1
|
Liu X, Nishikubo K, Ohgaki R, Okanishi H, Okuda S, Xu M, Kanai Y. Identification of tumor-suppressive miRNAs that target amino acid transporter LAT1 and exhibit anti-proliferative effects on cholangiocarcinoma cells. J Pharmacol Sci 2024; 154:301-311. [PMID: 38485348 DOI: 10.1016/j.jphs.2024.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/24/2024] [Accepted: 02/20/2024] [Indexed: 03/19/2024] Open
Abstract
Amino acid transporter LAT1 is highly upregulated in various cancer types, including cholangiocarcinoma (CHOL), and contributes to the rapid proliferation of cancer cells and disease progression. However, the molecular mechanisms underlying the pathological upregulation of LAT1 remain largely unknown. This study pursued the possibility of miRNA-mediated regulation of the LAT1 expression in CHOL cells. Using online target prediction methods, we extracted five candidate miRNAs commonly predicted to regulate the LAT1 expression. Three of them, miR-194-5p, miR-122-5p, and miR-126-3p, were significantly downregulated in CHOL cancer compared to normal tissues. Correlation analysis revealed weak-to-moderate negative correlations between the expression of these miRNAs and LAT1 mRNA in CHOL cancer tissues. We selected miR-194-5p and miR-122-5p for further analyses and found that both miRNAs functionally target 3'UTR of LAT1 mRNA by a luciferase-based reporter assay. Transfection of the miRNA mimics significantly suppressed the LAT1 expression at mRNA and protein levels and inhibited the proliferation of CHOL cells, with a trend of affecting intracellular amino acids and amino acid-related signaling pathways. This study indicates that the decreased expression of these LAT1-targeting tumor-suppressive miRNAs contributes to the upregulation of LAT1 and the proliferation of CHOL cells, highlighting their potential for developing novel cancer therapeutics and diagnostics.
Collapse
Affiliation(s)
- Xingming Liu
- Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kou Nishikubo
- Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Ryuichi Ohgaki
- Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Hiroki Okanishi
- Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Suguru Okuda
- Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Minhui Xu
- Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yoshikatsu Kanai
- Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| |
Collapse
|
2
|
Ray A, Sarkar A, Banerjee S, Biswas K. Non-Canonical Targets of MicroRNAs: Role in Transcriptional Regulation, Disease Pathogenesis and Potential for Therapeutic Targets. Microrna 2024; 13:83-95. [PMID: 38317474 DOI: 10.2174/0122115366278651240105071533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 12/12/2023] [Accepted: 12/29/2023] [Indexed: 02/07/2024]
Abstract
MicroRNAs are a class of regulatory, non-coding small ribonucleic acid (RNA) molecules found in eukaryotes. Dysregulated expression of microRNAs can lead to downregulation or upregulation of their target gene. In general, microRNAs bind with the Argonaute protein and its interacting partners to form a silencing complex. This silencing complex binds with fully or partial complementary sequences in the 3'-UTR of their cognate target mRNAs and leads to degradation of the transcripts or translational inhibition, respectively. However, recent developments point towards the ability of these microRNAs to bind to the promoters, enhancers or coding sequences, leading to upregulation of their target genes. This review briefly summarizes the various non-canonical binding sites of microRNAs and their regulatory roles in various diseased conditions.
Collapse
Affiliation(s)
- Aishwarya Ray
- Department of Biological Sciences, Bose Institute, Kolkata, West Bengal, 700091, India
| | - Abhisek Sarkar
- Department of Biological Sciences, Bose Institute, Kolkata, West Bengal, 700091, India
| | - Sounak Banerjee
- Department of Biological Sciences, Bose Institute, Kolkata, West Bengal, 700091, India
| | - Kaushik Biswas
- Department of Biological Sciences, Bose Institute, Kolkata, West Bengal, 700091, India
| |
Collapse
|
3
|
Wang YL, Feng LL, Shi J, Chen WY, Bie SY, Bai SM, Zeng GD, Wang RZ, Zheng J, Wan XB, Fan XJ. CiRS-7 Enhances the Liquid-liquid Phase Separation of miRISC and Promotes DNA Damage Repair. Nucleus 2023; 14:2293599. [PMID: 38105528 PMCID: PMC10730229 DOI: 10.1080/19491034.2023.2293599] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 12/07/2023] [Indexed: 12/19/2023] Open
Abstract
Noncoding RNAs have been found to play important roles in DNA damage repair, whereas the participation of circRNA remains undisclosed. Here, we characterized ciRS-7, a circRNA containing over 70 putative miR-7-binding sites, as an enhancer of miRISC condensation and DNA repair. Both in vivo and in vitro experiments confirmed the condensation of TNRC6B and AGO2, two core protein components of human miRISC. Moreover, overexpressing ciRS-7 largely increased the condensate number of TNRC6B and AGO2 in cells, while silencing ciRS-7 reduced it. Additionally, miR-7 overexpression also promoted miRISC condensation. Consistent with the previous report that AGO2 participated in RAD51-mediated DNA damage repair, the overexpression of ciRS-7 significantly promoted irradiation-induced DNA damage repair by enhancing RAD51 recruitment. Our results uncover a new role of circRNA in liquid-liquid phase separation and provide new insight into the regulatory mechanism of ciRS-7 on miRISC function and DNA repair.
Collapse
Affiliation(s)
- Yun-Long Wang
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R. China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, P.R. China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R.China
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| | - Li-Li Feng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, P.R. China
- Department of Radiology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, P.R. China
| | - Jie Shi
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| | - Wan-Ying Chen
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R. China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, P.R. China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R.China
| | - Shu-Ying Bie
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| | - Shao-Mei Bai
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| | - Guang-Dong Zeng
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| | - Rui-Zhi Wang
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| | - Jian Zheng
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| | - Xiang-Bo Wan
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R. China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, P.R. China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R.China
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| | - Xin-Juan Fan
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R. China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, P.R. China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| |
Collapse
|
4
|
Kiltschewskij DJ, Harrison PF, Fitzsimmons C, Beilharz T, Cairns M. Extension of mRNA poly(A) tails and 3'UTRs during neuronal differentiation exhibits variable association with post-transcriptional dynamics. Nucleic Acids Res 2023; 51:8181-8198. [PMID: 37293985 PMCID: PMC10450200 DOI: 10.1093/nar/gkad499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 05/24/2023] [Accepted: 05/26/2023] [Indexed: 06/10/2023] Open
Abstract
Differentiation of neural progenitor cells into mature neuronal phenotypes relies on extensive temporospatial coordination of mRNA expression to support the development of functional brain circuitry. Cleavage and polyadenylation of mRNA has tremendous regulatory capacity through the alteration of mRNA stability and modulation of microRNA (miRNA) function, however the extent of utilization in neuronal development is currently unclear. Here, we employed poly(A) tail sequencing, mRNA sequencing, ribosome profiling and small RNA sequencing to explore the functional relationship between mRNA abundance, translation, poly(A) tail length, alternative polyadenylation (APA) and miRNA expression in an in vitro model of neuronal differentiation. Differential analysis revealed a strong bias towards poly(A) tail and 3'UTR lengthening during differentiation, both of which were positively correlated with changes in mRNA abundance, but not translation. Globally, changes in miRNA expression were predominantly associated with mRNA abundance and translation, however several miRNA-mRNA pairings with potential to regulate poly(A) tail length were identified. Furthermore, 3'UTR lengthening was observed to significantly increase the inclusion of non-conserved miRNA binding sites, potentially enhancing the regulatory capacity of these molecules in mature neuronal cells. Together, our findings suggest poly(A) tail length and APA function as part of a rich post-transcriptional regulatory matrix during neuronal differentiation.
Collapse
Affiliation(s)
- Dylan J Kiltschewskij
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW 2308, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia
| | - Paul F Harrison
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Chantel Fitzsimmons
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW 2308, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia
| | - Traude H Beilharz
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Murray J Cairns
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW 2308, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia
| |
Collapse
|
5
|
Welte T, Goulois A, Stadler MB, Hess D, Soneson C, Neagu A, Azzi C, Wisser MJ, Seebacher J, Schmidt I, Estoppey D, Nigsch F, Reece-Hoyes J, Hoepfner D, Großhans H. Convergence of multiple RNA-silencing pathways on GW182/TNRC6. Mol Cell 2023:S1097-2765(23)00423-9. [PMID: 37369201 DOI: 10.1016/j.molcel.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 04/02/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023]
Abstract
The RNA-binding protein TRIM71/LIN-41 is a phylogenetically conserved developmental regulator that functions in mammalian stem cell reprogramming, brain development, and cancer. TRIM71 recognizes target mRNAs through hairpin motifs and silences them through molecular mechanisms that await identification. Here, we uncover that TRIM71 represses its targets through RNA-supported interaction with TNRC6/GW182, a core component of the miRNA-induced silencing complex (miRISC). We demonstrate that AGO2, TRIM71, and UPF1 each recruit TNRC6 to specific sets of transcripts to silence them. As cellular TNRC6 levels are limiting, competition occurs among the silencing pathways, such that the loss of AGO proteins or of AGO binding to TNRC6 enhances the activities of the other pathways. We conclude that a miRNA-like silencing activity is shared among different mRNA silencing pathways and that the use of TNRC6 as a central hub provides a means to integrate their activities.
Collapse
Affiliation(s)
- Thomas Welte
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; Department of Medicine IV, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Alison Goulois
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Michael B Stadler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; SIB Swiss Institute of Bioinformatics, Basel, Switzerland; Faculty of Natural Sciences, University of Basel, Basel, Switzerland
| | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Charlotte Soneson
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Anca Neagu
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Chiara Azzi
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Marlena J Wisser
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; Faculty of Natural Sciences, University of Basel, Basel, Switzerland
| | - Jan Seebacher
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Isabel Schmidt
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, 4002 Basel, Switzerland
| | - David Estoppey
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, 4002 Basel, Switzerland
| | - Florian Nigsch
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, 4002 Basel, Switzerland
| | - John Reece-Hoyes
- Department of Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Dominic Hoepfner
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, 4002 Basel, Switzerland
| | - Helge Großhans
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; Faculty of Natural Sciences, University of Basel, Basel, Switzerland.
| |
Collapse
|
6
|
Yuan L, Jiang X, Gong Q, Gao N. Arsenic resistance protein 2 and microRNA biogenesis: Biological implications in cancer development. Pharmacol Ther 2023; 244:108386. [PMID: 36933704 DOI: 10.1016/j.pharmthera.2023.108386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 03/12/2023] [Accepted: 03/15/2023] [Indexed: 03/18/2023]
Abstract
Arsenic resistance protein 2 (Ars2) is a nuclear protein that plays a critical role in the regulation of microRNA (miRNA) biogenesis. Ars2 is required for cell proliferation and for the early stages of mammalian development through a possible effect on miRNA processing. Increasing evidence reveal that Ars2 is highly expressed in proliferating cancer cells, suggesting that Ars2 may be a potential therapeutic target for cancer. Therefore, development of the novel Ars2 inhibitors could represent the novel therapeutic strategies for treatment of cancer. In this review, we briefly discuss the mechanisms by which Ars2 regulates miRNA biogenesis and its impact on cell proliferation and cancer development. Particularly, we mainly discuss the role of Ars2 in the regulation of cancer development and highlight pharmacological targeting of Ars2 as a promising cancer therapeutic strategy.
Collapse
Affiliation(s)
- Liang Yuan
- Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou 563006, China
| | - Xiuxing Jiang
- College of Pharmacy, Army Medical University, 30 Gaotanyan Street, Shapingba District, Chongqing 400038, China
| | - Qihai Gong
- Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou 563006, China.
| | - Ning Gao
- Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou 563006, China.
| |
Collapse
|
7
|
Allen G, Weiss B, Panasenko OO, Huch S, Villanyi Z, Albert B, Dilg D, Zagatti M, Schaughency P, Liao SE, Corden J, Polte C, Shore D, Ignatova Z, Pelechano V, Collart MA. Not1 and Not4 inversely determine mRNA solubility that sets the dynamics of co-translational events. Genome Biol 2023; 24:30. [PMID: 36803582 PMCID: PMC9940351 DOI: 10.1186/s13059-023-02871-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 02/10/2023] [Indexed: 02/22/2023] Open
Abstract
BACKGROUND The Ccr4-Not complex is mostly known as the major eukaryotic deadenylase. However, several studies have uncovered roles of the complex, in particular of the Not subunits, unrelated to deadenylation and relevant for translation. In particular, the existence of Not condensates that regulate translation elongation dynamics has been reported. Typical studies that evaluate translation efficiency rely on soluble extracts obtained after the disruption of cells and ribosome profiling. Yet cellular mRNAs in condensates can be actively translated and may not be present in such extracts. RESULTS In this work, by analyzing soluble and insoluble mRNA decay intermediates in yeast, we determine that insoluble mRNAs are enriched for ribosomes dwelling at non-optimal codons compared to soluble mRNAs. mRNA decay is higher for soluble RNAs, but the proportion of co-translational degradation relative to the overall mRNA decay is higher for insoluble mRNAs. We show that depletion of Not1 and Not4 inversely impacts mRNA solubilities and, for soluble mRNAs, ribosome dwelling according to codon optimality. Depletion of Not4 solubilizes mRNAs with lower non-optimal codon content and higher expression that are rendered insoluble by Not1 depletion. By contrast, depletion of Not1 solubilizes mitochondrial mRNAs, which are rendered insoluble upon Not4 depletion. CONCLUSIONS Our results reveal that mRNA solubility defines the dynamics of co-translation events and is oppositely regulated by Not1 and Not4, a mechanism that we additionally determine may already be set by Not1 promoter association in the nucleus.
