201
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MicroRNA-Based Drugs for Brain Tumors. Trends Cancer 2018; 4:222-238. [PMID: 29506672 DOI: 10.1016/j.trecan.2017.12.008] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 12/18/2017] [Accepted: 12/24/2017] [Indexed: 12/11/2022]
Abstract
MicroRNAs (miRNAs) are key regulatory elements encoded by the genome. A single miRNA can downregulate the expression of multiple genes involved in diverse functions. Because cancer is a disease with multiple gene aberrations, developing novel approaches to identify and modulate miRNA pathways may result in a breakthrough for cancer treatment. With a special focus on glioblastoma (GBM), this review provides an up-to-date summary of miRNA biogenesis, the role of miRNA in cancer resistance, and essential tools for modulating miRNA expression, as well as of clinically promising RNAi delivery systems and how they can be adapted for therapy.
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202
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Ma Y, Liu S, Wang Y, Zhao Y, Huang Y, Zhong L, Guan Z, Zhang L, Yang Z. Isonucleotide incorporation into middle and terminal siRNA duplexes exhibits high gene silencing efficacy and nuclease resistance. Org Biomol Chem 2018; 15:5161-5170. [PMID: 28585968 DOI: 10.1039/c7ob01065f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this study, we introduced a pair of nucleotide enantiomers, d-/l-isonucleotides (d-/l-isoNA), to examine the interactions between siRNAs and their related proteins. The serum stability and gene-silencing activity of the modified siRNAs were systematically evaluated. Gene-silencing activity had a site-specific effect, and the incorporation of a single d-isoNA at the 8th position (counting from the 5'-terminus) in the antisense strand improved the gene-silencing activity by improving RISC loading and affecting the movement of the PIWI domain. d-isoNA incorporated at the terminus of siRNA including the 2nd position in the antisense strand and 3'-overhangs in the sense strand, especially the latter, enhanced nuclease resistance and prolonged the silencing retention time. In addition, l-isoNA incorporation into the middle of the sense strand enhanced activity. These results provide a chemical strategy for the modulation of siRNA gene-silencing activity and nuclease resistance.
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Affiliation(s)
- Yuan Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China.
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203
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Wu Q, Ferry QRV, Baeumler TA, Michaels YS, Vitsios DM, Habib O, Arnold R, Jiang X, Maio S, Steinkraus BR, Tapia M, Piazza P, Xu N, Holländer GA, Milne TA, Kim JS, Enright AJ, Bassett AR, Fulga TA. In situ functional dissection of RNA cis-regulatory elements by multiplex CRISPR-Cas9 genome engineering. Nat Commun 2017; 8:2109. [PMID: 29235467 PMCID: PMC5727397 DOI: 10.1038/s41467-017-00686-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 07/19/2017] [Indexed: 12/21/2022] Open
Abstract
RNA regulatory elements (RREs) are an important yet relatively under-explored facet of gene regulation. Deciphering the prevalence and functional impact of this post-transcriptional control layer requires technologies for disrupting RREs without perturbing cellular homeostasis. Here we describe genome-engineering based evaluation of RNA regulatory element activity (GenERA), a clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 platform for in situ high-content functional analysis of RREs. We use GenERA to survey the entire regulatory landscape of a 3′UTR, and apply it in a multiplex fashion to analyse combinatorial interactions between sets of miRNA response elements (MREs), providing strong evidence for cooperative activity. We also employ this technology to probe the functionality of an entire MRE network under cellular homeostasis, and show that high-resolution analysis of the GenERA dataset can be used to extract functional features of MREs. This study provides a genome editing-based multiplex strategy for direct functional interrogation of RNA cis-regulatory elements in a native cellular environment. RNA regulatory elements (RREs) are important post-transcriptional control features but studying them requires disrupting their activity without disturbing cellular homeostasis. Here the authors present GenERA, a CRISPR-Cas9 screening platform of in situ analysis of native RREs.
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Affiliation(s)
- Qianxin Wu
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK.,Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Quentin R V Ferry
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Toni A Baeumler
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Yale S Michaels
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Dimitrios M Vitsios
- European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Omer Habib
- Center for Genome Engineering, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
| | - Roland Arnold
- Molecular and Population Genetics Laboratory, Oxford Centre for Cancer Gene Research, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Xiaowei Jiang
- Molecular and Population Genetics Laboratory, Oxford Centre for Cancer Gene Research, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Stefano Maio
- Weatherall Institute of Molecular Medicine, Developmental Immunology, University of Oxford, Oxford, OX3 9DS, UK
| | - Bruno R Steinkraus
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Marta Tapia
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, NIHR Oxford Biomedical Research Centre Programme, University of Oxford, Oxford, OX3 9DS, UK
| | - Paolo Piazza
- Wellcome Trust Centre for Human Genetics, Oxford, OX3 7BN, UK
| | - Ni Xu
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Georg A Holländer
- Weatherall Institute of Molecular Medicine, Developmental Immunology, University of Oxford, Oxford, OX3 9DS, UK.,Department of Biomedicine, Laboratory of Paediatric Immunology, University of Basel, CH-4058, Basel, Switzerland
| | - Thomas A Milne
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, NIHR Oxford Biomedical Research Centre Programme, University of Oxford, Oxford, OX3 9DS, UK
| | - Jin-Soo Kim
- Center for Genome Engineering, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea.,Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea
| | - Anton J Enright
- European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Andrew R Bassett
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RF, UK.,Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Tudor A Fulga
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK.
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204
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Sakakibara K, Siomi MC. The PIWI-Interacting RNA Molecular Pathway: Insights From Cultured Silkworm Germline Cells. Bioessays 2017; 40. [DOI: 10.1002/bies.201700068] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 09/26/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Kazuhiro Sakakibara
- Department of Biological Sciences; Graduate School of Science; The University of Tokyo; Tokyo 113-0032 Japan
| | - Mikiko C. Siomi
- Department of Biological Sciences; Graduate School of Science; The University of Tokyo; Tokyo 113-0032 Japan
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205
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Herrera-Carrillo E, Harwig A, Berkhout B. Influence of the loop size and nucleotide composition on AgoshRNA biogenesis and activity. RNA Biol 2017; 14:1559-1569. [PMID: 28569591 PMCID: PMC5785215 DOI: 10.1080/15476286.2017.1328349] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Short hairpin RNAs (shRNAs) are widely used for gene silencing by the RNA interference (RNAi) mechanism. The shRNA precursor is processed by the Dicer enzyme into active small interfering RNAs (siRNAs) that subsequently target a complementary mRNA for cleavage by the Argonaute 2 (Ago2) complex. Recent evidence indicates that shRNAs with a relatively short basepaired stem bypass Dicer and are instead processed by Ago2. We termed these molecules AgoshRNAs as both processing and silencing steps are mediated by Ago2 and proposed rules for the design of effective AgoshRNA molecules. Active and non-cytotoxic AgoshRNAs against HIV-1 RNA were generated, but their silencing activity was generally reduced compared with the matching shRNAs. Thus, further optimization of the AgoshRNA design is needed. In this study, we evaluated the importance of the single-stranded loop, in particular its size and nucleotide sequence, in AgoshRNA-mediated silencing. We document that the pyrimidine/purine content is important for AgoshRNA-mediated silencing activity.
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Affiliation(s)
- Elena Herrera-Carrillo
- a Laboratory of Experimental Virology, Department of Medical Microbiology , Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam , AZ Amsterdam , the Netherlands
| | - Alex Harwig
- a Laboratory of Experimental Virology, Department of Medical Microbiology , Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam , AZ Amsterdam , the Netherlands
| | - Ben Berkhout
- a Laboratory of Experimental Virology, Department of Medical Microbiology , Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam , AZ Amsterdam , the Netherlands
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206
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Wang Y, Xu YM, Zou YQ, Lin J, Huang B, Liu J, Li J, Zhang J, Yang WM, Min QH, Li SQ, Gao QF, Sun F, Chen QG, Zhang L, Jiang YH, Deng LB, Wang XZ. Identification of differential expressed PE exosomal miRNA in lung adenocarcinoma, tuberculosis, and other benign lesions. Medicine (Baltimore) 2017; 96:e8361. [PMID: 29095265 PMCID: PMC5682784 DOI: 10.1097/md.0000000000008361] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Pleural effusion (PE) is a common clinical complication of many pulmonary and systemic diseases, including lung cancer and tuberculosis. Nevertheless, there is no clinical effective biomarker to identify the cause of PE. We attempted to investigate differential expressed exosomal miRNAs in PEs of lung adenocarcinoma (APE), tuberculous (TPE), and other benign lesions (NPE) by using deep sequencing and quantitative polymerase chain reaction (qRT-PCR). As a result, 171 differentiated miRNAs were observed in 3 groups of PEs, and 11 significantly differentiated exosomal miRNAs were validated by qRT-PCR. We identified 9 miRNAs, including miR-205-5p, miR-483-5p, miR-375, miR-200c-3p, miR-429, miR-200b-3p, miR-200a-3p, miR-203a-3p, and miR-141-3p which were preferentially represented in exosomes derived from APE when compared with TPE or NPE, while 3 miRNAs, including miR-148a-3p, miR-451a, and miR-150-5p, were differentially expressed between TPE and NPE. These different miRNAs profiles may hold promise as biomarkers for differential diagnosis of PEs with more validation based on larger cohorts.
