51
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Salces-Ortiz J, Vargas-Chavez C, Guio L, Rech GE, González J. Transposable elements contribute to the genomic response to insecticides in Drosophila melanogaster. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190341. [PMID: 32075557 PMCID: PMC7061994 DOI: 10.1098/rstb.2019.0341] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Most of the genotype–phenotype analyses to date have largely centred attention on single nucleotide polymorphisms. However, transposable element (TE) insertions have arisen as a plausible addition to the study of the genotypic–phenotypic link because of to their role in genome function and evolution. In this work, we investigate the contribution of TE insertions to the regulation of gene expression in response to insecticides. We exposed four Drosophila melanogaster strains to malathion, a commonly used organophosphate insecticide. By combining information from different approaches, including RNA-seq and ATAC-seq, we found that TEs can contribute to the regulation of gene expression under insecticide exposure by rewiring cis-regulatory networks. This article is part of a discussion meeting issue ‘Crossroads between transposons and gene regulation’.
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Affiliation(s)
- Judit Salces-Ortiz
- Institute of Evolutionary Biology (IBE), CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Carlos Vargas-Chavez
- Institute of Evolutionary Biology (IBE), CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Lain Guio
- Institute of Evolutionary Biology (IBE), CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Gabriel E Rech
- Institute of Evolutionary Biology (IBE), CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Josefa González
- Institute of Evolutionary Biology (IBE), CSIC-Universitat Pompeu Fabra, Barcelona, Spain
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52
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Sun YH, Zhu J, Xie LH, Li Z, Meduri R, Zhu X, Song C, Chen C, Ricci EP, Weng Z, Li XZ. Ribosomes guide pachytene piRNA formation on long intergenic piRNA precursors. Nat Cell Biol 2020; 22:200-212. [PMID: 32015435 PMCID: PMC8041231 DOI: 10.1038/s41556-019-0457-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 12/16/2019] [Indexed: 11/09/2022]
Abstract
PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs essential for fertility. In adult mouse testes, most piRNAs are derived from long single-stranded RNAs lacking annotated open reading frames (ORFs). The mechanisms underlying how piRNA sequences are defined during the cleavages of piRNA precursors remain elusive. Here, we show that 80S ribosomes translate the 5'-proximal short ORFs (uORFs) of piRNA precursors. The MOV10L1/Armitage RNA helicase then facilitates the translocation of ribosomes into the uORF downstream regions (UDRs). The ribosome-bound UDRs are targeted by piRNA processing machinery, with the processed ribosome-protected regions becoming piRNAs. The dual modes of interaction between ribosomes and piRNA precursors underlie the distinct piRNA biogenesis requirements at uORFs and UDRs. Ribosomes also mediate piRNA processing in roosters and green lizards, implying that this mechanism is evolutionarily conserved in amniotes. Our results uncover a function for ribosomes on non-coding regions of RNAs and reveal the mechanisms underlying how piRNAs are defined.
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Affiliation(s)
- Yu H Sun
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, USA
| | - Jiang Zhu
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, USA
| | - Li Huitong Xie
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, USA
| | - Ziwei Li
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, USA
| | - Rajyalakshmi Meduri
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, USA
| | - Xiaopeng Zhu
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Chi Song
- College of Public Health, Division of Biostatistics, The Ohio State University, Columbus, OH, USA
| | - Chen Chen
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
| | - Emiliano P Ricci
- Université de Lyon, ENSL, UCBL, INSERM, CNRS, LBMC, Lyon, France
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Xin Zhiguo Li
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, USA. .,Department of Urology, University of Rochester Medical Center, Rochester, NY, USA.
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53
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Tharp ME, Malki S, Bortvin A. Maximizing the ovarian reserve in mice by evading LINE-1 genotoxicity. Nat Commun 2020; 11:330. [PMID: 31949138 PMCID: PMC6965193 DOI: 10.1038/s41467-019-14055-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 12/06/2019] [Indexed: 11/21/2022] Open
Abstract
Female reproductive success critically depends on the size and quality of a finite ovarian reserve. Paradoxically, mammals eliminate up to 80% of the initial oocyte pool through the enigmatic process of fetal oocyte attrition (FOA). Here, we interrogate the striking correlation of FOA with retrotransposon LINE-1 (L1) expression in mice to understand how L1 activity influences FOA and its biological relevance. We report that L1 activity triggers FOA through DNA damage-driven apoptosis and the complement system of immunity. We demonstrate this by combined inhibition of L1 reverse transcriptase activity and the Chk2-dependent DNA damage checkpoint to prevent FOA. Remarkably, reverse transcriptase inhibitor AZT-treated Chk2 mutant oocytes that evade FOA initially accumulate, but subsequently resolve, L1-instigated genotoxic threats independent of piRNAs and differentiate, resulting in an increased functional ovarian reserve. We conclude that FOA serves as quality control for oocyte genome integrity, and is not obligatory for oogenesis nor fertility.
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Affiliation(s)
- Marla E Tharp
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, 21218, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Safia Malki
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, 21218, USA
| | - Alex Bortvin
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, 21218, USA.
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54
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Özata DM, Yu T, Mou H, Gainetdinov I, Colpan C, Cecchini K, Kaymaz Y, Wu PH, Fan K, Kucukural A, Weng Z, Zamore PD. Evolutionarily conserved pachytene piRNA loci are highly divergent among modern humans. Nat Ecol Evol 2020; 4:156-168. [PMID: 31900453 PMCID: PMC6961462 DOI: 10.1038/s41559-019-1065-1] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 11/19/2019] [Indexed: 12/18/2022]
Abstract
In the fetal mouse testis, PIWI-interacting RNAs (piRNAs) guide PIWI proteins to silence transposons but, after birth, most post-pubertal pachytene piRNAs map to the genome uniquely and are thought to regulate genes required for male fertility. In the human male, the developmental classes, precise genomic origins and transcriptional regulation of postnatal piRNAs remain undefined. Here, we demarcate the genes and transcripts that produce postnatal piRNAs in human juvenile and adult testes. As in the mouse, human A-MYB drives transcription of both pachytene piRNA precursor transcripts and messenger RNAs encoding piRNA biogenesis factors. Although human piRNA genes are syntenic to those in other placental mammals, their sequences are poorly conserved. In fact, pachytene piRNA loci are rapidly diverging even among modern humans. Our findings suggest that, during mammalian evolution, pachytene piRNA genes are under few selective constraints. We speculate that pachytene piRNA diversity may provide a hitherto unrecognized driver of reproductive isolation.
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Affiliation(s)
- Deniz M Özata
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Tianxiong Yu
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
- Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai, People's Republic of China
| | - Haiwei Mou
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ildar Gainetdinov
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Cansu Colpan
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Katharine Cecchini
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
- Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Yasin Kaymaz
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Pei-Hsuan Wu
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Kaili Fan
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
- Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai, People's Republic of China
| | - Alper Kucukural
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA.
| | - Phillip D Zamore
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.
- Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA, USA.
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55
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Srivastav SP, Rahman R, Ma Q, Pierre J, Bandyopadhyay S, Lau NC. Har-P, a short P-element variant, weaponizes P-transposase to severely impair Drosophila development. eLife 2019; 8:49948. [PMID: 31845649 PMCID: PMC6917496 DOI: 10.7554/elife.49948] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 11/16/2019] [Indexed: 12/20/2022] Open
Abstract
Without transposon-silencing Piwi-interacting RNAs (piRNAs), transposition causes an ovarian atrophy syndrome in Drosophila called gonadal dysgenesis (GD). Harwich (Har) strains with P-elements cause severe GD in F1 daughters when Har fathers mate with mothers lacking P-element-piRNAs (i.e. ISO1 strain). To address the mystery of why Har induces severe GD, we bred hybrid Drosophila with Har genomic fragments into the ISO1 background to create HISR-D or HISR-N lines that still cause Dysgenesis or are Non-dysgenic, respectively. In these lines, we discovered a highly truncated P-element variant we named ‘Har-P’ as the most frequent de novo insertion. Although HISR-D lines still contain full-length P-elements, HISR-N lines lost functional P-transposase but retained Har-P’s that when crossed back to P-transposase restores GD induction. Finally, we uncovered P-element-piRNA-directed repression on Har-P’s transmitted paternally to suppress somatic transposition. The Drosophila short Har-P’s and full-length P-elements relationship parallels the MITEs/DNA-transposase in plants and SINEs/LINEs in mammals. DNA provides the instructions needed for life, a role that relies on it being a very stable and organized molecule. However, some sections of DNA are able to move from one place in the genome to another. When these “mobile genetic elements” move they may disrupt other genes and cause disease. For example, a mobile section of DNA known as the P-element causes a condition called gonadal dysgenesis in female fruit flies, leading to infertility. Only certain strains of fruit flies carry P-elements and the severity of gonadal dysgenesis in their daughters varies. For example, when male fruit flies of a strain known as Harwich (or Har for short) is crossed with female fruit flies that do not contain P-elements, all of their daughters develop severe gonadal dysgenesis and are infertile. However, if the cross is done the other way around, and female Har flies mate with males that do not contain P-elements, the daughters are fertile because the Har mothers provide their daughters with protective molecules that silence the P-elements. But it was a mystery as to why the P-elements from the Har fathers always caused such severe gonadal dysgenesis in all the daughters. Here, Srivastav et al. bred fruit flies to create offspring that had different pieces of Har DNA in a genetic background that was normally free from P-elements; they then analyzed the ‘hybrid’ offspring to identify which pieces of the Har genome caused gonadal dysgenesis in the daughter flies. These experiments showed that Har flies possess a very short variant of the P-element (named “Har-P”) that is more mobile than other variants. However, the Har-P variants still depended on an enzyme known as P-transposase encoded by the full-length P-elements to move around the genome. Further experiments showed that other strains of fruit flies that cause severe gonadal dysgenesis also had very short P-element variants that were almost identical to Har-P. These findings may explain why Har and some other strains of fruit flies drive severe gonadal dysgenesis. In the future, it may be possible to transfer P-transposase and Har-P into mosquitoes, ticks and other biting insects to make them infertile and help reduce the spread of certain diseases in humans.
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Affiliation(s)
- Satyam P Srivastav
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, United States
| | - Reazur Rahman
- Department of Biology, Brandeis University, Waltham, United States
| | - Qicheng Ma
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, United States
| | - Jasmine Pierre
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, United States
| | - Saptaparni Bandyopadhyay
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, United States
| | - Nelson C Lau
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, United States.,Department of Biology, Brandeis University, Waltham, United States.,Genome Science Institute, Boston University School of Medicine, Boston, United States
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56
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Di Bella S, La Ferlita A, Carapezza G, Alaimo S, Isacchi A, Ferro A, Pulvirenti A, Bosotti R. A benchmarking of pipelines for detecting ncRNAs from RNA-Seq data. Brief Bioinform 2019; 21:1987-1998. [PMID: 31740918 DOI: 10.1093/bib/bbz110] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/12/2019] [Accepted: 08/01/2019] [Indexed: 12/18/2022] Open
Abstract
Next-Generation Sequencing (NGS) is a high-throughput technology widely applied to genome sequencing and transcriptome profiling. RNA-Seq uses NGS to reveal RNA identities and quantities in a given sample. However, it produces a huge amount of raw data that need to be preprocessed with fast and effective computational methods. RNA-Seq can look at different populations of RNAs, including ncRNAs. Indeed, in the last few years, several ncRNAs pipelines have been developed for ncRNAs analysis from RNA-Seq experiments. In this paper, we analyze eight recent pipelines (iSmaRT, iSRAP, miARma-Seq, Oasis 2, SPORTS1.0, sRNAnalyzer, sRNApipe, sRNA workbench) which allows the analysis not only of single specific classes of ncRNAs but also of more than one ncRNA classes. Our systematic performance evaluation aims at guiding users to select the appropriate pipeline for processing each ncRNA class, focusing on three key points: (i) accuracy in ncRNAs identification, (ii) accuracy in read count estimation and (iii) deployment and ease of use.