Collapse
Affiliation(s)
- George Allen
- Departement of Microbiology and Molecular Medicine, Institute of Genetics and Genomics Geneva, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Benjamin Weiss
- Departement of Microbiology and Molecular Medicine, Institute of Genetics and Genomics Geneva, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Present address: Department of Biomolecular Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Olesya O. Panasenko
- Departement of Microbiology and Molecular Medicine, Institute of Genetics and Genomics Geneva, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Susanne Huch
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Zoltan Villanyi
- Departement of Microbiology and Molecular Medicine, Institute of Genetics and Genomics Geneva, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Benjamin Albert
- Department of Molecular and Cellular Biology, Faculty of Sciences, Institute of Genetics and Genomics Geneva, University of Geneva, Geneva, Switzerland
- Present Address: Molecular, Cellular & Developmental Biology (MCD), Center for Integrative Biology (CBI), University of 11, CNRS/UPS, Bâtiment IBCG, 118, Route de Narbonne, 31062 ToulouseToulouse Cedex 9, France
| | - Daniel Dilg
- Department of Molecular and Cellular Biology, Faculty of Sciences, Institute of Genetics and Genomics Geneva, University of Geneva, Geneva, Switzerland
| | - Marina Zagatti
- Departement of Microbiology and Molecular Medicine, Institute of Genetics and Genomics Geneva, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Paul Schaughency
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD USA
- Present Address: Axle Informatics, NIAID Collaborative Bioinformatics Resource, North Bethesda, MD USA
| | - Susan E. Liao
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD USA
- Present Address: Department of Computer Science, Courant Institute of Mathematical Sciences, New York University, New York, USA
| | - Jeff Corden
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Christine Polte
- Departement of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - David Shore
- Department of Molecular and Cellular Biology, Faculty of Sciences, Institute of Genetics and Genomics Geneva, University of Geneva, Geneva, Switzerland
| | - Zoya Ignatova
- Departement of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Martine A. Collart
- Departement of Microbiology and Molecular Medicine, Institute of Genetics and Genomics Geneva, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| |
Collapse
|
8
|
Mauro M, Berretta M, Palermo G, Cavalieri V, La Rocca G. The Multiplicity of Argonaute Complexes in Mammalian Cells. J Pharmacol Exp Ther 2023; 384:1-9. [PMID: 35667689 PMCID: PMC9827513 DOI: 10.1124/jpet.122.001158] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 01/12/2023] Open
Abstract
Argonautes (AGOs) are a highly conserved family of proteins found in most eukaryotes and involved in mechanisms of gene regulation, both at the transcriptional and post-transcriptional level. Among other functions, AGO proteins associate with microRNAs (miRNAs) to mediate the post-transcriptional repression of protein-coding genes. In this process, AGOs associate with members of the trinucleotide repeat containing 6 protein (TNRC6) family to form the core of the RNA-induced silencing complex (RISC), the effector machinery that mediates miRNA function. However, the description of the exact composition of the RISC has been a challenging task due to the fact the AGO's interactome is dynamically regulated in a cell type- and condition-specific manner. Here, we summarize some of the most significant studies that have identified AGO complexes in mammalian cells, as well as the approaches used to characterize them. Finally, we discuss possible opportunities to exploit what we have learned on the properties of the RISC to develop novel anti-cancer therapies. SIGNIFICANCE STATEMENT: The RNA-induced silencing complex (RISC) is the molecular machinery that mediates miRNA function in mammals. Studies over the past two decades have shed light on important biochemical and functional properties of this complex. However, many aspects of this complex await further elucidation, mostly due to technical limitations that have hindered full characterization. Here, we summarize some of the most significant studies on the mammalian RISC and discuss possible sources of biases in the approaches used to characterize it.
Collapse
Affiliation(s)
- Maurizio Mauro
- Department of Medicine, Albert Einstein College of Medicine, New York, New York (M.M.); Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy (M.B.); Gruppo Oncologico Ricercatori Italiani, GORI ONLUS, Pordenone, Italy (M.B.); Department of Biomedical and Biotechnological Sciences, University of Catania, Catania Italy (G.P.); Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy (V.C.); and Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York (G.L.R.)
| | - Massimiliano Berretta
- Department of Medicine, Albert Einstein College of Medicine, New York, New York (M.M.); Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy (M.B.); Gruppo Oncologico Ricercatori Italiani, GORI ONLUS, Pordenone, Italy (M.B.); Department of Biomedical and Biotechnological Sciences, University of Catania, Catania Italy (G.P.); Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy (V.C.); and Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York (G.L.R.)
| | - Giuseppe Palermo
- Department of Medicine, Albert Einstein College of Medicine, New York, New York (M.M.); Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy (M.B.); Gruppo Oncologico Ricercatori Italiani, GORI ONLUS, Pordenone, Italy (M.B.); Department of Biomedical and Biotechnological Sciences, University of Catania, Catania Italy (G.P.); Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy (V.C.); and Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York (G.L.R.)
| | - Vincenzo Cavalieri
- Department of Medicine, Albert Einstein College of Medicine, New York, New York (M.M.); Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy (M.B.); Gruppo Oncologico Ricercatori Italiani, GORI ONLUS, Pordenone, Italy (M.B.); Department of Biomedical and Biotechnological Sciences, University of Catania, Catania Italy (G.P.); Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy (V.C.); and Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York (G.L.R.)
| | - Gaspare La Rocca
- Department of Medicine, Albert Einstein College of Medicine, New York, New York (M.M.); Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy (M.B.); Gruppo Oncologico Ricercatori Italiani, GORI ONLUS, Pordenone, Italy (M.B.); Department of Biomedical and Biotechnological Sciences, University of Catania, Catania Italy (G.P.); Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy (V.C.); and Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York (G.L.R.)
| |
Collapse
|
9
|
Bhatt IS, Wilson N, Dias R, Torkamani A. A genome-wide association study of tinnitus reveals shared genetic links to neuropsychiatric disorders. Sci Rep 2022; 12:22511. [PMID: 36581688 PMCID: PMC9800371 DOI: 10.1038/s41598-022-26413-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 12/14/2022] [Indexed: 12/30/2022] Open
Abstract
Tinnitus, a phantom perception of sound in the absence of any external sound source, is a prevalent health condition often accompanied by psychiatric comorbidities. Recent genome-wide association studies (GWAS) highlighted a polygenic nature of tinnitus susceptibility. A shared genetic component between tinnitus and psychiatric conditions remains elusive. Here we present a GWAS using the UK Biobank to investigate the genetic processes linked to tinnitus and tinnitus-related distress, followed by gene-set enrichment analyses. The UK Biobank sample comprised 132,438 individuals with tinnitus and genotype data. Among the study sample, 38,525 individuals reported tinnitus, and 26,889 participants mentioned they experienced tinnitus-related distress in daily living. The genome-wide association analyses were conducted on tinnitus and tinnitus-related distress. We conducted enrichment analyses using FUMA to further understand the genetic processes linked to tinnitus and tinnitus-related distress. A genome-wide significant locus (lead SNP: rs71595470) for tinnitus was obtained in the vicinity of GPM6A. Nineteen independent loci reached suggestive association with tinnitus. Fifteen independent loci reached suggestive association with tinnitus-related distress. The enrichment analysis revealed a shared genetic component between tinnitus and psychiatric traits, such as bipolar disorder, feeling worried, cognitive ability, fast beta electroencephalogram, and sensation seeking. Metabolic, cardiovascular, hematological, and pharmacological gene sets revealed a significant association with tinnitus. Anxiety and stress-related gene sets revealed a significant association with tinnitus-related distress. The GWAS signals for tinnitus were enriched in the hippocampus and cortex, and for tinnitus-related distress were enriched in the brain and spinal cord. This study provides novel insights into genetic processes associated with tinnitus and tinnitus-related distress and demonstrates a shared genetic component underlying tinnitus and psychiatric conditions. Further collaborative attempts are necessary to identify genetic components underlying the phenotypic heterogeneity in tinnitus and provide biological insight into the etiology.
Collapse
Affiliation(s)
- Ishan Sunilkumar Bhatt
- grid.214572.70000 0004 1936 8294Department of Communication Sciences & Disorders, University of Iowa, 250 Hawkins Dr, Iowa City, IA 52242 USA
| | - Nicholas Wilson
- Department of Integrative Structural and Computational Biology Scripps Science Institute, La Jolla, CA 92037 USA
| | - Raquel Dias
- grid.15276.370000 0004 1936 8091Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32608 USA
| | - Ali Torkamani
- Department of Integrative Structural and Computational Biology Scripps Science Institute, La Jolla, CA 92037 USA
| |
Collapse
|
10
|
Hayder H, Shan Y, Chen Y, O’Brien JA, Peng C. Role of microRNAs in trophoblast invasion and spiral artery remodeling: Implications for preeclampsia. Front Cell Dev Biol 2022; 10:995462. [PMID: 36263015 PMCID: PMC9575991 DOI: 10.3389/fcell.2022.995462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/25/2022] [Indexed: 11/18/2022] Open
Abstract
It is now well-established that microRNAs (miRNAs) are important regulators of gene expression. The role of miRNAs in placental development and trophoblast function is constantly expanding. Trophoblast invasion and their ability to remodel uterine spiral arteries are essential for proper placental development and successful pregnancy outcome. Many miRNAs are reported to be dysregulated in pregnancy complications, especially preeclampsia and they exert various regulatory effects on trophoblasts. In this review, we provide a brief overview of miRNA biogenesis and their mechanism of action, as well as of trophoblasts differentiation, invasion and spiral artery remodeling. We then discuss the role of miRNAs in trophoblasts invasion and spiral artery remodeling, focusing on miRNAs that have been thoroughly investigated, especially using multiple model systems. We also discuss the potential role of miRNAs in the pathogenesis of preeclampsia.
Collapse
Affiliation(s)
- Heyam Hayder
- Department of Biology, York University, Toronto, ON, Canada
| | - Yanan Shan
- Department of Biology, York University, Toronto, ON, Canada
| | - Yan Chen
- Department of Biology, York University, Toronto, ON, Canada
| | | | - Chun Peng
- Department of Biology, York University, Toronto, ON, Canada
- Centre for Research on Biomolecular Interactions, York University, Toronto, ON, Canada
- *Correspondence: Chun Peng,
| |
Collapse
|
11
|
Guo M, Luo C, Wang Z, Chen S, Morris D, Ruan F, Chen Z, Yang L, Wei X, Wu C, Luo B, Lv Z, Huang J, Zhang D, Yu C, Gao Q, Wang H, Zhang Y, Sun F, Yan W, Tang C. Uncoupling transcription and translation through miRNA-dependent poly(A) length control in haploid male germ cells. Development 2022; 149:275470. [PMID: 35588208 PMCID: PMC9270972 DOI: 10.1242/dev.199573] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/05/2022] [Indexed: 01/31/2023]
Abstract
As one of the post-transcriptional regulatory mechanisms, uncoupling of transcription and translation plays an essential role in development and adulthood physiology. However, it remains elusive how thousands of mRNAs get translationally silenced while stability is maintained for hours or even days before translation. In addition to oocytes and neurons, developing spermatids display significant uncoupling of transcription and translation for delayed translation. Therefore, spermiogenesis represents an excellent in vivo model for investigating the mechanism underlying uncoupled transcription and translation. Through full-length poly(A) deep sequencing, we discovered dynamic changes in poly(A) length through deadenylation and re-polyadenylation. Deadenylation appeared to be mediated by microRNAs (miRNAs), and transcripts with shorter poly(A) tails tend to be sequestered into ribonucleoprotein (RNP) granules for translational repression and stabilization. In contrast, re-polyadenylation might allow for translocation of the translationally repressed transcripts from RNP granules to polysomes. Overall, our data suggest that miRNA-dependent poly(A) length control represents a previously unreported mechanism underlying uncoupled translation and transcription in haploid male mouse germ cells.