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Affiliation(s)
- Yan Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Jiangxi
- Department of Hematology, The Affiliated Hospital of Guizhou Medical University, Guizhou
| | - Yan-Mei Xu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Jiangxi
| | - Ye-Qing Zou
- The Key Laboratory of Molecular Medicine, The Second Affiliated Hospital of Nanchang University
| | - Jin Lin
- Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Jiangxi
| | - Bo Huang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Jiangxi
| | - Jing Liu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Jiangxi
| | - Jing Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University
| | - Jing Zhang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Jiangxi
| | - Wei-Ming Yang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Jiangxi
| | - Qing-Hua Min
- Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Jiangxi
| | - Shu-Qi Li
- Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Jiangxi
| | - Qiu-Fang Gao
- Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Jiangxi
| | - Fan Sun
- Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Jiangxi
| | - Qing-Gen Chen
- Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Jiangxi
| | - Lei Zhang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Jiangxi
| | - Yu-Huan Jiang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Jiangxi
| | - Li-Bin Deng
- Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Jiangxi
- Institute of Translational Medicine, Nanchang University, Jiangxi, China
| | - Xiao-Zhong Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Jiangxi
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207
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Lozada-Delgado EL, Grafals-Ruiz N, Vivas-Mejía PE. RNA interference for glioblastoma therapy: Innovation ladder from the bench to clinical trials. Life Sci 2017; 188:26-36. [PMID: 28864225 PMCID: PMC5617340 DOI: 10.1016/j.lfs.2017.08.027] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/24/2017] [Accepted: 08/28/2017] [Indexed: 02/07/2023]
Abstract
Glioblastoma multiforme (GBM) is the most common and deadliest type of primary brain tumor with a prognosis of 14months after diagnosis. Current treatment for GBM patients includes "total" tumor resection, temozolomide-based chemotherapy, radiotherapy or a combination of these options. Although, several targeted therapies, gene therapy, and immunotherapy are currently in the clinic and/or in clinical trials, the overall survival of GBM patients has hardly improved over the last two decades. Therefore, novel multitarget modalities are urgently needed. Recently, RNA interference (RNAi) has emerged as a novel strategy for the treatment of most cancers, including GBM. RNAi-based therapies consist of using small RNA oligonucleotides to regulate protein expression at the post-transcriptional level. Despite the therapeutic potential of RNAi molecules, systemic limitations including short circulatory stability and low release into the tumor tissue have halted their progress to the clinic. The effective delivery of RNAi molecules through the blood-brain barrier (BBB) represents an additional challenge. This review focuses on connecting the translational process of RNAi-based therapies from in vitro evidence to pre-clinical studies. We delineate the effect of RNAi in GBM cell lines, describe their effectiveness in glioma mouse models, and compare the proposed drug carriers for the effective transport of RNAi molecules through the BBB to reach the tumor in the brain. Furthermore, we summarize the most important obstacles to overcome before RNAi-based therapy becomes a reality for GBM treatment.
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Affiliation(s)
- Eunice L Lozada-Delgado
- Department of Biology, University of Puerto Rico, Rio Piedras Campus, San Juan, PR 00927, United States; Comprehensive Cancer Center, University of Puerto Rico, Medical Sciences Campus, San Juan, PR 00935, United States; Department of Biochemistry, University of Puerto Rico, Medical Sciences Campus, San Juan, PR 00935, United States
| | - Nilmary Grafals-Ruiz
- Comprehensive Cancer Center, University of Puerto Rico, Medical Sciences Campus, San Juan, PR 00935, United States; Department of Physiology, University of Puerto Rico, Medical Sciences Campus, San Juan, PR 00935, United States
| | - Pablo E Vivas-Mejía
- Comprehensive Cancer Center, University of Puerto Rico, Medical Sciences Campus, San Juan, PR 00935, United States; Department of Biochemistry, University of Puerto Rico, Medical Sciences Campus, San Juan, PR 00935, United States.
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208
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Herrera-Carrillo E, Berkhout B. Dicer-independent processing of small RNA duplexes: mechanistic insights and applications. Nucleic Acids Res 2017; 45:10369-10379. [PMID: 28977573 PMCID: PMC5737282 DOI: 10.1093/nar/gkx779] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 08/24/2017] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) play a pivotal role in the regulation of cellular gene expression via the conserved RNA interference (RNAi) mechanism. Biogenesis of the unusual miR-451 does not require Dicer. This molecule is instead processed by the Argonaute 2 (Ago2) enzyme. Similarly, unconventional short hairpin RNA (shRNA) molecules have been designed as miR-451 mimics that rely exclusively on Ago2 for maturation. We will review recent progress made in the understanding of this alternative processing route. Next, we describe different Dicer-independent shRNA designs that have been developed and discuss their therapeutic advantages and disadvantages. As an example, we will present the route towards development of a durable gene therapy against HIV-1.
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Affiliation(s)
- Elena Herrera-Carrillo
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, the Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, the Netherlands
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209
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Burke JM, Kincaid RP, Aloisio F, Welch N, Sullivan CS. Expression of short hairpin RNAs using the compact architecture of retroviral microRNA genes. Nucleic Acids Res 2017; 45:e154. [PMID: 28973449 PMCID: PMC5622367 DOI: 10.1093/nar/gkx653] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 07/19/2017] [Indexed: 12/03/2022] Open
Abstract
Short hairpin RNAs (shRNAs) are effective in generating stable repression of gene expression. RNA polymerase III (RNAP III) type III promoters (U6 or H1) are typically used to drive shRNA expression. While useful for some knockdown applications, the robust expression of U6/H1-driven shRNAs can induce toxicity and generate heterogeneous small RNAs with undesirable off-target effects. Additionally, typical U6/H1 promoters encompass the majority of the ∼270 base pairs (bp) of vector space required for shRNA expression. This can limit the efficacy and/or number of delivery vector options, particularly when delivery of multiple gene/shRNA combinations is required. Here, we develop a compact shRNA (cshRNA) expression system based on retroviral microRNA (miRNA) gene architecture that uses RNAP III type II promoters. We demonstrate that cshRNAs coded from as little as 100 bps of total coding space can precisely generate small interfering RNAs (siRNAs) that are active in the RNA-induced silencing complex (RISC). We provide an algorithm with a user-friendly interface to design cshRNAs for desired target genes. This cshRNA expression system reduces the coding space required for shRNA expression by >2-fold as compared to the typical U6/H1 promoters, which may facilitate therapeutic RNAi applications where delivery vector space is limiting.
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Affiliation(s)
- James M Burke
- The University of Texas at Austin, Institute for Cellular and Molecular Biology, Center for Synthetic and Systems Biology, Center for Infectious Disease and Department Molecular Biosciences, 1 University Station A5000, Austin, TX 78712-0162, USA
| | - Rodney P Kincaid
- The University of Texas at Austin, Institute for Cellular and Molecular Biology, Center for Synthetic and Systems Biology, Center for Infectious Disease and Department Molecular Biosciences, 1 University Station A5000, Austin, TX 78712-0162, USA
| | - Francesca Aloisio
- The University of Texas at Austin, Institute for Cellular and Molecular Biology, Center for Synthetic and Systems Biology, Center for Infectious Disease and Department Molecular Biosciences, 1 University Station A5000, Austin, TX 78712-0162, USA
| | - Nicole Welch
- The University of Texas at Austin, Institute for Cellular and Molecular Biology, Center for Synthetic and Systems Biology, Center for Infectious Disease and Department Molecular Biosciences, 1 University Station A5000, Austin, TX 78712-0162, USA
| | - Christopher S Sullivan
- The University of Texas at Austin, Institute for Cellular and Molecular Biology, Center for Synthetic and Systems Biology, Center for Infectious Disease and Department Molecular Biosciences, 1 University Station A5000, Austin, TX 78712-0162, USA
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210
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Muiwo P, Pandey P, Ahmad HM, Ramachandran SS, Bhattacharya A. IsomiR processing during differentiation of myelogenous leukemic cell line K562 by phorbol ester PMA. Gene 2017; 641:172-179. [PMID: 29051025 DOI: 10.1016/j.gene.2017.10.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 05/18/2017] [Accepted: 10/10/2017] [Indexed: 01/28/2023]
Abstract
Chronic myelocytic leukemia cell line K562 undergoes differentiation by phorbol esters to megakaryocytes and we have used this system to understand miRNA processing leading to isomiR generation. PMA treatment significantly altered the production of miRNA in K562 cells. Expression of 24.4% of miRNAs were found to be stimulated whereas expression of 10% miRNAs were inhibited by PMA treatment. Our results suggest that miRNA precursors are processed into isomiRs in a deterministic manner. The relative levels of different isomiRs of a miRNA remained mainly unchanged even after PMA treatment irrespective of overall changes in expression (either up-regulation or down-regulation). However, not all miRNAs behave in the same way, about 7% showed a variation of isomiR profiles after PMA treatment. Most of the later class of miRNAs were found to be oncogenic miRNAs. Further, it was also found that number of isomiRs was independent of abundance of a miRNA. Functional importance of different isomiRs was demonstrated using three different isomiRs of miR-22. Our results showed that different isomiRs could inhibit expression of targets genes with different efficiencies. Our study suggests that the heterogeneity of a miRNA population generated during processing is in general regulated and that variation in the generation of an isomiR can be a functionally important regulatory feature.
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Affiliation(s)
- Pamchui Muiwo
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.
| | - Priyatama Pandey
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
| | - Hafiz M Ahmad
- Department of Molecular Cell and Cancer Biology, Umass Medical School, Worcester, MA, USA.
| | | | - Alok Bhattacharya
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India; School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
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211
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Park JH, Shin SY, Shin C. Non-canonical targets destabilize microRNAs in human Argonautes. Nucleic Acids Res 2017; 45:1569-1583. [PMID: 28119422 PMCID: PMC5389725 DOI: 10.1093/nar/gkx029] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 01/15/2017] [Indexed: 01/06/2023] Open
Abstract
Although much is known about microRNA (miRNA) biogenesis and the mechanism by which miRNAs regulate their targets, little is known about the regulation of miRNA stability. Mature miRNAs are stabilized by binding to Argonaute (Ago) proteins, the core components of the RNA-induced silencing complex (RISC). Recent studies suggest that interactions between miRNAs and their highly complementary target RNAs promote release of miRNAs from Ago proteins, and this in turn can lead to destabilization of miRNAs. However, the physiological triggers of miRNA destabilization with molecular mechanisms remain largely unknown. Here, using an in vitro system that consists of a minimal human Ago2-RISC in HEK293T cell lysates, we sought to understand how miRNAs are destabilized by their targets. Strikingly, we showed that miRNA destabilization is dramatically enhanced by an interaction with seedless, non-canonical targets. We then showed that this process entails not only unloading of miRNAs from Ago, but also 3΄ end destabilization of miRNAs occurred within Ago. Furthermore, our mutation analysis indicates that conformational changes in the hinge region of the Ago PAZ domain are likely to be the main driving force of the miRNA destabilization. Our collective results suggest that non-canonical targets may provide a stability control mechanism in the regulation of miRNAs in humans.
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Affiliation(s)
- June Hyun Park
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sang-Yoon Shin
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea.,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, Republic of Korea
| | - Chanseok Shin
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea.,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, Republic of Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.,Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea
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212
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Herrera-Carrillo E, Gao ZL, Harwig A, Heemskerk MT, Berkhout B. The influence of the 5΄-terminal nucleotide on AgoshRNA activity and biogenesis: importance of the polymerase III transcription initiation site. Nucleic Acids Res 2017; 45:4036-4050. [PMID: 27928054 PMCID: PMC5397164 DOI: 10.1093/nar/gkw1203] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 11/29/2016] [Indexed: 12/21/2022] Open
Abstract
Recent evidence indicates that shRNAs with a relatively short basepaired stem do not require Dicer processing, but instead are processed by the Argonaute 2 protein (Ago2). We named these molecules AgoshRNAs as both their processing and silencing function are mediated by Ago2. This alternative processing yields only a single RNA guide strand, which can avoid off-target effects induced by the passenger strand of regular shRNAs. It is important to understand this alternative processing route in mechanistic detail such that one can design improved RNA reagents. We verified that AgoshRNAs trigger site-specific cleavage of a complementary mRNA. Second, we document the importance of the identity of the 5΄-terminal nucleotide and its basepairing status for AgoshRNA activity. AgoshRNA activity is significantly reduced or even abrogated with C or U at the 5΄-terminal and is enhanced by introduction of a bottom mismatch and 5΄-terminal nucleotide A or G. The 5΄-terminal RNA nucleotide also represents the +1 position of the transcriptional promoter in the DNA, thus further complicating the analysis. Indeed, we report that +1 modification affects the transcriptional efficiency and accuracy of start site selection, with A or G as optimal nucleotide. These combined results allow us to propose general rules for the design and expression of potent AgoshRNA molecules.