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Affiliation(s)
| | - Alessandro La Ferlita
- Department of Clinical and Experimental Medicine, Bioinformatics Unit, University of Catania, Catania, Italy.,Department of Physics and Astronomy, University of Catania, Catania, Italy
| | | | - Salvatore Alaimo
- Department of Clinical and Experimental Medicine, Bioinformatics Unit, University of Catania, Catania, Italy
| | | | - Alfredo Ferro
- Department of Clinical and Experimental Medicine, Bioinformatics Unit, University of Catania, Catania, Italy
| | - Alfredo Pulvirenti
- Department of Clinical and Experimental Medicine, Bioinformatics Unit, University of Catania, Catania, Italy
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57
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Osumi K, Sato K, Murano K, Siomi H, Siomi MC. Essential roles of Windei and nuclear monoubiquitination of Eggless/SETDB1 in transposon silencing. EMBO Rep 2019; 20:e48296. [PMID: 31576653 DOI: 10.15252/embr.201948296] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 09/02/2019] [Accepted: 09/11/2019] [Indexed: 11/09/2022] Open
Abstract
Eggless/SETDB1 (Egg), the only essential histone methyltransferase (HMT) in Drosophila, plays a role in gene repression, including piRNA-mediated transposon silencing in the ovaries. Previous studies suggested that Egg is post-translationally modified and showed that Windei (Wde) regulates Egg nuclear localization through protein-protein interaction. Monoubiquitination of mammalian SETDB1 is necessary for the HMT activity. Here, using cultured ovarian somatic cells, we show that Egg is monoubiquitinated and phosphorylated but that only monoubiquitination is required for piRNA-mediated transposon repression. Egg monoubiquitination occurs in the nucleus. Egg has its own nuclear localization signal, and the nuclear import of Egg is Wde-independent. Wde recruits Egg to the chromatin at target gene silencing loci, but their interaction is monoubiquitin-independent. The abundance of nuclear Egg is governed by that of nuclear Wde. These results illuminate essential roles of nuclear monoubiquitination of Egg and the role of Wde in piRNA-mediated transposon repression.
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Affiliation(s)
- Ken Osumi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Kaoru Sato
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Kensaku Murano
- Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan
| | - Haruhiko Siomi
- Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan
| | - Mikiko C Siomi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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58
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Bonnet S, Boucherat O, Paulin R, Wu D, Hindmarch CCT, Archer SL, Song R, Moore JB, Provencher S, Zhang L, Uchida S. Clinical value of non-coding RNAs in cardiovascular, pulmonary, and muscle diseases. Am J Physiol Cell Physiol 2019; 318:C1-C28. [PMID: 31483703 DOI: 10.1152/ajpcell.00078.2019] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Although a majority of the mammalian genome is transcribed to RNA, mounting evidence indicates that only a minor proportion of these transcriptional products are actually translated into proteins. Since the discovery of the first non-coding RNA (ncRNA) in the 1980s, the field has gone on to recognize ncRNAs as important molecular regulators of RNA activity and protein function, knowledge of which has stimulated the expansion of a scientific field that quests to understand the role of ncRNAs in cellular physiology, tissue homeostasis, and human disease. Although our knowledge of these molecules has significantly improved over the years, we have limited understanding of their precise functions, protein interacting partners, and tissue-specific activities. Adding to this complexity, it remains unknown exactly how many ncRNAs there are in existence. The increased use of high-throughput transcriptomics techniques has rapidly expanded the list of ncRNAs, which now includes classical ncRNAs (e.g., ribosomal RNAs and transfer RNAs), microRNAs, and long ncRNAs. In addition, splicing by-products of protein-coding genes and ncRNAs, so-called circular RNAs, are now being investigated. Because there is substantial heterogeneity in the functions of ncRNAs, we have summarized the present state of knowledge regarding the functions of ncRNAs in heart, lungs, and skeletal muscle. This review highlights the pathophysiologic relevance of these ncRNAs in the context of human cardiovascular, pulmonary, and muscle diseases.
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Affiliation(s)
- Sébastien Bonnet
- Pulmonary Hypertension and Vascular Biology Research Group, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Department of Medicine, Université Laval, Quebec City, Quebec, Canada.,Department of Medicine, Université Laval, Quebec City, Quebec, Canada
| | - Olivier Boucherat
- Pulmonary Hypertension and Vascular Biology Research Group, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Department of Medicine, Université Laval, Quebec City, Quebec, Canada.,Department of Medicine, Université Laval, Quebec City, Quebec, Canada
| | - Roxane Paulin
- Pulmonary Hypertension and Vascular Biology Research Group, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Department of Medicine, Université Laval, Quebec City, Quebec, Canada.,Department of Medicine, Université Laval, Quebec City, Quebec, Canada
| | - Danchen Wu
- Department of Medicine, Queen's University, Kingston, Ontario, Canada
| | - Charles C T Hindmarch
- Queen's Cardiopulmonary Unit, Translational Institute of Medicine, Department of Medicine, Queen's University, Kingston, Ontario, Canada
| | - Stephen L Archer
- Department of Medicine, Queen's University, Kingston, Ontario, Canada
| | - Rui Song
- Lawrence D. Longo, MD Center for Perinatal Biology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, California
| | - Joseph B Moore
- Diabetes and Obesity Center, University of Louisville, Louisville, Kentucky.,The Christina Lee Brown Envirome Institute, Department of Medicine, University of Louisville, Louisville, Kentucky
| | - Steeve Provencher
- Pulmonary Hypertension and Vascular Biology Research Group, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Department of Medicine, Université Laval, Quebec City, Quebec, Canada.,Department of Medicine, Université Laval, Quebec City, Quebec, Canada
| | - Lubo Zhang
- Lawrence D. Longo, MD Center for Perinatal Biology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, California
| | - Shizuka Uchida
- Diabetes and Obesity Center, University of Louisville, Louisville, Kentucky.,The Christina Lee Brown Envirome Institute, Department of Medicine, University of Louisville, Louisville, Kentucky.,Cardiovascular Innovation Institute, University of Louisville, Louisville, Kentucky
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59
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Zhu L, Kandasamy SK, Fukunaga R. Dicer partner protein tunes the length of miRNAs using base-mismatch in the pre-miRNA stem. Nucleic Acids Res 2019; 46:3726-3741. [PMID: 29373753 PMCID: PMC5909426 DOI: 10.1093/nar/gky043] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 01/17/2018] [Indexed: 12/19/2022] Open
Abstract
Dicer partner proteins Drosophila Loquacious-PB (Loqs-PB) and human TRBP tune the length of miRNAs produced by Dicer from a subset of pre-miRNAs and thereby alter their target repertoire, by an unknown mechanism. Here, we developed a novel high-throughput method that we named Dram-seq (Dice randomized pre-miRNA pool and seq) to study length distributions of miRNAs produced from thousands of different pre-miRNA variants. Using Dram-seq, we found that a base-mismatch in the pre-miRNA stem can alter the length of miRNAs compared with a base-pair at the same position in both Drosophila and human, and is important for the miRNA length tuning by Loqs-PB. Loqs-PB directly bound base-mismatched nucleotides in the pre-miRNA stem. We speculate that Loqs-PB tunes miRNA length by changing the conformation of base-mismatched nucleotides in the pre-miRNA stem to that of base-paired ones and thereby altering the distance of the pre-miRNA stem.
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Affiliation(s)
- Li Zhu
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, 521A Physiology Building, Baltimore, MD 21205, USA
| | - Suresh K Kandasamy
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, 521A Physiology Building, Baltimore, MD 21205, USA
| | - Ryuya Fukunaga
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, 521A Physiology Building, Baltimore, MD 21205, USA
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60
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Zhu L, Liao SE, Fukunaga R. Drosophila Regnase-1 RNase is required for mRNA and miRNA profile remodelling during larva-to-adult metamorphosis. RNA Biol 2019; 16:1386-1400. [PMID: 31195914 DOI: 10.1080/15476286.2019.1630799] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Metamorphosis is an intricate developmental process in which large-scale remodelling of mRNA and microRNA (miRNA) profiles leads to orchestrated tissue remodelling and organogenesis. Whether, which, and how, ribonucleases (RNases) are involved in the RNA profile remodelling during metamorphosis remain unknown. Human Regnase-1 (also known as MCPIP1 and Zc3h12a) RNase remodels RNA profile by cleaving specific RNAs and is a crucial modulator of immune-inflammatory and cellular defence. Here, we studied Drosophila CG10889, which we named Drosophila Regnase-1, an ortholog of human Regnase-1. The larva-to-adult metamorphosis in Drosophila includes two major transitions, larva-to-pupa and pupa-to-adult. regnase-1 knockout flies developed until the pupa stage but could not complete pupa-to-adult transition, dying in puparium case. Regnase-1 RNase activity is required for completion of pupa-to-adult transition as transgenic expression of wild-type Drosophila Regnase-1, but not the RNase catalytic-dead mutants, rescued the pupa-to-adult transition in regnase-1 knockout. High-throughput RNA sequencing revealed that regnase-1 knockout flies fail to remodel mRNA and miRNA profiles during the larva-to-pupa transition. Thus, we uncovered the roles of Drosophila Regnase-1 in the larva-to-adult metamorphosis and large-scale remodelling of mRNA and miRNA profiles during this metamorphosis process.
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Affiliation(s)
- Li Zhu
- Department of Biological Chemistry, Johns Hopkins University School of Medicine , Baltimore , MD , USA
| | - Susan E Liao
- Department of Biological Chemistry, Johns Hopkins University School of Medicine , Baltimore , MD , USA
| | - Ryuya Fukunaga
- Department of Biological Chemistry, Johns Hopkins University School of Medicine , Baltimore , MD , USA
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61
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Ge DT, Wang W, Tipping C, Gainetdinov I, Weng Z, Zamore PD. The RNA-Binding ATPase, Armitage, Couples piRNA Amplification in Nuage to Phased piRNA Production on Mitochondria. Mol Cell 2019; 74:982-995.e6. [PMID: 31076285 PMCID: PMC6636356 DOI: 10.1016/j.molcel.2019.04.006] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 01/24/2019] [Accepted: 04/01/2019] [Indexed: 12/13/2022]
Abstract
PIWI-interacting RNAs (piRNAs) silence transposons in Drosophila ovaries, ensuring female fertility. Two coupled pathways generate germline piRNAs: the ping-pong cycle, in which the PIWI proteins Aubergine and Ago3 increase the abundance of pre-existing piRNAs, and the phased piRNA pathway, which generates strings of tail-to-head piRNAs, one after another. Proteins acting in the ping-pong cycle localize to nuage, whereas phased piRNA production requires Zucchini, an endonuclease on the mitochondrial surface. Here, we report that Armitage (Armi), an RNA-binding ATPase localized to both nuage and mitochondria, links the ping-pong cycle to the phased piRNA pathway. Mutations that block phased piRNA production deplete Armi from nuage. Armi ATPase mutants cannot support phased piRNA production and inappropriately bind mRNA instead of piRNA precursors. We propose that Armi shuttles between nuage and mitochondria, feeding precursor piRNAs generated by Ago3 cleavage into the Zucchini-dependent production of Aubergine- and Piwi-bound piRNAs on the mitochondrial surface.
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Affiliation(s)
- Daniel Tianfang Ge
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Wei Wang
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA; Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Cindy Tipping
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Ildar Gainetdinov
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| | - Phillip D Zamore
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
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62
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Baumann B, Lugli G, Gao S, Zenner M, Nonn L. High levels of PIWI-interacting RNAs are present in the small RNA landscape of prostate epithelium from vitamin D clinical trial specimens. Prostate 2019; 79:840-855. [PMID: 30905091 PMCID: PMC6593815 DOI: 10.1002/pros.23789] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 01/31/2019] [Accepted: 02/19/2019] [Indexed: 02/02/2023]
Abstract
BACKGROUND Vitamin D, a hormone that acts through the nuclear vitamin D receptor (VDR), upregulates antitumorigenic microRNA in prostate epithelium. This may contribute to the lower levels of aggressive prostate cancer (PCa) observed in patients with high serum vitamin D. The small noncoding RNA (ncRNA) landscape includes many other RNA species that remain uncharacterized in prostate epithelium and their potential regulation by vitamin D is unknown. METHODS Laser capture microdissection (LCM) followed by small-RNA sequencing was used to identify ncRNAs in the prostate epithelium of tissues from a vitamin D-supplementation trial. VDR chromatin immunoprecipitation-sequencing was performed to identify vitamin D genomic targets in primary prostate epithelial cells. RESULTS Isolation of epithelium by LCM increased sample homogeneity and captured more diversity in ncRNA species compared with publicly available small-RNA sequencing data from benign whole prostate. An abundance of PIWI-interacting RNAs (piRNAs) was detected in normal prostate epithelium. The obligate binding partners of piRNAs, PIWI-like (PIWIL) proteins, were also detected in prostate epithelium. High prostatic vitamin D levels were associated with increased expression of piRNAs. VDR binding sites were located near several ncRNA biogenesis genes and genes regulating translation and differentiation. CONCLUSIONS Benign prostate epithelium expresses both piRNA and PIWIL proteins, suggesting that these small ncRNA may serve an unknown function in the prostate. Vitamin D may increase the expression of prostatic piRNAs. VDR binding sites in primary prostate epithelial cells are consistent with its reported antitumorigenic functions and a role in ncRNA biogenesis.
