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Munafò M, Lawless VR, Passera A, MacMillan S, Bornelöv S, Haussmann IU, Soller M, Hannon GJ, Czech B. Channel nuclear pore complex subunits are required for transposon silencing in Drosophila. eLife 2021; 10:e66321. [PMID: 33856346 PMCID: PMC8133776 DOI: 10.7554/elife.66321] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 04/14/2021] [Indexed: 12/21/2022] Open
Abstract
The nuclear pore complex (NPC) is the principal gateway between nucleus and cytoplasm that enables exchange of macromolecular cargo. Composed of multiple copies of ~30 different nucleoporins (Nups), the NPC acts as a selective portal, interacting with factors which individually license passage of specific cargo classes. Here we show that two Nups of the inner channel, Nup54 and Nup58, are essential for transposon silencing via the PIWI-interacting RNA (piRNA) pathway in the Drosophila ovary. In ovarian follicle cells, loss of Nup54 and Nup58 results in compromised piRNA biogenesis exclusively from the flamenco locus, whereas knockdowns of other NPC subunits have widespread consequences. This provides evidence that some Nups can acquire specialised roles in tissue-specific contexts. Our findings consolidate the idea that the NPC has functions beyond simply constituting a barrier to nuclear/cytoplasmic exchange as genomic loci subjected to strong selective pressure can exploit NPC subunits to facilitate their expression.
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Affiliation(s)
- Marzia Munafò
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Victoria R Lawless
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Alessandro Passera
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Serena MacMillan
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Susanne Bornelöv
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Irmgard U Haussmann
- Department of Life Science, Faculty of Health, Education and Life Sciences, Birmingham City UniversityBirminghamUnited Kingdom
- School of Biosciences, College of Life and Environmental Sciences, University of BirminghamBirminghamUnited Kingdom
| | - Matthias Soller
- School of Biosciences, College of Life and Environmental Sciences, University of BirminghamBirminghamUnited Kingdom
- Birmingham Center for Genome Biology, University of BirminghamBirminghamUnited Kingdom
| | - Gregory J Hannon
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Benjamin Czech
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
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2
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Zorn P, Misiak D, Gekle M, Köhn M. Identification and initial characterization of POLIII-driven transcripts by msRNA-sequencing. RNA Biol 2021; 18:1807-1817. [PMID: 33404286 PMCID: PMC8583065 DOI: 10.1080/15476286.2020.1871216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Non-coding RNAs (ncRNAs) are powerful regulators of gene expression but medium-sized (50–300 nts in length) ncRNAs (msRNAs) are barely picked-up precisely by RNA-sequencing. Here we describe msRNA-sequencing (msRNAseq), a modified protocol that associated with a computational analyses pipeline identified about ~1800 msRNA loci, including over 300 putatively novel msRNAs, in human and murine cells. We focused on the identification and initial characterization of three POLIII-derived transcripts. The validation of these uncharacterized msRNAs identified an ncRNA in antisense orientation from the POLR3E locus transcribed by POLIII. This msRNA, termed POLAR (POLR3E Antisense RNA), has a strikingly short half-life, localizes to paraspeckles (PSPs) and associates with PSP-associated proteins indicating that msRNAseq identifies functional msRNAs. Thus, our analyses will pave the way for analysing the roles of msRNAs in cells, development and diseases.
