 11724, USA; Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Oliver H Tam
- Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA
| | - Ralph Burgess
- Howard Hughes Medical Institute, Cold Spring Harbor, New York 11724, USA; Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA
| | - Oliver Meikar
- Institute of Biomedicine, Department of Physiology, University of Turku, Turku FI-20520, Finland
| | - Noora Kotaja
- Institute of Biomedicine, Department of Physiology, University of Turku, Turku FI-20520, Finland
| | - Molly Hammell
- Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA
| | - Gregory J Hannon
- Howard Hughes Medical Institute, Cold Spring Harbor, New York 11724, USA; Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK;
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231
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Mohn F, Handler D, Brennecke J. Noncoding RNA. piRNA-guided slicing specifies transcripts for Zucchini-dependent, phased piRNA biogenesis. Science 2015; 348:812-817. [PMID: 25977553 PMCID: PMC4988486 DOI: 10.1126/science.aaa1039] [Citation(s) in RCA: 243] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In animal gonads, PIWI-clade Argonaute proteins repress transposons sequence-specifically via bound Piwi-interacting RNAs (piRNAs). These are processed from single-stranded precursor RNAs by largely unknown mechanisms. Here we show that primary piRNA biogenesis is a 3'-directed and phased process that, in the Drosophila germ line, is initiated by secondary piRNA-guided transcript cleavage. Phasing results from consecutive endonucleolytic cleavages catalyzed by Zucchini, implying coupled formation of 3' and 5' ends of flanking piRNAs. Unexpectedly, Zucchini also participates in 3' end formation of secondary piRNAs. Its function can, however, be bypassed by downstream piRNA-guided precursor cleavages coupled to exonucleolytic trimming. Our data uncover an evolutionarily conserved piRNA biogenesis mechanism in which Zucchini plays a central role in defining piRNA 5' and 3' ends.
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Affiliation(s)
- Fabio Mohn
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr. Bohrgasse 3, 1030 Vienna, Austria
| | - Dominik Handler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr. Bohrgasse 3, 1030 Vienna, Austria
| | - Julius Brennecke
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr. Bohrgasse 3, 1030 Vienna, Austria
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232
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Rosenkranz D, Rudloff S, Bastuck K, Ketting RF, Zischler H. Tupaia small RNAs provide insights into function and evolution of RNAi-based transposon defense in mammals. RNA (NEW YORK, N.Y.) 2015; 21:911-22. [PMID: 25802409 PMCID: PMC4408798 DOI: 10.1261/rna.048603.114] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 01/10/2015] [Indexed: 05/25/2023]
Abstract
Argonaute proteins comprising Piwi-like and Argonaute-like proteins and their guiding small RNAs combat mobile DNA on the transcriptional and post-transcriptional level. While Piwi-like proteins and associated piRNAs are generally restricted to the germline, Argonaute-like proteins and siRNAs have been linked with transposon control in the germline as well as in the soma. Intriguingly, evolution has realized distinct Argonaute subfunctionalization patterns in different species but our knowledge about mammalian RNA interference pathways relies mainly on findings from the mouse model. However, mice differ from other mammals by absence of functional Piwil3 and expression of an oocyte-specific Dicer isoform. Thus, studies beyond the mouse model are required for a thorough understanding of function and evolution of mammalian RNA interference pathways. We high-throughput sequenced small RNAs from the male Tupaia belangeri germline, which represents a close outgroup to primates, hence phylogenetically links mice with humans. We identified transposon-derived piRNAs as well as siRNAs clearly contrasting the separation of piRNA- and siRNA-pathways into male and female germline as seen in mice. Genome-wide analysis of tree shrew transposons reveal that putative siRNAs map to transposon sites that form foldback secondary structures thus representing suitable Dicer substrates. In contrast piRNAs target transposon sites that remain accessible. With this we provide a basic mechanistic explanation how secondary structure of transposon transcripts influences piRNA- and siRNA-pathway utilization. Finally, our analyses of tree shrew piRNA clusters indicate A-Myb and the testis-expressed transcription factor RFX4 to be involved in the transcriptional regulation of mammalian piRNA clusters.