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Affiliation(s)
- Bethany Baumann
- Department of Pathology, College of MedicineUniversity of Illinois at ChicagoChicagoIllinois
| | - Giovanni Lugli
- Department of Pathology, College of MedicineUniversity of Illinois at ChicagoChicagoIllinois
| | - Shang Gao
- Department of BioengineeringUniversity of Illinois at ChicagoChicagoIllinois
| | - Morgan Zenner
- Department of Pathology, College of MedicineUniversity of Illinois at ChicagoChicagoIllinois
| | - Larisa Nonn
- Department of Pathology, College of MedicineUniversity of Illinois at ChicagoChicagoIllinois
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63
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Zhu L, Liao SE, Ai Y, Fukunaga R. RNA methyltransferase BCDIN3D is crucial for female fertility and miRNA and mRNA profiles in Drosophila ovaries. PLoS One 2019; 14:e0217603. [PMID: 31145769 PMCID: PMC6542536 DOI: 10.1371/journal.pone.0217603] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 05/14/2019] [Indexed: 11/18/2022] Open
Abstract
RNA methyltransferases post-transcriptionally add methyl groups to RNAs, which can regulate their fates and functions. Human BCDIN3D (Bicoid interacting 3 domain containing RNA methyltransferase) has been reported to specifically methylate the 5′-monophosphates of pre-miR-145 and cytoplasmic tRNAHis. Methylation of the 5′-monophosphate of pre-miR-145 blocks its cleavage by the miRNA generating enzyme Dicer, preventing generation of miR-145. Elevated expression of BCDIN3D has been associated with poor prognosis in breast cancer. However, the biological functions of BCDIN3D and its orthologs remain unknown. Here we studied the biological and molecular functions of CG1239, a Drosophila ortholog of BCDIN3D. We found that ovary-specific knockdown of Drosophila BCDIN3D causes female sterility. High-throughput sequencing revealed that miRNA and mRNA profiles are dysregulated in BCDIN3D knockdown ovaries. Pathway analysis showed that many of the dysregulated genes are involved in metabolic processes, ribonucleoprotein complex regulation, and translational control. Our results reveal BCDIN3D’s biological role in female fertility and its molecular role in defining miRNA and mRNA profiles in ovaries.
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Affiliation(s)
- Li Zhu
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Susan E. Liao
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Yiwei Ai
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Ryuya Fukunaga
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
- * E-mail:
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64
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Karunanithi S, Simon M, Schulz MH. Automated analysis of small RNA datasets with RAPID. PeerJ 2019; 7:e6710. [PMID: 30993044 PMCID: PMC6462184 DOI: 10.7717/peerj.6710] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/01/2019] [Indexed: 02/06/2023] Open
Abstract
Understanding the role of short-interfering RNA (siRNA) in diverse biological processes is of current interest and often approached through small RNA sequencing. However, analysis of these datasets is difficult due to the complexity of biological RNA processing pathways, which differ between species. Several properties like strand specificity, length distribution, and distribution of soft-clipped bases are few parameters known to guide researchers in understanding the role of siRNAs. We present RAPID, a generic eukaryotic siRNA analysis pipeline, which captures information inherent in the datasets and automatically produces numerous visualizations as user-friendly HTML reports, covering multiple categories required for siRNA analysis. RAPID also facilitates an automated comparison of multiple datasets, with one of the normalization techniques dedicated for siRNA knockdown analysis, and integrates differential expression analysis using DESeq2.
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Affiliation(s)
- Sivarajan Karunanithi
- Cluster of Excellence for Multimodal Computing and Interaction, and Department for Computational Biology & Applied Algorithms, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany.,Graduate School of Computer Science, Saarland Informatics Campus, Universität des Saarlandes, Saarbrücken, Germany.,Institute for Cardiovascular Regeneration, Goethe University Hospital, Frankfurt am Main, Germany
| | - Martin Simon
- Molecular Cell Biology and Microbiology, Wuppertal University, Wuppertal, Germany
| | - Marcel H Schulz
- Cluster of Excellence for Multimodal Computing and Interaction, and Department for Computational Biology & Applied Algorithms, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany.,Institute for Cardiovascular Regeneration, Goethe University Hospital, Frankfurt am Main, Germany.,German Centre for Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt am Main, Germany
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65
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Lerat E, Casacuberta J, Chaparro C, Vieira C. On the Importance to Acknowledge Transposable Elements in Epigenomic Analyses. Genes (Basel) 2019; 10:genes10040258. [PMID: 30935103 PMCID: PMC6523952 DOI: 10.3390/genes10040258] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 03/27/2019] [Accepted: 03/27/2019] [Indexed: 12/21/2022] Open
Abstract
Eukaryotic genomes comprise a large proportion of repeated sequences, an important fraction of which are transposable elements (TEs). TEs are mobile elements that have a significant impact on genome evolution and on gene functioning. Although some TE insertions could provide adaptive advantages to species, transposition is a highly mutagenic event that has to be tightly controlled to ensure its viability. Genomes have evolved sophisticated mechanisms to control TE activity, the most important being epigenetic silencing. However, the epigenetic control of TEs can also affect genes located nearby that can become epigenetically regulated. It has been proposed that the combination of TE mobilization and the induced changes in the epigenetic landscape could allow a rapid phenotypic adaptation to global environmental changes. In this review, we argue the crucial need to take into account the repeated part of genomes when studying the global impact of epigenetic modifications on an organism. We emphasize more particularly why it is important to carefully consider TEs and what bioinformatic tools can be used to do so.
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Affiliation(s)
- Emmanuelle Lerat
- CNRS, Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, UMR 5558, F-69622 Villeurbanne, France.
| | - Josep Casacuberta
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, 08193 Barcelona, Spain.
| | - Cristian Chaparro
- CNRS, IHPE UMR 5244, University of Perpignan Via Domitia, IFREMER, University Montpellier, F-66860 Perpignan, France.
| | - Cristina Vieira
- CNRS, Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, UMR 5558, F-69622 Villeurbanne, France.
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66
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A Transgenic Flock House Virus Replicon Reveals an RNAi Independent Antiviral Mechanism Acting in Drosophila Follicular Somatic Cells. G3-GENES GENOMES GENETICS 2019; 9:403-412. [PMID: 30530643 PMCID: PMC6385967 DOI: 10.1534/g3.118.200872] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The small interfering RNA (siRNA) pathway is the main and best studied invertebrate antiviral response. Other poorly characterized protein based antiviral mechanisms also contribute to the control of viral replication in insects. In addition, it remains unclear whether tissue specific factors contribute to RNA and protein-based antiviral immunity mechanisms. In vivo screens to identify such factors are challenging and time consuming. In addition, the scored phenotype is usually limited to survival and/or viral load. Transgenic viral replicons are valuable tools to overcome these limitations and screen for novel antiviral factors. Here we describe transgenic Drosophila melanogaster lines encoding a Flock House Virus-derived replicon (FHV∆B2eGFP), expressing GFP as a reporter of viral replication. This replicon is efficiently controlled by the siRNA pathway in most somatic tissues, with GFP fluorescence providing a reliable marker for the activity of antiviral RNAi. Interestingly, in follicular somatic cells (FSC) of ovaries, this replicon is still partially repressed in an siRNA independent manner. We did not detect replicon derived Piwi-interacting RNAs in FSCs and identified 31 differentially expressed genes between restrictive and permissive FSCs. Altogether, our results uncovered a yet unidentified RNAi-independent mechanism controlling FHV replication in FSCs of ovaries and validate the FHV∆B2eGFP replicon as a tool to screen for novel tissue specific antiviral mechanisms.
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67
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Chang TH, Mattei E, Gainetdinov I, Colpan C, Weng Z, Zamore PD. Maelstrom Represses Canonical Polymerase II Transcription within Bi-directional piRNA Clusters in Drosophila melanogaster. Mol Cell 2019; 73:291-303.e6. [PMID: 30527661 PMCID: PMC6551610 DOI: 10.1016/j.molcel.2018.10.038] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 10/05/2018] [Accepted: 10/24/2018] [Indexed: 11/18/2022]
Abstract
In Drosophila, 23-30 nt long PIWI-interacting RNAs (piRNAs) direct the protein Piwi to silence germline transposon transcription. Most germline piRNAs derive from dual-strand piRNA clusters, heterochromatic transposon graveyards that are transcribed from both genomic strands. These piRNA sources are marked by the heterochromatin protein 1 homolog Rhino (Rhi), which facilitates their promoter-independent transcription, suppresses splicing, and inhibits transcriptional termination. Here, we report that the protein Maelstrom (Mael) represses canonical, promoter-dependent transcription in dual-strand clusters, allowing Rhi to initiate piRNA precursor transcription. Mael also represses promoter-dependent transcription at sites outside clusters. At some loci, Mael repression requires the piRNA pathway, while at others, piRNAs play no role. We propose that by repressing canonical transcription of individual transposon mRNAs, Mael helps Rhi drive non-canonical transcription of piRNA precursors without generating mRNAs encoding transposon proteins.
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MESH Headings
- Animals
- Argonaute Proteins/genetics
- Argonaute Proteins/metabolism
- Binding Sites
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- DNA Transposable Elements
- Drosophila Proteins/genetics
- Drosophila Proteins/metabolism
- Drosophila melanogaster/enzymology
- Drosophila melanogaster/genetics
- Gene Expression Regulation
- Promoter Regions, Genetic
- Protein Binding
- RNA Helicases/genetics
- RNA Helicases/metabolism
- RNA Polymerase II/genetics
- RNA Polymerase II/metabolism
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- RNA, Small Interfering/biosynthesis
- RNA, Small Interfering/genetics
- Transcription, Genetic
- RNA, Guide, CRISPR-Cas Systems
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Affiliation(s)
- Timothy H Chang
- RNA Therapeutics Institute and Howard Hughes Medical Institute, Worcester, MA, USA
| | - Eugenio Mattei
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Ildar Gainetdinov
- RNA Therapeutics Institute and Howard Hughes Medical Institute, Worcester, MA, USA
| | - Cansu Colpan
- RNA Therapeutics Institute and Howard Hughes Medical Institute, Worcester, MA, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA.
| | - Phillip D Zamore
- RNA Therapeutics Institute and Howard Hughes Medical Institute, Worcester, MA, USA.
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68
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O'Neill K, Liao WW, Patel A, Hammell MG. TEsmall Identifies Small RNAs Associated With Targeted Inhibitor Resistance in Melanoma. Front Genet 2018; 9:461. [PMID: 30349559 PMCID: PMC6186986 DOI: 10.3389/fgene.2018.00461] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/20/2018] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs) are small 21–22 nt RNAs that act to regulate the expression of mRNA target genes through direct binding to mRNA targets. While miRNAs typically dominate small RNA (sRNA) transcriptomes, many other classes are present including tRNAs, snoRNAs, snRNAs, Y-RNAs, piRNAs, and siRNAs. Interactions between processing machinery and targeting networks of these various sRNA classes remains unclear, largely because these sRNAs are typically analyzed separately. Here, we present TEsmall, a tool that allows for the simultaneous processing and analysis of sRNAs from each annotated class in a single integrated workflow. The pipeline begins with raw fastq reads and proceeds all the way to producing count tables formatted for differential expression analysis. Several interactive charts are also produced to look at overall distributions in length and annotation classes. We next applied the TEsmall pipeline to sRNA libraries generated from melanoma cells responding to targeted inhibitors of the MAPK pathway. Targeted oncogene inhibitors have emerged as way to tailor cancer therapies to the particular mutations present in a given tumor. While these targeted strategies are typically effective for short intervals, the emergence of resistance is extremely common, limiting the effectiveness of single-agent therapeutics and driving the need for a better understanding of resistance mechanisms. Using TEsmall, we identified several microRNAs and other sRNA classes that are enriched in inhibitor resistant melanoma cells in multiple melanoma cell lines and may be able to serve as markers of resistant populations more generally.
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Affiliation(s)
- Kathryn O'Neill
- Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Wen-Wei Liao
- McDonnell Genome Institute, School of Medicine, Washington University in St. Louis, St. Louis, MO, United States
| | - Ami Patel
- Icahn School of Medicine at Mount Sinai, New York City, NY, United States
| | - Molly Gale Hammell
- Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
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69
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70
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Lerat E, Fablet M, Modolo L, Lopez-Maestre H, Vieira C. TEtools facilitates big data expression analysis of transposable elements and reveals an antagonism between their activity and that of piRNA genes. Nucleic Acids Res 2018; 45:e17. [PMID: 28204592 PMCID: PMC5389681 DOI: 10.1093/nar/gkw953] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 09/29/2016] [Accepted: 10/11/2016] [Indexed: 11/24/2022] Open
Abstract
Over recent decades, substantial efforts have been made to understand the interactions between host genomes and transposable elements (TEs). The impact of TEs on the regulation of host genes is well known, with TEs acting as platforms of regulatory sequences. Nevertheless, due to their repetitive nature it is considerably hard to integrate TE analysis into genome-wide studies. Here, we developed a specific tool for the analysis of TE expression: TEtools. This tool takes into account the TE sequence diversity of the genome, it can be applied to unannotated or unassembled genomes and is freely available under the GPL3 (https://github.com/l-modolo/TEtools). TEtools performs the mapping of RNA-seq data obtained from classical mRNAs or small RNAs onto a list of TE sequences and performs differential expression analyses with statistical relevance. Using this tool, we analyzed TE expression from five Drosophila wild-type strains. Our data show for the first time that the activity of TEs is strictly linked to the activity of the genes implicated in the piwi-interacting RNA biogenesis and therefore fits an arms race scenario between TE sequences and host control genes.