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Affiliation(s)
- Elena Herrera-Carrillo
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, the Netherlands
| | - Zong-Liang Gao
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, the Netherlands
| | - Alex Harwig
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, the Netherlands
| | - Matthias T Heemskerk
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, the Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, the Netherlands
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213
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Grimaldi A, Zarone MR, Irace C, Zappavigna S, Lombardi A, Kawasaki H, Caraglia M, Misso G. Non-coding RNAs as a new dawn in tumor diagnosis. Semin Cell Dev Biol 2017; 78:37-50. [PMID: 28765094 DOI: 10.1016/j.semcdb.2017.07.035] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/19/2017] [Accepted: 07/21/2017] [Indexed: 12/12/2022]
Abstract
The current knowledge about non-coding RNAs (ncRNAs) as important regulators of gene expression in both physiological and pathological conditions, has been the main engine for the design of innovative platforms to finalize the pharmacological application of ncRNAs as either therapeutic tools or as molecular biomarkers in cancer. Biochemical alterations of cancer cells are, in fact, largely supported by ncRNA disregulation in the tumor site, which, in turn, reflects the cancer-associated specific modification of circulating ncRNA expression pattern. The aim of this review is to describe the state of the art of pre-clinical and clinical studies that analyze the involvement of miRNAs and lncRNAs in cancer-related processes, such as proliferation, invasion and metastases, giving emphasis to their functional role. A central node of our work has been also the examination of advantages and criticisms correlated with the clinical use of ncRNAs, taking into account the pressing need to refine the profiling methods aimed at identify novel diagnostic and prognostic markers and the request to optimize the delivery of such nucleic acids for a therapeutic use in an imminent future.
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Affiliation(s)
- Anna Grimaldi
- Department of Biochemistry, Biophysics and General Pathology, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy
| | - Mayra Rachele Zarone
- Department of Biochemistry, Biophysics and General Pathology, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy
| | - Carlo Irace
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | - Silvia Zappavigna
- Department of Biochemistry, Biophysics and General Pathology, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy
| | - Angela Lombardi
- Department of Biochemistry, Biophysics and General Pathology, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy
| | - Hiromichi Kawasaki
- Department of Biochemistry, Biophysics and General Pathology, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy; Wakunaga Pharmaceutical Co. LTD, 4-5-36 Miyahara, Yodogawa-ku, Osaka 532-0003 Japan
| | - Michele Caraglia
- Department of Biochemistry, Biophysics and General Pathology, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy.
| | - Gabriella Misso
- Department of Biochemistry, Biophysics and General Pathology, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy.
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214
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Haraszti RA, Roux L, Coles AH, Turanov AA, Alterman JF, Echeverria D, Godinho BM, Aronin N, Khvorova A. 5΄-Vinylphosphonate improves tissue accumulation and efficacy of conjugated siRNAs in vivo. Nucleic Acids Res 2017; 45:7581-7592. [PMID: 28591791 PMCID: PMC5570069 DOI: 10.1093/nar/gkx507] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 05/23/2017] [Accepted: 05/31/2017] [Indexed: 12/20/2022] Open
Abstract
5΄-Vinylphosphonate modification of siRNAs protects them from phosphatases, and improves silencing activity. Here, we show that 5΄-vinylphosphonate confers novel properties to siRNAs. Specifically, 5΄-vinylphosphonate (i) increases siRNA accumulation in tissues, (ii) extends duration of silencing in multiple organs and (iii) protects siRNAs from 5΄-to-3΄ exonucleases. Delivery of conjugated siRNAs requires extensive chemical modifications to achieve stability in vivo. Because chemically modified siRNAs are poor substrates for phosphorylation by kinases, and 5΄-phosphate is required for loading into RNA-induced silencing complex, the synthetic addition of a 5΄-phosphate on a fully modified siRNA guide strand is expected to be beneficial. Here, we show that synthetic phosphorylation of fully modified cholesterol-conjugated siRNAs increases their potency and efficacy in vitro, but when delivered systemically to mice, the 5΄-phosphate is removed within 2 hours. The 5΄-phosphate mimic 5΄-(E)-vinylphosphonate stabilizes the 5΄ end of the guide strand by protecting it from phosphatases and 5΄-to-3΄ exonucleases. The improved stability increases guide strand accumulation and retention in tissues, which significantly enhances the efficacy of cholesterol-conjugated siRNAs and the duration of silencing in vivo. Moreover, we show that 5΄-(E)-vinylphosphonate stabilizes 5΄ phosphate, thereby enabling systemic delivery to and silencing in kidney and heart.
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Affiliation(s)
- Reka A. Haraszti
- RNA Therapeutics Institute, University of Massachusetts Medical School, 01605 Worcester, MA, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, 01605 Worcester, MA, USA
| | - Loic Roux
- RNA Therapeutics Institute, University of Massachusetts Medical School, 01605 Worcester, MA, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, 01605 Worcester, MA, USA
| | - Andrew H. Coles
- RNA Therapeutics Institute, University of Massachusetts Medical School, 01605 Worcester, MA, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, 01605 Worcester, MA, USA
| | - Anton A. Turanov
- RNA Therapeutics Institute, University of Massachusetts Medical School, 01605 Worcester, MA, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, 01605 Worcester, MA, USA
| | - Julia F. Alterman
- RNA Therapeutics Institute, University of Massachusetts Medical School, 01605 Worcester, MA, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, 01605 Worcester, MA, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Medical School, 01605 Worcester, MA, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, 01605 Worcester, MA, USA
| | - Bruno M.D.C. Godinho
- RNA Therapeutics Institute, University of Massachusetts Medical School, 01605 Worcester, MA, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, 01605 Worcester, MA, USA
| | - Neil Aronin
- RNA Therapeutics Institute, University of Massachusetts Medical School, 01605 Worcester, MA, USA
- Department of Medicine, University of Massachusetts Medical School, 01605 Worcester, MA, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, 01605 Worcester, MA, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, 01605 Worcester, MA, USA
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215
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Structural Foundations of RNA Silencing by Argonaute. J Mol Biol 2017; 429:2619-2639. [PMID: 28757069 DOI: 10.1016/j.jmb.2017.07.018] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 07/24/2017] [Accepted: 07/25/2017] [Indexed: 12/19/2022]
Abstract
Nearly every cell in the human body contains a set of programmable gene-silencing proteins named Argonaute. Argonaute proteins mediate gene regulation by small RNAs and thereby contribute to cellular homeostasis during diverse physiological process, such as stem cell maintenance, fertilization, and heart development. Over the last decade, remarkable progress has been made toward understanding Argonaute proteins, small RNAs, and their roles in eukaryotic biology. Here, we review current understanding of Argonaute proteins from a structural prospective and discuss unanswered questions surrounding this fascinating class of enzymes.
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216
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Xu JY, Chen GH, Yang YJ. Exosomes: A Rising Star in Falling Hearts. Front Physiol 2017; 8:494. [PMID: 28751864 PMCID: PMC5508217 DOI: 10.3389/fphys.2017.00494] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 06/28/2017] [Indexed: 12/20/2022] Open
Abstract
Although exosomes were previously recognized as a mechanism for discharging useless cellular components, growing evidence has elucidated their roles in conveying information between cells. They contribute to cell-cell communication by carrying nucleic acids, proteins and lipids that can, in turn, regulate behavior of the target cells. Recent research suggested that exosomes extensively participate in progression of diverse cardiovascular diseases (CVDs), such as myocardial infarction, cardiomyopathy, pulmonary arterial hypertension and others. Here, we summarize effects of exosome-derived molecules (mainly microRNAs and proteins) on cardiac function, to examine their potential applications as biomarkers or therapeutics in CVDs.
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Affiliation(s)
- Jun-Yan Xu
- State Key Laboratory of Cardiovascular Disease, Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Science and Peking Union Medical CollegeBeijing, China
| | - Gui-Hao Chen
- State Key Laboratory of Cardiovascular Disease, Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Science and Peking Union Medical CollegeBeijing, China
| | - Yue-Jin Yang
- State Key Laboratory of Cardiovascular Disease, Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Science and Peking Union Medical CollegeBeijing, China
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217
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Sun G, Riggs AD. A Simple and Cost-Effective Approach for In Vitro Production of Sliced siRNAs as Potent Triggers for RNAi. MOLECULAR THERAPY. NUCLEIC ACIDS 2017; 8:345-355. [PMID: 28918034 PMCID: PMC5537206 DOI: 10.1016/j.omtn.2017.07.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 07/08/2017] [Accepted: 07/09/2017] [Indexed: 12/25/2022]
Abstract
We have studied the molecular properties of in-vitro-transcribed sliced small interfering RNAs (tsli-siRNAs) as an alternative RNAi agent for chemically synthesized siRNA. We describe here a simple and cost-effective procedure for high-purity production of tsli-siRNA using bacteriophage T7 RNA polymerases. tsli-siRNAs exhibit potent gene knockdown effects, with efficacy comparable with that of chemically synthesized sli-siRNAs and classical siRNAs. Furthermore, we found that it is very easy to prepare potent tsli-siRNAs with modified bases, such as 2′-fluorine- or biotin-16-modified tsli-siRNAs. tsli-siRNAs can cause a mild innate immune response, which can be easily eliminated by alkaline phosphatase treatment. On the other hand, this feature, which can be useful as a trigger of the innate immune response, can be enhanced by polynucleotide kinase treatment. Because of the simplicity of preparation and purification, the procedure presented here could be useful for the production of RNAi or immunostimulatory reagents.
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Affiliation(s)
- Guihua Sun
- Department of Diabetes Complications & Metabolism, Diabetes & Metabolism Research Institute, Beckman Research Institute, City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA.
| | - Arthur D Riggs
- Department of Diabetes Complications & Metabolism, Diabetes & Metabolism Research Institute, Beckman Research Institute, City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA.