Collapse
Affiliation(s)
- Mei Guo
- R&D Department, BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Chunhai Luo
- Institute of Reproductive Medicine, Nantong University School of Medicine, Nantong University, Nantong 226001, Jiangsu, China
| | - Zhuqing Wang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, 1664 North Virginia Street, MS575, Reno, NV 89557, USA,Department of Endocrinology and Metabolism, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Sheng Chen
- Department of Endocrinology and Metabolism, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA,China Medical University, Department of Laboratory Animal Science, Shenyang 110122, China
| | - Dayton Morris
- Department of Endocrinology and Metabolism, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Fengying Ruan
- R&D Department, BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhichao Chen
- R&D Department, BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Linfeng Yang
- R&D Department, BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Xiongyi Wei
- Institute of Reproductive Medicine, Nantong University School of Medicine, Nantong University, Nantong 226001, Jiangsu, China
| | - Chuanwen Wu
- R&D Department, BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Bei Luo
- R&D Department, BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhou Lv
- R&D Department, BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Jin Huang
- R&D Department, BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Dong Zhang
- R&D Department, BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Cong Yu
- R&D Department, BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Qiang Gao
- R&D Department, BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Hongqi Wang
- R&D Department, BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Ying Zhang
- Institute of Reproductive Medicine, Nantong University School of Medicine, Nantong University, Nantong 226001, Jiangsu, China,Authors for correspondence (; ; ; )
| | - Fei Sun
- Institute of Reproductive Medicine, Nantong University School of Medicine, Nantong University, Nantong 226001, Jiangsu, China,Authors for correspondence (; ; ; )
| | - Wei Yan
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, 1664 North Virginia Street, MS575, Reno, NV 89557, USA,Department of Endocrinology and Metabolism, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA,Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA,Authors for correspondence (; ; ; )
| | - Chong Tang
- R&D Department, BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China,Institute of Reproductive Medicine, Nantong University School of Medicine, Nantong University, Nantong 226001, Jiangsu, China,Authors for correspondence (; ; ; )
| |
Collapse
|
12
|
Rojas-Pirela M, Andrade-Alviárez D, Medina L, Castillo C, Liempi A, Guerrero-Muñoz J, Ortega Y, Maya JD, Rojas V, Quiñones W, Michels PA, Kemmerling U. MicroRNAs: master regulators in host-parasitic protist interactions. Open Biol 2022; 12:210395. [PMID: 35702995 PMCID: PMC9198802 DOI: 10.1098/rsob.210395] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
MicroRNAs (miRNAs) are a group of small non-coding RNAs present in a wide diversity of organisms. MiRNAs regulate gene expression at a post-transcriptional level through their interaction with the 3' untranslated regions of target mRNAs, inducing translational inhibition or mRNA destabilization and degradation. Thus, miRNAs regulate key biological processes, such as cell death, signal transduction, development, cellular proliferation and differentiation. The dysregulation of miRNAs biogenesis and function is related to the pathogenesis of diseases, including parasite infection. Moreover, during host-parasite interactions, parasites and host miRNAs determine the probability of infection and progression of the disease. The present review is focused on the possible role of miRNAs in the pathogenesis of diseases of clinical interest caused by parasitic protists. In addition, the potential role of miRNAs as targets for the design of drugs and diagnostic and prognostic markers of parasitic diseases is also discussed.
Collapse
Affiliation(s)
- Maura Rojas-Pirela
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile,Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile,Facultad de Farmacia y Bioanálisis, Universidad de Los Andes, Mérida, Venezuela
| | - Diego Andrade-Alviárez
- Laboratorio de Enzimología de Parásitos, Facultad de Ciencias, Universidad de Los Andes, Mérida, Venezuela
| | - Lisvaneth Medina
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile
| | - Christian Castillo
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile,Núcleo de Investigación Aplicada en Ciencias Veterinarias y Agronómicas, Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Chile
| | - Ana Liempi
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile
| | - Jesús Guerrero-Muñoz
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile
| | - Yessica Ortega
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile,Facultad de Farmacia y Bioanálisis, Universidad de Los Andes, Mérida, Venezuela
| | - Juan Diego Maya
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile
| | - Verónica Rojas
- Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile
| | - Wilfredo Quiñones
- Laboratorio de Enzimología de Parásitos, Facultad de Ciencias, Universidad de Los Andes, Mérida, Venezuela
| | - Paul A. Michels
- Centre for Immunity, Infection and Evolution and Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Ulrike Kemmerling
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile
| |
Collapse
|
13
|
Guz M, Jeleniewicz W, Cybulski M. An Insight into miR-1290: An Oncogenic miRNA with Diagnostic Potential. Int J Mol Sci 2022; 23:1234. [PMID: 35163157 PMCID: PMC8835968 DOI: 10.3390/ijms23031234] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/11/2022] [Accepted: 01/19/2022] [Indexed: 12/12/2022] Open
Abstract
For more than two decades, the view of the roles of non-coding RNAs (ncRNAs) has been radically changing. These RNA molecules that are transcribed from our genome do not have the capacity to encode proteins, but are critical regulators of gene expression at different levels. Our knowledge is constantly enriched by new reports revealing the role of these new molecular players in the development of many pathological conditions, including cancer. One of the ncRNA classes includes short RNA molecules called microRNAs (miRNAs), which are involved in the post-transcriptional control of gene expression affecting various cellular processes. The aberrant expression of miRNAs with oncogenic and tumor-suppressive function is associated with cancer initiation, promotion, malignant transformation, progression and metastasis. Oncogenic miRNAs, also known as oncomirs, mediate the downregulation of tumor-suppressor genes and their expression is upregulated in cancer. Nowadays, miRNAs show promising application in diagnosis, prediction, disease monitoring and therapy response. Our review presents a current view of the oncogenic role of miR-1290 with emphasis on its properties as a cancer biomarker in clinical medicine.
Collapse
Affiliation(s)
- Małgorzata Guz
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, 20-093 Lublin, Poland; (W.J.); (M.C.)
| | | | | |
Collapse
|
14
|
Epstein-Barr Virus BGLF2 commandeers RISC to interfere with cellular miRNA function. PLoS Pathog 2022; 18:e1010235. [PMID: 35007297 PMCID: PMC8782528 DOI: 10.1371/journal.ppat.1010235] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 01/21/2022] [Accepted: 12/27/2021] [Indexed: 01/27/2023] Open
Abstract
The Epstein-Barr virus (EBV) BGLF2 protein is a tegument protein with multiple effects on the cellular environment, including induction of SUMOylation of cellular proteins. Using affinity-purification coupled to mass-spectrometry, we identified the miRNA-Induced Silencing Complex (RISC), essential for miRNA function, as a top interactor of BGLF2. We confirmed BGLF2 interaction with the Ago2 and TNRC6 components of RISC in multiple cell lines and their co-localization in cytoplasmic bodies that also contain the stress granule marker G3BP1. In addition, BGLF2 expression led to the loss of processing bodies in multiple cell types, suggesting disruption of RISC function in mRNA regulation. Consistent with this observation, BGLF2 disrupted Ago2 association with multiple miRNAs. Using let-7 miRNAs as a model, we tested the hypothesis that BGLF2 interfered with the function of RISC in miRNA-mediated mRNA silencing. Using multiple reporter constructs with 3’UTRs containing let-7a regulated sites, we showed that BGLF2 inhibited let-7a miRNA activity dependent on these 3’UTRs, including those from SUMO transcripts which are known to be regulated by let-7 miRNAs. In keeping with these results, we showed that BGLF2 increased the cellular level of unconjugated SUMO proteins without affecting the level of SUMO transcripts. Such an increase in free SUMO is known to drive SUMOylation and would account for the effect of BGLF2 in inducing SUMOylation. We further showed that BGLF2 expression inhibited the loading of let-7 miRNAs into Ago2 proteins, and conversely, that lytic infection with EBV lacking BGLF2 resulted in increased interaction of let-7a and SUMO transcripts with Ago2, relative to WT EBV infection. Therefore, we have identified a novel role for BGLF2 as a miRNA regulator and shown that one outcome of this activity is the dysregulation of SUMO transcripts that leads to increased levels of free SUMO proteins and SUMOylation. Epstein-Barr virus (EBV) infects most people worldwide, persists for life and is associated with several kinds of cancer. In order to undergo efficient lytic infection, EBV must manipulate multiple cellular pathways. BGLF2 is an EBV lytic protein known to modulate several cellular processes including increasing the modification of cellular proteins with the Small Ubiquitin-Like Modifier (SUMO), a process referred to as SUMOylation. Here we show for the first time that BGLF2 interacts with a cellular complex (RISC) required for miRNA function and interferes with the function of some cellular miRNAs by sequestering this complex. One of the consequences of this effect is the increased expression of SUMO proteins, due to inhibition of the miRNAs that normally downregulate their expression. The resulting increase in SUMO proteins drives SUMOylation, providing a mechanism for the previously reported BGLF2-induced SUMOylation of cellular proteins. In addition, the discovery of BGLF2 as a miRNA regulator suggests that this EBV protein can control many cellular pathways by interfering with cellular miRNAs that normally regulate them.
Collapse
|
15
|
Iwakawa HO, Tomari Y. Life of RISC: Formation, action, and degradation of RNA-induced silencing complex. Mol Cell 2021; 82:30-43. [PMID: 34942118 DOI: 10.1016/j.molcel.2021.11.026] [Citation(s) in RCA: 144] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/23/2021] [Accepted: 11/23/2021] [Indexed: 01/12/2023]
Abstract
Small RNAs regulate a wide variety of biological processes by repressing the expression of target genes at the transcriptional and post-transcriptional levels. To achieve these functions, small RNAs form RNA-induced silencing complex (RISC) together with a member of the Argonaute (AGO) protein family. RISC is directed by its bound small RNA to target complementary RNAs and represses their expression through mRNA cleavage, degradation, and/or translational repression. Many different factors fine-tune RISC activity and stability-from guide-target RNA complementarity to the recruitment of other protein partners to post-translational modifications of RISC itself. Here, we review recent progress in understanding RISC formation, action, and degradation, and discuss new, intriguing questions in the field.
Collapse
Affiliation(s)
- Hiro-Oki Iwakawa
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan.
| | - Yukihide Tomari
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan.
| |
Collapse
|
16
|
La Rocca G, King B, Shui B, Li X, Zhang M, Akat KM, Ogrodowski P, Mastroleo C, Chen K, Cavalieri V, Ma Y, Anelli V, Betel D, Vidigal J, Tuschl T, Meister G, Thompson CB, Lindsten T, Haigis K, Ventura A. Inducible and reversible inhibition of miRNA-mediated gene repression in vivo. eLife 2021; 10:e70948. [PMID: 34463618 PMCID: PMC8476124 DOI: 10.7554/elife.70948] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/24/2021] [Indexed: 12/23/2022] Open
Abstract
Although virtually all gene networks are predicted to be controlled by miRNAs, the contribution of this important layer of gene regulation to tissue homeostasis in adult animals remains unclear. Gain and loss-of-function experiments have provided key insights into the specific function of individual miRNAs, but effective genetic tools to study the functional consequences of global inhibition of miRNA activity in vivo are lacking. Here we report the generation and characterization of a genetically engineered mouse strain in which miRNA-mediated gene repression can be reversibly inhibited without affecting miRNA biogenesis or abundance. We demonstrate the usefulness of this strategy by investigating the consequences of acute inhibition of miRNA function in adult animals. We find that different tissues and organs respond differently to global loss of miRNA function. While miRNA-mediated gene repression is essential for the homeostasis of the heart and the skeletal muscle, it is largely dispensable in the majority of other organs. Even in tissues where it is not required for homeostasis, such as the intestine and hematopoietic system, miRNA activity can become essential during regeneration following acute injury. These data support a model where many metazoan tissues primarily rely on miRNA function to respond to potentially pathogenic events.
