1
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Larivera S, Neumeier J, Meister G. Post-transcriptional gene silencing in a dynamic RNP world. Biol Chem 2023; 404:1051-1067. [PMID: 37739934 DOI: 10.1515/hsz-2023-0203] [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: 05/05/2023] [Accepted: 08/04/2023] [Indexed: 09/24/2023]
Abstract
MicroRNA (miRNA)-guided gene silencing is a key regulatory process in various organisms and linked to many human diseases. MiRNAs are processed from precursor molecules and associate with Argonaute proteins to repress the expression of complementary target mRNAs. Excellent work by numerous labs has contributed to a detailed understanding of the mechanisms of miRNA function. However, miRNA effects have mostly been analyzed and viewed as isolated events and their natural environment as part of complex RNA-protein particles (RNPs) is often neglected. RNA binding proteins (RBPs) regulate key enzymes of the miRNA processing machinery and furthermore RBPs or readers of RNA modifications may modulate miRNA activity on mRNAs. Such proteins may function similarly to miRNAs and add their own contributions to the overall expression level of a particular gene. Therefore, post-transcriptional gene regulation might be more the sum of individual regulatory events and should be viewed as part of a dynamic and complex RNP world.
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Affiliation(s)
- Simone Larivera
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, D-93053, Regensburg, Germany
| | - Julia Neumeier
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, D-93053, Regensburg, Germany
| | - Gunter Meister
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, D-93053, Regensburg, Germany
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2
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Singh R, Hussain J, Kaur A, Jamdare BG, Pathak D, Garg K, Kaur R, Shankar S, Sunkaria A. The hidden players: Shedding light on the significance of post-translational modifications and miRNAs in Alzheimer's disease development. Ageing Res Rev 2023; 90:102002. [PMID: 37423542 DOI: 10.1016/j.arr.2023.102002] [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: 05/26/2023] [Revised: 06/29/2023] [Accepted: 07/03/2023] [Indexed: 07/11/2023]
Abstract
Alzheimer's disease (AD) is the most prevalent, expensive, lethal, and burdening neurodegenerative disease of this century. The initial stages of this disease are characterized by a reduced ability to encode and store new memories. Subsequent cognitive and behavioral deterioration occurs during the later stages. Abnormal cleavage of amyloid precursor protein (APP) resulting in amyloid-beta (Aβ) accumulation along with hyperphosphorylation of tau protein are the two characteristic hallmarks of AD. Recently, several post-translational modifications (PTMs) have been identified on both Aβ as well as tau proteins. However, a complete understanding of how different PTMs influence the structure and function of proteins in both healthy and diseased conditions is still lacking. It has been speculated that these PTMs might play vital roles in the progression of AD. In addition, several short non-coding microRNA (miRNA) sequences have been found to be deregulated in the peripheral blood of Alzheimer patients. The miRNAs are single-stranded RNAs that control gene expression by causing mRNA degradation, deadenylation, or translational repression and have been implicated in the regulation of several neuronal and glial activities. The lack of comprehensive understanding regarding disease mechanisms, biomarkers, and therapeutic targets greatly hampers the development of effective strategies for early diagnosis and the identification of viable therapeutic targets. Moreover, existing treatment options for managing the disease have proven to be ineffective and provide only temporary relief. Therefore, understanding the role of miRNAs and PTMs in AD can provide valuable insights into disease mechanisms, aid in the identification of biomarkers, facilitate the discovery of novel therapeutic targets, and inspire innovative treatments for this challenging condition.
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Affiliation(s)
- Ravinder Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Julfequar Hussain
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Amandeep Kaur
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Balaji Gokul Jamdare
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Deepti Pathak
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Kanchan Garg
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Ramanpreet Kaur
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Shivani Shankar
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Aditya Sunkaria
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India.