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Affiliation(s)
- Emmanuelle Lerat
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, Université de Lyon, Villeurbanne 69622, France
| | - Marie Fablet
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, Université de Lyon, Villeurbanne 69622, France
| | - Laurent Modolo
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, Université de Lyon, Villeurbanne 69622, France
| | - Hélène Lopez-Maestre
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, Université de Lyon, Villeurbanne 69622, France
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, Université de Lyon, Villeurbanne 69622, France
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71
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Gainetdinov I, Colpan C, Arif A, Cecchini K, Zamore PD. A Single Mechanism of Biogenesis, Initiated and Directed by PIWI Proteins, Explains piRNA Production in Most Animals. Mol Cell 2018; 71:775-790.e5. [PMID: 30193099 PMCID: PMC6130920 DOI: 10.1016/j.molcel.2018.08.007] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 06/21/2018] [Accepted: 08/03/2018] [Indexed: 01/20/2023]
Abstract
In animals, PIWI-interacting RNAs (piRNAs) guide PIWI proteins to silence transposons and regulate gene expression. The mechanisms for making piRNAs have been proposed to differ among cell types, tissues, and animals. Our data instead suggest a single model that explains piRNA production in most animals. piRNAs initiate piRNA production by guiding PIWI proteins to slice precursor transcripts. Next, PIWI proteins direct the stepwise fragmentation of the sliced precursor transcripts, yielding tail-to-head strings of phased precursor piRNAs (pre-piRNAs). Our analyses detect evidence for this piRNA biogenesis strategy across an evolutionarily broad range of animals, including humans. Thus, PIWI proteins initiate and sustain piRNA biogenesis by the same mechanism in species whose last common ancestor predates the branching of most animal lineages. The unified model places PIWI-clade Argonautes at the center of piRNA biology and suggests that the ancestral animal-the Urmetazoan-used PIWI proteins both to generate piRNA guides and to execute piRNA function.
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Affiliation(s)
- Ildar Gainetdinov
- RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Cansu Colpan
- RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Amena Arif
- RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Katharine Cecchini
- RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Phillip D Zamore
- RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
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72
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Pogorelcnik R, Vaury C, Pouchin P, Jensen S, Brasset E. sRNAPipe: a Galaxy-based pipeline for bioinformatic in-depth exploration of small RNAseq data. Mob DNA 2018; 9:25. [PMID: 30079119 PMCID: PMC6069783 DOI: 10.1186/s13100-018-0130-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 07/16/2018] [Indexed: 12/12/2022] Open
Abstract
Background The field of small RNA is one of the most investigated research areas since they were shown to regulate transposable elements and gene expression and play essential roles in fundamental biological processes. Small RNA deep sequencing (sRNA-seq) is now routinely used for large-scale analyses of small RNA. Such high-throughput sequencing typically produces several millions reads. Results Here we present a computational pipeline (sRNAPipe: small RNA pipeline) based on the Galaxy framework that takes as input a fastq file of small RNA-seq reads and performs successive steps of mapping to categories of genomic sequences: transposable elements, gene transcripts, microRNAs, small nuclear RNAs, ribosomal RNAs and transfer RNAs. It also provides individual mapping and counting for chromosomes, transposable elements and gene transcripts, normalization, small RNA length analysis and plotting of the data along genomic coordinates to build publication-quality graphs and figures. sRNAPipe evaluates 10-nucleotide 5′-overlaps of reads on opposite strands to test ping-pong amplification for putative PIWI-interacting RNAs, providing counts of overlaps and corresponding z-scores. Conclusions sRNAPipe is easy to use and does not require command-line or coding knowledge. This pipeline gives quick visual and quantitative results, which are usable for publications. sRNAPipe is freely available as a Galaxy tool and via GitHub. Electronic supplementary material The online version of this article (10.1186/s13100-018-0130-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Romain Pogorelcnik
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 10448, 63001 Clermont-Ferrand, France
| | - Chantal Vaury
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 10448, 63001 Clermont-Ferrand, France
| | - Pierre Pouchin
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 10448, 63001 Clermont-Ferrand, France
| | - Silke Jensen
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 10448, 63001 Clermont-Ferrand, France
| | - Emilie Brasset
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 10448, 63001 Clermont-Ferrand, France
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73
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An RNA-binding protein Blanks plays important roles in defining small RNA and mRNA profiles in Drosophila testes. Heliyon 2018; 4:e00706. [PMID: 30094376 PMCID: PMC6074722 DOI: 10.1016/j.heliyon.2018.e00706] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 07/10/2018] [Accepted: 07/20/2018] [Indexed: 01/03/2023] Open
Abstract
Drosophila Blanks is a testes-specific RNA-binding protein required for post-meiotic spermiogenesis. However, Blanks's role in regulating RNA populations in the testes remains unknown. We performed small RNA and mRNA high-throughput sequencing in blanks mutant testes and controls. We identified two miRNAs, one siRNA, and hundreds of mRNAs that are significantly upregulated or downregulated in blanks mutant testes. Pathway analysis revealed that differentially expressed mRNAs are involved in catabolic and metabolic processes, anion and cation transport, mating, and reproductive behavior. Our results reveal that Blanks plays important roles in defining testicular small RNA and mRNA profiles.
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74
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Fu Y, Wu PH, Beane T, Zamore PD, Weng Z. Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers. BMC Genomics 2018; 19:531. [PMID: 30001700 PMCID: PMC6044086 DOI: 10.1186/s12864-018-4933-1] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 07/08/2018] [Indexed: 12/12/2022] Open
Abstract
Background RNA-seq and small RNA-seq are powerful, quantitative tools to study gene regulation and function. Common high-throughput sequencing methods rely on polymerase chain reaction (PCR) to expand the starting material, but not every molecule amplifies equally, causing some to be overrepresented. Unique molecular identifiers (UMIs) can be used to distinguish undesirable PCR duplicates derived from a single molecule and identical but biologically meaningful reads from different molecules. Results We have incorporated UMIs into RNA-seq and small RNA-seq protocols and developed tools to analyze the resulting data. Our UMIs contain stretches of random nucleotides whose lengths sufficiently capture diverse molecule species in both RNA-seq and small RNA-seq libraries generated from mouse testis. Our approach yields high-quality data while allowing unique tagging of all molecules in high-depth libraries. Conclusions Using simulated and real datasets, we demonstrate that our methods increase the reproducibility of RNA-seq and small RNA-seq data. Notably, we find that the amount of starting material and sequencing depth, but not the number of PCR cycles, determine PCR duplicate frequency. Finally, we show that computational removal of PCR duplicates based only on their mapping coordinates introduces substantial bias into data analysis. Electronic supplementary material The online version of this article (10.1186/s12864-018-4933-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yu Fu
- Bioinformatics Program, Boston University, 44 Cummington Mall, Boston, MA, 02215, USA.,Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Pei-Hsuan Wu
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Timothy Beane
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Phillip D Zamore
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA.
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA. .,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA.
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75
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Berrens RV, Andrews S, Spensberger D, Santos F, Dean W, Gould P, Sharif J, Olova N, Chandra T, Koseki H, von Meyenn F, Reik W. An endosiRNA-Based Repression Mechanism Counteracts Transposon Activation during Global DNA Demethylation in Embryonic Stem Cells. Cell Stem Cell 2018; 21:694-703.e7. [PMID: 29100015 PMCID: PMC5678422 DOI: 10.1016/j.stem.2017.10.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 08/14/2017] [Accepted: 10/12/2017] [Indexed: 12/28/2022]
Abstract
Erasure of DNA methylation and repressive chromatin marks in the mammalian germline leads to risk of transcriptional activation of transposable elements (TEs). Here, we used mouse embryonic stem cells (ESCs) to identify an endosiRNA-based mechanism involved in suppression of TE transcription. In ESCs with DNA demethylation induced by acute deletion of Dnmt1, we saw an increase in sense transcription at TEs, resulting in an abundance of sense/antisense transcripts leading to high levels of ARGONAUTE2 (AGO2)-bound small RNAs. Inhibition of Dicer or Ago2 expression revealed that small RNAs are involved in an immediate response to demethylation-induced transposon activation, while the deposition of repressive histone marks follows as a chronic response. In vivo, we also found TE-specific endosiRNAs present during primordial germ cell development. Our results suggest that antisense TE transcription is a “trap” that elicits an endosiRNA response to restrain acute transposon activity during epigenetic reprogramming in the mammalian germline. Global DNA demethylation in embryonic stem cells leads to transposon activation Transposon activation increases the abundance of sense/antisense transcripts ARGONAUTE2-bound endosiRNAs accumulate at high levels for acute repression Longer-term transposon repression depends on repressive histone marks
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Affiliation(s)
- Rebecca V Berrens
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK; University of Cambridge, The Old Schools, Trinity Lane, Cambridge CB2 1TN, UK.
| | - Simon Andrews
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | | | - Fátima Santos
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK; University of Cambridge, The Old Schools, Trinity Lane, Cambridge CB2 1TN, UK
| | - Wendy Dean
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Poppy Gould
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Jafar Sharif
- RIKEN Research Center for Allergy and Immunology, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Kanagawa, Japan
| | - Nelly Olova
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Tamir Chandra
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Haruhiko Koseki
- RIKEN Research Center for Allergy and Immunology, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Kanagawa, Japan
| | | | - Wolf Reik
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK; University of Cambridge, The Old Schools, Trinity Lane, Cambridge CB2 1TN, UK; Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.
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76
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Yu B, Lin YA, Parhad SS, Jin Z, Ma J, Theurkauf WE, Zhang ZZ, Huang Y. Structural insights into Rhino-Deadlock complex for germline piRNA cluster specification. EMBO Rep 2018; 19:embr.201745418. [PMID: 29858487 DOI: 10.15252/embr.201745418] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 04/28/2018] [Accepted: 05/14/2018] [Indexed: 11/09/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) silence transposons in germ cells to maintain genome stability and animal fertility. Rhino, a rapidly evolving heterochromatin protein 1 (HP1) family protein, binds Deadlock in a species-specific manner and so defines the piRNA-producing loci in the Drosophila genome. Here, we determine the crystal structures of Rhino-Deadlock complex in Drosophila melanogaster and simulans In both species, one Rhino binds the N-terminal helix-hairpin-helix motif of one Deadlock protein through a novel interface formed by the beta-sheet in the Rhino chromoshadow domain. Disrupting the interface leads to infertility and transposon hyperactivation in flies. Our structural and functional experiments indicate that electrostatic repulsion at the interaction interface causes cross-species incompatibility between the sibling species. By determining the molecular architecture of this piRNA-producing machinery, we discover a novel HP1-partner interacting mode that is crucial to piRNA biogenesis and transposon silencing. We thus explain the cross-species incompatibility of two sibling species at the molecular level.
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Affiliation(s)
- Bowen Yu
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yu An Lin
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA
| | - Swapnil S Parhad
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Zhaohui Jin
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - William E Theurkauf
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Zz Zhao Zhang
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA
| | - Ying Huang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
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77
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Parikh RY, Lin H, Gangaraju VK. A critical role for nucleoporin 358 (Nup358) in transposon silencing and piRNA biogenesis in Drosophila. J Biol Chem 2018; 293:9140-9147. [PMID: 29735528 DOI: 10.1074/jbc.ac118.003264] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 04/27/2018] [Indexed: 01/10/2023] Open
Abstract
Piwi-interacting RNAs (piRNAs) are a class of small noncoding RNAs that bind Piwi proteins to silence transposons and to regulate gene expression. In Drosophila germ cells, the Aubergine (Aub)-Argonaute 3 (Ago3)-dependent ping-pong cycle generates most germline piRNAs. Loading of antisense piRNAs amplified by this cycle enables Piwi to enter the nucleus and silence transposons. Nuclear localization is crucial for Piwi function in transposon silencing, but how this process is regulated remains unknown. It is also not known whether any of the components of the nuclear pore complex (NPC) directly function in the piRNA pathway. Here, we show that nucleoporin 358 (Nup358) and Piwi interact with each other and that a germline knockdown (GLKD) of Nup358 with short hairpin RNA prevents Piwi entry into the nucleus. The Nup358 GLKD also activated transposons, increased genomic instability, and derailed piRNA biogenesis because of a combination of decreased piRNA precursor transcription and a collapse of the ping-pong cycle. Our results point to a critical role for Nup358 in the piRNA pathway, laying the foundation for future studies to fully elucidate the mechanisms by which Nup358 contributes to piRNA biogenesis and transposon silencing.