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Affiliation(s)
| | - Danny Misiak
- Institute of Molecular Medicine, University of Halle-Wittenberg, Halle (Saale), Germany
| | - Michael Gekle
- Julius-Bernstein-Institute of Physiology, University of Halle-Wittenberg, Germany
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3
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Grentzinger T, Oberlin S, Schott G, Handler D, Svozil J, Barragan-Borrero V, Humbert A, Duharcourt S, Brennecke J, Voinnet O. A universal method for the rapid isolation of all known classes of functional silencing small RNAs. Nucleic Acids Res 2020; 48:e79. [PMID: 32496553 PMCID: PMC7641303 DOI: 10.1093/nar/gkaa472] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 05/05/2020] [Accepted: 05/25/2020] [Indexed: 01/30/2023] Open
Abstract
Diverse classes of silencing small (s)RNAs operate via ARGONAUTE-family proteins within RNA-induced-silencing-complexes (RISCs). Here, we have streamlined various embodiments of a Q-sepharose-based RISC-purification method that relies on conserved biochemical properties of all ARGONAUTEs. We show, in multiple benchmarking assays, that the resulting 15-min benchtop extraction procedure allows simultaneous purification of all known classes of RISC-associated sRNAs without prior knowledge of the samples-intrinsic ARGONAUTE repertoires. Optimized under a user-friendly format, the method – coined ‘TraPR’ for Trans-kingdom, rapid, affordable Purification of RISCs – operates irrespectively of the organism, tissue, cell type or bio-fluid of interest, and scales to minute amounts of input material. The method is highly suited for direct profiling of silencing sRNAs, with TraPR-generated sequencing libraries outperforming those obtained via gold-standard procedures that require immunoprecipitations and/or lengthy polyacrylamide gel-selection. TraPR considerably improves the quality and consistency of silencing sRNA sample preparation including from notoriously difficult-to-handle tissues/bio-fluids such as starchy storage roots or mammalian plasma, and regardless of RNA contaminants or RNA degradation status of samples.
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Affiliation(s)
- Thomas Grentzinger
- Department of Biology, Swiss Federal Institute of Technology (ETH), Zürich, 8092, Switzerland
| | - Stefan Oberlin
- Department of Biology, Swiss Federal Institute of Technology (ETH), Zürich, 8092, Switzerland
| | - Gregory Schott
- Department of Biology, Swiss Federal Institute of Technology (ETH), Zürich, 8092, Switzerland
| | - Dominik Handler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, 1030, Austria
| | - Julia Svozil
- Department of Biology, Swiss Federal Institute of Technology (ETH), Zürich, 8092, Switzerland
| | | | - Adeline Humbert
- Institut Jacques Monod, Université de Paris, CNRS, Paris, 75013, France
| | - Sandra Duharcourt
- Institut Jacques Monod, Université de Paris, CNRS, Paris, 75013, France
| | - Julius Brennecke
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, 1030, Austria
| | - Olivier Voinnet
- Department of Biology, Swiss Federal Institute of Technology (ETH), Zürich, 8092, Switzerland
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4
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Liu W, Guo J, Luo J, Ren Q, Chen Z, Qu Z, Wu Z, Ni J, Xu X, Rashid M, Luo J, Yin H, Yang Z, Liu G. Analysis of microRNA expression profiles dynamic in different life stages of Haemaphysalis longicornis ticks by deep sequencing of small RNA libraries. Ticks Tick Borne Dis 2020; 11:101427. [PMID: 32370927 DOI: 10.1016/j.ttbdis.2020.101427] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 03/18/2020] [Accepted: 03/23/2020] [Indexed: 10/24/2022]
Abstract
The three-host tick Haemaphysalis longicornis is an obligate blood-sucking ectoparasite. In life-stage transitions, microRNAs (miRNAs) show a variety of expression changes. To investigate these changes, deep sequencing technology was applied to identify the conserved and potentially novel miRNAs expressed during the different life stages of H. longicornis. Total RNA from eggs, unfed larvae, unfed nymphs and unfed adults was extracted for deep sequence analysis. Deep sequencing on a Hiseq 4000 generated a total of 111,192,069 reads, grouped into four small RNA (sRNA) libraries, one for each of the four developmental stages of H. longicornis. Among these sequences, 78 conserved and 55 potentially novel miRNAs were identified, including stage-specific and differentially expressed miRNAs. Gene ontology (GO) analysis indicated significantly enriched GO terms related to cell proliferation and differentiation, including specific terms for the processes of development, growth, metabolism, regulation of biological functions, reproduction, and membrane enzyme regular activity. Kyoto Encyclopedia of Gene and Genomes (KEGG) analysis revealed a significant enrichment of the insulin, notch, Hippo, and Wnt signaling pathways for growth and development. Our data highlight the abundance of miRNA changes (conserved and potentially novel) in the different life stages of H. longicornis. In particular, stage-specific miRNAs, as observed, are essential regulators for the development of H. longicornis.