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Affiliation(s)
- David Rosenkranz
- Institute of Anthropology, Johannes Gutenberg-University, Mainz, Rheinland-Pfalz 55128, Germany
| | - Stefanie Rudloff
- Institute of Anthropology, Johannes Gutenberg-University, Mainz, Rheinland-Pfalz 55128, Germany
| | - Katharina Bastuck
- Institute of Anthropology, Johannes Gutenberg-University, Mainz, Rheinland-Pfalz 55128, Germany
| | - René F Ketting
- Institute of Molecular Biology, IMB. Mainz, Rheinland-Pfalz 55128, Germany
| | - Hans Zischler
- Institute of Anthropology, Johannes Gutenberg-University, Mainz, Rheinland-Pfalz 55128, Germany
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233
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Darde TA, Sallou O, Becker E, Evrard B, Monjeaud C, Le Bras Y, Jégou B, Collin O, Rolland AD, Chalmel F. The ReproGenomics Viewer: an integrative cross-species toolbox for the reproductive science community. Nucleic Acids Res 2015; 43:W109-16. [PMID: 25883147 PMCID: PMC4489245 DOI: 10.1093/nar/gkv345] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 04/06/2015] [Indexed: 12/23/2022] Open
Abstract
We report the development of the ReproGenomics Viewer (RGV), a multi- and cross-species working environment for the visualization, mining and comparison of published omics data sets for the reproductive science community. The system currently embeds 15 published data sets related to gametogenesis from nine model organisms. Data sets have been curated and conveniently organized into broad categories including biological topics, technologies, species and publications. RGV's modular design for both organisms and genomic tools enables users to upload and compare their data with that from the data sets embedded in the system in a cross-species manner. The RGV is freely available at http://rgv.genouest.org.
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Affiliation(s)
- Thomas A Darde
- Inserm U1085-Irset, Université de Rennes 1, F-35042 Rennes, France Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA/INRIA) - GenOuest platform, Université de Rennes 1, F-35042 Rennes, France
| | - Olivier Sallou
- Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA/INRIA) - GenOuest platform, Université de Rennes 1, F-35042 Rennes, France
| | | | - Bertrand Evrard
- Inserm U1085-Irset, Université de Rennes 1, F-35042 Rennes, France
| | - Cyril Monjeaud
- Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA/INRIA) - GenOuest platform, Université de Rennes 1, F-35042 Rennes, France
| | - Yvan Le Bras
- Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA/INRIA) - GenOuest platform, Université de Rennes 1, F-35042 Rennes, France
| | - Bernard Jégou
- Inserm U1085-Irset, Université de Rennes 1, F-35042 Rennes, France Ecole des Hautes Études en Santé Publique, Avenue du Professeur Léon-Bernard, F-35043 Rennes, France
| | - Olivier Collin
- Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA/INRIA) - GenOuest platform, Université de Rennes 1, F-35042 Rennes, France
| | | | - Frédéric Chalmel
- Inserm U1085-Irset, Université de Rennes 1, F-35042 Rennes, France
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234
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Roy CK, Olson S, Graveley BR, Zamore PD, Moore MJ. Assessing long-distance RNA sequence connectivity via RNA-templated DNA-DNA ligation. eLife 2015; 4. [PMID: 25866926 PMCID: PMC4442144 DOI: 10.7554/elife.03700] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 04/12/2015] [Indexed: 02/04/2023] Open
Abstract
Many RNAs, including pre-mRNAs and long non-coding RNAs, can be thousands of nucleotides long and undergo complex post-transcriptional processing. Multiple sites of alternative splicing within a single gene exponentially increase the number of possible spliced isoforms, with most human genes currently estimated to express at least ten. To understand the mechanisms underlying these complex isoform expression patterns, methods are needed that faithfully maintain long-range exon connectivity information in individual RNA molecules. In this study, we describe SeqZip, a methodology that uses RNA-templated DNA–DNA ligation to retain and compress connectivity between distant sequences within single RNA molecules. Using this assay, we test proposed coordination between distant sites of alternative exon utilization in mouse Fn1, and we characterize the extraordinary exon diversity of Drosophila melanogaster Dscam1. DOI:http://dx.doi.org/10.7554/eLife.03700.001 A flow chart can show how an outcome can be achieved from a particular start point by breaking down an activity into a list of possible steps. Often, a flow chart contains several alternative steps, not all of which are taken every time the flow chart is used. The same can be said of genes, which are biological instructions that often contain many options within their DNA sequences. Proteins—which perform many roles in cells—are built following the instructions contained in genes. First, the DNA sequence of the gene is copied. This produces a molecule of ribonucleic acid (RNA), which is able to move around the cell to find the machinery that can use the genetic information to make a protein. Genes and their RNA copies contain instructions with more