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218
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Zhang K, Yang XJ, Zhao W, Xu MC, Xu JJ, Chen HY. Regulation and imaging of gene expression via an RNA interference antagonistic biomimetic probe. Chem Sci 2017; 8:4973-4977. [PMID: 28959421 PMCID: PMC5607853 DOI: 10.1039/c7sc00909g] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 05/05/2017] [Indexed: 11/21/2022] Open
Abstract
Regulation of gene expression is highly important in the area of cell biology. In this work a novel convenient and versatile strategy is reported which permits both gene regulation and imaging in living cells. An oligonucleotide-based biomimetic probe was designed to target an RNA-induced silencing complex (RISC) and served as an agent for the modulation of c-Myc protein expression in living cells through regulating the RNA interference (RNAi) pathway. In this probe, a DNA strand (Strand1) serving as the frame was immobilized on a AuNP with a thiol group at the 5' end. Strand2, designed to recognize the target RISC with an RNA fragment, was hybridized with the complementary sequence of Strand1. In the original state, the fluorescence of the Cy3 modifier at the 5' end of Strand2 was quenched by both the AuNP and BHQ2, which labelled the 3' end of Strand1. In the presence of RISC, Strand2 was cleaved, resulting in a shorter oligo part with a corresponding lower melting temperature than that of the original full-length Strand2. The shorter oligonucleotide strand containing the Cy3 fluorophore was released, accompanied by a recovered fluorescence signal. Through evaluating the fluorescence intensity, the competition for RISC was dynamically monitored in single cells. Furthermore, capturing RISC by this probe resulted not only in restored fluorescence intensity but also increased c-Myc oncogene expression. Hence, gene expression could be selectively and precisely regulated and imaged via the RISC targeting probe. The synthetic method for the biomimetic probe is universally applicable, and facilitates the fundamental study of RNAi pathways, or development of a gene regulation strategy without cytokine activation. The gene regulation and imaging strategy will accelerate the unveiling of the basic role of the RISC cleavage interaction, the mystery of RNA-silencing and therapeutic monitoring of cancer.
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Affiliation(s)
- Kai Zhang
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China . ;
- Key Laboratory of Nuclear Medicine , Ministry of Health , Jiangsu Key Laboratory of Molecular Nuclear Medicine , Jiangsu Institute of Nuclear Medicine , Wuxi , Jiangsu 214063 , China
| | - Xue-Jiao Yang
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China . ;
| | - Wei Zhao
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China . ;
| | - Ming-Chen Xu
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China . ;
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China . ;
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China . ;
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219
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Burke JM, Kincaid RP, Nottingham RM, Lambowitz AM, Sullivan CS. DUSP11 activity on triphosphorylated transcripts promotes Argonaute association with noncanonical viral microRNAs and regulates steady-state levels of cellular noncoding RNAs. Genes Dev 2017; 30:2076-2092. [PMID: 27798849 PMCID: PMC5066614 DOI: 10.1101/gad.282616.116] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 09/02/2016] [Indexed: 12/22/2022]
Abstract
Here, Burke et al. delineate a new pathway for mammalian small RNAs to enter the RNAi gene silencing machinery. They show that DUSP11 directly dephosphorylates viral triphosphate ncRNA transcripts and that this is required for efficient silencing by RISC, suggesting that mammalian viral pathogens can use DUSP11 to generate atypical microRNAs. RNA silencing is a conserved eukaryotic gene expression regulatory mechanism mediated by small RNAs. In Caenorhabditis elegans, the accumulation of a distinct class of siRNAs synthesized by an RNA-dependent RNA polymerase (RdRP) requires the PIR-1 phosphatase. However, the function of PIR-1 in RNAi has remained unclear. Since mammals lack an analogous siRNA biogenesis pathway, an RNA silencing role for the mammalian PIR-1 homolog (dual specificity phosphatase 11 [DUSP11]) was unexpected. Here, we show that the RNA triphosphatase activity of DUSP11 promotes the RNA silencing activity of viral microRNAs (miRNAs) derived from RNA polymerase III (RNAP III) transcribed precursors. Our results demonstrate that DUSP11 converts the 5′ triphosphate of miRNA precursors to a 5′ monophosphate, promoting loading of derivative 5p miRNAs into Argonaute proteins via a Dicer-coupled 5′ monophosphate-dependent strand selection mechanism. This mechanistic insight supports a likely shared function for PIR-1 in C. elegans. Furthermore, we show that DUSP11 modulates the 5′ end phosphate group and/or steady-state level of several host RNAP III transcripts, including vault RNAs and Alu transcripts. This study shows that steady-state levels of select noncoding RNAs are regulated by DUSP11 and defines a previously unknown portal for small RNA-mediated silencing in mammals, revealing that DUSP11-dependent RNA silencing activities are shared among diverse metazoans.
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Affiliation(s)
- James M Burke
- Institute for Cellular and Molecular Biology, College of Natural Sciences, The University of Texas at Austin, Austin, Texas 78712, USA.,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, USA.,Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, Texas 78712, USA.,John Ring LaMontagne Center for Infectious Disease, College of Natural Sciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Rodney P Kincaid
- Institute for Cellular and Molecular Biology, College of Natural Sciences, The University of Texas at Austin, Austin, Texas 78712, USA.,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, USA.,Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, Texas 78712, USA.,John Ring LaMontagne Center for Infectious Disease, College of Natural Sciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Ryan M Nottingham
- Institute for Cellular and Molecular Biology, College of Natural Sciences, The University of Texas at Austin, Austin, Texas 78712, USA.,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, USA.,Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Alan M Lambowitz
- Institute for Cellular and Molecular Biology, College of Natural Sciences, The University of Texas at Austin, Austin, Texas 78712, USA.,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, USA.,Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Christopher S Sullivan
- Institute for Cellular and Molecular Biology, College of Natural Sciences, The University of Texas at Austin, Austin, Texas 78712, USA.,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, USA.,Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, Texas 78712, USA.,John Ring LaMontagne Center for Infectious Disease, College of Natural Sciences, The University of Texas at Austin, Austin, Texas 78712, USA
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220
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Gao Z, Harwig A, Berkhout B, Herrera-Carrillo E. Mutation of nucleotides around the +1 position of type 3 polymerase III promoters: The effect on transcriptional activity and start site usage. Transcription 2017; 8:275-287. [PMID: 28598252 PMCID: PMC5703244 DOI: 10.1080/21541264.2017.1322170] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 04/18/2017] [Accepted: 04/18/2017] [Indexed: 11/24/2022] Open
Abstract
Type 3 RNA polymerase III (Pol III) promoters are widely used for the expression of small RNAs such as short hairpin RNA and guide RNA in the popular RNAi and CRISPR-Cas gene regulation systems. Although it is generally believed that type 3 Pol III promoters use a defined transcription start site (+1 position), most man-made promoter constructs contain local sequence alterations of which the impact on transcription efficiency and initiation accuracy is not known. For three human type 3 Pol III promoters (7SK, U6, and H1), we demonstrated that the nucleotides around the +1 position affect both the transcriptional efficiency and start site selection. Human 7SK and U6 promoters with A or G at the +1 position efficiently produced small RNAs with a precise +1 start site. The human H1 promoter with +1A or G also efficiently produced small RNAs but from multiple start sites in the -3/-1 window. These results provide new insights for the design of vectors for accurate expression of designed small RNAs for research and therapeutic purposes.
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Affiliation(s)
- Zongliang Gao
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Alex Harwig
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Elena Herrera-Carrillo
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
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221
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Paces J, Nic M, Novotny T, Svoboda P. Literature review of baseline information to support the risk assessment of RNAi‐based GM plants. ACTA ACUST UNITED AC 2017. [PMCID: PMC7163844 DOI: 10.2903/sp.efsa.2017.en-1246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Paces
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
| | | | | | - Petr Svoboda
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
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222
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Pawlina K, Gurgul A, Szmatoła T, Koch C, Mählmann K, Witkowski M, Bugno-Poniewierska M. Comprehensive characteristics of microRNA expression profile of equine sarcoids. Biochimie 2017; 137:20-28. [DOI: 10.1016/j.biochi.2017.02.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 02/28/2017] [Indexed: 12/21/2022]
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223
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Iribe H, Miyamoto K, Takahashi T, Kobayashi Y, Leo J, Aida M, Ui-Tei K. Chemical Modification of the siRNA Seed Region Suppresses Off-Target Effects by Steric Hindrance to Base-Pairing with Targets. ACS OMEGA 2017; 2:2055-2064. [PMID: 29450406 PMCID: PMC5808362 DOI: 10.1021/acsomega.7b00291] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 05/05/2017] [Indexed: 05/12/2023]
Abstract
Chemical modifications of 2'-O-methyl (2'-OMe) and locked nucleic acid (LNA) of the nucleotides in the seed region (positions 2-8) of the small interfering RNA (siRNA) guide strand significantly reduced seed-matched (SM) off-target effects. The siRNA with 2'-OMe modifications inhibited the expression of a completely-matched (CM) target gene, whereas that with LNA modifications did not inhibit the expression of the CM target. By computational predictions of conformational changes of siRNA by these modifications, we revealed that both modifications in the siRNA seed region reduce SM off-target effects by steric hindrance to base-pairing with target transcripts but LNA modifications also disturb the association of the siRNA guide strand with the Argonaute (AGO) protein by altering RNA conformation. Thus, chemical modifications of the siRNA guide strand, which alter steric conformation to disturb base-pairing with target transcripts but do not disturb the association with the AGO protein, may successfully suppress off-target effects without substantial loss of RNA silencing activity.
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Affiliation(s)
- Hanna Iribe
- Department
of Computational Biology and Medical Science, Graduate School of Frontier
Sciences, The University of Tokyo, Chiba 277-8581, Japan
| | - Kengo Miyamoto
- Center
for Quantum Life Sciences and Department of Chemistry, Graduate School
of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Tomoko Takahashi
- Department
of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yoshiaki Kobayashi
- Department
of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Jastina Leo
- Department
of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
- Faculty
of Microbiology, Immunology and Molecular Genetics, University of California, Los
Angeles, California 90095, United States
| | - Misako Aida
- Center
for Quantum Life Sciences and Department of Chemistry, Graduate School
of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Kumiko Ui-Tei
- Department
of Computational Biology and Medical Science, Graduate School of Frontier
Sciences, The University of Tokyo, Chiba 277-8581, Japan
- Department
of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
- E-mail:
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224
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Herrera-Carrillo E, Harwig A, Berkhout B. Silencing of HIV-1 by AgoshRNA molecules. Gene Ther 2017; 24:453-461. [DOI: 10.1038/gt.2017.44] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 04/13/2017] [Accepted: 05/12/2017] [Indexed: 12/17/2022]
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225
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Elkayam E, Parmar R, Brown CR, Willoughby JL, Theile CS, Manoharan M, Joshua-Tor L. siRNA carrying an (E)-vinylphosphonate moiety at the 5΄ end of the guide strand augments gene silencing by enhanced binding to human Argonaute-2. Nucleic Acids Res 2017; 45:3528-3536. [PMID: 27903888 PMCID: PMC5389677 DOI: 10.1093/nar/gkw1171] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 11/03/2016] [Accepted: 11/09/2016] [Indexed: 01/20/2023] Open
Abstract
Efficient gene silencing by RNA interference (RNAi) in vivo requires the recognition and binding of the 5΄- phosphate of the guide strand of an siRNA by the Argonaute protein. However, for exogenous siRNAs it is limited by the rapid removal of the 5΄- phosphate of the guide strand by metabolic enzymes. Here, we have determined the crystal structure of human Argonaute-2 in complex with the metabolically stable 5΄-(E)-vinylphosphonate (5΄-E-VP) guide RNA at 2.5-Å resolution. The structure demonstrates how the 5΄ binding site in the Mid domain of human Argonaute-2 is able to adjust the key residues in the 5΄-nucleotide binding pocket to compensate for the change introduced by the modified nucleotide. This observation also explains improved binding affinity of the 5΄-E-VP -modified siRNA to human Argonaute-2 in-vitro, as well as the enhanced silencing in the context of the trivalent N-acetylgalactosamine (GalNAc)-conjugated siRNA in mice relative to the un-modified siRNA.