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Affiliation(s)
- Wenge Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China; College of Animal Veterinary Medicine, Northwest A & F University, Yangling, China.
| | - Junhui Guo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China.
| | - Jin Luo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China.
| | - Qiaoyun Ren
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China.
| | - Ze Chen
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China.
| | - Zhiqiang Qu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China.
| | - Zegong Wu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China.
| | - Jun Ni
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China.
| | - Xiaofeng Xu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China.
| | - Muhammad Rashid
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China.
| | - Jianxun Luo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China.
| | - Hong Yin
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.
| | - Zengqi Yang
- College of Animal Veterinary Medicine, Northwest A & F University, Yangling, China.
| | - Guangyuan Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China.
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5
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Kneuss E, Munafò M, Eastwood EL, Deumer US, Preall JB, Hannon GJ, Czech B. Specialization of the Drosophila nuclear export family protein Nxf3 for piRNA precursor export. Genes Dev 2019; 33:1208-1220. [PMID: 31416967 PMCID: PMC6719614 DOI: 10.1101/gad.328690.119] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 07/15/2019] [Indexed: 12/29/2022]
Abstract
The PIWI-interacting RNA (piRNA) pathway is a conserved small RNA-based immune system that protects animal germ cell genomes from the harmful effects of transposon mobilization. In Drosophila ovaries, most piRNAs originate from dual-strand clusters, which generate piRNAs from both genomic strands. Dual-strand clusters use noncanonical transcription mechanisms. Although transcribed by RNA polymerase II, cluster transcripts lack splicing signatures and poly(A) tails. mRNA processing is important for general mRNA export mediated by nuclear export factor 1 (Nxf1). Although UAP56, a component of the transcription and export complex, has been implicated in piRNA precursor export, it remains unknown how dual-strand cluster transcripts are specifically targeted for piRNA biogenesis by export from the nucleus to cytoplasmic processing centers. Here we report that dual-strand cluster transcript export requires CG13741/Bootlegger and the Drosophila nuclear export factor family protein Nxf3. Bootlegger is specifically recruited to piRNA clusters and in turn brings Nxf3. We found that Nxf3 specifically binds to piRNA precursors and is essential for their export to piRNA biogenesis sites, a process that is critical for germline transposon silencing. Our data shed light on how dual-strand clusters compensate for a lack of canonical features of mature mRNAs to be specifically exported via Nxf3, ensuring proper piRNA production.
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Affiliation(s)
- Emma Kneuss
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Marzia Munafò
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Evelyn L Eastwood
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Undine-Sophie Deumer
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Jonathan B Preall
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Gregory J Hannon
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Benjamin Czech
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
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6
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Munafò M, Manelli V, Falconio FA, Sawle A, Kneuss E, Eastwood EL, Seah JWE, Czech B, Hannon GJ. Daedalus and Gasz recruit Armitage to mitochondria, bringing piRNA precursors to the biogenesis machinery. Genes Dev 2019; 33:844-856. [PMID: 31123065 PMCID: PMC6601507 DOI: 10.1101/gad.325662.119] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 04/16/2019] [Indexed: 11/28/2022]
Abstract
The Piwi-interacting RNA (piRNA) pathway is a small RNA-based immune system that silences mobile genetic elements in animal germlines. piRNA biogenesis requires a specialized machinery that converts long single-stranded precursors into small RNAs of ∼25-nucleotides in length. This process involves factors that operate in two different subcellular compartments: the nuage/Yb body and mitochondria. How these two sites communicate to achieve accurate substrate selection and efficient processing remains unclear. Here, we investigate a previously uncharacterized piRNA biogenesis factor, Daedalus (Daed), that is located on the outer mitochondrial membrane. Daed is essential for Zucchini-mediated piRNA production and the correct localization of the indispensable piRNA biogenesis factor Armitage (Armi). We found that Gasz and Daed interact with each other and likely provide a mitochondrial "anchoring platform" to ensure that Armi is held in place, proximal to Zucchini, during piRNA processing. Our data suggest that Armi initially identifies piRNA precursors in nuage/Yb bodies in a manner that depends on Piwi and then moves to mitochondria to present precursors to the mitochondrial biogenesis machinery. These results represent a significant step in understanding a critical aspect of transposon silencing; namely, how RNAs are chosen to instruct the piRNA machinery in the nature of its silencing targets.