steps—called exons—than are necessary to make a working protein, so extra exons are removed (‘spliced’) from the RNA copies. Different combinations of exons can be removed, so splicing can make different versions of the RNA called isoforms. These allow a single gene to build many different proteins. In fruit flies, for example, the different exons of the gene Dscam1 can be spliced into one of 38,016 unique RNA isoforms. Current technology only allows researchers to deduce the sequence of RNA molecules by combining sequences recorded from short fragments of the molecule. However, before splicing, RNA molecules tend to be much longer than this, so this restricts our understanding of the RNA isoforms found in cells. Here, Roy et al. devised and tested a new method called SeqZip to solve this problem. SeqZip uses short fragments of DNA called ligamers that can only stick to the sections of RNA that will remain after the molecule has been spliced. After splicing, the ligamers can be stuck together to make a DNA replica of the spliced RNA. The end product is at least 49 times shorter than the original RNA, so it is easier to sequence. In addition, the combinations of the ligamers in the DNA replica show which exons of a specific gene are kept and which ones are spliced out. To test the method, Roy et al. studied a mouse gene that has six RNA isoforms. SeqZip reduced the length of the RNA by five times and made it possible to measure how frequently the different isoforms naturally arise. Roy et al. also used SeqZip to work out which isoforms of the Dscam1 gene are used at different stages in the life of fruit fly larvae. SeqZip can provide insights into how complex organisms like flies, mice, and humans have evolved with relatively few—a little over 20,000—genes in their genomes. DOI:http://dx.doi.org/10.7554/eLife.03700.002
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Affiliation(s)
- Christian K Roy
- RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, United States
| | - Sara Olson
- Institute for Systems Genomics, Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, United States
| | - Brenton R Graveley
- Institute for Systems Genomics, Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, United States
| | - Phillip D Zamore
- RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, United States
| | - Melissa J Moore
- RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, United States
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235
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Roovers EF, Rosenkranz D, Mahdipour M, Han CT, He N, Chuva de Sousa Lopes SM, van der Westerlaken LAJ, Zischler H, Butter F, Roelen BAJ, Ketting RF. Piwi proteins and piRNAs in mammalian oocytes and early embryos. Cell Rep 2015; 10:2069-82. [PMID: 25818294 DOI: 10.1016/j.celrep.2015.02.062] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 02/12/2015] [Accepted: 02/24/2015] [Indexed: 10/23/2022] Open
Abstract
Germ cells of most animals critically depend on piRNAs and Piwi proteins. Surprisingly, piRNAs in mouse oocytes are relatively rare and dispensable. We present compelling evidence for strong Piwi and piRNA expression in oocytes of other mammals. Human fetal oocytes express PIWIL2 and transposon-enriched piRNAs. Oocytes in adult human ovary express PIWIL1 and PIWIL2, whereas those in bovine ovary only express PIWIL1. In human, macaque, and bovine ovaries, we find piRNAs that resemble testis-borne pachytene piRNAs. Isolated bovine follicular oocytes were shown to contain abundant, relatively short piRNAs that preferentially target transposable elements. Using label-free quantitative proteome analysis, we show that these maturing oocytes strongly and specifically express the PIWIL3 protein, alongside other, known piRNA-pathway components. A piRNA pool is still present in early bovine embryos, revealing a potential impact of piRNAs on mammalian embryogenesis. Our results reveal that there are highly dynamic piRNA pathways in mammalian oocytes and early embryos.
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Affiliation(s)
- Elke F Roovers
- Biology of Non-coding RNA Group, Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - David Rosenkranz
- Johannes Gutenberg-University Mainz, Institute of Anthropology, Anselm-Franz-von-Bentzel-Weg 7, 55128 Mainz, Germany
| | - Mahdi Mahdipour
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, the Netherlands
| | - Chung-Ting Han
- Genomics Core Facility, Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Nannan He
- Department of Anatomy and Embryology, Leiden University Medical Center, Einthovenweg 20, 2333 ZA Leiden, the Netherlands
| | - Susana M Chuva de Sousa Lopes
- Department of Anatomy and Embryology, Leiden University Medical Center, Einthovenweg 20, 2333 ZA Leiden, the Netherlands
| | | | - Hans Zischler
- Johannes Gutenberg-University Mainz, Institute of Anthropology, Anselm-Franz-von-Bentzel-Weg 7, 55128 Mainz, Germany
| | - Falk Butter
- Quantitative Proteomics Group, Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Bernard A J Roelen
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, the Netherlands
| | - René F Ketting
- Biology of Non-coding RNA Group, Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany.