Collapse
Affiliation(s)
- Gaspare La Rocca
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Bryan King
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Bing Shui
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, United States
| | - Xiaoyi Li
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Minsi Zhang
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Kemal M Akat
- Laboratory of RNA Molecular Biology, The Rockefeller University, New York, United States
| | - Paul Ogrodowski
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Chiara Mastroleo
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Kevin Chen
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Vincenzo Cavalieri
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy
| | - Yilun Ma
- Weill Cornell/Rockefeller/Sloan-Kettering Tri-Institutional MD-PhD Program, New York, United States
| | - Viviana Anelli
- Center of Integrative Biology, University of Trento, Trento, Italy
| | - Doron Betel
- Hem/Oncology, Medicine and Institution for Computational Biomedicine, Weill Cornell Medical College, New York, United States
| | - Joana Vidigal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, United States
| | - Thomas Tuschl
- Laboratory of RNA Molecular Biology, The Rockefeller University, New York, United States
| | - Gunter Meister
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Craig B Thompson
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Tullia Lindsten
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Kevin Haigis
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, United States
| | - Andrea Ventura
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
| |
Collapse
|
17
|
Jia H, Kang L, Ma Z, Lu S, Huang B, Wang C, Zou Y, Sun Y. MicroRNAs involve in bicuspid aortic aneurysm: pathogenesis and biomarkers. J Cardiothorac Surg 2021; 16:230. [PMID: 34384454 PMCID: PMC8359579 DOI: 10.1186/s13019-021-01613-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 08/03/2021] [Indexed: 01/27/2023] Open
Abstract
The incidence of bicuspid aortic valves (BAV) is high in the whole population, BAV-related thoracic aortic aneurysm (TAA) is accompanied by many adverse vascular events. So far, there are two key points in dealing with BAV-related TAA. First is fully understanding on its pathogenesis. Second is optimizing surgical intervention time. This review aims to illustrate the potential role of miRNAs in both aspects, that is, how miRNAs are involved in the occurrence and progression of BAV-related TAA, and the feasibilities of miRNAs as biomarkers.
Collapse
Affiliation(s)
- Hao Jia
- Department of Cardiac Surgery, Zhongshan Hospital, Fudan University, 1069 Xietu Road, 200032, Shanghai, People's Republic of China
| | - Le Kang
- Department of Cardiac Surgery, Zhongshan Hospital, Fudan University, 1069 Xietu Road, 200032, Shanghai, People's Republic of China
| | - Zhen Ma
- Central Laboratory of Cardiovascular Institute, Zhongshan Hospital, Fudan University, 1069 Xietu Road, 200032, Shanghai, People's Republic of China
| | - Shuyang Lu
- Department of Cardiac Surgery, Zhongshan Hospital, Fudan University, 1069 Xietu Road, 200032, Shanghai, People's Republic of China
| | - Ben Huang
- Department of Cardiac Surgery, Zhongshan Hospital, Fudan University, 1069 Xietu Road, 200032, Shanghai, People's Republic of China
| | - Chunsheng Wang
- Department of Cardiac Surgery, Zhongshan Hospital, Fudan University, 1069 Xietu Road, 200032, Shanghai, People's Republic of China.
| | - Yunzeng Zou
- Central Laboratory of Cardiovascular Institute, Zhongshan Hospital, Fudan University, 1069 Xietu Road, 200032, Shanghai, People's Republic of China.
| | - Yongxin Sun
- Department of Cardiac Surgery, Zhongshan Hospital, Fudan University, 1069 Xietu Road, 200032, Shanghai, People's Republic of China.
| |
Collapse
|
18
|
Translation Initiation Regulated by RNA-Binding Protein in Mammals: The Modulation of Translation Initiation Complex by Trans-Acting Factors. Cells 2021; 10:cells10071711. [PMID: 34359885 PMCID: PMC8306974 DOI: 10.3390/cells10071711] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/03/2021] [Accepted: 07/04/2021] [Indexed: 12/15/2022] Open
Abstract
Protein synthesis is tightly regulated at each step of translation. In particular, the formation of the basic cap-binding complex, eukaryotic initiation factor 4F (eIF4F) complex, on the 5' cap structure of mRNA is positioned as the rate-limiting step, and various cis-elements on mRNA contribute to fine-tune spatiotemporal protein expression. The cis-element on mRNAs is recognized and bound to the trans-acting factors, which enable the regulation of the translation rate or mRNA stability. In this review, we focus on the molecular mechanism of how the assembly of the eIF4F complex is regulated on the cap structure of mRNAs. We also summarize the fine-tuned regulation of translation initiation by various trans-acting factors through cis-elements on mRNAs.
Collapse
|
19
|
Zhao W, Quansah E, Yuan M, Li P, Yi C, Cai X, Zhu J. Next-generation sequencing analysis reveals segmental patterns of microRNA expression in yak epididymis. Reprod Fertil Dev 2021; 32:1067-1083. [PMID: 32758354 DOI: 10.1071/rd20113] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 06/16/2020] [Indexed: 12/26/2022] Open
Abstract
MicroRNAs (miRNAs) have emerged as potent regulators of gene expression and are widely expressed in biological systems. In reproduction, they have been shown to have a significant role in the acquisition and maintenance of male fertility, whereby deletion of Dicer in mouse germ cells leads to infertility. Evidence indicates that this role of miRNAs extends from the testis into the epididymis, controlling gene expression and contributing to regional variations in gene expression. In this study, RNA sequencing technology was used to investigate miRNA expression patterns in the yak epididymis. Region-specific miRNA expression was found in the yak epididymis. In all, 683 differentially expressed known miRNAs were obtained; 190, 186 and 307 differentially expressed miRNAs were identified for caput versus corpus, corpus versus cauda and caput versus cauda region pairs respectively. Kyoto Encyclopedia of Genes and Genomes results showed endocytosis as the most enriched pathway across region pairs, followed by protein processing in the endoplasmic reticulum, phagosome, spliceosome and biosynthesis of amino acids in region pair-specific hierarchical order. Gene ontology results showed varied enrichment in terms including cell, biogenesis, localisation, binding and locomotion across region pairs. In addition, significantly higher miR-34c expression was seen in the yak caput epididymidis relative to the corpus and cauda epididymidis.
Collapse
Affiliation(s)
- Wangsheng Zhao
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010 Sichuan, China
| | - Eugene Quansah
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010 Sichuan, China
| | - Meng Yuan
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010 Sichuan, China
| | - Pengcheng Li
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010 Sichuan, China
| | - Chuanping Yi
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010 Sichuan, China
| | - Xin Cai
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilisation (Southwest Minzu University), Ministry of Education, Chengdu, Sichuan 610041, China; and Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilisation Key Laboratory of Sichuan Province, Chengdu, Sichuan 610041, China; and Corresponding authors. ;
| | - Jiangjiang Zhu
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilisation (Southwest Minzu University), Ministry of Education, Chengdu, Sichuan 610041, China; and Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilisation Key Laboratory of Sichuan Province, Chengdu, Sichuan 610041, China; and Corresponding authors. ;
| |
Collapse
|
20
|
Kubik TD, Snell TK, Saavedra-Rodriguez K, Wilusz J, Anderson JR, Lozano-Fuentes S, Black WC, Campbell CL. Aedes aegypti miRNA-33 modulates permethrin induced toxicity by regulating VGSC transcripts. Sci Rep 2021; 11:7301. [PMID: 33790374 PMCID: PMC8012613 DOI: 10.1038/s41598-021-86665-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 03/18/2021] [Indexed: 12/12/2022] Open
Abstract
Aedes aegypti is a major vector of Zika, dengue, and other arboviruses. Permethrin adulticidal spraying, which targets the voltage-gated sodium channel (VGSC), is commonly done to reduce local mosquito populations and protect humans from exposure to arbovirus pathogens transmitted by this dangerous pest. Permethrin resistance, however, is a growing problem and understanding its underlying molecular basis may identify avenues to combat it. We identified a single G:C polymorphism in pre-miR-33 that was genetically associated with permethrin resistance; resulting isoforms had structural differences that may affect DICER-1/pre-miRNA processing rates. We then assessed the effects of overexpression of pre-miR-33 isoforms on permethrin toxicological phenotypes, VGSC transcript abundance and protein levels for two genetically related mosquito strains. One strain had its naturally high permethrin resistance levels maintained by periodic treatment, and the other was released from selection. VGSC protein levels were lower in the permethrin resistant strain than in the related permethrin-susceptible strain. Overexpression of the G-pre-miR-33 isoform reduced VGSC expression levels in both strains. To further elucidate changes in gene expression associated with permethrin resistance, exome-capture gDNA deep sequencing, genetic association mapping and subsequent gene set enrichment analysis revealed that transport genes, in particular, were selected in resistant versus susceptible mosquitoes. Collectively, these data indicate that miR-33 regulates VGSC expression as part of a nuanced system of neuronal regulation that contributes to a network of heritable features determining permethrin resistance.
Collapse
Affiliation(s)
- Tristan D Kubik
- Department of Microbiology, Immunology and Pathology, Colorado State University, Campus Delivery 1685, Fort Collins, CO, 80523, USA
| | - Trey K Snell
- Department of Microbiology, Immunology and Pathology, Colorado State University, Campus Delivery 1685, Fort Collins, CO, 80523, USA
| | - Karla Saavedra-Rodriguez
- Department of Microbiology, Immunology and Pathology, Colorado State University, Campus Delivery 1685, Fort Collins, CO, 80523, USA
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Campus Delivery 1685, Fort Collins, CO, 80523, USA
| | - John R Anderson
- Department of Microbiology, Immunology and Pathology, Colorado State University, Campus Delivery 1685, Fort Collins, CO, 80523, USA
| | - Saul Lozano-Fuentes
- Department of Microbiology, Immunology and Pathology, Colorado State University, Campus Delivery 1685, Fort Collins, CO, 80523, USA
| | - William C Black
- Department of Microbiology, Immunology and Pathology, Colorado State University, Campus Delivery 1685, Fort Collins, CO, 80523, USA
| | - Corey L Campbell
- Department of Microbiology, Immunology and Pathology, Colorado State University, Campus Delivery 1685, Fort Collins, CO, 80523, USA.
| |
Collapse
|
21
|
Holzner G, Mateescu B, van Leeuwen D, Cereghetti G, Dechant R, Stavrakis S, deMello A. High-throughput multiparametric imaging flow cytometry: toward diffraction-limited sub-cellular detection and monitoring of sub-cellular processes. Cell Rep 2021; 34:108824. [PMID: 33691119 DOI: 10.1016/j.celrep.2021.108824] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/07/2020] [Accepted: 02/12/2021] [Indexed: 02/06/2023] Open
Abstract
We present a sheathless, microfluidic imaging flow cytometer that incorporates stroboscopic illumination for blur-free fluorescence detection at ultra-high analytical throughput. The imaging platform is capable of multiparametric fluorescence quantification and sub-cellular localization of these structures down to 500 nm with microscopy image quality. We demonstrate the efficacy of the approach through the analysis and localization of P-bodies and stress granules in yeast and human cells using fluorescence and bright-field detection at analytical throughputs in excess of 60,000 and 400,000 cells/s, respectively. Results highlight the utility of our imaging flow cytometer in directly investigating phase-separated compartments within cellular environments and screening rare events at the sub-cellular level for a range of diagnostic applications.
Collapse
Affiliation(s)
- Gregor Holzner
- Institute for Chemical & Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland
| | - Bogdan Mateescu
- Brain Research Institute, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Daniel van Leeuwen
- Department of Biology, ETH Zürich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Gea Cereghetti
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Reinhard Dechant
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Stavros Stavrakis
- Institute for Chemical & Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland.
| | - Andrew deMello
- Institute for Chemical & Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland.
| |
Collapse
|
22
|
Cai Z, Zhai T, Muhanhali D, Ling Y. TNRC6C Functions as a Tumor Suppressor and Is Frequently Downregulated in Papillary Thyroid Cancer. Int J Endocrinol 2021; 2021:6686998. [PMID: 33564303 PMCID: PMC7867448 DOI: 10.1155/2021/6686998] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/29/2020] [Accepted: 01/22/2021] [Indexed: 12/21/2022] Open
Abstract
Our previous study found that trinucleotide repeat containing adaptor 6C (TNRC6C) may act as a tumor suppressor in papillary thyroid cancer (PTC). In this study, we aimed to confirm the effect of TNRC6C on PTC and investigate the underlying molecular mechanism. The difference of mRNA level of TNRC6C between PTC tissue and noncancerous thyroid tissue and the association of expression level of TNRC6C with clinicopathological features of PTC were analyzed using TCGA data. Immunohistochemical assay was performed to detect the protein expression of TNRC6C in PTC and its adjacent noncancerous tissue. Cell proliferation, migration, invasion, and apoptosis were analyzed after knockdown or overexpression of TNRC6C in BCPAP cells. RNA-sequencing was performed to find the target genes of TNRC6C, and potential targets were validated in BCPAP and TPC1 cells. Our results showed that TNRC6C was downregulated in PTC, and lower expression level of TNRC6C was associated with worse clinicopathological features. Overexpression of TNRC6C significantly inhibited proliferation, migration, and invasion of BCPAP cells and promoted its apoptosis, while knockdown of TNRC6C acted the opposite role. By analyzing RNA-sequencing data and TCGA data, 12 genes (SCD, CRLF1, APCDD1L, CTHRC1, PTPRU, ALDH1A3, VCAN, TNC, ECE1, COL1A1, CAMK2N2, and MMP14) were considered as potential target genes of TNRC6C, and most of them were associated with clinicopathological features of PTC in TCGA. All of them except CAMK2N2 were significantly downregulated after overexpressing TNRC6C. Our study demonstrated that TNRC6C functions as a tumor suppressor in PTC and may serve as a useful therapeutic target and prognostic marker for PTC patients.