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Affiliation(s)
- Rasesh Y Parikh
- From the Department of Biochemistry and Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425 and
| | - Haifan Lin
- Yale Stem Cell Center and Department of Cell Biology, Yale University, New Haven, Connecticut 06510
| | - Vamsi K Gangaraju
- From the Department of Biochemistry and Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425 and
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78
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Nishimura T, Nagamori I, Nakatani T, Izumi N, Tomari Y, Kuramochi-Miyagawa S, Nakano T. PNLDC1, mouse pre-piRNA Trimmer, is required for meiotic and post-meiotic male germ cell development. EMBO Rep 2018; 19:embr.201744957. [PMID: 29444933 PMCID: PMC5836094 DOI: 10.15252/embr.201744957] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 01/05/2018] [Accepted: 01/17/2018] [Indexed: 11/09/2022] Open
Abstract
PIWI‐interacting RNAs (piRNAs) are germ cell‐specific small RNAs essential for retrotransposon gene silencing and male germ cell development. In piRNA biogenesis, the endonuclease MitoPLD/Zucchini cleaves long, single‐stranded RNAs to generate 5′ termini of precursor piRNAs (pre‐piRNAs) that are consecutively loaded into PIWI‐family proteins. Subsequently, these pre‐piRNAs are trimmed at their 3′‐end by an exonuclease called Trimmer. Recently, poly(A)‐specific ribonuclease‐like domain‐containing 1 (PNLDC1) was identified as the pre‐piRNA Trimmer in silkworms. However, the function of PNLDC1 in other species remains unknown. Here, we generate Pnldc1 mutant mice and analyze small RNAs in their testes. Our results demonstrate that mouse PNLDC1 functions in the trimming of both embryonic and post‐natal pre‐piRNAs. In addition, piRNA trimming defects in embryonic and post‐natal testes cause impaired DNA methylation and reduced MIWI expression, respectively. Phenotypically, both meiotic and post‐meiotic arrests are evident in the same individual Pnldc1 mutant mouse. The former and latter phenotypes are similar to those of MILI and MIWI mutant mice, respectively. Thus, PNLDC1‐mediated piRNA trimming is indispensable for the function of piRNAs throughout mouse spermatogenesis.
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Affiliation(s)
- Toru Nishimura
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Ippei Nagamori
- Department of Pathology, Osaka University, Suita, Osaka, Japan
| | | | - Natsuko Izumi
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku Tokyo, Japan
| | - Yukihide Tomari
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku Tokyo, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku Tokyo, Japan
| | - Satomi Kuramochi-Miyagawa
- Department of Pathology, Osaka University, Suita, Osaka, Japan .,CREST, Japan Science and Technology Agency (JST), Saitama, Japan
| | - Toru Nakano
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan .,Department of Pathology, Osaka University, Suita, Osaka, Japan.,CREST, Japan Science and Technology Agency (JST), Saitama, Japan
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79
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Fu Y, Yang Y, Zhang H, Farley G, Wang J, Quarles KA, Weng Z, Zamore PD. The genome of the Hi5 germ cell line from Trichoplusia ni, an agricultural pest and novel model for small RNA biology. eLife 2018; 7:31628. [PMID: 29376823 PMCID: PMC5844692 DOI: 10.7554/elife.31628] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 01/26/2018] [Indexed: 12/30/2022] Open
Abstract
We report a draft assembly of the genome of Hi5 cells from the lepidopteran insect pest, Trichoplusia ni, assigning 90.6% of bases to one of 28 chromosomes and predicting 14,037 protein-coding genes. Chemoreception and detoxification gene families reveal T. ni-specific gene expansions that may explain its widespread distribution and rapid adaptation to insecticides. Transcriptome and small RNA data from thorax, ovary, testis, and the germline-derived Hi5 cell line show distinct expression profiles for 295 microRNA- and >393 piRNA-producing loci, as well as 39 genes encoding small RNA pathway proteins. Nearly all of the W chromosome is devoted to piRNA production, and T. ni siRNAs are not 2´-O-methylated. To enable use of Hi5 cells as a model system, we have established genome editing and single-cell cloning protocols. The T. ni genome provides insights into pest control and allows Hi5 cells to become a new tool for studying small RNAs ex vivo. A common moth called the cabbage looper is becoming increasingly relevant to the scientific community. Its caterpillars are a serious threat to cabbage, broccoli and cauliflower crops, and they have started to resist the pesticides normally used to control them. Moreover, the insect’s germline cells – the ones that will produce sperm and eggs – are used in laboratories as ‘factories’ to artificially produce proteins of interest. The germline cells also host a group of genetic mechanisms called RNA silencing. One of these processes is known as piRNA, and it protects the genome against ‘jumping genes’. These genetic elements can cause mutations by moving from place to place in the DNA: in germline cells, piRNA suppresses them before the genetic information is transmitted to the next generation. Not all germline cells grow equally well under experimental conditions, or are easy to use to examine piRNA mechanisms in a laboratory. The germline cells from the cabbage looper, on the other hand, have certain characteristics that would make them ideal to study piRNA in insects. However, the genome of the moth had not yet been fully resolved. This hinders research on new ways of controlling the pest, on how to use the germline cells to produce more useful proteins, or on piRNA. Decoding a genome requires several steps. First, the entire genetic information is broken in short sections that can then be deciphered. Next, these segments need to be ‘assembled’ – put together, and in the right order, to reconstitute the entire genome. Certain portions of the genome, which are formed of repeats of the same sections, can be difficult to assemble. Finally, the genome must be annotated: the different regions – such as the genes – need to be identified and labeled. Here, Fu et al. assembled and annotated the genome of the cabbage looper, and in the process developed strategies that could be used for other species with a lot of repeated sequences in their genomes. Having access to the looper’s full genetic information makes it possible to use their germline cells to produce new types of proteins, for example for pharmaceutical purposes. Fu et al. went on to make working with these cells even easier by refining protocols so that modern research techniques, such as the gene-editing technology CRISPR-Cas9, can be used on the looper germline cells. The mapping of the genome also revealed that the genes involved in removing toxins from the insects’ bodies are rapidly evolving, which may explain why the moths readily become resistant to insecticides. This knowledge could help finding new ways of controlling the pest. Finally, the genes involved in RNA silencing were labeled: results show that an entire chromosome is the source of piRNAs. Combined with the new protocols developed by Fu et al., this could make cabbage looper germline cells the default option for any research into the piRNA mechanism. How piRNA works in the moth could inform work on human piRNA, as these processes are highly similar across the animal kingdom.
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Affiliation(s)
- Yu Fu
- Bioinformatics Program, Boston University, Boston, United States.,Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, United States
| | - Yujing Yang
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, United States
| | - Han Zhang
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, United States
| | - Gwen Farley
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, United States
| | - Junling Wang
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, United States
| | - Kaycee A Quarles
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, United States
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, United States
| | - Phillip D Zamore
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, United States
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80
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Penke TJR, McKay DJ, Strahl BD, Matera AG, Duronio RJ. Functional Redundancy of Variant and Canonical Histone H3 Lysine 9 Modification in Drosophila. Genetics 2018; 208:229-244. [PMID: 29133298 PMCID: PMC5753860 DOI: 10.1534/genetics.117.300480] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 11/10/2017] [Indexed: 01/07/2023] Open
Abstract
Histone post-translational modifications (PTMs) and differential incorporation of variant and canonical histones into chromatin are central modes of epigenetic regulation. Despite similar protein sequences, histone variants are enriched for different suites of PTMs compared to their canonical counterparts. For example, variant histone H3.3 occurs primarily in transcribed regions and is enriched for "active" histone PTMs like Lys9 acetylation (H3.3K9ac), whereas the canonical histone H3 is enriched for Lys9 methylation (H3K9me), which is found in transcriptionally silent heterochromatin. To determine the functions of K9 modification on variant vs. canonical H3, we compared the phenotypes caused by engineering H3.3K9R and H3K9R mutant genotypes in Drosophila melanogaster Whereas most H3.3K9R , and a small number of H3K9R , mutant animals are capable of completing development and do not have substantially altered protein-coding transcriptomes, all H3.3K9R H3K9R combined mutants die soon after embryogenesis and display decreased expression of genes enriched for K9ac. These data suggest that the role of K9ac in gene activation during development can be provided by either H3 or H3.3. Conversely, we found that H3.3K9 is methylated at telomeric transposons and that this mark contributes to repressive chromatin architecture, supporting a role for H3.3 in heterochromatin that is distinct from that of H3. Thus, our genetic and molecular analyses demonstrate that K9 modification of variant and canonical H3 have overlapping roles in development and transcriptional regulation, though to differing extents in euchromatin and heterochromatin.
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Affiliation(s)
- Taylor J R Penke
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, North Carolina 27599
| | - Daniel J McKay
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, North Carolina 27599
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, North Carolina 27599
- Department of Genetics, The University of North Carolina at Chapel Hill, North Carolina 27599
- Department of Biology, The University of North Carolina at Chapel Hill, North Carolina 27599
| | - Brian D Strahl
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, North Carolina 27599
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, North Carolina 27599
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, North Carolina 27599
| | - A Gregory Matera
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, North Carolina 27599
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, North Carolina 27599
- Department of Genetics, The University of North Carolina at Chapel Hill, North Carolina 27599
- Department of Biology, The University of North Carolina at Chapel Hill, North Carolina 27599
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, North Carolina 27599
| | - Robert J Duronio
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, North Carolina 27599
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, North Carolina 27599
- Department of Genetics, The University of North Carolina at Chapel Hill, North Carolina 27599
- Department of Biology, The University of North Carolina at Chapel Hill, North Carolina 27599
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, North Carolina 27599
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81
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piRNA-mediated regulation of transposon alternative splicing in the soma and germ line. Nature 2017; 552:268-272. [PMID: 29211718 PMCID: PMC5933846 DOI: 10.1038/nature25018] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 11/06/2017] [Indexed: 12/31/2022]
Abstract
Transposable elements can drive genome evolution, but their enhanced activity is detrimental to the host and therefore must be tightly regulated1. The piwi-interacting small RNAs (piRNAs) pathway is critically important for transposable element regulation, by inducing transcriptional silencing or post-transcriptional decay of mRNAs2. Here, we show that piRNAs and piRNA biogenesis components regulate pre-mRNA splicing of P transposable element transcripts in vivo, leading to the production of the non-transposase-encoding mature mRNA isoform in germ cells. Unexpectedly, we show that the piRNA pathway components do not act to reduce P-element transposon transcript levels during P-M hybrid dysgenesis, a syndrome that affects germline development in Drosophila3,4. Instead, splicing regulation is mechanistically achieved in concert with piRNA-mediated changes to repressive chromatin states, and relies on the function of the Piwi-piRNA complex proteins Asterix/Gtsf15–7 and Panoramix/Silencio8,9, as well as Heterochromatin Protein 1a (Su(var)205/HP1a). Furthermore, we show that this machinery, together with the piRNA Flamenco cluster10, not only controls the accumulation of Gypsy retrotransposon transcripts11 but also regulates splicing of Gypsy mRNAs in cultured ovarian somatic cells, a process required for the production of infectious particles that can lead to heritable transposition events12,13. Our findings identify splicing regulation as a new role and essential function for the Piwi pathway in protecting the genome against transposon mobility, and provide a model system for studying the role of chromatin structure in modulating alternative splicing during development.