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236
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Vourekas A, Zheng K, Fu Q, Maragkakis M, Alexiou P, Ma J, Pillai RS, Mourelatos Z, Wang PJ. The RNA helicase MOV10L1 binds piRNA precursors to initiate piRNA processing. Genes Dev 2015; 29:617-29. [PMID: 25762440 PMCID: PMC4378194 DOI: 10.1101/gad.254631.114] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Piwi-piRNA ribonucleoproteins (piRNPs) enforce retrotransposon silencing, a function critical for preserving genome integrity of germ cells. Vourekas et al. found that MOV10L1 exhibits 5? to 3? directional RNA unwinding activity in vitro and that a point mutation that abolishes this activity causes a failure in primary piRNA biogenesis in vivo. MOV10L1 selectively binds piRNA precursor transcripts and is essential for the generation of intermediate piRNA processing fragments that are subsequently loaded to Piwi proteins. Piwi–piRNA (Piwi-interacting RNA) ribonucleoproteins (piRNPs) enforce retrotransposon silencing, a function critical for preserving the genome integrity of germ cells. The molecular functions of most of the factors that have been genetically implicated in primary piRNA biogenesis are still elusive. Here we show that MOV10L1 exhibits 5′-to-3′ directional RNA-unwinding activity in vitro and that a point mutation that abolishes this activity causes a failure in primary piRNA biogenesis in vivo. We demonstrate that MOV10L1 selectively binds piRNA precursor transcripts and is essential for the generation of intermediate piRNA processing fragments that are subsequently loaded to Piwi proteins. Multiple analyses suggest an intimate coupling of piRNA precursor processing with elements of local secondary structures such as G quadruplexes. Our results support a model in which MOV10L1 RNA helicase activity promotes unwinding and funneling of the single-stranded piRNA precursor transcripts to the endonuclease that catalyzes the first cleavage step of piRNA processing.
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Affiliation(s)
- Anastassios Vourekas
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Ke Zheng
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, China;
| | - Qi Fu
- Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Manolis Maragkakis
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Panagiotis Alexiou
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Jing Ma
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, China
| | - Ramesh S Pillai
- European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble, Cedex 9, France
| | - Zissimos Mourelatos
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
| | - P Jeremy Wang
- Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
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237
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Abstract
PIWI-interacting RNAs (piRNAs) are a class of small RNAs that are 24-31 nucleotides in length. They associate with PIWI proteins, which constitute a germline-specific subclade of the Argonaute family, to form effector complexes known as piRNA-induced silencing complexes, which repress transposons via transcriptional or posttranscriptional mechanisms and maintain germline genome integrity. In addition to having a role in transposon silencing, piRNAs in diverse organisms function in the regulation of cellular genes. In some cases, piRNAs have shown transgenerational inheritance to pass on the memory of "self" and "nonself," suggesting a contribution to various cellular processes over generations. Many piRNA factors have been identified; however, both the molecular mechanisms leading to the production of mature piRNAs and the effector phases of gene silencing are still enigmatic. Here, we summarize the current state of our knowledge on the biogenesis of piRNA, its biological functions, and the underlying mechanisms.
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Affiliation(s)
- Yuka W Iwasaki
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan;
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238
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239
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Chen YCA, Aravin AA. Non-Coding RNAs in Transcriptional Regulation: The review for Current Molecular Biology Reports. ACTA ACUST UNITED AC 2015; 1:10-18. [PMID: 26120554 DOI: 10.1007/s40610-015-0002-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transcriptional gene silencing guided by small RNAs is a process conserved from protozoa to mammals. Small RNAs loaded into Argonaute family proteins direct repressive histone modifications or DNA cytosine methylation to homologous regions of the genome. Small RNA-mediated transcriptional silencing is required for many biological processes, including repression of transposable elements, maintaining the genome stability/integrity, and epigenetic inheritance of gene expression. Here we will summarize the current knowledge about small RNA biogenesis and mechanisms of transcriptional regulation in plants, Drosophila, C. elegans and mice. Furthermore, a rapidly growing number long non-coding RNAs (lncRNAs) have been implicated as important players in transcription regulation. We will discuss current models for long non-coding RNA-mediated gene regulation.