Collapse
Affiliation(s)
- Zhenqin Cai
- Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, No.180 Fenglin Road, Shanghai 200032, China
| | - Tianyu Zhai
- Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, No.180 Fenglin Road, Shanghai 200032, China
| | - Dilidaer Muhanhali
- Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, No.180 Fenglin Road, Shanghai 200032, China
| | - Yan Ling
- Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, No.180 Fenglin Road, Shanghai 200032, China
| |
Collapse
|
23
|
Sebastian-delaCruz M, Gonzalez-Moro I, Olazagoitia-Garmendia A, Castellanos-Rubio A, Santin I. The Role of lncRNAs in Gene Expression Regulation through mRNA Stabilization. Noncoding RNA 2021; 7:ncrna7010003. [PMID: 33466464 PMCID: PMC7839045 DOI: 10.3390/ncrna7010003] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 12/28/2020] [Accepted: 12/30/2020] [Indexed: 12/12/2022] Open
Abstract
mRNA stability influences gene expression and translation in almost all living organisms, and the levels of mRNA molecules in the cell are determined by a balance between production and decay. Maintaining an accurate balance is crucial for the correct function of a wide variety of biological processes and to maintain an appropriate cellular homeostasis. Long non-coding RNAs (lncRNAs) have been shown to participate in the regulation of gene expression through different molecular mechanisms, including mRNA stabilization. In this review we provide an overview on the molecular mechanisms by which lncRNAs modulate mRNA stability and decay. We focus on how lncRNAs interact with RNA binding proteins and microRNAs to avoid mRNA degradation, and also on how lncRNAs modulate epitranscriptomic marks that directly impact on mRNA stability.
Collapse
Affiliation(s)
- Maialen Sebastian-delaCruz
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, 48940 Leioa, Spain; (M.S.-d.); (A.O.-G.); (A.C.-R.)
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain;
| | - Itziar Gonzalez-Moro
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain;
- Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain
| | - Ane Olazagoitia-Garmendia
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, 48940 Leioa, Spain; (M.S.-d.); (A.O.-G.); (A.C.-R.)
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain;
| | - Ainara Castellanos-Rubio
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, 48940 Leioa, Spain; (M.S.-d.); (A.O.-G.); (A.C.-R.)
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain;
- Ikerbasque, Basque Foundation for Science, 48009 Bilbao, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Izortze Santin
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain;
- Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Correspondence: ; Tel.: +34-94-601-32-09
| |
Collapse
|
24
|
Inagaki H, Hosoda N, Tsuiji H, Hoshino SI. Direct evidence that Ataxin-2 is a translational activator mediating cytoplasmic polyadenylation. J Biol Chem 2020; 295:15810-15825. [PMID: 32989052 DOI: 10.1074/jbc.ra120.013835] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 09/13/2020] [Indexed: 12/27/2022] Open
Abstract
The RNA-binding protein Ataxin-2 binds to and stabilizes a number of mRNA sequences, including that of the transactive response DNA-binding protein of 43 kDa (TDP-43). Ataxin-2 is additionally involved in several processes requiring translation, such as germline formation, long-term habituation, and circadian rhythm formation. However, it has yet to be unambiguously demonstrated that Ataxin-2 is actually involved in activating the translation of its target mRNAs. Here we provide direct evidence from a polysome profile analysis showing that Ataxin-2 enhances translation of target mRNAs. Our recently established method for transcriptional pulse-chase analysis under conditions of suppressing deadenylation revealed that Ataxin-2 promotes post-transcriptional polyadenylation of the target mRNAs. Furthermore, Ataxin-2 binds to a poly(A)-binding protein PABPC1 and a noncanonical poly(A) polymerase PAPD4 via its intrinsically disordered region (amino acids 906-1095) to recruit PAPD4 to the targets. Post-transcriptional polyadenylation by Ataxin-2 explains not only how it activates translation but also how it stabilizes target mRNAs, including TDP-43 mRNA. Ataxin-2 is known to be a potent modifier of TDP-43 proteinopathies and to play a causative role in the neurodegenerative disease spinocerebellar ataxia type 2, so these findings suggest that Ataxin-2-induced cytoplasmic polyadenylation and activation of translation might impact neurodegeneration (i.e. TDP-43 proteinopathies), and this process could be a therapeutic target for Ataxin-2-related neurodegenerative disorders.
Collapse
Affiliation(s)
- Hiroto Inagaki
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan
| | - Nao Hosoda
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan
| | - Hitomi Tsuiji
- Department of Biomedical Science, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan
| | - Shin-Ichi Hoshino
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan.
| |
Collapse
|
25
|
Therapeutically Significant MicroRNAs in Primary and Metastatic Brain Malignancies. Cancers (Basel) 2020; 12:cancers12092534. [PMID: 32906592 PMCID: PMC7564168 DOI: 10.3390/cancers12092534] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/31/2020] [Accepted: 09/03/2020] [Indexed: 12/11/2022] Open
Abstract
Simple Summary The overall survival of brain cancer patients remains grim, with conventional therapies such as chemotherapy and radiotherapy only providing marginal benefits to patient survival. Cancers are complex, with multiple pathways being dysregulated simultaneously. Non-coding RNAs such as microRNA (miRNAs) are gaining importance due to their potential in regulating a variety of targets implicated in the pathology of cancers. This could be leveraged for the development of targeted and personalized therapies for cancers. Since miRNAs can upregulate and/or downregulate proteins, this review aims to understand the role of these miRNAs in primary and metastatic brain cancers. Here, we discuss the regulatory mechanisms of ten miRNAs that are highly dysregulated in glioblastoma and metastatic brain tumors. This will enable researchers to develop miRNA-based targeted cancer therapies and identify potential prognostic biomarkers. Abstract Brain cancer is one among the rare cancers with high mortality rate that affects both children and adults. The most aggressive form of primary brain tumor is glioblastoma. Secondary brain tumors most commonly metastasize from primary cancers of lung, breast, or melanoma. The five-year survival of primary and secondary brain tumors is 34% and 2.4%, respectively. Owing to poor prognosis, tumor heterogeneity, increased tumor relapse, and resistance to therapies, brain cancers have high mortality and poor survival rates compared to other cancers. Early diagnosis, effective targeted treatments, and improved prognosis have the potential to increase the survival rate of patients with primary and secondary brain malignancies. MicroRNAs (miRNAs) are short noncoding RNAs of approximately 18–22 nucleotides that play a significant role in the regulation of multiple genes. With growing interest in the development of miRNA-based therapeutics, it is crucial to understand the differential role of these miRNAs in the given cancer scenario. This review focuses on the differential expression of ten miRNAs (miR-145, miR-31, miR-451, miR-19a, miR-143, miR-125b, miR-328, miR-210, miR-146a, and miR-126) in glioblastoma and brain metastasis. These miRNAs are highly dysregulated in both primary and metastatic brain tumors, which necessitates a better understanding of their role in these cancers. In the context of the tumor microenvironment and the expression of different genes, these miRNAs possess both oncogenic and/or tumor-suppressive roles within the same cancer.
Collapse
|
26
|
Bah I, Alkhateeb T, Kumbhare A, Youssef D, Yao ZQ, Hawkin GA, McCall CE, El Gazzar M. HuR promotes miRNA-mediated upregulation of NFI-A protein expression in MDSCs during murine sepsis. Mol Immunol 2020; 123:97-105. [PMID: 32474254 DOI: 10.1016/j.molimm.2020.04.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 04/09/2020] [Accepted: 04/14/2020] [Indexed: 01/04/2023]
Abstract
Myeloid-derived suppressor cells (MDSCs) contribute to high mortality rates during sepsis, but how sepsis induces MDSCs is unclear. Previously we reported that microRNA (miR)-21 and miR-181b reprogram MDSCs in septic mice by increasing levels of DNA binding transcription factor, nuclear factor 1 (NFI-A). Here, we provide evidence that miR-21 and miR-181b stabilize NFI-A mRNA and increase NFI-A protein levels by recruiting RNA-binding proteins HuR and Ago1 to its 3' untranslated region (3'UTR). We also find that the NFI-A GU-rich element (GRE)-binding protein CUGBP1 counters miR-21 and miR-181b dependent NFI-A mRNA stabilization and decreases protein production by replacing 3'UTR bound Ago1 with Ago2. We confirmed the miR-21 and miR-181b dependent reprogramming pathway in MDSCs transfected with a luciferase reporter construct containing an NFI-A 3'UTR fragment with point mutations in the miRNA binding sites. These results suggest that targeting NFI-A in MDSCs during sepsis may enhance resistance to uncontrolled infection.
Collapse
Affiliation(s)
- Isatou Bah
- Department of Internal Medicine, East Tennessee State University College of Medicine, Johnson City, TN, 37614, USA
| | - Tuqa Alkhateeb
- Department of Internal Medicine, East Tennessee State University College of Medicine, Johnson City, TN, 37614, USA
| | - Ajinkya Kumbhare
- Department of Internal Medicine, East Tennessee State University College of Medicine, Johnson City, TN, 37614, USA
| | - Dima Youssef
- Department of Internal Medicine, East Tennessee State University College of Medicine, Johnson City, TN, 37614, USA
| | - Zhi Q Yao
- Department of Internal Medicine, East Tennessee State University College of Medicine, Johnson City, TN, 37614, USA
| | - Gregory A Hawkin
- Department of Biochemistry and Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, 27157, USA
| | - Charles E McCall
- Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, 27157, USA
| | - Mohamed El Gazzar
- Department of Internal Medicine, East Tennessee State University College of Medicine, Johnson City, TN, 37614, USA.
| |
Collapse
|
27
|
Eisen TJ, Eichhorn SW, Subtelny AO, Bartel DP. MicroRNAs Cause Accelerated Decay of Short-Tailed Target mRNAs. Mol Cell 2020; 77:775-785.e8. [PMID: 31902668 DOI: 10.1016/j.molcel.2019.12.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/25/2019] [Accepted: 12/06/2019] [Indexed: 01/05/2023]
Abstract
MicroRNAs (miRNAs) specify the recruitment of deadenylases to mRNA targets. Despite this recruitment, we find that miRNAs have almost no effect on steady-state poly(A)-tail lengths of their targets in mouse fibroblasts, which motivates the acquisition of pre-steady-state measurements of the effects of miRNAs on tail lengths, mRNA levels, and translational efficiencies. Effects on translational efficiency are minimal compared to effects on mRNA levels, even for newly transcribed target mRNAs. Effects on target mRNA levels accumulate as the mRNA population approaches steady state, whereas effects on tail lengths peak for recently transcribed target mRNAs and then subside. Computational modeling of this phenomenon reveals that miRNAs cause not only accelerated deadenylation of their targets but also accelerated decay of short-tailed target molecules. This unanticipated effect of miRNAs largely prevents short-tailed target mRNAs from accumulating despite accelerated target deadenylation. The net result is a nearly imperceptible change to the steady-state tail-length distribution of targeted mRNAs.
Collapse
Affiliation(s)
- Timothy J Eisen
- Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Stephen W Eichhorn
- Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alexander O Subtelny
- Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David P Bartel
- Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| |
Collapse
|
28
|
Linck-Paulus L, Hellerbrand C, Bosserhoff AK, Dietrich P. Dissimilar Appearances Are Deceptive-Common microRNAs and Therapeutic Strategies in Liver Cancer and Melanoma. Cells 2020; 9:E114. [PMID: 31906510 PMCID: PMC7017070 DOI: 10.3390/cells9010114] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/20/2019] [Accepted: 12/23/2019] [Indexed: 12/13/2022] Open
Abstract
: In this review, we summarize the current knowledge on miRNAs as therapeutic targets in two cancer types that were frequently described to be driven by miRNAs-melanoma and hepatocellular carcinoma (HCC). By focusing on common microRNAs and associated pathways in these-at first sight-dissimilar cancer types, we aim at revealing similar molecular mechanisms that are evolved in microRNA-biology to drive cancer progression. Thereby, we also want to outlay potential novel therapeutic strategies. After providing a brief introduction to general miRNA biology and basic information about HCC and melanoma, this review depicts prominent examples of potent oncomiRs and tumor-suppressor miRNAs, which have been proven to drive diverse cancer types including melanoma and HCC. To develop and apply miRNA-based therapeutics for cancer treatment in the future, it is essential to understand how miRNA dysregulation evolves during malignant transformation. Therefore, we highlight important aspects such as genetic alterations, miRNA editing and transcriptional regulation based on concrete examples. Furthermore, we expand our illustration by focusing on miRNA-associated proteins as well as other regulators of miRNAs which could also provide therapeutic targets. Finally, design and delivery strategies of miRNA-associated therapeutic agents as well as potential drawbacks are discussed to address the question of how miRNAs might contribute to cancer therapy in the future.