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3
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Sharma S, Kajjo S, Harra Z, Hasaj B, Delisle V, Ray D, Gutierrez RL, Carrier I, Kleinman C, Morris Q, Hughes TR, McInnes R, Fabian MR. Uncovering a mammalian neural-specific poly(A) binding protein with unique properties. Genes Dev 2023; 37:760-777. [PMID: 37704377 PMCID: PMC10546976 DOI: 10.1101/gad.350597.123] [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: 03/03/2023] [Accepted: 08/29/2023] [Indexed: 09/15/2023]
Abstract
The mRNA 3' poly(A) tail plays a critical role in regulating both mRNA translation and turnover. It is bound by the cytoplasmic poly(A) binding protein (PABPC), an evolutionarily conserved protein that can interact with translation factors and mRNA decay machineries to regulate gene expression. Mammalian PABPC1, the prototypical PABPC, is expressed in most tissues and interacts with eukaryotic translation initiation factor 4G (eIF4G) to stimulate translation in specific contexts. In this study, we uncovered a new mammalian PABPC, which we named neural PABP (neuPABP), as it is predominantly expressed in the brain. neuPABP maintains a unique architecture as compared with other PABPCs, containing only two RNA recognition motifs (RRMs) and maintaining a unique N-terminal domain of unknown function. neuPABP expression is activated in neurons as they mature during synaptogenesis, where neuPABP localizes to the soma and postsynaptic densities. neuPABP interacts with the noncoding RNA BC1, as well as mRNAs coding for ribosomal and mitochondrial proteins. However, in contrast to PABPC1, neuPABP does not associate with actively translating mRNAs in the brain. In keeping with this, we show that neuPABP has evolved such that it does not bind eIF4G and as a result fails to support protein synthesis in vitro. Taken together, these results indicate that mammals have expanded their PABPC repertoire in the brain and propose that neuPABP may support the translational repression of select mRNAs.
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Affiliation(s)
- Sahil Sharma
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Sam Kajjo
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Zineb Harra
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Benedeta Hasaj
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Victoria Delisle
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Debashish Ray
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Rodrigo L Gutierrez
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Isabelle Carrier
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Claudia Kleinman
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Quaid Morris
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Timothy R Hughes
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Roderick McInnes
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Marc R Fabian
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada;
- Department of Biochemistry, McGill University, Montreal, Quebec H3A 0G4, Canada
- Department of Oncology, McGill University, Montreal, Quebec H3A 0G4, Canada
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4
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Johnson KC, Johnson ST, Liu J, Chu Y, Arana C, Han Y, Wang T, Corey DR. Consequences of depleting TNRC6, AGO, and DROSHA proteins on expression of microRNAs. RNA (NEW YORK, N.Y.) 2023; 29:1166-1184. [PMID: 37169394 PMCID: PMC10351893 DOI: 10.1261/rna.079647.123] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 04/21/2023] [Indexed: 05/13/2023]
Abstract
The potential for microRNAs (miRNAs) to regulate gene expression remains incompletely understood. DROSHA initiates the biogenesis of miRNAs while variants of Argonaute (AGO) and trinucleotide repeat containing six (TNRC6) family proteins form complexes with miRNAs to facilitate RNA recognition and gene regulation. Here we investigate the fate of miRNAs in the absence of these critical RNAi protein factors. Knockout of DROSHA expression reduces levels of some miRNAs annotated in miRBase but not others. The identity of miRNAs with reduced expression matches the identity of miRNAs previously identified by experimental approaches. The MirGeneDB resource offers the closest alignment with experimental results. In contrast, the loss of TNRC6 proteins had much smaller effects on miRNA levels. Knocking out AGO proteins, which directly contact the mature miRNA, decreased expression of the miRNAs most strongly associated with AGO2 as determined from enhanced crosslinking immunoprecipitation (AGO2-eCLIP). Evaluation of miRNA binding to endogenously expressed AGO proteins revealed that miRNA:AGO association was similar for AGO1, AGO2, AGO3, and AGO4. Our data emphasize the need to evaluate annotated miRNAs based on approximate cellular abundance, DROSHA-dependence, and physical association with AGO when forming hypotheses related to their function.