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Affiliation(s)
- Yung-Chia Ariel Chen
- California Institute of Technology, Division of Biology and Biological Engineering, 147-75, 1200 E. California Blvd., Pasadena, CA 91125, USA
| | - Alexei A Aravin
- California Institute of Technology, Division of Biology and Biological Engineering, 147-75, 1200 E. California Blvd., Pasadena, CA 91125, USA
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240
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Kasper DM, Wang G, Gardner KE, Johnstone TG, Reinke V. The C. elegans SNAPc component SNPC-4 coats piRNA domains and is globally required for piRNA abundance. Dev Cell 2015; 31:145-58. [PMID: 25373775 DOI: 10.1016/j.devcel.2014.09.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 08/25/2014] [Accepted: 09/25/2014] [Indexed: 11/26/2022]
Abstract
The Piwi/Piwi-interacting RNA (piRNA) pathway protects the germline from the activity of foreign sequences such as transposons. Remarkably, tens of thousands of piRNAs arise from a minimal number of discrete genomic regions. The extent to which clustering of these small RNA genes contributes to their coordinated expression remains unclear. We show that C. elegans SNPC-4, the Myb-like DNA-binding subunit of the small nuclear RNA activating protein complex, binds piRNA clusters in a germline-specific manner and is required for global piRNA expression. SNPC-4 localization is mutually dependent with localization of piRNA biogenesis factor PRDE-1. SNPC-4 exhibits an atypical widely distributed binding pattern that "coats" piRNA domains. Discrete peaks within the domains occur frequently at RNA-polymerase-III-occupied transfer RNA (tRNA) genes, which have been implicated in chromatin organization. We suggest that SNPC-4 binding establishes a positive expression environment across piRNA domains, providing an explanation for the conserved clustering of individually transcribed piRNA genes.
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Affiliation(s)
- Dionna M Kasper
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Guilin Wang
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Kathryn E Gardner
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Timothy G Johnstone
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Valerie Reinke
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA.
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241
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Watanabe T, Cheng EC, Zhong M, Lin H. Retrotransposons and pseudogenes regulate mRNAs and lncRNAs via the piRNA pathway in the germline. Genome Res 2014; 25:368-80. [PMID: 25480952 PMCID: PMC4352877 DOI: 10.1101/gr.180802.114] [Citation(s) in RCA: 175] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The eukaryotic genome has vast intergenic regions containing transposons, pseudogenes, and other repetitive sequences. They produce numerous long noncoding RNAs (lncRNAs) and Piwi-interacting RNAs (piRNAs), yet the functions of the vast intergenic regions remain largely unknown. Mammalian piRNAs are abundantly expressed from the spermatocyte to round spermatid stage, coinciding with the widespread expression of lncRNAs in these cells. Here, we show that piRNAs derived from transposons and pseudogenes mediate the degradation of a large number of mRNAs and lncRNAs in mouse late spermatocytes. In particular, they have a large impact on the lncRNA transcriptome, as a quarter of lncRNAs expressed in late spermatocytes are up-regulated in mice deficient in the piRNA pathway. Furthermore, our genomic and in vivo functional analyses reveal that retrotransposon sequences in the 3′ UTR of mRNAs are targeted by piRNAs for degradation. Similarly, the degradation of spermatogenic cell-specific lncRNAs by piRNAs is mediated by retrotransposon sequences. Moreover, we show that pseudogenes regulate mRNA stability via the piRNA pathway. The degradation of mRNAs and lncRNAs by piRNAs requires PIWIL1 (also known as MIWI) and, at least in part, depends on its slicer activity. Together, these findings reveal the presence of a highly complex and global RNA regulatory network mediated by piRNAs with retrotransposons and pseudogenes as regulatory sequences.
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Affiliation(s)
- Toshiaki Watanabe
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06519, USA
| | - Ee-chun Cheng
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06519, USA
| | - Mei Zhong
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06519, USA
| | - Haifan Lin
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06519, USA
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242
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Théron E, Dennis C, Brasset E, Vaury C. Distinct features of the piRNA pathway in somatic and germ cells: from piRNA cluster transcription to piRNA processing and amplification. Mob DNA 2014; 5:28. [PMID: 25525472 PMCID: PMC4269861 DOI: 10.1186/s13100-014-0028-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 11/12/2014] [Indexed: 02/05/2023] Open
Abstract
Transposable elements (TEs) are major components of genomes. Their mobilization may affect genomic expression and be a threat to genetic stability. This is why they have to be tightly regulated by a dedicated system. In the reproductive tissues of a large range of organisms, they are repressed by a subclass of small interfering RNAs called piRNAs (PIWI interacting RNAs). In Drosophila melanogaster, piRNAs are produced both in the ovarian germline cells and in their surrounding somatic cells. Accumulating evidence suggests that germinal and somatic piRNA pathways are far more different than previously thought. Here we review the current knowledge on piRNA production in both these cell types, and explore their similarities and differences.