Collapse
Affiliation(s)
- Lisa Linck-Paulus
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University Erlangen-Nürnberg, 91054 Erlangen, Germany; (L.L.-P.); (C.H.)
| | - Claus Hellerbrand
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University Erlangen-Nürnberg, 91054 Erlangen, Germany; (L.L.-P.); (C.H.)
- Comprehensive Cancer Center (CCC) Erlangen-EMN, 91054 Erlangen, Germany
| | - Anja K. Bosserhoff
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University Erlangen-Nürnberg, 91054 Erlangen, Germany; (L.L.-P.); (C.H.)
- Comprehensive Cancer Center (CCC) Erlangen-EMN, 91054 Erlangen, Germany
| | - Peter Dietrich
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University Erlangen-Nürnberg, 91054 Erlangen, Germany; (L.L.-P.); (C.H.)
- Department of Medicine 1, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, 91054 Erlangen, Germany
| |
Collapse
|
29
|
Sala L, Chandrasekhar S, Vidigal JA. AGO unchained: Canonical and non-canonical roles of Argonaute proteins in mammals. Front Biosci (Landmark Ed) 2020; 25:1-42. [PMID: 31585876 DOI: 10.2741/4793] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Argonaute (AGO) proteins play key roles in animal physiology by binding to small RNAs and regulating the expression of their targets. In mammals, they do so through two distinct pathways: the miRNA pathway represses genes through a multiprotein complex that promotes both decay and translational repression; the siRNA pathway represses transcripts through direct Ago2-mediated cleavage. Here, we review our current knowledge of mechanistic details and physiological requirements of both these pathways and briefly discuss their implications to human disease.
Collapse
Affiliation(s)
- Laura Sala
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Srividya Chandrasekhar
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Joana A Vidigal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, MD 20892, USA,
| |
Collapse
|
30
|
Wilczynska A, Gillen SL, Schmidt T, Meijer HA, Jukes-Jones R, Langlais C, Kopra K, Lu WT, Godfrey JD, Hawley BR, Hodge K, Zanivan S, Cain K, Le Quesne J, Bushell M. eIF4A2 drives repression of translation at initiation by Ccr4-Not through purine-rich motifs in the 5'UTR. Genome Biol 2019; 20:262. [PMID: 31791371 PMCID: PMC6886185 DOI: 10.1186/s13059-019-1857-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 10/10/2019] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Regulation of the mRNA life cycle is central to gene expression control and determination of cell fate. miRNAs represent a critical mRNA regulatory mechanism, but despite decades of research, their mode of action is still not fully understood. RESULTS Here, we show that eIF4A2 is a major effector of the repressive miRNA pathway functioning via the Ccr4-Not complex. We demonstrate that while DDX6 interacts with Ccr4-Not, its effects in the mechanism are not as pronounced. Through its interaction with the Ccr4-Not complex, eIF4A2 represses mRNAs at translation initiation. We show evidence that native eIF4A2 has similar RNA selectivity to chemically inhibited eIF4A1. eIF4A2 exerts its repressive effect by binding purine-rich motifs which are enriched in the 5'UTR of target mRNAs directly upstream of the AUG start codon. CONCLUSIONS Our data support a model whereby purine motifs towards the 3' end of the 5'UTR are associated with increased ribosome occupancy and possible uORF activation upon eIF4A2 binding.
Collapse
Affiliation(s)
- Ania Wilczynska
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK.
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK.
| | - Sarah L Gillen
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
- MRC Toxicology Unit, Lancaster Road, Leicester, LE1 9HN, UK
| | - Tobias Schmidt
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - Hedda A Meijer
- MRC Toxicology Unit, Lancaster Road, Leicester, LE1 9HN, UK
- Present Address: Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | | | | | - Kari Kopra
- MRC Toxicology Unit, Lancaster Road, Leicester, LE1 9HN, UK
- Present Address: Department of Chemistry, University of Turku, Vatselankatu 2, FI-20500, Turku, Finland
| | - Wei-Ting Lu
- MRC Toxicology Unit, Lancaster Road, Leicester, LE1 9HN, UK
| | - Jack D Godfrey
- MRC Toxicology Unit, Lancaster Road, Leicester, LE1 9HN, UK
| | | | - Kelly Hodge
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - Sara Zanivan
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Kelvin Cain
- MRC Toxicology Unit, Lancaster Road, Leicester, LE1 9HN, UK
| | - John Le Quesne
- MRC Toxicology Unit, Lancaster Road, Leicester, LE1 9HN, UK
| | - Martin Bushell
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK.
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK.
| |
Collapse
|
31
|
Narula A, Ellis J, Taliaferro JM, Rissland OS. Coding regions affect mRNA stability in human cells. RNA (NEW YORK, N.Y.) 2019; 25:1751-1764. [PMID: 31527111 PMCID: PMC6859850 DOI: 10.1261/rna.073239.119] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 09/09/2019] [Indexed: 05/05/2023]
Abstract
A new paradigm has emerged that coding regions can regulate mRNA stability in model organisms. Here, due to differences in cognate tRNA abundance, synonymous codons are translated at different speeds, and slow codons then stimulate mRNA decay. To ask if this phenomenon also occurs in humans, we isolated RNA stability effects due to coding regions using the human ORFeome collection. We find that many open reading frame (ORF) characteristics, such as length and secondary structure, fail to provide explanations for how coding regions alter mRNA stability, and, instead, that the ORF relies on translation to impact mRNA stability. Consistent with what has been seen in other organisms, codon use is related to the effects of ORFs on transcript stability. Importantly, we found instability-associated codons have longer A-site dwell times, suggesting for the first time in humans a connection between elongation speed and mRNA decay. Thus, we propose that codon usage alters decoding speeds and so affects human mRNA stability.
Collapse
Affiliation(s)
- Ashrut Narula
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - James Ellis
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - J Matthew Taliaferro
- RNA Bioscience Initiative and Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Olivia S Rissland
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| |
Collapse
|
32
|
Sun Y, Zhang X. Role of DCP1-DCP2 complex regulated by viral and host microRNAs in DNA virus infection. FISH & SHELLFISH IMMUNOLOGY 2019; 92:21-30. [PMID: 31146005 DOI: 10.1016/j.fsi.2019.05.058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/23/2019] [Accepted: 05/25/2019] [Indexed: 06/09/2023]
Abstract
The DCP1-DCP2 complex can regulate the antiviral immunity of animals by the decapping of retrovirus RNAs and the suppression of RNAi during RNA virus infection. However, the influence of DCP1-DCP2 complex on DNA virus infection and the regulation of DCP1-DCP2 complex by microRNAs (miRNAs) remain unclear. In this study, the role of miRNA-regulated DCP1-DCP2 complex in DNA virus infection was characterized. Our results showed that the DCP1-DCP2 complex played a positive role in the infection of white spot syndrome virus (WSSV), a DNA virus of shrimp. In the DCP1-DCP2 complex, the N-terminal regulatory domain of DCP2 was interacted with the EVH1 domain of DCP1. Furthermore, shrimp miRNA miR-87 inhibited WSSV infection by targeting the host DCP2 gene and viral miRNA WSSV-miR-N46 took a negative effect on WSSV replication by targeting the host DCP1 gene. Therefore, our study provided novel insights into the underlying mechanism of DCP1-DCP2 complex and its regulation by miRNAs in virus-host interactions. IMPORTANCE: During RNA virus infection, the DCP1-DCP2 complex can play important roles in the animal antiviral immunity by decapping retrovirus RNAs and suppressing RNAi. In the present study, the findings indicated that the silencing of DCP1 and DCP2 inhibited the infection of WSSV, a DNA virus of shrimp, suggesting that the DCP1-DCP2 complex facilitated DNA virus infection. Due to the suppressive role of the DCP1-DCP2 complex in shrimp RNAi against WSSV infection, the DCP1-DCP2 complex could promote WSSV infection in shrimp. The results showed that WSSV-miR-N46 and shrimp miR-87 could respectively suppress the expressions of DCP1 and DCP2 to affect virus infection. Therefore, our study contributed novel aspects of the DCP1-DCP2 complex and its regulation by miRNAs in virus-host interactions.
Collapse
Affiliation(s)
- Yuechao Sun
- College of Life Sciences and Laboratory for Marine Biology and Biotechnology of Qingdao National Laboratory for Marine Science and Technology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Xiaobo Zhang
- College of Life Sciences and Laboratory for Marine Biology and Biotechnology of Qingdao National Laboratory for Marine Science and Technology, Zhejiang University, Hangzhou, 310058, People's Republic of China.
| |
Collapse
|
33
|
Cui TJ, Joo C. Facilitated diffusion of Argonaute-mediated target search. RNA Biol 2019; 16:1093-1107. [PMID: 31068066 PMCID: PMC6693542 DOI: 10.1080/15476286.2019.1616353] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 04/29/2019] [Accepted: 05/01/2019] [Indexed: 10/26/2022] Open
Abstract
Argonaute (Ago) proteins are of key importance in many cellular processes. In eukaryotes, Ago can induce translational repression followed by deadenylation and degradation of mRNA molecules through base pairing of microRNAs (miRNAs) with a complementary target on a mRNA sequence. In bacteria, Ago eliminates foreign DNA through base pairing of siDNA (small interfering DNA) with a target on a DNA sequence. Effective targeting activities of Ago require fast recognition of the cognate target sequence among numerous off-target sites. Other target search proteins such as transcription factors (TFs) are known to rely on facilitated diffusion for this goal, but it is undetermined to what extent these small nucleic acid-guided proteins utilize this mechanism. Here, we review recent single-molecule studies on Ago target search. We discuss the consequences of the recent findings on the search mechanism. Furthermore, we discuss the open standing research questions that need to be addressed for a complete picture of facilitated target search by small nucleic acids.
Collapse
Affiliation(s)
- Tao Ju Cui
- Kavli Institute of Nanoscience and Department of Bionanoscience, Delft University of Technology, Delft, The Netherlands
| | - Chirlmin Joo
- Kavli Institute of Nanoscience and Department of Bionanoscience, Delft University of Technology, Delft, The Netherlands
| |
Collapse
|
34
|
Kiltschewskij D, Cairns MJ. Temporospatial guidance of activity-dependent gene expression by microRNA: mechanisms and functional implications for neural plasticity. Nucleic Acids Res 2019; 47:533-545. [PMID: 30535081 PMCID: PMC6344879 DOI: 10.1093/nar/gky1235] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 11/30/2018] [Indexed: 01/08/2023] Open
Abstract
MicroRNA are major regulators of neuronal gene expression at the post-transcriptional and translational levels. This layer of control is critical for spatially and temporally restricted gene expression, facilitating highly dynamic changes to cellular structure and function associated with neural plasticity. Investigation of microRNA function in the neural system, however, is at an early stage, and many aspects of the mechanisms employing these small non-coding RNAs remain unclear. In this article, we critically review current knowledge pertaining to microRNA function in neural activity, with emphasis on mechanisms of microRNA repression, their subcellular remodelling and functional impacts on neural plasticity and behavioural phenotypes.
Collapse
Affiliation(s)
- Dylan Kiltschewskij
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, 2323, Australia.,Centre for Brain and Mental Health Research, Hunter Medical Research Institute, New Lambton, NSW, 2323, Australia
| | - Murray J Cairns
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, 2323, Australia.,Centre for Brain and Mental Health Research, Hunter Medical Research Institute, New Lambton, NSW, 2323, Australia
| |
Collapse
|
35
|
Interpreting and integrating big data in non-coding RNA research. Emerg Top Life Sci 2019; 3:343-355. [PMID: 33523206 DOI: 10.1042/etls20190004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 07/10/2019] [Accepted: 07/15/2019] [Indexed: 12/17/2022]
Abstract
In the last two decades, we have witnessed an impressive crescendo of non-coding RNA studies, due to both the development of high-throughput RNA-sequencing strategies and an ever-increasing awareness of the involvement of newly discovered ncRNA classes in complex regulatory networks. Together with excitement for the possibility to explore previously unknown layers of gene regulation, these advancements led to the realization of the need for shared criteria of data collection and analysis and for novel integrative perspectives and tools aimed at making biological sense of very large bodies of molecular information. In the last few years, efforts to respond to this need have been devoted mainly to the regulatory interactions involving ncRNAs as direct or indirect regulators of protein-coding mRNAs. Such efforts resulted in the development of new computational tools, allowing the exploitation of the information spread in numerous different ncRNA data sets to interpret transcriptome changes under physiological and pathological cell responses. While experimental validation remains essential to identify key RNA regulatory interactions, the integration of ncRNA big data, in combination with systematic literature mining, is proving to be invaluable in identifying potential new players, biomarkers and therapeutic targets in cancer and other diseases.