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Affiliation(s)
- Marzia Munafò
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Vera Manelli
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Federica A Falconio
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Ashley Sawle
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Emma Kneuss
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Evelyn L Eastwood
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Jun Wen Eugene Seah
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Benjamin Czech
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Gregory J Hannon
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
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7
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Yu J, Yu Y, Li Q, Chen M, Shen H, Zhang R, Song M, Hu W. Comprehensive analysis of miRNA profiles reveals the role of Schistosoma japonicum miRNAs at different developmental stages. Vet Res 2019; 50:23. [PMID: 30947738 PMCID: PMC6449929 DOI: 10.1186/s13567-019-0642-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 02/19/2019] [Indexed: 12/13/2022] Open
Abstract
Schistosomiasis is an important zoonotic disease affecting up to 40 kinds of animals and 250 million people. It has been reported that the miRNAs play a role in the metabolism, differentiation, development and reproduction in many organisms. However, the roles of miRNAs regulating the development, maturation and production in schistosome in both females and males remains unclear. Here we present the dynamic transcriptome analysis of all 79 known Schistosoma japonicum miRNAs from pairing to production, including 14 days post-infection (dpi), 16, 18, 20, 22, 24, 26, 28 dpi female and male, by small RNA sequencing. The miRNA expression profiles showed time-related characteristics in male and female from paring to production, which could be clustered into three patterns, characterized by pairing stage highly expressed (cluster 1), maturating stage highly expressed (cluster 2), and egg producing stage highly expressed (cluster 3). The enrichment of miRNA cluster targeted genes in female and male were distinctly different. Network analysis of miRNAs and their target regulation showed that cluster 1 had 15 miRNAs involved in the regulation of interaction, communication, immune response in female–male and parasite–host. The other 11 miRNAs were involved in gender differentiation and the meiotic cell cycle process. In cluster 2, 11 miRNAs were involved in development and sexual maturation. In cluster 3, 45 miRNAs possibly regulate metabolism and synthesis of the substance for egg production. Analysis of the miRNA regulation network would contribute to understanding the molecular mechanism in S. japonicum development and egg production.
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Affiliation(s)
- Jie Yu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China.,State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ying Yu
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Qing Li
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Muxin Chen
- Joint Research Laboratory of Genetics and Ecology on Parasite-host Interaction, Chinese Center for Disease Control and Prevention & Fudan University, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology Ministry of Health, National Institute of Parasitic Diseases, Shanghai, 200025, China
| | - Haimo Shen
- Joint Research Laboratory of Genetics and Ecology on Parasite-host Interaction, Chinese Center for Disease Control and Prevention & Fudan University, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology Ministry of Health, National Institute of Parasitic Diseases, Shanghai, 200025, China
| | - RuiXiang Zhang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Mingxin Song
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China. .,Heilongjiang Key Laboratory for Zoonosis, Harbin, 150030, China.
| | - Wei Hu
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438, China. .,Joint Research Laboratory of Genetics and Ecology on Parasite-host Interaction, Chinese Center for Disease Control and Prevention & Fudan University, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology Ministry of Health, National Institute of Parasitic Diseases, Shanghai, 200025, China.