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Affiliation(s)
- Emmanuelle Théron
- Laboratoire GReD, Faculté de Médecine, Clermont Université, Université d'Auvergne, 28 Place H Dunant, 63000 Clermont-Ferrand, France.,Inserm, U 1103, F-63001 Clermont-Ferrand, France.,CNRS, UMR 6293, F-63001 Clermont-Ferrand, France
| | - Cynthia Dennis
- Laboratoire GReD, Faculté de Médecine, Clermont Université, Université d'Auvergne, 28 Place H Dunant, 63000 Clermont-Ferrand, France.,Inserm, U 1103, F-63001 Clermont-Ferrand, France.,CNRS, UMR 6293, F-63001 Clermont-Ferrand, France
| | - Emilie Brasset
- Laboratoire GReD, Faculté de Médecine, Clermont Université, Université d'Auvergne, 28 Place H Dunant, 63000 Clermont-Ferrand, France.,Inserm, U 1103, F-63001 Clermont-Ferrand, France.,CNRS, UMR 6293, F-63001 Clermont-Ferrand, France
| | - Chantal Vaury
- Laboratoire GReD, Faculté de Médecine, Clermont Université, Université d'Auvergne, 28 Place H Dunant, 63000 Clermont-Ferrand, France.,Inserm, U 1103, F-63001 Clermont-Ferrand, France.,CNRS, UMR 6293, F-63001 Clermont-Ferrand, France
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243
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Abstract
Distinguishing self from non-self plays a crucial role in safeguarding the germlines of metazoa from mobile DNA elements. Since their discovery less than a decade ago, Piwi-interacting RNAs (piRNAs) have been shown to repress transposable elements in the germline and, hence, have been at the forefront of research aimed at understanding the mechanisms that maintain germline integrity. More recently, roles for piRNAs in gene regulation have emerged. In this Review, we highlight recent advances made in understanding piRNA function, highlighting the divergent nature of piRNA biogenesis in different organisms, and discussing the mechanisms of piRNA action during transcriptional regulation and in transgenerational epigenetic inheritance.
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Affiliation(s)
- Eva-Maria Weick
- Wellcome Trust Cancer Research UK Gurdon Institute, Department of Biochemistry and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Eric A Miska
- Wellcome Trust Cancer Research UK Gurdon Institute, Department of Biochemistry and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
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244
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Ortogero N, Schuster AS, Oliver DK, Riordan CR, Hong AS, Hennig GW, Luong D, Bao J, Bhetwal BP, Ro S, McCarrey JR, Yan W. A novel class of somatic small RNAs similar to germ cell pachytene PIWI-interacting small RNAs. J Biol Chem 2014; 289:32824-34. [PMID: 25320077 DOI: 10.1074/jbc.m114.613232] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) are small noncoding RNAs that bind PIWI family proteins exclusively expressed in the germ cells of mammalian gonads. MIWI2-associated piRNAs are essential for silencing transposons during primordial germ cell development, and MIWI-bound piRNAs are required for normal spermatogenesis during adulthood in mice. Although piRNAs have long been regarded as germ cell-specific, increasing lines of evidence suggest that somatic cells also express piRNA-like RNAs (pilRNAs). Here, we report the detection of abundant pilRNAs in somatic cells, which are similar to MIWI-associated piRNAs mainly expressed in pachytene spermatocytes and round spermatids in the testis. Based on small RNA deep sequencing and quantitative PCR analyses, pilRNA expression is dynamic and displays tissue specificity. Although pilRNAs are similar to pachytene piRNAs in both size and genomic origins, they have a distinct ping-pong signature. Furthermore, pilRNA biogenesis appears to utilize a yet to be identified pathway, which is different from all currently known small RNA biogenetic pathways. In addition, pilRNAs appear to preferentially target the 3'-UTRs of mRNAs in a partially complementary manner. Our data suggest that pilRNAs, as an integral component of the small RNA transcriptome in somatic cell lineages, represent a distinct population of small RNAs that may have functions similar to germ cell piRNAs.