Collapse
|
36
|
Amaya Ramirez CC, Hubbe P, Mandel N, Béthune J. 4EHP-independent repression of endogenous mRNAs by the RNA-binding protein GIGYF2. Nucleic Acids Res 2019; 46:5792-5808. [PMID: 29554310 PMCID: PMC6009589 DOI: 10.1093/nar/gky198] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 03/07/2018] [Indexed: 11/12/2022] Open
Abstract
Initially identified as a factor involved in tyrosine kinase receptor signaling, Grb10-interacting GYF protein 2 (GIGYF2) has later been shown to interact with the 5′ cap-binding protein 4EHP as part of a translation repression complex, and to mediate post-transcriptional repression of tethered reporter mRNAs. A current model proposes that GIGYF2 is indirectly recruited to mRNAs by specific RNA-binding proteins (RBPs) leading to translation repression through its association with 4EHP. Accordingly, we recently observed that GIGYF2 also interacts with the miRNA-induced silencing complex and probably modulates its translation repression activity. Here we have further investigated how GIGYF2 represses mRNA function. In a tethering reporter assay, we identify three independent domains of GIGYF2 with repressive activity. In this assay, GIGYF2-mediated repression is independent of 4EHP but largely dependent on the CCR4/NOT complex that GIGYF2 recruits through multiple interfaces. Importantly, we show that GIGYF2 is an RBP and identify for the first time endogenous mRNA targets that recapitulate 4EHP-independent repression. Altogether, we propose that GIGYF2 has two distinct mechanisms of repression: one depends on 4EHP binding and mainly affects translation; the other is 4EHP-independent and involves the CCR4/NOT complex and its deadenylation activity.
Collapse
Affiliation(s)
- Cinthia C Amaya Ramirez
- CellNetworks Junior Research Group Posttranscriptional Regulation of mRNA Expression and Localization, Heidelberg University, D-69120 Heidelberg, Germany.,Biochemistry Center, Heidelberg University, D-69120 Heidelberg, Germany
| | - Petra Hubbe
- CellNetworks Junior Research Group Posttranscriptional Regulation of mRNA Expression and Localization, Heidelberg University, D-69120 Heidelberg, Germany.,Biochemistry Center, Heidelberg University, D-69120 Heidelberg, Germany
| | - Nicolas Mandel
- CellNetworks Junior Research Group Posttranscriptional Regulation of mRNA Expression and Localization, Heidelberg University, D-69120 Heidelberg, Germany.,Biochemistry Center, Heidelberg University, D-69120 Heidelberg, Germany
| | - Julien Béthune
- CellNetworks Junior Research Group Posttranscriptional Regulation of mRNA Expression and Localization, Heidelberg University, D-69120 Heidelberg, Germany.,Biochemistry Center, Heidelberg University, D-69120 Heidelberg, Germany
| |
Collapse
|
37
|
Li Y, Wang L, Rivera-Serrano EE, Chen X, Lemon SM. TNRC6 proteins modulate hepatitis C virus replication by spatially regulating the binding of miR-122/Ago2 complexes to viral RNA. Nucleic Acids Res 2019; 47:6411-6424. [PMID: 30997501 PMCID: PMC6614814 DOI: 10.1093/nar/gkz278] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 04/03/2019] [Accepted: 04/16/2019] [Indexed: 01/17/2023] Open
Abstract
The liver-specific microRNA, miR-122, is an essential host factor for replication of the hepatitis C virus (HCV). miR-122 stabilizes the positive-strand HCV RNA genome and promotes its synthesis by binding two sites (S1 and S2) near its 5' end in association with Ago2. Ago2 is essential for both host factor activities, but whether other host proteins are involved is unknown. Using an unbiased quantitative proteomics screen, we identified the TNRC6 protein paralogs, TNRC6B and TNRC6C, as functionally important but redundant components of the miR-122/Ago2 host factor complex. Doubly depleting TNRC6B and TNRC6C proteins reduced HCV replication in human hepatoma cells, dampening miR-122 stimulation of viral RNA synthesis without reducing the stability or translational activity of the viral RNA. TNRC6B/C were required for optimal miR-122 host factor activity only when S1 was able to bind miR-122, and restricted replication when S1 was mutated and only S2 bound by miR-122. TNRC6B/C preferentially associated with S1, and TNRC6B/C depletion enhanced Ago2 association at S2. Collectively, these data suggest a model in which TNRC6B/C regulate the assembly of miR-122/Ago complexes on HCV RNA, preferentially directing miR-122/Ago2 to S1 while restricting its association with S2, thereby fine-tuning the spatial organization of miR-122/Ago2 complexes on the viral genome.
Collapse
Affiliation(s)
- You Li
- Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Li Wang
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Efraín E Rivera-Serrano
- Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Xian Chen
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stanley M Lemon
- Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| |
Collapse
|
38
|
PABP Cooperates with the CCR4-NOT Complex to Promote mRNA Deadenylation and Block Precocious Decay. Mol Cell 2019; 70:1081-1088.e5. [PMID: 29932901 DOI: 10.1016/j.molcel.2018.05.009] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 04/16/2018] [Accepted: 05/04/2018] [Indexed: 12/18/2022]
Abstract
Multiple deadenylases are known in vertebrates, the PAN2-PAN3 (PAN2/3) and CCR4-NOT (CNOT) complexes, and PARN, yet their differential functions remain ambiguous. Moreover, the role of poly(A) binding protein (PABP) is obscure, limiting our understanding of the deadenylation mechanism. Here, we show that CNOT serves as a predominant nonspecific deadenylase for cytoplasmic poly(A)+ RNAs, and PABP promotes deadenylation while preventing premature uridylation and decay. PAN2/3 selectively trims long tails (>∼150 nt) with minimal effect on transcriptome, whereas PARN does not affect mRNA deadenylation. CAF1 and CCR4, catalytic subunits of CNOT, display distinct activities: CAF1 trims naked poly(A) segments and is blocked by PABPC, whereas CCR4 is activated by PABPC to shorten PABPC-protected sequences. Concerted actions of CAF1 and CCR4 delineate the ∼27 nt periodic PABPC footprints along shortening tail. Our study unveils distinct functions of deadenylases and PABPC, re-drawing the view on mRNA deadenylation and regulation.
Collapse
|
39
|
Duchaine TF, Fabian MR. Mechanistic Insights into MicroRNA-Mediated Gene Silencing. Cold Spring Harb Perspect Biol 2019; 11:cshperspect.a032771. [PMID: 29959194 DOI: 10.1101/cshperspect.a032771] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs) posttranscriptionally regulate gene expression by repressing protein synthesis and exert a broad influence over development, physiology, adaptation, and disease. Over the past two decades, great strides have been made toward elucidating how miRNAs go about shutting down messenger RNA (mRNA) translation and promoting mRNA decay.
Collapse
Affiliation(s)
- Thomas F Duchaine
- Department of Biochemistry & Goodman Cancer Research Centre, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Marc R Fabian
- Department of Oncology, McGill University, Montreal, Quebec H3G 1Y6, Canada.,Lady Davis Institute, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| |
Collapse
|
40
|
Abstract
Since their serendipitous discovery in nematodes, microRNAs (miRNAs) have emerged as key regulators of biological processes in animals. These small RNAs form complex networks that regulate cell differentiation, development and homeostasis. Deregulation of miRNA function is associated with an increasing number of human diseases, particularly cancer. Recent discoveries have expanded our understanding of the control of miRNA function. Here, we review the mechanisms that modulate miRNA activity, stability and cellular localization through alternative processing and maturation, sequence editing, post-translational modifications of Argonaute proteins, viral factors, transport from the cytoplasm and regulation of miRNA-target interactions. We conclude by discussing intriguing, unresolved research questions.
Collapse
Affiliation(s)
- Luca F R Gebert
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ian J MacRae
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
| |
Collapse
|
41
|
Cai Y, Wan J. Competing Endogenous RNA Regulations in Neurodegenerative Disorders: Current Challenges and Emerging Insights. Front Mol Neurosci 2018; 11:370. [PMID: 30344479 PMCID: PMC6182084 DOI: 10.3389/fnmol.2018.00370] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 09/18/2018] [Indexed: 12/14/2022] Open
Abstract
The past decade has witnessed exciting breakthroughs that have contributed to the richness and complexity of a burgeoning modern RNA world, and one particular breakthrough-the competing endogenous RNA (ceRNA) hypothesis-has been described as the "Rosetta Stone" for decoding the RNA language used in regulating RNA crosstalk and modulating biological functions. The proposed far-reaching mechanism unites diverse RNA species and provides new insights into previously unrecognized RNA-RNA interactions and RNA regulatory networks that perhaps determine gene expression in an organized, hierarchical manner. The recently uncovered ceRNA regulatory loops and networks have emphasized the power of ceRNA regulation in a wide range of developmental stages and pathological contexts, such as in tumorigenesis and neurodegenerative disorders. Although the ceRNA hypothesis drastically enhanced our understanding of RNA biology, shortly after the hypothesis was proposed, disputes arose in relation mainly to minor discrepancies in the reported effects of ceRNA regulation under physiological conditions, and this resulted in ceRNA regulation becoming an extensively studied and fast-growing research field. Here, we focus on the evidence supporting ceRNA regulation in neurodegenerative disorders and address three critical points related to the ceRNA regulatory mechanism: the microRNA (miRNA) and ceRNA hierarchies in cross-regulations; the balance between destabilization and stable binding in ceRNA-miRNA interactions; and the true extent to which ceRNA regulatory mechanisms are involved in both health and disease, and the experimental shortcomings in current ceRNA studies.
Collapse
Affiliation(s)
- Yifei Cai
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Jun Wan
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center, Shenzhen, China.,Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| |
Collapse
|
42
|
Role of GW182 protein in the cell. Int J Biochem Cell Biol 2018; 101:29-38. [PMID: 29791863 DOI: 10.1016/j.biocel.2018.05.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 04/23/2018] [Accepted: 05/17/2018] [Indexed: 12/27/2022]
Abstract
GW182 proteins interact directly with the argonaute proteins and constitute key components of miRNA repressor complexes (miRISC) in metazoans. As argonautes are insufficient for silencing they recruit the GW182 s that act as scaffold proteins inducing downstream translational repression, target mRNA deadenylation and exonucleolytic mRNA degradation. Besides their role as part of repressor complexes inside the cell, they function in wide variety of cellular processes as highlighted in this review. The present review summarises and discusses in detail our current knowledge of the GW182 s and their role inside the cell.
Collapse
|
43
|
Jalali S, Gandhi S, Scaria V. Distinct and Modular Organization of Protein Interacting Sites in Long Non-coding RNAs. Front Mol Biosci 2018; 5:27. [PMID: 29670884 PMCID: PMC5893854 DOI: 10.3389/fmolb.2018.00027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 03/14/2018] [Indexed: 12/11/2022] Open
Abstract
Background: Long non-coding RNAs (lncRNAs), are being reported to be extensively involved in diverse regulatory roles and have exhibited numerous disease associations. LncRNAs modulate their function through interaction with other biomolecules in the cell including DNA, RNA, and proteins. The availability of genome-scale experimental datasets of RNA binding proteins (RBP) motivated us to understand the role of lncRNAs in terms of its interactions with these proteins. In the current report, we demonstrate a comprehensive study of interactions between RBP and lncRNAs at a transcriptome scale through extensive analysis of the crosslinking and immunoprecipitation (CLIP) experimental datasets available for 70 RNA binding proteins. Results: Our analysis suggests that density of interaction sites for these proteins was significantly higher for specific sub-classes of lncRNAs when compared to protein-coding transcripts. We also observe a positional preference of these RBPs across lncRNA and protein coding transcripts in addition to a significant co-occurrence of RBPs having similar functions, suggesting a modular organization of these elements across lncRNAs. Conclusion: The significant enrichment of RBP sites across some lncRNA classes is suggestive that these interactions might be important in understanding the functional role of lncRNA. We observed a significant enrichment of RBPs which are involved in functional roles such as silencing, splicing, mRNA processing, and transport, indicating the potential participation of lncRNAs in such processes.