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Affiliation(s)
- Elad Elkayam
- Keck Structural Biology Lab, Cold Spring Harbor, NY 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor, NY 11724, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Rubina Parmar
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | | | | | | | | | - Leemor Joshua-Tor
- Keck Structural Biology Lab, Cold Spring Harbor, NY 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor, NY 11724, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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226
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Harikrishna S, Pradeepkumar PI. Probing the Binding Interactions between Chemically Modified siRNAs and Human Argonaute 2 Using Microsecond Molecular Dynamics Simulations. J Chem Inf Model 2017; 57:883-896. [DOI: 10.1021/acs.jcim.6b00773] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- S. Harikrishna
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai−400076, India
| | - P. I. Pradeepkumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai−400076, India
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227
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Zander A, Willkomm S, Ofer S, van Wolferen M, Egert L, Buchmeier S, Stöckl S, Tinnefeld P, Schneider S, Klingl A, Albers SV, Werner F, Grohmann D. Guide-independent DNA cleavage by archaeal Argonaute from Methanocaldococcus jannaschii. Nat Microbiol 2017; 2:17034. [PMID: 28319081 DOI: 10.1038/nmicrobiol.2017.34] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 02/10/2017] [Indexed: 12/17/2022]
Abstract
Prokaryotic Argonaute proteins acquire guide strands derived from invading or mobile genetic elements, via an unknown pathway, to direct guide-dependent cleavage of foreign DNA. Here, we report that Argonaute from the archaeal organism Methanocaldococcus jannaschii (MjAgo) possesses two modes of action: the canonical guide-dependent endonuclease activity and a non-guided DNA endonuclease activity. The latter allows MjAgo to process long double-stranded DNAs, including circular plasmid DNAs and genomic DNAs. Degradation of substrates in a guide-independent fashion primes MjAgo for subsequent rounds of DNA cleavage. Chromatinized genomic DNA is resistant to MjAgo degradation, and recombinant histones protect DNA from cleavage in vitro. Mutational analysis shows that key residues important for guide-dependent target processing are also involved in guide-independent MjAgo function. This is the first characterization of guide-independent cleavage activity for an Argonaute protein potentially serving as a guide biogenesis pathway in a prokaryotic system.
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Affiliation(s)
- Adrian Zander
- Department of Microbiology &Archaea Centre, University of Regensburg, Regensburg 93053, Germany
| | - Sarah Willkomm
- Department of Microbiology &Archaea Centre, University of Regensburg, Regensburg 93053, Germany
| | - Sapir Ofer
- Institute for Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
| | - Marleen van Wolferen
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Microbiology, Schaenzlestraße 1, 79104 Freiburg, Germany
| | - Luisa Egert
- Department of Microbiology &Archaea Centre, University of Regensburg, Regensburg 93053, Germany
| | - Sabine Buchmeier
- Institute of Physical and Theoretical Chemistry - NanoBioSciences, Technische Universität Braunschweig-BRICS, Rebenring 56, 38106 Braunschweig, Germany
| | - Sarah Stöckl
- Department of Microbiology &Archaea Centre, University of Regensburg, Regensburg 93053, Germany
| | - Philip Tinnefeld
- Institute of Physical and Theoretical Chemistry - NanoBioSciences, Technische Universität Braunschweig-BRICS, Rebenring 56, 38106 Braunschweig, Germany
| | - Sabine Schneider
- Center for Integrated Protein Science Munich CIPSM, Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Andreas Klingl
- Biocentre of the LMU Munich, Department Biology I - Plant Development, Großhadernerstraße 2-4, 82152 Planegg-Martinstried, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Microbiology, Schaenzlestraße 1, 79104 Freiburg, Germany
| | - Finn Werner
- Institute for Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
| | - Dina Grohmann
- Department of Microbiology &Archaea Centre, University of Regensburg, Regensburg 93053, Germany
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228
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Willkomm S, Oellig CA, Zander A, Restle T, Keegan R, Grohmann D, Schneider S. Structural and mechanistic insights into an archaeal DNA-guided Argonaute protein. Nat Microbiol 2017; 2:17035. [PMID: 28319084 DOI: 10.1038/nmicrobiol.2017.35] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 02/10/2017] [Indexed: 12/17/2022]
Abstract
Argonaute (Ago) proteins in eukaryotes are known as key players in post-transcriptional gene silencing1, while recent studies on prokaryotic Agos hint at their role in the protection against invading DNA2,3. Here, we present crystal structures of the apo enzyme and a binary Ago-guide complex of the archaeal Methanocaldococcus jannaschii (Mj) Ago. Binding of a guide DNA leads to large structural rearrangements. This includes the structural transformation of a hinge region containing a switch helix, which has been shown for human Ago2 to be critical for the dynamic target search process4-6. To identify key residues crucial for MjAgo function, we analysed the effect of several MjAgo mutants. We observe that the nature of the 3' and 5' nucleotides in particular, as well as the switch helix, appear to impact MjAgo cleavage activity. In summary, we provide insights into the molecular mechanisms that drive DNA-guided DNA silencing by an archaeal Ago.
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Affiliation(s)
- Sarah Willkomm
- Institute of Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Christine A Oellig
- Center for Integrated Protein Science Munich CIPSM, Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Adrian Zander
- Institute of Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Tobias Restle
- Institute for Molecular Medicine, University of Lübeck, 23538 Lübeck, Germany
| | - Ronan Keegan
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, UK.,Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Dina Grohmann
- Institute of Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Sabine Schneider
- Center for Integrated Protein Science Munich CIPSM, Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany
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229
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Martelli F, Giannecchini S. Polyomavirus microRNAs circulating in biological fluids during viral persistence. Rev Med Virol 2017; 27:e1927. [DOI: 10.1002/rmv.1927] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 02/13/2017] [Accepted: 02/14/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Francesco Martelli
- Department of Experimental and Clinical Medicine; University of Florence; Florence Italy
| | - Simone Giannecchini
- Department of Experimental and Clinical Medicine; University of Florence; Florence Italy
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230
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Chen J, Guan X, Hu Y, Tian H, Chen X. Peptide-Based and Polypeptide-Based Gene Delivery Systems. Top Curr Chem (Cham) 2017; 375:32. [DOI: 10.1007/s41061-017-0115-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 01/28/2017] [Indexed: 12/15/2022]
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231
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Swarts DC, Szczepaniak M, Sheng G, Chandradoss SD, Zhu Y, Timmers EM, Zhang Y, Zhao H, Lou J, Wang Y, Joo C, van der Oost J. Autonomous Generation and Loading of DNA Guides by Bacterial Argonaute. Mol Cell 2017; 65:985-998.e6. [PMID: 28262506 DOI: 10.1016/j.molcel.2017.01.033] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 12/09/2016] [Accepted: 01/27/2017] [Indexed: 01/20/2023]
Abstract
Several prokaryotic Argonaute proteins (pAgos) utilize small DNA guides to mediate host defense by targeting invading DNA complementary to the DNA guide. It is unknown how these DNA guides are being generated and loaded onto pAgo. Here, we demonstrate that guide-free Argonaute from Thermus thermophilus (TtAgo) can degrade double-stranded DNA (dsDNA), thereby generating small dsDNA fragments that subsequently are loaded onto TtAgo. Combining single-molecule fluorescence, molecular dynamic simulations, and structural studies, we show that TtAgo loads dsDNA molecules with a preference toward a deoxyguanosine on the passenger strand at the position opposite to the 5' end of the guide strand. This explains why in vivo TtAgo is preferentially loaded with guides with a 5' end deoxycytidine. Our data demonstrate that TtAgo can independently generate and selectively load functional DNA guides.
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Affiliation(s)
- Daan C Swarts
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6708 WE Wageningen, the Netherlands
| | - Malwina Szczepaniak
- Kavli Institute of NanoScience, Department of BioNanoScience, Delft University of Technology, 2628 CD Delft, the Netherlands
| | - Gang Sheng
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Stanley D Chandradoss
- Kavli Institute of NanoScience, Department of BioNanoScience, Delft University of Technology, 2628 CD Delft, the Netherlands
| | - Yifan Zhu
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6708 WE Wageningen, the Netherlands
| | - Elizabeth M Timmers
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6708 WE Wageningen, the Netherlands
| | - Yong Zhang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Hongtu Zhao
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jizhong Lou
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanli Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Chirlmin Joo
- Kavli Institute of NanoScience, Department of BioNanoScience, Delft University of Technology, 2628 CD Delft, the Netherlands.
| | - John van der Oost
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6708 WE Wageningen, the Netherlands.
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232
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Tarabay Y, Achour M, Teletin M, Ye T, Teissandier A, Mark M, Bourc'his D, Viville S. Tex19 paralogs are new members of the piRNA pathway controlling retrotransposon suppression. J Cell Sci 2017; 130:1463-1474. [PMID: 28254886 DOI: 10.1242/jcs.188763] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 02/27/2017] [Indexed: 01/29/2023] Open
Abstract
Tex19 genes are mammalian specific and duplicated to give Tex19.1 and Tex19.2 in some species, such as the mouse and rat. It has been demonstrated that mutant Tex19.1 males display a variable degree of infertility whereas they all upregulate MMERVK10C transposons in their germ line. In order to study the function of both paralogs in the mouse, we generated and studied Tex19 double knockout (Tex19DKO) mutant mice. Adult Tex19DKO males exhibited a fully penetrant phenotype, similar to the most severe phenotype observed in the single Tex19.1KO mice, with small testes and impaired spermatogenesis, defects in meiotic chromosome synapsis, persistence of DNA double-strand breaks during meiosis, lack of post-meiotic germ cells and upregulation of MMERVK10C expression. The phenotypic similarities to mice with knockouts in the Piwi family genes prompted us to check and then demonstrate, by immunoprecipitation and GST pulldown followed by mass spectrometry analyses, that TEX19 paralogs interact with PIWI proteins and the TEX19 VPTEL domain directly binds Piwi-interacting RNAs (piRNAs) in adult testes. We therefore identified two new members of the postnatal piRNA pathway.