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Affiliation(s)
- Nicole Ortogero
- From the Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada 89557 and
| | - Andrew S Schuster
- From the Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada 89557 and
| | - Daniel K Oliver
- From the Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada 89557 and
| | - Connor R Riordan
- From the Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada 89557 and
| | - Annie S Hong
- From the Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada 89557 and
| | - Grant W Hennig
- From the Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada 89557 and
| | - Dickson Luong
- From the Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada 89557 and
| | - Jianqiang Bao
- From the Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada 89557 and
| | - Bhupal P Bhetwal
- From the Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada 89557 and
| | - Seungil Ro
- From the Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada 89557 and
| | - John R McCarrey
- the Department of Biology, University of Texas at San Antonio, San Antonio, Texas 78249
| | - Wei Yan
- From the Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada 89557 and
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245
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Rizzo F, Hashim A, Marchese G, Ravo M, Tarallo R, Nassa G, Giurato G, Rinaldi A, Cordella A, Persico M, Sulas P, Perra A, Ledda-Columbano GM, Columbano A, Weisz A. Timed regulation of P-element-induced wimpy testis-interacting RNA expression during rat liver regeneration. Hepatology 2014; 60:798-806. [PMID: 24930433 DOI: 10.1002/hep.27267] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 06/11/2014] [Accepted: 06/12/2014] [Indexed: 12/21/2022]
Abstract
UNLABELLED Small noncoding RNAs comprise a growing family of molecules that regulate key cellular processes, including messenger RNA (mRNA) degradation, translational repression, and transcriptional gene silencing. P-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs) represent a class of small RNAs initially identified in the germline of a variety of species, where they contribute to maintenance of genome stability, and recently found expressed also in stem and somatic cells, where their role and responsiveness to physiopathological signals remain elusive. Here, we investigated piRNA expression in rat liver and its response to the stimuli exerted by regenerative proliferation of this organ. Quantitative polymerase chain reaction analysis identify in the liver the RNAs encoding PIWIL2/HILI, PIWIL4/HIWI2, and other components of the piRNA biogenesis pathways, suggesting that this is indeed functional. RNA sequencing before, during, and after the wave of cell proliferation that follows partial hepatectomy (PH) identified ∼1,400 mammalian germline piRNAs expressed in rat liver, including 72 showing timed changes in expression 24-48 hours post-PH, a timing that corresponds to cell transition through the S phase, returning to basal levels by 168 hours, when organ regeneration is completed and hepatocytes reach quiescence. CONCLUSION The piRNA pathway is active in somatic cells of the liver and is subject to regulation during the pathophysiological process of organ regeneration, when these molecules are available to exert their regulatory functions on the cell genome and transcriptome, as demonstrated by the identification of several liver mRNAs representing candidate targets of these regulatory RNAs.
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Affiliation(s)
- Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine and Surgery, University of Salerno, Baronissi, Italy
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246
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Sree S, Radhakrishnan K, Indu S, Kumar PG. Dramatic Changes in 67 miRNAs During Initiation of First Wave of Spermatogenesis in Mus musculusTestis: Global Regulatory Insights Generated by miRNA-mRNA Network Analysis1. Biol Reprod 2014; 91:69. [DOI: 10.1095/biolreprod.114.119305] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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247
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Abstract
Precursors for most Piwi-interacting RNAs (piRNAs) are indistinguishable from other RNA polymerase II-transcribed long noncoding RNAs. So, it is currently unclear how they are recognized as substrates by the piRNA processing machinery that resides in cytoplasmic granules called nuage. In this issue, Castaneda et al (2014) reveal a role for the nuage component and nucleo-cytoplasmic shuttling protein Maelstrom in mouse piRNA biogenesis.
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Affiliation(s)
- Radha Raman Pandey
- European Molecular Biology Laboratory, Grenoble Outstation, Grenoble, France Unit for Virus Host Cell Interactions, University Grenoble Alpes-EMBL-CNRS, Grenoble, France
| | - Ramesh S Pillai
- European Molecular Biology Laboratory, Grenoble Outstation, Grenoble, France Unit for Virus Host Cell Interactions, University Grenoble Alpes-EMBL-CNRS, Grenoble, France
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248
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Abstract
The generation of piRNAs from long primary transcripts requires specialized factors that distinguish these precursors from canonical RNA polymerase II transcripts. Mohn et al. and Zhang et al. provide evidence that in Drosophila melanogaster noncanonical transcription coupled with splicing inhibition differentiates piRNA precursors from mRNAs and ensures their correct processing.
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Affiliation(s)
- Alexandra Sapetschnig
- Wellcome Trust/Cancer Research Gurdon Institute, Department of Biochemistry and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Eric A Miska
- Wellcome Trust/Cancer Research Gurdon Institute, Department of Biochemistry and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.