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8
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Wang R, Xu J, Liu H, Zhao Z. Peripheral leukocyte microRNAs as novel biomarkers for COPD. Int J Chron Obstruct Pulmon Dis 2017; 12:1101-1112. [PMID: 28435243 PMCID: PMC5388252 DOI: 10.2147/copd.s130416] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
COPD is a multifactorial disease caused by environmental determinants as well as genetic risk factors. The prevalence and mortality of COPD continue to increase, and underdiagnosis of COPD remains a critical issue. Previous reports investigated promising microRNAs (miRNAs) to reveal the molecular mechanism for the development of COPD; however, diagnostic and therapeutic markers for COPD have not yet been found. For this study, 20 representative COPD patients were separated into four groups based on increasing severity (A, B, C, and D) and compared to six healthy controls. Small RNA profiles of peripheral leukocytes were differentially expressed miRNAs (analyzed via next-generation sequencing) were validated via quantitative reverse transcriptase-polymerase chain reaction. Compared to healthy controls, 19 differentially expressed miRNAs were found in COPD patients. For all COPD groups, miR-3177-3p was downregulated, while 17 miRNAs were upregulated. Furthermore, the results revealed 21 differentially expressed miRNAs, of which miR-183-5p was continually downregulated from A to B to D. Between respective bronchodilator reversibility positive and negative groups of COPD different groups (A, B, C, and D), 10 miRNAs were differentially expressed, while miR-100-5p was upregulated in the negative groups. In conclusion, miR-106b-5p, miR-125a-5p, miR-183-5p, and miR-100-5p are central for the development of COPD. The severity of COPD was attenuated by miR-106b-5p, thus suggesting this miRNA as potential target for disease treatment.
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Affiliation(s)
- Ruiying Wang
- Department of Respiratory, Shanxi Dayi Hospital Affiliated to Shanxi Medical University, Taiyuan, Shanxi, People's Republic of China
| | - Jianying Xu
- Department of Respiratory, Shanxi Dayi Hospital Affiliated to Shanxi Medical University, Taiyuan, Shanxi, People's Republic of China
| | - Hu Liu
- Department of Respiratory, Shanxi Dayi Hospital Affiliated to Shanxi Medical University, Taiyuan, Shanxi, People's Republic of China
| | - Zhiping Zhao
- Department of Respiratory, Shanxi Dayi Hospital Affiliated to Shanxi Medical University, Taiyuan, Shanxi, People's Republic of China
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9
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Abstract
In the past decade, deep-sequencing approaches have greatly improved our knowledge of the genome's potential and have become a crucial milestone for new discoveries in genomics. Transcription is the first step of gene expression; therefore, the detection and measurement of transcription rates is of great interest. Here, a detailed protocol for global run-on sequencing (GRO-seq) library preparation from Drosophila ovaries is described. The method relies on rapid isolation of nuclei with halted transcription, then restarting transcription in physiological conditions in the presence of a labeled nucleotide. The newly transcribed nascent RNA is then isolated and cloned using a small RNA cloning protocol. Although it is time-consuming, the global run-on method allows the user to profile the position, orientation and amount of transcriptionally engaged RNA polymerases across the genome, therefore providing a snapshot of genome-wide transcription.
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10
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Kang YJ, Lee T, Lee J, Shim S, Jeong H, Satyawan D, Kim MY, Lee SH. Translational genomics for plant breeding with the genome sequence explosion. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1057-69. [PMID: 26269219 PMCID: PMC5042036 DOI: 10.1111/pbi.12449] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 07/04/2015] [Accepted: 07/10/2015] [Indexed: 05/22/2023]
Abstract
The use of next-generation sequencers and advanced genotyping technologies has propelled the field of plant genomics in model crops and plants and enhanced the discovery of hidden bridges between genotypes and phenotypes. The newly generated reference sequences of unstudied minor plants can be annotated by the knowledge of model plants via translational genomics approaches. Here, we reviewed the strategies of translational genomics and suggested perspectives on the current databases of genomic resources and the database structures of translated information on the new genome. As a draft picture of phenotypic annotation, translational genomics on newly sequenced plants will provide valuable assistance for breeders and researchers who are interested in genetic studies.
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Affiliation(s)
- Yang Jae Kang
- Department of Plant Science Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Taeyoung Lee
- Department of Plant Science Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Jayern Lee
- Department of Plant Science Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Sangrea Shim
- Department of Plant Science Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Haneul Jeong
- Department of Plant Science Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Dani Satyawan
- Department of Plant Science Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
- Indonesian Center for Agricultural Biotechnology and Genomic resources Research and Development (ICABIOGRAD-IAARD), Bogor, Indonesia
| | - Moon Young Kim
- Department of Plant Science Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Suk-Ha Lee
- Department of Plant Science Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
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