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82
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Panero R, Rinaldi A, Memoli D, Nassa G, Ravo M, Rizzo F, Tarallo R, Milanesi L, Weisz A, Giurato G. iSmaRT: a toolkit for a comprehensive analysis of small RNA-Seq data. Bioinformatics 2017; 33:938-940. [PMID: 28057684 DOI: 10.1093/bioinformatics/btw734] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 11/15/2016] [Indexed: 11/13/2022] Open
Abstract
Summary The interest in investigating the biological roles of small non-coding RNAs (sncRNAs) is increasing, due to the pleiotropic effects of these molecules exert in many biological contexts. While several methods and tools are available to study microRNAs (miRNAs), only few focus on novel classes of sncRNAs, in particular PIWI-interacting RNAs (piRNAs). To overcome these limitations, we implemented iSmaRT ( i ntegrative Sm all R NA T ool-kit), an automated pipeline to analyze smallRNA-Seq data. Availability and Implementation iSmaRT is a collection of bioinformatics tools and own algorithms, interconnected through a Graphical User Interface (GUI). In addition to performing comprehensive analyses on miRNAs, it implements specific computational modules to analyze piRNAs, predicting novel ones and identifying their RNA targets. A smallRNA-Seq dataset generated from brain samples of Huntington's Disease patients was used here to illustrate iSmaRT performances, demonstrating how the pipeline can provide, in a rapid and user friendly way, a comprehensive analysis of different classes of sncRNAs. iSmaRT is freely available on the web at ftp://labmedmolge-1.unisa.it (User: iSmart - Password: password). Contact aweisz@unisa.it or ggiurato@unisa.it. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Riccardo Panero
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy.,Department of Molecular Biotechnology and Health Sciences, University of Torino, via Nizza 52, Torino, Italy
| | - Antonio Rinaldi
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy
| | - Domenico Memoli
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy
| | - Giovanni Nassa
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy.,Genomix4Life, University of Salerno, Baronissi, SA, Italy
| | - Maria Ravo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy
| | - Roberta Tarallo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy
| | - Luciano Milanesi
- Institute for Biomedical Technologies, National Research Council, Segrate, MI, Italy
| | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy.,Genomix4Life, University of Salerno, Baronissi, SA, Italy
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83
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Kandasamy SK, Zhu L, Fukunaga R. The C-terminal dsRNA-binding domain of Drosophila Dicer-2 is crucial for efficient and high-fidelity production of siRNA and loading of siRNA to Argonaute2. RNA (NEW YORK, N.Y.) 2017; 23:1139-1153. [PMID: 28416567 PMCID: PMC5473147 DOI: 10.1261/rna.059915.116] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 04/10/2017] [Indexed: 05/25/2023]
Abstract
Drosophila Dicer-2 efficiently and precisely produces 21-nucleotide (nt) siRNAs from long double-stranded RNA (dsRNA) substrates and loads these siRNAs onto the effector protein Argonaute2 for RNA silencing. The functional roles of each domain of the multidomain Dicer-2 enzyme in the production and loading of siRNAs are not fully understood. Here we characterized Dicer-2 mutants lacking either the N-terminal helicase domain or the C-terminal dsRNA-binding domain (CdsRBD) (ΔHelicase and ΔCdsRBD, respectively) in vivo and in vitro. We found that ΔCdsRBD Dicer-2 produces siRNAs with lowered efficiency and length fidelity, producing a smaller ratio of 21-nt siRNAs and higher ratios of 20- and 22-nt siRNAs in vivo and in vitro. We also found that ΔCdsRBD Dicer-2 cannot load siRNA duplexes to Argonaute2 in vitro. Consistent with these findings, we found that ΔCdsRBD Dicer-2 causes partial loss of RNA silencing activity in vivo. Thus, Dicer-2 CdsRBD is crucial for the efficiency and length fidelity in siRNA production and for siRNA loading. Together with our previously published findings, we propose that CdsRBD binds the proximal body region of a long dsRNA substrate whose 5'-monophosphate end is anchored by the phosphate-binding pocket in the PAZ domain. CdsRBD aligns the RNA to the RNA cleavage active site in the RNase III domain for efficient and high-fidelity siRNA production. This study reveals multifunctions of Dicer-2 CdsRBD and sheds light on the molecular mechanism by which Dicer-2 produces 21-nt siRNAs with a high efficiency and fidelity for efficient RNA silencing.
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Affiliation(s)
- Suresh K Kandasamy
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Li Zhu
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Ryuya Fukunaga
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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84
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Comparative Principles of DNA Methylation Reprogramming during Human and Mouse In Vitro Primordial Germ Cell Specification. Dev Cell 2017; 39:104-115. [PMID: 27728778 PMCID: PMC5064768 DOI: 10.1016/j.devcel.2016.09.015] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Revised: 08/24/2016] [Accepted: 09/14/2016] [Indexed: 12/22/2022]
Abstract
Primordial germ cell (PGC) development is characterized by global epigenetic remodeling, which resets genomic potential and establishes an epigenetic ground state. Here we recapitulate PGC specification in vitro from naive embryonic stem cells and characterize the early events of epigenetic reprogramming during the formation of the human and mouse germline. Following rapid de novo DNA methylation during priming to epiblast-like cells, methylation is globally erased in PGC-like cells. Repressive chromatin marks (H3K9me2/3) and transposable elements are enriched at demethylation-resistant regions, while active chromatin marks (H3K4me3 or H3K27ac) are more prominent at regions that demethylate faster. The dynamics of specification and epigenetic reprogramming show species-specific differences, in particular markedly slower reprogramming kinetics in the human germline. Differences in developmental kinetics may be explained by differential regulation of epigenetic modifiers. Our work establishes a robust and faithful experimental system of the early events of epigenetic reprogramming and regulation in the germline.
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85
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Iwasaki YW, Ishino K, Siomi H. Deep sequencing and high-throughput analysis of PIWI-associated small RNAs. Methods 2017; 126:66-75. [PMID: 28552266 DOI: 10.1016/j.ymeth.2017.05.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/08/2017] [Accepted: 05/21/2017] [Indexed: 02/07/2023] Open
Abstract
Small RNAs are now known to be major regulatory factors of gene expression. Emerging methods based on deep-sequencing have enabled the analysis of small RNA expression in a high-throughput manner, leading to the identification of large numbers of small RNAs in various species. Moreover, profiling small RNA data together with transcriptome data enables transcriptional and post-transcriptional regulation mediated by small RNAs to be hypothesized. Here, we isolated PIWIL1 (MIWI)-associated small RNAs from mouse testes, and performed small RNA-seq analysis. In addition, directional RNA-seq was performed using Piwil1 mutant mouse testes. Using these data, we describe protocols for analyzing small RNA-seq reads to obtain profiles of small RNAs associated with PIWI proteins. We also present bioinformatic protocols for analyzing RNA-seq reads that aim to annotate expression of piRNA clusters and identify genes regulated by piRNAs.
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Affiliation(s)
- Yuka W Iwasaki
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Kyoko Ishino
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Haruhiko Siomi
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan.
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86
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Akkouche A, Mugat B, Barckmann B, Varela-Chavez C, Li B, Raffel R, Pélisson A, Chambeyron S. Piwi Is Required during Drosophila Embryogenesis to License Dual-Strand piRNA Clusters for Transposon Repression in Adult Ovaries. Mol Cell 2017; 66:411-419.e4. [PMID: 28457744 DOI: 10.1016/j.molcel.2017.03.017] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 01/13/2017] [Accepted: 03/24/2017] [Indexed: 12/22/2022]
Abstract
Most piRNAs in the Drosophila female germline are transcribed from heterochromatic regions called dual-strand piRNA clusters. Histone 3 lysine 9 trimethylation (H3K9me3) is required for licensing piRNA production by these clusters. However, it is unclear when and how they acquire this permissive heterochromatic state. Here, we show that transient Piwi depletion in Drosophila embryos results in H3K9me3 decrease at piRNA clusters in ovaries. This is accompanied by impaired biogenesis of ovarian piRNAs, accumulation of transposable element transcripts, and female sterility. Conversely, Piwi depletion at later developmental stages does not disturb piRNA cluster licensing. These results indicate that the identity of piRNA clusters is epigenetically acquired in a Piwi-dependent manner during embryonic development, which is reminiscent of the widespread genome reprogramming occurring during early mammalian zygotic development.
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Affiliation(s)
- Abdou Akkouche
- Institut de Génétique Humaine, UMR9002 CNRS-Université de Montpellier, 34396 Montpellier, France
| | - Bruno Mugat
- Institut de Génétique Humaine, UMR9002 CNRS-Université de Montpellier, 34396 Montpellier, France
| | - Bridlin Barckmann
- Institut de Génétique Humaine, UMR9002 CNRS-Université de Montpellier, 34396 Montpellier, France
| | - Carolina Varela-Chavez
- Institut de Génétique Humaine, UMR9002 CNRS-Université de Montpellier, 34396 Montpellier, France
| | - Blaise Li
- Institut de Génétique Humaine, UMR9002 CNRS-Université de Montpellier, 34396 Montpellier, France
| | - Raoul Raffel
- Institut de Génétique Humaine, UMR9002 CNRS-Université de Montpellier, 34396 Montpellier, France
| | - Alain Pélisson
- Institut de Génétique Humaine, UMR9002 CNRS-Université de Montpellier, 34396 Montpellier, France
| | - Séverine Chambeyron
- Institut de Génétique Humaine, UMR9002 CNRS-Université de Montpellier, 34396 Montpellier, France.
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87
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Sun YH, Xie LH, Zhuo X, Chen Q, Ghoneim D, Zhang B, Jagne J, Yang C, Li XZ. Domestic chickens activate a piRNA defense against avian leukosis virus. eLife 2017; 6. [PMID: 28384097 PMCID: PMC5383398 DOI: 10.7554/elife.24695] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 03/04/2017] [Indexed: 12/12/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) protect the germ line by targeting transposable elements (TEs) through the base-pair complementarity. We do not know how piRNAs co-evolve with TEs in chickens. Here we reported that all active TEs in the chicken germ line are targeted by piRNAs, and as TEs lose their activity, the corresponding piRNAs erode away. We observed de novo piRNA birth as host responds to a recent retroviral invasion. Avian leukosis virus (ALV) has endogenized prior to chicken domestication, remains infectious, and threatens poultry industry. Domestic fowl produce piRNAs targeting ALV from one ALV provirus that was known to render its host ALV resistant. This proviral locus does not produce piRNAs in undomesticated wild chickens. Our findings uncover rapid piRNA evolution reflecting contemporary TE activity, identify a new piRNA acquisition modality by activating a pre-existing genomic locus, and extend piRNA defense roles to include the period when endogenous retroviruses are still infectious. DOI:http://dx.doi.org/10.7554/eLife.24695.001 Viruses called retroviruses can infect animal cells and merge their genetic information with those of the animal causing damage to the animal’s genetic blueprints. Once retroviruses are integrated into a cell they can sometimes get passed down through the generations over the centuries. Almost half of the human genetic code, for example, is made from ancient retroviruses and other foreign sequences. Over time many of these ancient viruses lost the ability to infect other cells and became trapped within cells but they can still jump out and damage the animal’s genetic code under certain circumstances. These trapped foreign sequences are called transposable elements. Animal cells produce molecules called piRNAs to shut down transposable elements. Most piRNAs are produced from genetic information that originally came from integrated retroviruses and that has been hijacked to defend the cell, a similar strategy as Crisper system in bacteria. Domestic chickens produce piRNAs against a virus called avian leukosis virus (or ALV for short) – which commonly infects domestic fowl. The virus also infected the wild ancestors of chickens, known as red jungle fowl, but these birds do not produce piRNAs. This provides an ideal setting to study the evolution of piRNAs in an animal that is not too distantly related to humans (chickens and humans both have backbones, and are therefore both warm-blooded vertebrates). Sun et al. examined cells from the testicles of domestic chickens and red jungle fowl as an example of the role of piRNAs in protecting genetic information in vertebrates. The investigation revealed that piRNAs against all previously trapped viruses in the chicken’s genetic code are produced in chickens to stop them from causing more damage. Sun et al. also observed the creation of piRNAs in chickens in response to ALV that had not yet become trapped in the chicken’s genetic code. Importantly, the piRNAs could control these retroviruses while they were still infectious. The experiments also revealed that piRNAs against ALV are produced from a single copy of ALV that is found in both domestic and wild chickens. The results showed that cells can produce new piRNAs using these pre-existing viral copies within their own genetics. This illustrates that production of piRNA from existing genetic material can be activated in response to certain cues. Further work will seek to discover how existing genetic information becomes a source of piRNAs. In the United States, 8 billion domestic chickens are consumed each year, and a better understanding of how these birds defend themselves against viral infections could increase the productivity of the poultry industry around the world. Moreover, because other viruses trapped in the chicken’s genetic code are related to similar viruses in humans, future discoveries made in this area could help to guide research that will benefit human health as well. DOI:http://dx.doi.org/10.7554/eLife.24695.002
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Affiliation(s)
- Yu Huining Sun
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, Department of Urology, University of Rochester Medical Center, Rochester, United States
| | - Li Huitong Xie
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, Department of Urology, University of Rochester Medical Center, Rochester, United States
| | - Xiaoyu Zhuo
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, United States
| | - Qiang Chen
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, Department of Urology, University of Rochester Medical Center, Rochester, United States
| | - Dalia Ghoneim
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, Department of Urology, University of Rochester Medical Center, Rochester, United States
| | - Bin Zhang
- Department of Pathology and Laboratory Medicine, Department of Pediatrics, University of Rochester Medical Center, Rochester, United States
| | - Jarra Jagne
- Animal Health Diagnostic Center, Cornell University College of Veterinary Medicine, Ithaca, United States
| | - Chengbo Yang
- Department of Animal Science, University of Manitoba, Winnipeg, Canada
| | - Xin Zhiguo Li
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, Department of Urology, University of Rochester Medical Center, Rochester, United States
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88
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Loudig O, Wang T, Ye K, Lin J, Wang Y, Ramnauth A, Liu C, Stark A, Chitale D, Greenlee R, Multerer D, Honda S, Daida Y, Spencer Feigelson H, Glass A, Couch FJ, Rohan T, Ben-Dov IZ. Evaluation and Adaptation of a Laboratory-Based cDNA Library Preparation Protocol for Retrospective Sequencing of Archived MicroRNAs from up to 35-Year-Old Clinical FFPE Specimens. Int J Mol Sci 2017; 18:ijms18030627. [PMID: 28335433 PMCID: PMC5372640 DOI: 10.3390/ijms18030627] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 03/02/2017] [Accepted: 03/08/2017] [Indexed: 01/30/2023] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) specimens, when used in conjunction with patient clinical data history, represent an invaluable resource for molecular studies of cancer. Even though nucleic acids extracted from archived FFPE tissues are degraded, their molecular analysis has become possible. In this study, we optimized a laboratory-based next-generation sequencing barcoded cDNA library preparation protocol for analysis of small RNAs recovered from archived FFPE tissues. Using matched fresh and FFPE specimens, we evaluated the robustness and reproducibility of our optimized approach, as well as its applicability to archived clinical specimens stored for up to 35 years. We then evaluated this cDNA library preparation protocol by performing a miRNA expression analysis of archived breast ductal carcinoma in situ (DCIS) specimens, selected for their relation to the risk of subsequent breast cancer development and obtained from six different institutions. Our analyses identified six miRNAs (miR-29a, miR-221, miR-375, miR-184, miR-363, miR-455-5p) differentially expressed between DCIS lesions from women who subsequently developed an invasive breast cancer (cases) and women who did not develop invasive breast cancer within the same time interval (control). Our thorough evaluation and application of this laboratory-based miRNA sequencing analysis indicates that the preparation of small RNA cDNA libraries can reliably be performed on older, archived, clinically-classified specimens.