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Affiliation(s)
- Yara Tarabay
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964/Centre National de Recherche Scientifique (CNRS) UMR 1704/Université de Strasbourg, Illkirch 67404, France
| | - Mayada Achour
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964/Centre National de Recherche Scientifique (CNRS) UMR 1704/Université de Strasbourg, Illkirch 67404, France
| | - Marius Teletin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964/Centre National de Recherche Scientifique (CNRS) UMR 1704/Université de Strasbourg, Illkirch 67404, France.,Service de Biologie de la Reproduction, Centre Hospitalier Universitaire, Strasbourg 67000, France
| | - Tao Ye
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964/Centre National de Recherche Scientifique (CNRS) UMR 1704/Université de Strasbourg, Illkirch 67404, France
| | - Aurélie Teissandier
- Institut Curie, department of Genetics and Developmental Biology, CNRS UMR3215, INSERM U934, 75005 Paris, France
| | - Manuel Mark
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964/Centre National de Recherche Scientifique (CNRS) UMR 1704/Université de Strasbourg, Illkirch 67404, France.,Service de Biologie de la Reproduction, Centre Hospitalier Universitaire, Strasbourg 67000, France
| | - Déborah Bourc'his
- Institut Curie, department of Genetics and Developmental Biology, CNRS UMR3215, INSERM U934, 75005 Paris, France
| | - Stéphane Viville
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964/Centre National de Recherche Scientifique (CNRS) UMR 1704/Université de Strasbourg, Illkirch 67404, France .,Centre Hospitalier Universitaire, Strasbourg 67000, France
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233
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Khvorova A, Watts JK. The chemical evolution of oligonucleotide therapies of clinical utility. Nat Biotechnol 2017; 35:238-248. [PMID: 28244990 PMCID: PMC5517098 DOI: 10.1038/nbt.3765] [Citation(s) in RCA: 749] [Impact Index Per Article: 107.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 12/12/2016] [Indexed: 02/07/2023]
Abstract
After nearly 40 years of development, oligonucleotide therapeutics are nearing meaningful clinical productivity. One of the key advantages of oligonucleotide drugs is that their delivery and potency are derived primarily from the chemical structure of the oligonucleotide whereas their target is defined by the base sequence. Thus, as oligonucleotides with a particular chemical design show appropriate distribution and safety profiles for clinical gene silencing in a particular tissue, this will open the door to the rapid development of additional drugs targeting other disease-associated genes in the same tissue. To achieve clinical productivity, the chemical architecture of the oligonucleotide needs to be optimized with a combination of sugar, backbone, nucleobase, and 3'- and 5'-terminal modifications. A portfolio of chemistries can be used to confer drug-like properties onto the oligonucleotide as a whole, with minor chemical changes often translating into major improvements in clinical efficacy. One outstanding challenge in oligonucleotide chemical development is the optimization of chemical architectures to ensure long-term safety. There are multiple designs that enable effective targeting of the liver, but a second challenge is to develop architectures that enable robust clinical efficacy in additional tissues.
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Affiliation(s)
- Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Jonathan K Watts
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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234
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Cock JM, Liu F, Duan D, Bourdareau S, Lipinska AP, Coelho SM, Tarver JE. Rapid Evolution of microRNA Loci in the Brown Algae. Genome Biol Evol 2017; 9:740-749. [PMID: 28338896 PMCID: PMC5381526 DOI: 10.1093/gbe/evx038] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2017] [Indexed: 02/06/2023] Open
Abstract
Stringent searches for microRNAs (miRNAs) have so far only identified these molecules in animals, land plants, chlorophyte green algae, slime molds and brown algae. The identification of miRNAs in brown algae was based on the analysis of a single species, the filamentous brown alga Ectocarpus sp. Here, we have used deep sequencing of small RNAs and a recently published genome sequence to identify miRNAs in a second brown alga, the kelp Saccharina japonica. S. japonica possesses a large number of miRNAs (117) and these miRNAs are highly diverse, falling into 98 different families. Surprisingly, none of the S. japonica miRNAs share significant sequence similarity with the Ectocarpus sp. miRNAs. However, the miRNA repertoires of the two species share a number of structural and genomic features indicating that they were generated by similar evolutionary processes and therefore probably evolved within the context of a common, ancestral miRNA system. This lack of sequence similarity suggests that miRNAs evolve rapidly in the brown algae (the two species are separated by ∼95 Myr of evolution). The sets of predicted targets of miRNAs in the two species were also very different suggesting that the divergence of the miRNAs may have had significant consequences for miRNA function.
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Affiliation(s)
- J. Mark Cock
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Fuli Liu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Delin Duan
- Key Lab of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Qingdao National Laboratory for Marine Science and Technology, Lab for Marine Biology and Biotechnology, Qingdao, China
| | - Simon Bourdareau
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Agnieszka P. Lipinska
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Susana M. Coelho
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - James E. Tarver
- School of Earth Sciences, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, United Kingdom
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235
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Bellissimo T, Masciarelli S, Poser E, Genovese I, Del Rio A, Colotti G, Fazi F. Small Molecules Targeting the miRNA-Binding Domain of Argonaute 2: From Computer-Aided Molecular Design to RNA Immunoprecipitation. Methods Mol Biol 2017; 1517:211-221. [PMID: 27924485 DOI: 10.1007/978-1-4939-6563-2_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The development of small-molecule-based target therapy design for human disease and cancer is object of growing attention. Recently, specific microRNA (miRNA) mimicking compounds able to bind the miRNA-binding domain of Argonaute 2 protein (AGO2) to inhibit miRNA loading and its functional activity were described. Computer-aided molecular design techniques and RNA immunoprecipitation represent suitable approaches to identify and experimentally determine if a compound is able to impair the loading of miRNAs on AGO2 protein. Here, we describe these two methodologies that we recently used to select a specific compound able to interfere with the AGO2 functional activity and able to improve the retinoic acid-dependent myeloid differentiation of leukemic cells.
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Affiliation(s)
- Teresa Bellissimo
- Department of Anatomical, Histological, Forensic & Orthopaedic Sciences, Section of Histology & Medical Embryology, Sapienza University of Rome, Via A. Scarpa, 14-16, 00161, Rome, Italy
| | - Silvia Masciarelli
- Department of Anatomical, Histological, Forensic & Orthopaedic Sciences, Section of Histology & Medical Embryology, Sapienza University of Rome, Via A. Scarpa, 14-16, 00161, Rome, Italy
| | - Elena Poser
- Pathology, Italian National Research Council, Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, 00161, Rome, Italy
| | - Ilaria Genovese
- Pathology, Italian National Research Council, Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, 00161, Rome, Italy
| | - Alberto Del Rio
- CNR-National Research Council of Italy, Institute for Organic Chemistry and Photoreactivity, Via P. Gobetti 101, 40129, Bologna, Italy. .,Innovamol Srls, Viale A. Corassori 24, 41124, Modena, Italy.
| | - Gianni Colotti
- Pathology, Italian National Research Council, Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, 00161, Rome, Italy.
| | - Francesco Fazi
- Department of Anatomical, Histological, Forensic & Orthopaedic Sciences, Section of Histology & Medical Embryology, Sapienza University of Rome, Via A. Scarpa, 14-16, 00161, Rome, Italy.
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236
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Abstract
RNA interference is a convenient and highly effective technique to investigate the biological function of genes. Adequately designed RNA molecules introduced into an oocyte are able to bind specific endogenous mRNAs and trigger their degradation. Subsequent fertilization of these oocytes will result in the generation of embryos in which the expression of the gene of interest is downregulated, and following the degradation of maternal proteins the role of the gene product can be studied. Here, we describe the approach how post-transcriptional gene silencing can be achieved in oocytes and early embryos using siRNA.
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Affiliation(s)
- Lu Zhang
- Department of Animal Sciences, Purdue University, Lilly Hall of Life Sciences, 915 W. State Street, West Lafayette, IN, 47907, USA
| | - Zoltan Machaty
- Department of Animal Sciences, Purdue University, Lilly Hall of Life Sciences, 915 W. State Street, West Lafayette, IN, 47907, USA.
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237
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Iki T. Messages on small RNA duplexes in plants. JOURNAL OF PLANT RESEARCH 2017; 130:7-16. [PMID: 27878651 DOI: 10.1007/s10265-016-0876-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/12/2016] [Indexed: 06/06/2023]
Abstract
Small RNA-mediated gene silencing encompasses diverse developmental events, stress responses, defense against pathogens, and maintenance of genome integrity. Extensive studies in model organisms have unveiled the molecular mechanisms underpinning the RNA silencing phenomena, and the accumulating knowledge have characterized the intricate pathways and the repertoire of proteins responsible for the actions of small RNAs characterized as microRNAs (miRNAs) or small interfering RNAs (siRNAs). Although the single-stranded, matured guide small RNAs direct the effector ribonucleoprotein complexes to induce gene silencing in sequence-specific manner, the double-stranded intermediate, the small RNA duplexes, which are processed as nascent products of the RNase III enzyme activities, act as key to determine the downstream molecular pathways and the fate of small RNAs. Based at the small RNA duplex-centered view, this review describes the recent advances in understanding the small RNA pathways in plants.
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Affiliation(s)
- Taichiro Iki
- Graduate School of Frontier Biosciences, Osaka University, Yamadaoka 1-3, Suita, Osaka, 565-0871, Japan.
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238
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Elucidating Mechanisms of Molecular Recognition Between Human Argonaute and miRNA Using Computational Approaches. Methods Mol Biol 2016. [PMID: 27924488 DOI: 10.1007/978-1-4939-6563-2_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
MicroRNA (miRNA) and Argonaute (AGO) protein together form the RNA-induced silencing complex (RISC) that plays an essential role in the regulation of gene expression. Elucidating the underlying mechanism of AGO-miRNA recognition is thus of great importance not only for the in-depth understanding of miRNA function but also for inspiring new drugs targeting miRNAs. In this chapter we introduce a combined computational approach of molecular dynamics (MD) simulations, Markov state models (MSMs), and protein-RNA docking to investigate AGO-miRNA recognition. Constructed from MD simulations, MSMs can elucidate the conformational dynamics of AGO at biologically relevant timescales. Protein-RNA docking can then efficiently identify the AGO conformations that are geometrically accessible to miRNA. Using our recent work on human AGO2 as an example, we explain the rationale and the workflow of our method in details. This combined approach holds great promise to complement experiments in unraveling the mechanisms of molecular recognition between large, flexible, and complex biomolecules.