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249
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Hirano T, Iwasaki YW, Lin ZYC, Imamura M, Seki NM, Sasaki E, Saito K, Okano H, Siomi MC, Siomi H. Small RNA profiling and characterization of piRNA clusters in the adult testes of the common marmoset, a model primate. RNA (NEW YORK, N.Y.) 2014; 20:1223-1237. [PMID: 24914035 PMCID: PMC4105748 DOI: 10.1261/rna.045310.114] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 05/05/2014] [Indexed: 06/01/2023]
Abstract
Small RNAs mediate gene silencing by binding Argonaute/Piwi proteins to regulate target RNAs. Here, we describe small RNA profiling of the adult testes of Callithrix jacchus, the common marmoset. The most abundant class of small RNAs in the adult testis was piRNAs, although 353 novel miRNAs but few endo-siRNAs were also identified. MARWI, a marmoset homolog of mouse MIWI and a very abundant PIWI in adult testes, associates with piRNAs that show characteristics of mouse pachytene piRNAs. As in other mammals, most marmoset piRNAs are derived from conserved clustered regions in the genome, which are annotated as intergenic regions. However, unlike in mice, marmoset piRNA clusters are also found on the X chromosome, suggesting escape from meiotic sex chromosome inactivation by the X-linked clusters. Some of the piRNA clusters identified contain antisense-orientated pseudogenes, suggesting the possibility that pseudogene-derived piRNAs may regulate parental functional protein-coding genes. More piRNAs map to transposable element (TE) subfamilies when they have copies in piRNA clusters. In addition, the strand bias observed for piRNAs mapped to each TE subfamily correlates with the polarity of copies inserted in clusters. These findings suggest that pachytene piRNA clusters determine the abundance and strand-bias of TE-derived piRNAs, may regulate protein-coding genes via pseudogene-derived piRNAs, and may even play roles in meiosis in the adult marmoset testis.
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Affiliation(s)
- Takamasa Hirano
- Department of Molecular Biology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Yuka W Iwasaki
- Department of Molecular Biology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Zachary Yu-Ching Lin
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Masanori Imamura
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan Molecular Biology Section, Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
| | - Naomi M Seki
- Department of Molecular Biology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Erika Sasaki
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan Central Institute for Experimental Animals, Kawasaki, Kanagawa 210-0821, Japan
| | - Kuniaki Saito
- Department of Molecular Biology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Mikiko C Siomi
- Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Haruhiko Siomi
- Department of Molecular Biology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
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250
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Keam SP, Young PE, McCorkindale AL, Dang THY, Clancy JL, Humphreys DT, Preiss T, Hutvagner G, Martin DIK, Cropley JE, Suter CM. The human Piwi protein Hiwi2 associates with tRNA-derived piRNAs in somatic cells. Nucleic Acids Res 2014; 42:8984-95. [PMID: 25038252 PMCID: PMC4132735 DOI: 10.1093/nar/gku620] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 06/26/2014] [Accepted: 06/26/2014] [Indexed: 01/31/2023] Open
Abstract
The Piwi-piRNA pathway is active in animal germ cells where its functions are required for germ cell maintenance and gamete differentiation. Piwi proteins and piRNAs have been detected outside germline tissue in multiple phyla, but activity of the pathway in mammalian somatic cells has been little explored. In particular, Piwi expression has been observed in cancer cells, but nothing is known about the piRNA partners or the function of the system in these cells. We have surveyed the expression of the three human Piwi genes, Hiwi, Hili and Hiwi2, in multiple normal tissues and cancer cell lines. We find that Hiwi2 is ubiquitously expressed; in cancer cells the protein is largely restricted to the cytoplasm and is associated with translating ribosomes. Immunoprecipitation of Hiwi2 from MDAMB231 cancer cells enriches for piRNAs that are predominantly derived from processed tRNAs and expressed genes, species which can also be found in adult human testis. Our studies indicate that a Piwi-piRNA pathway is present in human somatic cells, with an uncharacterised function linked to translation. Taking this evidence together with evidence from primitive organisms, we propose that this somatic function of the pathway predates the germline functions of the pathway in modern animals.
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Affiliation(s)
- Simon P Keam
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, 2010, Australia Faculty of Engineering and Information Technology, Centre of Health Technologies, University of Technology Sydney, 235 Jones Street, Ultimo, NSW, 2007, Australia
| | - Paul E Young
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, 2010, Australia
| | - Alexandra L McCorkindale
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, 2010, Australia
| | - Thurston H Y Dang
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, 2010, Australia
| | - Jennifer L Clancy
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, 2010, Australia
| | - David T Humphreys
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, 2010, Australia
| | - Thomas Preiss
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, 2010, Australia
| | - Gyorgy Hutvagner
- Faculty of Engineering and Information Technology, Centre of Health Technologies, University of Technology Sydney, 235 Jones Street, Ultimo, NSW, 2007, Australia
| | - David I K Martin
- Center for Genetics, Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland, CA 94609, USA
| | - Jennifer E Cropley
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, 2010, Australia Faculty of Medicine, University of New South Wales, Kensington, 2052, Australia
| | - Catherine M Suter
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, 2010, Australia Faculty of Medicine, University of New South Wales, Kensington, 2052, Australia
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