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Affiliation(s)
- Olivier Loudig
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Tao Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Kenny Ye
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Juan Lin
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Yihong Wang
- Department of Pathology, Rhode Island Hospital, Providence, RI 02903, USA.
| | - Andrew Ramnauth
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Christina Liu
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Azadeh Stark
- Department of Pathology and Breast Oncology Program, Henry Ford Health System, Detroit, MI 48202, USA.
| | - Dhananjay Chitale
- Department of Pathology and Breast Oncology Program, Henry Ford Health System, Detroit, MI 48202, USA.
| | - Robert Greenlee
- Center for Clinical Epidemiology and Population Health, Marshfield Clinic Research Foundation, Marshfield, WI 54449, USA.
| | - Deborah Multerer
- Center for Clinical Epidemiology and Population Health, Marshfield Clinic Research Foundation, Marshfield, WI 54449, USA.
| | - Stacey Honda
- Department of Pathology, Center for Health Research, Kaiser Permanente, 3288 Moanalua Road, Honolulu, HI 96819, USA.
| | - Yihe Daida
- Department of Pathology, Center for Health Research, Kaiser Permanente, 3288 Moanalua Road, Honolulu, HI 96819, USA.
| | | | - Andrew Glass
- Center for Health Research, Kaiser Permanente Northwest, Portland, OR 97227, USA.
| | - Fergus J Couch
- Health Sciences Research, Mayo Clinic, Rochester, NY 55902, USA.
| | - Thomas Rohan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
- Montefiore Medical Center, Bronx, NY 10467, USA.
| | - Iddo Z Ben-Dov
- Laboratory of Medical Transcriptomics, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel.
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89
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Karam JA, Parikh RY, Nayak D, Rosenkranz D, Gangaraju VK. Co-chaperone Hsp70/Hsp90-organizing protein (Hop) is required for transposon silencing and Piwi-interacting RNA (piRNA) biogenesis. J Biol Chem 2017; 292:6039-6046. [PMID: 28193840 DOI: 10.1074/jbc.c117.777730] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 02/08/2017] [Indexed: 11/06/2022] Open
Abstract
Piwi-interacting RNAs (piRNAs) are 26-30-nucleotide germ line-specific small non-coding RNAs that have evolutionarily conserved function in mobile genetic element (transposons) silencing and maintenance of genome integrity. Drosophila Hsp70/90-organizing protein homolog (Hop), a co-chaperone, interacts with piRNA-binding protein Piwi and mediates silencing of phenotypic variations. However, it is not known whether Hop has a direct role in piRNA biogenesis and transposon silencing. Here, we show that knockdown of Hop in the germ line nurse cells (GLKD) of Drosophila ovaries leads to activation of transposons. Hop GLKD females can lay eggs at the same rate as wild-type counterparts, but the eggs do not hatch into larvae. Hop GLKD leads to the accumulation of γ-H2Av foci in the germ line, indicating increased DNA damage in the ovary. We also show that Hop GLKD-induced transposon up-regulation is due to inefficient piRNA biogenesis. Based on these results, we conclude that Hop is a critical component of the piRNA pathway and that it maintains genome integrity by silencing transposons.
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Affiliation(s)
- Joseph A Karam
- From the Department of Biochemistry and Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425 and
| | - Rasesh Y Parikh
- From the Department of Biochemistry and Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425 and
| | - Dhananjaya Nayak
- From the Department of Biochemistry and Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425 and
| | - David Rosenkranz
- the Institute of Organismic and Molecular Evolutionary Biology, Johannes Gutenberg-Universität Mainz, 55122 Mainz, Germany
| | - Vamsi K Gangaraju
- From the Department of Biochemistry and Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425 and
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90
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De Luca L, Trino S, Laurenzana I, Simeon V, Calice G, Raimondo S, Podestà M, Santodirocco M, Di Mauro L, La Rocca F, Caivano A, Morano A, Frassoni F, Cilloni D, Del Vecchio L, Musto P. MiRNAs and piRNAs from bone marrow mesenchymal stem cell extracellular vesicles induce cell survival and inhibit cell differentiation of cord blood hematopoietic stem cells: a new insight in transplantation. Oncotarget 2017; 7:6676-92. [PMID: 26760763 PMCID: PMC4872742 DOI: 10.18632/oncotarget.6791] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 12/05/2015] [Indexed: 12/18/2022] Open
Abstract
Hematopoietic stem cells (HSC), including umbilical cord blood CD34+ stem cells (UCB-CD34+), are used for the treatment of several diseases. Although different studies suggest that bone marrow mesenchymal stem cells (BM-MSC) support hematopoiesis, the exact mechanism remains unclear. Recently, extracellular vesicles (EVs) have been described as a novel avenue of cell communication, which may mediate BM-MSC effect on HSC. In this work, we studied the interaction between UCB-CD34+ cells and BM-MSC derived EVs. First, by sequencing EV derived miRNAs and piRNAs we found that EVs contain RNAs able to influence UCB-CD34+ cell fate. Accordingly, a gene expression profile of UCB-CD34+ cells treated with EVs, identified about 100 down-regulated genes among those targeted by EV-derived miRNAs and piRNAs (e.g. miR-27b/MPL, miR-21/ANXA1, miR-181/EGR2), indicating that EV content was able to modify gene expression profile of receiving cells. Moreover, we demonstrated that UCB-CD34+ cells, exposed to EVs, significantly changed different biological functions, becoming more viable and less differentiated. UCB-CD34+ gene expression profile also identified 103 up-regulated genes, most of them codifying for chemokines, cytokines and their receptors, involved in chemotaxis of different BM cells, an essential function of hematopoietic reconstitution. Finally, the exposure of UCB-CD34+ cells to EVs caused an increased expression CXCR4, paralleled by an in vivo augmented migration from peripheral blood to BM niche in NSG mice. This study demonstrates the existence of a powerful cross talk between BM-MSC and UCB-CD34+ cells, mediated by EVs, providing new insight in the biology of cord blood transplantation.
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Affiliation(s)
- Luciana De Luca
- Laboratory of Preclinical and Translational Research, IRCCS-Centro di Riferimento Oncologico della Basilicata (CROB), Rionero in Vulture, 85028 (PZ), Italy
| | - Stefania Trino
- Laboratory of Preclinical and Translational Research, IRCCS-Centro di Riferimento Oncologico della Basilicata (CROB), Rionero in Vulture, 85028 (PZ), Italy
| | - Ilaria Laurenzana
- Laboratory of Preclinical and Translational Research, IRCCS-Centro di Riferimento Oncologico della Basilicata (CROB), Rionero in Vulture, 85028 (PZ), Italy
| | - Vittorio Simeon
- Laboratory of Preclinical and Translational Research, IRCCS-Centro di Riferimento Oncologico della Basilicata (CROB), Rionero in Vulture, 85028 (PZ), Italy
| | - Giovanni Calice
- Laboratory of Preclinical and Translational Research, IRCCS-Centro di Riferimento Oncologico della Basilicata (CROB), Rionero in Vulture, 85028 (PZ), Italy
| | - Stefania Raimondo
- Department of Clinical and Biological Sciences, University of Turin, Turin 10126, Italy
| | - Marina Podestà
- Stem Cell Center, S. Martino Hospital, Genova 16132, Italy
| | - Michele Santodirocco
- Transfusion Medicine Unit, Puglia Cord Blood Bank, IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 (FG), Italy
| | - Lazzaro Di Mauro
- Transfusion Medicine Unit, Puglia Cord Blood Bank, IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 (FG), Italy
| | - Francesco La Rocca
- Laboratory of Preclinical and Translational Research, IRCCS-Centro di Riferimento Oncologico della Basilicata (CROB), Rionero in Vulture, 85028 (PZ), Italy
| | - Antonella Caivano
- Laboratory of Preclinical and Translational Research, IRCCS-Centro di Riferimento Oncologico della Basilicata (CROB), Rionero in Vulture, 85028 (PZ), Italy
| | - Annalisa Morano
- Laboratory of Preclinical and Translational Research, IRCCS-Centro di Riferimento Oncologico della Basilicata (CROB), Rionero in Vulture, 85028 (PZ), Italy
| | - Francesco Frassoni
- Laboratorio Cellule Staminali Post Natali e Terapie Cellulari, Giannina Gaslini Institute, Genova 16148, Italy
| | - Daniela Cilloni
- Department of Clinical and Biological Sciences, University of Turin, Turin 10126, Italy
| | - Luigi Del Vecchio
- CEINGE-Biotecnologie Avanzate S.C.a R.L., Naples, 80145, Italy.,Department of Molecular Medicine and Medical Biotechnologies, Federico II University, Naples 80131, Italy
| | - Pellegrino Musto
- Scientific Direction, IRCCS-Centro di Riferimento Oncologico Basilicata (CROB), Rionero in Vulture, 85028 (PZ), Italy
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91
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Da Ros M, Lehtiniemi T, Olotu O, Fischer D, Zhang FP, Vihinen H, Jokitalo E, Sironen A, Toppari J, Kotaja N. FYCO1 and autophagy control the integrity of the haploid male germ cell-specific RNP granules. Autophagy 2016; 13:302-321. [PMID: 27929729 PMCID: PMC5324852 DOI: 10.1080/15548627.2016.1261319] [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: 02/04/2023] Open
Abstract
Ribonucleoprotein (RNP) granules play a major role in compartmentalizing cytoplasmic RNA regulation. Haploid round spermatids that have exceptionally diverse transcriptomes are characterized by a unique germ cell-specific RNP granule, the chromatoid body (CB). The CB shares many characteristics with somatic RNP granules but also has germline-specific features. The CB appears to be a central structure in PIWI-interacting RNA (piRNA)-targeted RNA regulation. Here, we identified a novel CB component, FYCO1, which is involved in the intracellular transport of autophagic vesicles in somatic cells. We demonstrated that the CB is associated with autophagic activity. Induction of autophagy leads to the recruitment of lysosomal vesicles onto the CB in a FYCO1-dependent manner as demonstrated by the analysis of a germ cell-specific Fyco1 conditional knockout mouse model. Furthermore, in the absence of FYCO1, the integrity of the CB was affected and the CB was fragmented. Our results suggest that RNP granule homeostasis is regulated by FYCO1-mediated autophagy.