Collapse
Affiliation(s)
- Saakshi Jalali
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, New Delhi, India.,CSIR Institute of Genomics and Integrative Biology, Academy of Scientific and Innovative Research, New Delhi, India
| | - Shrey Gandhi
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, New Delhi, India
| | - Vinod Scaria
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, New Delhi, India.,CSIR Institute of Genomics and Integrative Biology, Academy of Scientific and Innovative Research, New Delhi, India
| |
Collapse
|
44
|
Sheu-Gruttadauria J, MacRae IJ. Phase Transitions in the Assembly and Function of Human miRISC. Cell 2018; 173:946-957.e16. [PMID: 29576456 DOI: 10.1016/j.cell.2018.02.051] [Citation(s) in RCA: 178] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 12/08/2017] [Accepted: 02/21/2018] [Indexed: 12/16/2022]
Abstract
miRISC is a multi-protein assembly that uses microRNAs (miRNAs) to identify mRNAs targeted for repression. Dozens of miRISC-associated proteins have been identified, and interactions between many factors have been examined in detail. However, the physical nature of the complex remains unknown. Here, we show that two core protein components of human miRISC, Argonaute2 (Ago2) and TNRC6B, condense into phase-separated droplets in vitro and in live cells. Phase separation is promoted by multivalent interactions between the glycine/tryptophan (GW)-rich domain of TNRC6B and three evenly spaced tryptophan-binding pockets in the Ago2 PIWI domain. miRISC droplets formed in vitro recruit deadenylation factors and sequester target RNAs from the bulk solution. The condensation of miRISC is accompanied by accelerated deadenylation of target RNAs bound to Ago2. The combined results may explain how miRISC silences mRNAs of varying size and structure and provide experimental evidence that protein-mediated phase separation can facilitate an RNA processing reaction.
Collapse
Affiliation(s)
- Jessica Sheu-Gruttadauria
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian J MacRae
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| |
Collapse
|
45
|
Muhanhali D, Zhai T, Jiang J, Ai Z, Zhu W, Ling Y. Long Non-coding Antisense RNA TNRC6C-AS1 Is Activated in Papillary Thyroid Cancer and Promotes Cancer Progression by Suppressing TNRC6C Expression. Front Endocrinol (Lausanne) 2018; 9:360. [PMID: 30038597 PMCID: PMC6046411 DOI: 10.3389/fendo.2018.00360] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 06/18/2018] [Indexed: 01/08/2023] Open
Abstract
Context: Evidences have shown the important role of long non-coding antisense RNAs in regulating its cognate sense gene in cancer biology. Objective: Investigate the regulatory role of a long non-coding antisense RNA TNRC6C-AS1 on its sense partner TNRC6C, and their effects on the aggressiveness and iodine-uptake ability of papillary thyroid cancer (PTC). Design: TNRC6C-AS1 was identified as the target long non-coding RNA in PTC by using microarray analysis and computational analysis. In vitro gain/loss-of-function experiments were performed to investigate the effects of TNRC6C-AS1 and TNRC6C on proliferation, apoptosis, migration, invasion and iodine-uptake ability of TPC1 cells. Expression levels of TNRC6C-AS1 and TNRC6C of 30 cases of PTC tissues and its adjacent normal thyroid tissues were determined. Results: Downregulation of TNRC6C-AS1 or overexpression of TNRC6C inhibited proliferation, migration and invasion of TPC1 cells, while apoptosis and iodine uptake was promoted in TPC1 cells. Suppression of TNRC6C-AS1 significantly increased the expression of TNRC6C in TPC1 cells. The inhibitory effect of TNRC6C-AS1 knockdown on cell proliferation, migration and invasion was attenuated when the expression of TNRC6C was suppressed simultaneously, indicating TNRC6C is a functional target of TNRC6C-AS1. The expression of TNRC6C-AS1 was significantly higher, while the TNRC6C mRNA and protein were significantly lower in PTC tissues than normal adjacent tissues. There was a significant inverse correlation between TNRC6C-AS1 and TNRC6C mRNA in PTC tissue samples. Conclusions: TNRC6C-AS1 promotes the progression of PTC and inhibits its ability of iodine accumulation by suppressing the expression of TNRC6C. Targeting TNRC6C-AS1 - TNRC6C axis may be a new promising treatment for PTC.
Collapse
Affiliation(s)
- Dilidaer Muhanhali
- Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Tianyu Zhai
- Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jingjing Jiang
- Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhilong Ai
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wei Zhu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yan Ling
- Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai, China
- *Correspondence: Yan Ling
| |
Collapse
|
46
|
Dittmann K, Mayer C, Czemmel S, Huber SM, Rodemann HP. New roles for nuclear EGFR in regulating the stability and translation of mRNAs associated with VEGF signaling. PLoS One 2017; 12:e0189087. [PMID: 29253018 PMCID: PMC5734708 DOI: 10.1371/journal.pone.0189087] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 11/18/2017] [Indexed: 11/21/2022] Open
Abstract
Cell membrane-associated epidermal growth factor receptor (EGFR) translocates into a perinuclear/nuclear location upon stimulation, where it complexes with mRNAs. Treatment with radiation and cisplatin decreases the amounts of mRNAs present within this complex. Gene array analyses of mRNAs in complex with immunoprecipitated nEGFR revealed significant enrichment of different mRNA species compared to the control immunoprecipitation. Functional annotation with help of DAVID Gene Ontology Analysis identified under other terms the HIF-1A/VEGF signaling pathway as one of the top scoring KEGG pathways. RT-PCR and western blots revealed the radiation-induced expression of mRNAs and proteins involved in HIF-1A/VEGF signaling. Simultaneously, the levels of the corresponding validated miRNAs within the complex containing nEGFR and mRNAs were decreased. This finding argues that an mRNA/miRNA/nEGFR complex regulates protein expression. Indeed, we detected the GW182, AGO2, PABPC1 and cNOT1 proteins, which belong to the deadenylase complex, in a complex with nuclear EGFR. Erlotinib-mediated inhibition of EGFR kinase reduced the radiation-induced increase in mRNA expression. In this context, erlotinib reduced AGO2 phosphorylation by the EGFR kinase at residue Y393, which was associated with increased cNOT1 deadenylase activity and reduced mRNA stability. To prove the roles of miRNAs in this context, we transfected cells with an inhibitor of Hsa-mir-1180p5, which targets the NFATC4 mRNA, an mRNA associated with VEGF signaling, or pretreated cells with erlotinib. Indeed, Hsa-mir-1180p5 knockdown increased and the erlotinib treatment decreased the expression of the NFATC4 protein. The expression of the NFATC4 protein controlled the cloning efficiency and radiosensitivity of A549 and FaDu tumor cells. Thus, this study is the first to show that a membrane-located tyrosine kinase receptor, such as EGFR, is internalized to a nuclear/perinuclear location upon exposure to stress and modulates the stability and translation of miRNA-selected mRNAs. This mechanism enables cells to directly express proteins in response to EGFR activation and may contribute to treatment resistance in EGFR-overexpressing tumors.
Collapse
Affiliation(s)
- Klaus Dittmann
- Division of Radiobiology and Molecular Environmental Research, University of Tuebingen, Tuebingen, Germany
- Department of Radiation Oncology, University of Tuebingen, Tuebingen, Germany
- German Cancer Consortium (DKTK), partner site Tuebingen and German Cancer Research Center (DKFZ), Heidelberg, Germany
- * E-mail:
| | - Claus Mayer
- Division of Radiobiology and Molecular Environmental Research, University of Tuebingen, Tuebingen, Germany
- Department of Radiation Oncology, University of Tuebingen, Tuebingen, Germany
- German Cancer Consortium (DKTK), partner site Tuebingen and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Czemmel
- Quantitative Biology Center (QBiC), University of Tuebingen, Tuebingen, Germany
| | - Stephan M. Huber
- Department of Radiation Oncology, University of Tuebingen, Tuebingen, Germany
- German Cancer Consortium (DKTK), partner site Tuebingen and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - H. Peter Rodemann
- Division of Radiobiology and Molecular Environmental Research, University of Tuebingen, Tuebingen, Germany
- Department of Radiation Oncology, University of Tuebingen, Tuebingen, Germany
- German Cancer Consortium (DKTK), partner site Tuebingen and German Cancer Research Center (DKFZ), Heidelberg, Germany
| |
Collapse
|
47
|
Rissland OS, Subtelny AO, Wang M, Lugowski A, Nicholson B, Laver JD, Sidhu SS, Smibert CA, Lipshitz HD, Bartel DP. The influence of microRNAs and poly(A) tail length on endogenous mRNA-protein complexes. Genome Biol 2017; 18:211. [PMID: 29089021 PMCID: PMC5664449 DOI: 10.1186/s13059-017-1330-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 09/29/2017] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND All mRNAs are bound in vivo by proteins to form mRNA-protein complexes (mRNPs), but changes in the composition of mRNPs during posttranscriptional regulation remain largely unexplored. Here, we have analyzed, on a transcriptome-wide scale, how microRNA-mediated repression modulates the associations of the core mRNP components eIF4E, eIF4G, and PABP and of the decay factor DDX6 in human cells. RESULTS Despite the transient nature of repressed intermediates, we detect significant changes in mRNP composition, marked by dissociation of eIF4G and PABP, and by recruitment of DDX6. Furthermore, although poly(A)-tail length has been considered critical in post-transcriptional regulation, differences in steady-state tail length explain little of the variation in either PABP association or mRNP organization more generally. Instead, relative occupancy of core components correlates best with gene expression. CONCLUSIONS These results indicate that posttranscriptional regulatory factors, such as microRNAs, influence the associations of PABP and other core factors, and do so without substantially affecting steady-state tail length.
Collapse
Affiliation(s)
- Olivia S Rissland
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA.
- Howard Hughes Medical Institute, Cambridge, MA, 02142, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.
- Present address: Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
| | - Alexander O Subtelny
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Cambridge, MA, 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Miranda Wang
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Andrew Lugowski
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Beth Nicholson
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - John D Laver
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Sachdev S Sidhu
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Craig A Smibert
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Howard D Lipshitz
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - David P Bartel
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA.
- Howard Hughes Medical Institute, Cambridge, MA, 02142, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| |
Collapse
|
48
|
Comprehensive Identification of Nuclear and Cytoplasmic TNRC6A-Associating Proteins. J Mol Biol 2017; 429:3319-3333. [DOI: 10.1016/j.jmb.2017.04.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 04/18/2017] [Accepted: 04/24/2017] [Indexed: 11/20/2022]
|
49
|
Chen CYA, Zhang Y, Xiang Y, Han L, Chang JT, Shyu AB. Antagonistic actions of two human Pan3 isoforms on global mRNA turnover. RNA (NEW YORK, N.Y.) 2017; 23:1404-1418. [PMID: 28559491 PMCID: PMC5558910 DOI: 10.1261/rna.061556.117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 05/25/2017] [Indexed: 05/03/2023]
Abstract
Deadenylation is a fundamental process that regulates eukaryotic gene expression. Mammalian deadenylation exhibits biphasic kinetics, with the Pan2-Pan3 and Ccr4-Caf1 deadenylase complexes mediating the first and second phase, respectively; however, the significance of the biphasic nature of deadenylation in mRNA turnover remains unclear. In this study, we discovered that two distinct isoforms of human Pan3 display opposing properties necessary for coordinating the two phases of deadenylation. The shorter isoform (Pan3S) interacts more strongly with PABP than the longer isoform (Pan3L) does. Pan2 deadenylase activity is enhanced by Pan3S but suppressed by Pan3L. Knocking down individual Pan3 isoforms has opposing effects on the global poly(A) tail length profile, P-body formation, and different mRNA decay pathways. Transcriptome-wide analysis of Pan3 knockdown effects on mRNA turnover shows that depleting either Pan3 isoform causes profound and extensive changes in mRNA stability globally. These results reveal a new fundamental step governing mammalian mRNA metabolism. We propose that the first phase of deadenylation, coordinated through the interplay among the two Pan3 isoforms, Pan2, and PABP, represents a cytoplasmic mRNA maturation step important for proper mRNA turnover.
Collapse
Affiliation(s)
- Chyi-Ying A Chen
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Yueqiang Zhang
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Yu Xiang
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Leng Han
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Jeffrey T Chang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Ann-Bin Shyu
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| |
Collapse
|
50
|
Chaston JJ, Stewart AG, Christie M. Structural characterisation of TNRC6A nuclear localisation signal in complex with importin-alpha. PLoS One 2017; 12:e0183587. [PMID: 28837617 PMCID: PMC5570423 DOI: 10.1371/journal.pone.0183587] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 08/06/2017] [Indexed: 12/16/2022] Open
Abstract
The GW182/TNRC6 family of proteins are central scaffolds that link microRNA-associated Argonaute proteins to the cytoplasmic decay machinery for targeted mRNA degradation processes. Although nuclear roles for the GW182/TNRC6 proteins are unknown, recent reports have demonstrated nucleocytoplasmic shuttling activity that utilises the importin-α and importin-β transport receptors for nuclear translocation. Here we describe the structure of mouse importin-α in complex with the TNRC6A nuclear localisation signal peptide. We further show that the interactions observed between TNRC6A and importin-α are conserved between mouse and human complexes. Our results highlight the ability of monopartite cNLS sequences to maximise contacts at the importin-α major binding site, as well as regions outside the main binding cavities.
Collapse
Affiliation(s)
- Jessica J. Chaston
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Alastair Gordon Stewart
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Mary Christie
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| |
Collapse
|