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239
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Gene silencing pathways found in the green alga Volvox carteri reveal insights into evolution and origins of small RNA systems in plants. BMC Genomics 2016; 17:853. [PMID: 27806710 PMCID: PMC5093975 DOI: 10.1186/s12864-016-3202-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 10/25/2016] [Indexed: 11/14/2022] Open
Abstract
Background Volvox carteri (V. carteri) is a multicellular green alga used as model system for the evolution of multicellularity. So far, the contribution of small RNA pathways to these phenomena is not understood. Thus, we have sequenced V. carteri Argonaute 3 (VcAGO3)-associated small RNAs from different developmental stages. Results Using this functional approach, we define the Volvox microRNA (miRNA) repertoire and show that miRNAs are not conserved in the closely related unicellular alga Chlamydomonas reinhardtii. Furthermore, we find that miRNAs are differentially expressed during different life stages of V. carteri. In addition to miRNAs, transposon-associated small RNAs or phased siRNA loci, which are common in higher land plants, are highly abundant in Volvox as well. Transposons not only give rise to miRNAs and other small RNAs, they are also targets of small RNAs. Conclusion Our analyses reveal a surprisingly complex small RNA network in Volvox as elaborate as in higher land plants. At least the identified VcAGO3-associated miRNAs are not conserved in C. reinhardtii suggesting fast evolution of small RNA systems. Thus, distinct small RNAs may contribute to multicellularity and also division of labor in reproductive and somatic cells. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3202-4) contains supplementary material, which is available to authorized users.
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240
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Willkomm S, Zander A, Grohmann D, Restle T. Mechanistic Insights into Archaeal and Human Argonaute Substrate Binding and Cleavage Properties. PLoS One 2016; 11:e0164695. [PMID: 27741323 PMCID: PMC5065165 DOI: 10.1371/journal.pone.0164695] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 09/29/2016] [Indexed: 12/17/2022] Open
Abstract
Argonaute (Ago) proteins from all three domains of life are key players in processes that specifically regulate cellular nucleic acid levels. Some of these Ago proteins, among them human Argonaute2 (hAgo2) and Ago from the archaeal organism Methanocaldococcus jannaschii (MjAgo), are able to cleave nucleic acid target strands that are recognised via an Ago-associated complementary guide strand. Here we present an in-depth kinetic side-by-side analysis of hAgo2 and MjAgo guide and target substrate binding as well as target strand cleavage, which enabled us to disclose similarities and differences in the mechanistic pathways as a function of the chemical nature of the substrate. Testing all possible guide-target combinations (i.e. RNA/RNA, RNA/DNA, DNA/RNA and DNA/DNA) with both Ago variants we demonstrate that the molecular mechanism of substrate association is highly conserved among archaeal-eukaryotic Argonautes. Furthermore, we show that hAgo2 binds RNA and DNA guide strands in the same fashion. On the other hand, despite striking homology between the two Ago variants, MjAgo cannot orientate guide RNA substrates in a way that allows interaction with the target DNA in a cleavage-compatible orientation.
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Affiliation(s)
- Sarah Willkomm
- Institute of Molecular Medicine, Universitätsklinikum Schleswig-Holstein, Universität zu Lübeck, Lübeck, 23538, Germany
| | - Adrian Zander
- Department of Biochemistry, Genetics and Microbiology, Institute of Microbiology- Archaea Centre, University of Regensburg, Regensburg, 93053, Germany
| | - Dina Grohmann
- Department of Biochemistry, Genetics and Microbiology, Institute of Microbiology- Archaea Centre, University of Regensburg, Regensburg, 93053, Germany
| | - Tobias Restle
- Institute of Molecular Medicine, Universitätsklinikum Schleswig-Holstein, Universität zu Lübeck, Lübeck, 23538, Germany
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241
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Angart PA, Carlson RJ, Adu-Berchie K, Walton SP. Terminal Duplex Stability and Nucleotide Identity Differentially Control siRNA Loading and Activity in RNA Interference. Nucleic Acid Ther 2016; 26:309-317. [PMID: 27399870 PMCID: PMC5067871 DOI: 10.1089/nat.2016.0612] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/06/2016] [Indexed: 01/17/2023] Open
Abstract
Efficient short interfering RNA (siRNA)-mediated gene silencing requires selection of a sequence that is complementary to the intended target and possesses sequence and structural features that encourage favorable functional interactions with the RNA interference (RNAi) pathway proteins. In this study, we investigated how terminal sequence and structural characteristics of siRNAs contribute to siRNA strand loading and silencing activity and how these characteristics ultimately result in a functionally asymmetric duplex in cultured HeLa cells. Our results reiterate that the most important characteristic in determining siRNA activity is the 5' terminal nucleotide identity. Our findings further suggest that siRNA loading is controlled principally by the hybridization stability of the 5' terminus (Nucleotides: 1-2) of each siRNA strand, independent of the opposing terminus. Postloading, RNA-induced silencing complex (RISC)-specific activity was found to be improved by lower hybridization stability in the 5' terminus (Nucleotides: 3-4) of the loaded siRNA strand and greater hybridization stability toward the 3' terminus (Nucleotides: 17-18). Concomitantly, specific recognition of the 5' terminal nucleotide sequence by human Argonaute 2 (Ago2) improves RISC half-life. These findings indicate that careful selection of siRNA sequences can maximize both the loading and the specific activity of the intended guide strand.
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Affiliation(s)
- Phillip A Angart
- Department of Chemical Engineering and Materials Science, Michigan State University , East Lansing, Michigan
| | - Rebecca J Carlson
- Department of Chemical Engineering and Materials Science, Michigan State University , East Lansing, Michigan
| | - Kwasi Adu-Berchie
- Department of Chemical Engineering and Materials Science, Michigan State University , East Lansing, Michigan
| | - S Patrick Walton
- Department of Chemical Engineering and Materials Science, Michigan State University , East Lansing, Michigan
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242
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Matsumoto N, Nishimasu H, Sakakibara K, Nishida KM, Hirano T, Ishitani R, Siomi H, Siomi MC, Nureki O. Crystal Structure of Silkworm PIWI-Clade Argonaute Siwi Bound to piRNA. Cell 2016; 167:484-497.e9. [DOI: 10.1016/j.cell.2016.09.002] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 08/29/2016] [Accepted: 08/31/2016] [Indexed: 12/11/2022]
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243
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Zhu L, Jiang H, Sheong FK, Cui X, Wang Y, Gao X, Huang X. Understanding the core of RNA interference: The dynamic aspects of Argonaute-mediated processes. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2016; 128:39-46. [PMID: 27697475 DOI: 10.1016/j.pbiomolbio.2016.09.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 09/04/2016] [Accepted: 09/26/2016] [Indexed: 12/14/2022]
Abstract
At the core of RNA interference, the Argonaute proteins (Ago) load and utilize small guide nucleic acids to silence mRNAs or cleave foreign nucleic acids in a sequence specific manner. In recent years, based on extensive structural studies of Ago and its interaction with the nucleic acids, considerable progress has been made to reveal the dynamic aspects of various Ago-mediated processes. Here we review these novel insights into the guide-strand loading, duplex unwinding, and effects of seed mismatch, with a focus on two representative Agos, the human Ago 2 (hAgo2) and the bacterial Thermus thermophilus Ago (TtAgo). In particular, comprehensive molecular simulation studies revealed that although sharing similar overall structures, the two Agos have vastly different conformational landscapes and guide-strand loading mechanisms because of the distinct rigidity of their L1-PAZ hinge. Given the central role of the PAZ motions in regulating the exposure of the nucleic acid binding channel, these findings exemplify the importance of protein motions in distinguishing the overlapping, yet distinct, mechanisms of Ago-mediated processes in different organisms.
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Affiliation(s)
- Lizhe Zhu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong; Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Hanlun Jiang
- Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong; Bioengineering Graduate Program, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Fu Kit Sheong
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Xuefeng Cui
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, 23955, Saudi Arabia
| | - Yanli Wang
- Laboratory of Non-Coding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xin Gao
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, 23955, Saudi Arabia
| | - Xuhui Huang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong; Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong; Bioengineering Graduate Program, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
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244
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Hooykaas MJG, Kruse E, Wiertz EJHJ, Lebbink RJ. Comprehensive profiling of functional Epstein-Barr virus miRNA expression in human cell lines. BMC Genomics 2016; 17:644. [PMID: 27531524 PMCID: PMC4987988 DOI: 10.1186/s12864-016-2978-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 07/28/2016] [Indexed: 12/21/2022] Open
Abstract
Background Epstein-Barr virus (EBV) establishes lifelong infections in its human host. The virus is associated with a broad range of malignancies of lymphoid and epithelial origin, including Burkitt’s lymphoma, post-transplant lymphoproliferative disease, nasopharyngeal carcinoma and gastric carcinoma. During the latent phase of its life cycle, EBV expresses more than 40 mature miRNAs that are highly abundant in tumor cells and may contribute to oncogenesis. Although multiple studies have assessed the relative expression profiles of EBV miRNAs in tumor cells, data linking these expression levels to functional target knockdown are mostly lacking. Therefore we set out to systematically assess the EBV miRNA expression levels in EBV+ tumor cell lines, and correlate this to their functional silencing capacity in these cells. Results We provide comprehensive EBV miRNA expression profiles of the EBV+ cell lines C666-1 (nasopharyngeal carcinoma), SNU-719 (gastric carcinoma), Jijoye (Burkitt’s lymphoma), and AKBM (Burkitt’s lymphoma) and of EBV− cells ectopically expressing the BART miRNA cluster. By deep sequencing the small RNA population and conducting miRNA-reporter experiments to assay miRNA potency, we were able to compare the expression profiles of the EBV miRNAs with their functional silencing efficacy. We observe a strong correlation between miRNA expression levels and functional miRNA activity. There is large variation in expression levels between EBV miRNAs in a given cell line, whereas the relative expression profiles are well maintained between cell lines. Furthermore, we show that miRNA arm selection bias is less pronounced for gamma-herpesvirus miRNAs than for human miRNAs. Conclusion We provide an in depth assessment of the expression levels and silencing activity of all EBV miRNAs in B- and epithelial cell lines of different latency stages. Our data show a good correlation between relative EBV miRNA expression levels and silencing capacity, and suggest preferential processing of particular EBV miRNAs irrespective of cell-type. In addition to encoding the largest number of precursor miRNAs of all human herpesviruses, EBV expresses many miRNAs precursors that yield two functional miRNA strands, rather than one guide strand and a non-functional passenger strand. This reduced strand bias may increase the size of the EBV miRNA targetome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2978-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marjolein J G Hooykaas
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Elisabeth Kruse
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Emmanuel J H J Wiertz
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
| | - Robert Jan Lebbink
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
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245
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Åsman AKM, Fogelqvist J, Vetukuri RR, Dixelius C. Phytophthora infestans Argonaute 1 binds microRNA and small RNAs from effector genes and transposable elements. THE NEW PHYTOLOGIST 2016; 211:993-1007. [PMID: 27010746 DOI: 10.1111/nph.13946] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 02/26/2016] [Indexed: 06/05/2023]
Abstract
Phytophthora spp. encode large sets of effector proteins and distinct populations of small RNAs (sRNAs). Recent evidence has suggested that pathogen-derived sRNAs can modulate the expression of plant defense genes. Here, we studied the sRNA classes and functions associated with Phytophthora infestans Argonaute (Ago) proteins. sRNAs were co-immunoprecipitated with three PiAgo proteins and deep sequenced. Twenty- to twenty-two-nucleotide (nt) sRNAs were identified as the main interaction partners of PiAgo1 and high enrichment of 24-26-nt sRNAs was seen in the PiAgo4-bound sample. The frequencies and sizes of transposable element (TE)-derived sRNAs in the different PiAgo libraries suggested diversified roles of the PiAgo proteins in the control of different TE classes. We further provide evidence for the involvement of PiAgo1 in the P. infestans microRNA (miRNA) pathway. Protein-coding genes are probably regulated by the shared action of PiAgo1 and PiAgo5, as demonstrated by analysis of differential expression. An abundance of sRNAs from genes encoding host cell death-inducing Crinkler (CRN) effectors was bound to PiAgo1, implicating this protein in the regulation of the expanded CRN gene family. The data suggest that PiAgo1 plays an essential role in gene regulation and that at least two RNA silencing pathways regulate TEs in the plant-pathogenic oomycete P. infestans.