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Affiliation(s)
- Matteo Da Ros
- a Institute of Biomedicine, Department of Physiology , University of Turku , Turku , Finland.,b Department of Cellular and Molecular Biology , Faculty of Medicine, University of Ottawa , Ottawa , ON , Canada
| | - Tiina Lehtiniemi
- a Institute of Biomedicine, Department of Physiology , University of Turku , Turku , Finland
| | - Opeyemi Olotu
- a Institute of Biomedicine, Department of Physiology , University of Turku , Turku , Finland
| | - Daniel Fischer
- c Natural Resources Institute Finland (Luke), Green Technology , Jokioinen , Finland
| | - Fu-Ping Zhang
- a Institute of Biomedicine, Department of Physiology , University of Turku , Turku , Finland.,d Turku Center for Disease Modeling, University of Turku , Turku , Finland
| | - Helena Vihinen
- e Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki , Helsinki , Finland
| | - Eija Jokitalo
- e Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki , Helsinki , Finland
| | - Anu Sironen
- c Natural Resources Institute Finland (Luke), Green Technology , Jokioinen , Finland
| | - Jorma Toppari
- a Institute of Biomedicine, Department of Physiology , University of Turku , Turku , Finland.,f Department of Pediatrics , University of Turku and Turku University Hospital , Turku , Finland
| | - Noora Kotaja
- a Institute of Biomedicine, Department of Physiology , University of Turku , Turku , Finland
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92
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Phosphate-binding pocket in Dicer-2 PAZ domain for high-fidelity siRNA production. Proc Natl Acad Sci U S A 2016; 113:14031-14036. [PMID: 27872309 DOI: 10.1073/pnas.1612393113] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The enzyme Dicer produces small silencing RNAs such as micro-RNAs (miRNAs) and small interfering RNAs (siRNAs). In Drosophila, Dicer-1 produces ∼22-24-nt miRNAs from pre-miRNAs, whereas Dicer-2 makes 21-nt siRNAs from long double-stranded RNAs (dsRNAs). How Dicer-2 precisely makes 21-nt siRNAs with a remarkably high fidelity is unknown. Here we report that recognition of the 5'-monophosphate of a long dsRNA substrate by a phosphate-binding pocket in the Dicer-2 PAZ (Piwi, Argonaute, and Zwille/Pinhead) domain is crucial for the length fidelity, but not the efficiency, in 21-nt siRNA production. Loss of the length fidelity, meaning increased length heterogeneity of siRNAs, caused by point mutations in the phosphate-binding pocket of the Dicer-2 PAZ domain decreased RNA silencing activity in vivo, showing the importance of the high fidelity to make 21-nt siRNAs. We propose that the 5'-monophosphate of a long dsRNA substrate is anchored by the phosphate-binding pocket in the Dicer-2 PAZ domain and the distance between the pocket and the RNA cleavage active site in the RNaseIII domain corresponds to the 21-nt pitch in the A-form duplex of a long dsRNA substrate, resulting in high-fidelity 21-nt siRNA production. This study sheds light on the molecular mechanism by which Dicer-2 produces 21-nt siRNAs with a remarkably high fidelity for efficient RNA silencing.
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93
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Veneziano D, Di Bella S, Nigita G, Laganà A, Ferro A, Croce CM. Noncoding RNA: Current Deep Sequencing Data Analysis Approaches and Challenges. Hum Mutat 2016; 37:1283-1298. [PMID: 27516218 DOI: 10.1002/humu.23066] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/09/2016] [Indexed: 02/06/2023]
Abstract
One of the most significant biological discoveries of the last decade is represented by the reality that the vast majority of the transcribed genomic output comprises diverse classes of noncoding RNAs (ncRNAs) that may play key roles and/or be affected by many biochemical cellular processes (i.e., RNA editing), with implications in human health and disease. With 90% of the human genome being transcribed and novel classes of ncRNA emerging (tRNA-derived small RNAs and circular RNAs among others), the great majority of the human transcriptome suggests that many important ncRNA functions/processes are yet to be discovered. An approach to filling such vast void of knowledge has been recently provided by the increasing application of next-generation sequencing (NGS), offering the unprecedented opportunity to obtain a more accurate profiling with higher resolution, increased throughput, sequencing depth, and low experimental complexity, concurrently posing an increasing challenge in terms of efficiency, accuracy, and usability of data analysis software. This review provides an overview of ncRNAs, NGS technology, and the most recent/popular computational approaches and the challenges they attempt to solve, which are essential to a more sensitive and comprehensive ncRNA annotation capable of furthering our understanding of this still vastly uncharted genomic territory.
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Affiliation(s)
- Dario Veneziano
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, 43210
| | | | - Giovanni Nigita
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, 43210
| | - Alessandro Laganà
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, 10029
| | - Afredo Ferro
- Department of Clinical and Molecular Biomedicine, University of Catania, Catania, 95125, Italy
| | - Carlo M Croce
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, 43210
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94
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Penke TJR, McKay DJ, Strahl BD, Matera AG, Duronio RJ. Direct interrogation of the role of H3K9 in metazoan heterochromatin function. Genes Dev 2016; 30:1866-80. [PMID: 27566777 PMCID: PMC5024684 DOI: 10.1101/gad.286278.116] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 08/05/2016] [Indexed: 11/24/2022]
Abstract
A defining feature of heterochromatin is methylation of Lys9 of histone H3 (H3K9me), a binding site for heterochromatin protein 1 (HP1). Penke et al. generated and analyzed H3K9R mutant flies, separating the functions of H3K9 and nonhistone substrates of H3K9 methyltransferases. A defining feature of heterochromatin is methylation of Lys9 of histone H3 (H3K9me), a binding site for heterochromatin protein 1 (HP1). Although H3K9 methyltransferases and HP1 are necessary for proper heterochromatin structure, the specific contribution of H3K9 to heterochromatin function and animal development is unknown. Using our recently developed platform to engineer histone genes in Drosophila, we generated H3K9R mutant flies, separating the functions of H3K9 and nonhistone substrates of H3K9 methyltransferases. Nucleosome occupancy and HP1a binding at pericentromeric heterochromatin are markedly decreased in H3K9R mutants. Despite these changes in chromosome architecture, a small percentage of H3K9R mutants complete development. Consistent with this result, expression of most protein-coding genes, including those within heterochromatin, is similar between H3K9R and controls. In contrast, H3K9R mutants exhibit increased open chromatin and transcription from piRNA clusters and transposons, resulting in transposon mobilization. Hence, transposon silencing is a major developmental function of H3K9.
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Affiliation(s)
- Taylor J R Penke
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Daniel J McKay
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Brian D Strahl
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - A Gregory Matera
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Robert J Duronio
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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95
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Wang H, Ma Z, Niu K, Xiao Y, Wu X, Pan C, Zhao Y, Wang K, Zhang Y, Liu N. Antagonistic roles of Nibbler and Hen1 in modulating piRNA 3' ends in Drosophila. Development 2015; 143:530-9. [PMID: 26718004 PMCID: PMC4760310 DOI: 10.1242/dev.128116] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 12/22/2015] [Indexed: 12/19/2022]
Abstract
In eukaryotes, aberrant expression of transposable elements (TEs) is detrimental to the host genome. Piwi-interacting RNAs (piRNAs) of ∼23 to 30 nucleotides bound to PIWI clade Argonaute proteins silence transposons in a manner that is strictly dependent on their sequence complementarity. Hence, a key goal in understanding piRNA pathways is to determine mechanisms that modulate piRNA sequences. Here, we identify a protein-protein interaction between the 3′-to-5′ exoribonuclease Nibbler (Nbr) and Piwi that links Nbr activity with piRNA pathways. We show that there is a delicate balance in the interplay between Nbr and Hen1, a methyltransferase involved in 2′-O-methylation at the 3′ terminal nucleotides of piRNAs, thus connecting two genes with opposing activities in the biogenesis of piRNA 3′ ends. With age, piRNAs become shorter and fewer in number, which is coupled with the derepression of select TEs. We demonstrate that activities of Nbr and Hen1 inherently contribute to TE silencing and age-dependent profiles of piRNAs. We propose that antagonistic roles of Nbr and Hen1 define a mechanism to modulate piRNA 3′ ends. Summary: Antagonism between Nbr and Hen1 represents a novel mechanism for the modulation of piRNA sequences, revealing new players involved in the silencing of transposable elements.
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Affiliation(s)
- Hui Wang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China
| | - Zaijun Ma
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China
| | - Kongyan Niu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yi Xiao
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xiaofen Wu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China
| | - Chenyu Pan
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yun Zhao
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Kai Wang
- Zilkha Neurogenetic Institute, University of South California, Los Angeles, CA 90033, USA
| | - Yaoyang Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China
| | - Nan Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
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96
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Wang W, Han BW, Tipping C, Ge DT, Zhang Z, Weng Z, Zamore PD. Slicing and Binding by Ago3 or Aub Trigger Piwi-Bound piRNA Production by Distinct Mechanisms. Mol Cell 2015; 59:819-30. [PMID: 26340424 DOI: 10.1016/j.molcel.2015.08.007] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 08/08/2015] [Accepted: 08/12/2015] [Indexed: 12/11/2022]
Abstract
In Drosophila ovarian germ cells, PIWI-interacting RNAs (piRNAs) direct Aubergine and Argonaute3 to cleave transposon transcripts and instruct Piwi to repress transposon transcription, thereby safeguarding the germline genome. Here, we report that RNA cleavage by Argonaute3 initiates production of most Piwi-bound piRNAs. We find that the cardinal function of Argonaute3, whose piRNA guides predominantly correspond to sense transposon sequences, is to produce antisense piRNAs that direct transcriptional silencing by Piwi, rather than to make piRNAs that guide post-transcriptional silencing by Aubergine. We also find that the Tudor domain protein Qin prevents Aubergine's cleavage products from becoming Piwi-bound piRNAs, ensuring that antisense piRNAs guide Piwi. Although Argonaute3 slicing is required to efficiently trigger phased piRNA production, an alternative, slicing-independent pathway suffices to generate Piwi-bound piRNAs that repress transcription of a subset of transposon families. This alternative pathway may help flies silence newly acquired transposons for which they lack extensively complementary piRNAs.
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Affiliation(s)
- Wei Wang
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA; RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Bo W Han
- RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Cindy Tipping
- RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Daniel Tianfang Ge
- RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Zhao Zhang
- RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
| | - Phillip D Zamore
- RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
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97
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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: 2.2] [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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98
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Jin Y, Tam OH, Paniagua E, Hammell M. TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets. Bioinformatics 2015. [PMID: 26206304 DOI: 10.1093/bioinformatics/btv422] [Citation(s) in RCA: 405] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Most RNA-seq data analysis software packages are not designed to handle the complexities involved in properly apportioning short sequencing reads to highly repetitive regions of the genome. These regions are often occupied by transposable elements (TEs), which make up between 20 and 80% of eukaryotic genomes. They can contribute a substantial portion of transcriptomic and genomic sequence reads, but are typically ignored in most analyses. RESULTS Here, we present a method and software package for including both gene- and TE-associated ambiguously mapped reads in differential expression analysis. Our method shows improved recovery of TE transcripts over other published expression analysis methods, in both synthetic data and qPCR/NanoString-validated published datasets. AVAILABILITY AND IMPLEMENTATION The source code, associated GTF files for TE annotation, and testing data are freely available at http://hammelllab.labsites.cshl.edu/software. CONTACT mhammell@cshl.edu. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ying Jin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Oliver H Tam
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Eric Paniagua
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Molly Hammell
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
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99
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Poplawski A, Marini F, Hess M, Zeller T, Mazur J, Binder H. Systematically evaluating interfaces for RNA-seq analysis from a life scientist perspective. Brief Bioinform 2015; 17:213-23. [PMID: 26108229 DOI: 10.1093/bib/bbv036] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Indexed: 11/13/2022] Open
Abstract
RNA-sequencing (RNA-seq) has become an established way for measuring gene expression in model organisms and humans. While methods development for refining the corresponding data processing and analysis pipeline is ongoing, protocols for typical steps have been proposed and are widely used. Several user interfaces have been developed for making such analysis steps accessible to life scientists without extensive knowledge of command line tools. We performed a systematic search and evaluation of such interfaces to investigate to what extent these can indeed facilitate RNA-seq data analysis. We found a total of 29 open source interfaces, and six of the more widely used interfaces were evaluated in detail. Central criteria for evaluation were ease of configuration, documentation, usability, computational demand and reporting. No interface scored best in all of these criteria, indicating that the final choice will depend on the specific perspective of users and the corresponding weighting of criteria. Considerable technical hurdles had to be overcome in our evaluation. For many users, this will diminish potential benefits compared with command line tools, leaving room for future improvement of interfaces.
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100
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Han BW, Wang W, Li C, Weng Z, Zamore PD. Noncoding RNA. piRNA-guided transposon cleavage initiates Zucchini-dependent, phased piRNA production. Science 2015; 348:817-21. [PMID: 25977554 PMCID: PMC4545291 DOI: 10.1126/science.aaa1264] [Citation(s) in RCA: 281] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PIWI-interacting RNAs (piRNAs) protect the animal germ line by silencing transposons. Primary piRNAs, generated from transcripts of genomic transposon "junkyards" (piRNA clusters), are amplified by the "ping-pong" pathway, yielding secondary piRNAs. We report that secondary piRNAs, bound to the PIWI protein Ago3, can initiate primary piRNA production from cleaved transposon RNAs. The first ~26 nucleotides (nt) of each cleaved RNA becomes a secondary piRNA, but the subsequent ~26 nt become the first in a series of phased primary piRNAs that bind Piwi, allowing piRNAs to spread beyond the site of RNA cleavage. The ping-pong pathway increases only the abundance of piRNAs, whereas production of phased primary piRNAs from cleaved transposon RNAs adds sequence diversity to the piRNA pool, allowing adaptation to changes in transposon sequence.
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Affiliation(s)
- Bo W Han
- RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA. Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Wei Wang
- RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA. Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA. Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Chengjian Li
- RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA. Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Zhiping Weng
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA. Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
| | - Phillip D Zamore
- RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA. Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
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