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Affiliation(s)
- Anna K M Åsman
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Linnéan Center for Plant Biology, PO Box 7080, SE-75007, Uppsala, Sweden
| | - Johan Fogelqvist
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Linnéan Center for Plant Biology, PO Box 7080, SE-75007, Uppsala, Sweden
| | - Ramesh R Vetukuri
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Resistance Biology Unit, PO Box 102, SE-23053, Alnarp, Sweden
| | - Christina Dixelius
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Linnéan Center for Plant Biology, PO Box 7080, SE-75007, Uppsala, Sweden
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246
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Swamy MN, Wu H, Shankar P. Recent advances in RNAi-based strategies for therapy and prevention of HIV-1/AIDS. Adv Drug Deliv Rev 2016; 103:174-186. [PMID: 27013255 PMCID: PMC4935623 DOI: 10.1016/j.addr.2016.03.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 03/10/2016] [Accepted: 03/11/2016] [Indexed: 12/15/2022]
Abstract
RNA interference (RNAi) provides a powerful tool to silence specific gene expression and has been widely used to suppress host factors such as CCR5 and/or viral genes involved in HIV-1 replication. Newer nuclease-based gene-editing technologies, such as zinc finger nucleases (ZFN), transcription activator-like effector nucleases (TALEN) and the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system, also provide powerful tools to ablate specific genes. Because of differences in co-receptor usage and the high mutability of the HIV-1 genome, a combination of host factors and viral genes needs to be suppressed for effective prevention and treatment of HIV-1 infection. Whereas the continued presence of small interfering/short hairpin RNA (si/shRNA) mediators is needed for RNAi to be effective, the continued expression of nucleases in the gene-editing systems is undesirable. Thus, RNAi provides the only practical way for expression of multiple silencers in infected and uninfected cells, which is needed for effective prevention/treatment of infection. There have been several advances in the RNAi field in terms of si/shRNA design, targeted delivery to HIV-1 susceptible cells, and testing for efficacy in preclinical humanized mouse models. Here, we comprehensively review the latest advances in RNAi technology towards prevention and treatment of HIV-1.
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Affiliation(s)
- Manjunath N Swamy
- Center of Emphasis in Infectious Disease, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX 79905, USA.
| | - Haoquan Wu
- Center of Emphasis in Infectious Disease, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX 79905, USA
| | - Premlata Shankar
- Center of Emphasis in Infectious Disease, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX 79905, USA.
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247
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Shelton SB, Reinsborough C, Xhemalce B. Who Watches the Watchmen: Roles of RNA Modifications in the RNA Interference Pathway. PLoS Genet 2016; 12:e1006139. [PMID: 27441695 PMCID: PMC4956115 DOI: 10.1371/journal.pgen.1006139] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
RNA levels are widely thought to be predictive of RNA function. However, the existence of more than a hundred chemically distinct modifications of RNA alone is a major indication that these moieties may impart distinct functions to subgroups of RNA molecules that share a primary sequence but display distinct RNA “epigenetic” marks. RNAs can be modified on many sites, including 5′ and 3′ ends, the sugar phosphate backbone, or internal bases, which collectively provide many opportunities for posttranscriptional regulation through a variety of mechanisms. Here, we will focus on how modifications on messenger and microRNAs may affect the process of RNA interference in mammalian cells. We believe that taking RNA modifications into account will not only advance our understanding of this crucial pathway in disease and cancer but will also open the path to exploiting the enzymes that “write” and “erase” them as targets for therapeutic drug development.
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Affiliation(s)
- Samantha B. Shelton
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Calder Reinsborough
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Blerta Xhemalce
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
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248
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Suter SR, Sheu-Gruttadauria J, Schirle NT, Valenzuela R, Ball-Jones AA, Onizuka K, MacRae IJ, Beal PA. Structure-Guided Control of siRNA Off-Target Effects. J Am Chem Soc 2016; 138:8667-9. [PMID: 27387838 DOI: 10.1021/jacs.6b06137] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Short interfering RNAs (siRNAs) are promising therapeutics that make use of the RNA interference (RNAi) pathway, but liabilities arising from the native RNA structure necessitate chemical modification for drug development. Advances in the structural characterization of components of the human RNAi pathway have enabled structure-guided optimization of siRNA properties. Here we report the 2.3 Å resolution crystal structure of human Argonaute 2 (hAgo2), a key nuclease in the RNAi pathway, bound to an siRNA guide strand bearing an unnatural triazolyl nucleotide at position 1 (g1). Unlike natural nucleotides, this analogue inserts deeply into hAgo2's central RNA binding cleft and thus is able to modulate pairing between guide and target RNAs. The affinity of the hAgo2-siRNA complex for a seed-only matched target was significantly reduced by the triazolyl modification, while the affinity for a fully matched target was unchanged. In addition, siRNA potency for off-target repression was reduced (4-fold increase in IC50) by the modification, while on-target knockdown was improved (2-fold reduction in IC50). Controlling siRNA on-target versus microRNA (miRNA)-like off-target potency by projection of substituent groups into the hAgo2 central cleft from g1 is a new approach to enhance siRNA selectivity with a strong structural rationale.
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Affiliation(s)
- Scott R Suter
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
| | - Jessica Sheu-Gruttadauria
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Nicole T Schirle
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Rachel Valenzuela
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
| | - Alexi A Ball-Jones
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
| | - Kazumitsu Onizuka
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
| | - Ian J MacRae
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Peter A Beal
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
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249
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Bofill-De Ros X, Gu S. Guidelines for the optimal design of miRNA-based shRNAs. Methods 2016; 103:157-66. [PMID: 27083402 PMCID: PMC4921303 DOI: 10.1016/j.ymeth.2016.04.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 03/28/2016] [Accepted: 04/04/2016] [Indexed: 12/21/2022] Open
Abstract
RNA interference (RNAi) is an extremely useful tool for inhibiting gene expression. It can be triggered by transfected synthetic small interfering RNA (siRNA) or by expressed small hairpin RNA (shRNA). The cellular machinery processes the latter into siRNA in vivo. shRNA is preferred or required in genetic screens and specific RNAi approaches in gene therapy settings. Despite its many successes, the field of shRNAs faces many challenges. Insufficient knockdowns and off-target effects become obstacles for shRNA usage in many applications. Numerous failures are triggered by pitfalls in shRNA design that is often associated with impoverished biogenesis. Here, based on current understanding of the miRNA maturation pathway, we discuss the principles of different shRNA design (pre-miRNA-like, pri-miRNA-like and Ago-shRNA) with an emphasis on the RNA structure. We also provide detailed instructions for an optimal design of pre-miRNA-like shRNA.
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Affiliation(s)
- Xavier Bofill-De Ros
- Gene Regulation and Chromosome Biology Laboratory, Center For Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Shuo Gu
- Gene Regulation and Chromosome Biology Laboratory, Center For Cancer Research, National Cancer Institute, Frederick, MD, United States.
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250
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Han J, Xu G, Xu T. The miiuy croaker microRNA transcriptome and microRNA regulation of RIG-I like receptor signaling pathway after poly(I:C) stimulation. FISH & SHELLFISH IMMUNOLOGY 2016; 54:419-426. [PMID: 27131903 DOI: 10.1016/j.fsi.2016.04.126] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 04/18/2016] [Accepted: 04/26/2016] [Indexed: 06/05/2023]
Abstract
MicroRNAs (miRNAs) as endogenous small non-coding RNAs play key regulatory roles in diverse biological processes via degrading the target mRNAs or inhibiting protein translation. Previously many researchers have reported the identification, characteristic of miRNAs and the interaction with its target gene. But, the study on the regulation of miRNAs to biological processes via regulatory the key signaling pathway was still limited. In order to comprehend the regulatory mechanism of miRNAs, two small RNA libraries from the spleen of miiuy croaker individuals with or without poly(I:C) infection were constructed. The 197 conserved miRNAs and 75 novel miRNAs were identified, and 14 conserved and 8 novel miRNAs appeared significant variations. Those differently expressed miRNAs relate to immune regulation of miiuy croaker. Furthermore, expressions of four differently expressed miRNAs were validated by qRT-PCR, and the result was consistent with sequencing data. The target genes of the differently expressed miRNAs in the two libraries were predicted, and some candidate target genes were involved in the RIG-I-like receptor (RLR) signaling pathway. The negative regulation of miRNAs to target genes were confirmed by comparing the expression pattern of miRNAs and their target genes. The results of regulating target genes were that firstly directly or indirectly activating the downstream signaling cascades and subsequent inducting the type I interferon, inflammatory cytokines and apoptosis. These studies could help us to deeper understand the roles of miRNAs played in the fish immune system, and provide a new way to investigate the defense mechanism of fish.
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Affiliation(s)
- Jingjing Han
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Guoliang Xu
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Tianjun Xu
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316022, China.
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