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Affiliation(s)
- Krystal C Johnson
- Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, Dallas, Texas 75205, USA
| | | | - Jing Liu
- Iris Medicine, Palo Alto, California 94304, USA
| | | | - Carlos Arana
- Genomics Core, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Yi Han
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Tao Wang
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - David R Corey
- Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, Dallas, Texas 75205, USA
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5
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Quesnelle DC, Bendena WG, Chin-Sang ID. A Compilation of the Diverse miRNA Functions in Caenorhabditis elegans and Drosophila melanogaster Development. Int J Mol Sci 2023; 24:ijms24086963. [PMID: 37108126 PMCID: PMC10139094 DOI: 10.3390/ijms24086963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
MicroRNAs are critical regulators of post-transcriptional gene expression in a wide range of taxa, including invertebrates, mammals, and plants. Since their discovery in the nematode, Caenorhabditis elegans, miRNA research has exploded, and they are being identified in almost every facet of development. Invertebrate model organisms, particularly C. elegans, and Drosophila melanogaster, are ideal systems for studying miRNA function, and the roles of many miRNAs are known in these animals. In this review, we compiled the functions of many of the miRNAs that are involved in the development of these invertebrate model species. We examine how gene regulation by miRNAs shapes both embryonic and larval development and show that, although many different aspects of development are regulated, several trends are apparent in the nature of their regulation.
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Affiliation(s)
| | - William G Bendena
- Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Ian D Chin-Sang
- Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada
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6
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Schaible P, Bethge W, Lengerke C, Haraszti RA. RNA Therapeutics for Improving CAR T-cell Safety and Efficacy. Cancer Res 2023; 83:354-362. [PMID: 36512627 PMCID: PMC7614194 DOI: 10.1158/0008-5472.can-22-2155] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 11/02/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022]
Abstract
Autologous chimeric antigen receptor (CAR) T cells have recently emerged as potent tools in the fight against cancer, with promising therapeutic efficacy against hematological malignancies. However, several limitations hamper their widespread clinical use, including availability of target antigen, severe toxic effects, primary and secondary resistance, heterogeneous quality of autologous T cells, variable persistence, and low activity against solid tumors. Development of allogeneic off-the-shelf CAR T cells could help address some of these limitations but is impeded by alloimmunity with either rejection and limited expansion of allo-CAR T cells or CAR T cells versus host reactions. RNA therapeutics, such as small interfering RNAs, microRNAs, and antisense oligonucleotides, are able to silence transcripts in a sequence-specific and proliferation-sensitive way, which may offer a way to overcome some of the challenges facing CAR T-cell development and clinical utility. Here, we review how different RNA therapeutics or a combination of RNA therapeutics and genetic engineering could be harnessed to improve the safety and efficacy of autologous and allogeneic CAR T-cell therapy.
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Affiliation(s)
- Philipp Schaible
- Department of Internal Medicine II, Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Wolfgang Bethge
- Department of Internal Medicine II, Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Claudia Lengerke
- Department of Internal Medicine II, Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Reka Agnes Haraszti
- Department of Internal Medicine II, Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
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7
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Dai L, Liang W, Shi Z, Li X, Zhou S, Hu W, Yang Z, Wang X. Systematic characterization and biological functions of non-coding RNAs in glioblastoma. Cell Prolif 2022; 56:e13375. [PMID: 36457281 PMCID: PMC9977673 DOI: 10.1111/cpr.13375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/02/2022] [Accepted: 11/22/2022] [Indexed: 12/05/2022] Open
Abstract
Glioblastoma multiforme (GBM) is the most malignant and aggressive type of glioma. Non-coding RNAs (ncRNAs) are RNAs that do not encode proteins but widely exist in eukaryotic cells. The common characteristics of these RNAs are that they can all be transcribed from the genome without being translated into proteins, thus performing biological functions, particularly microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs. Studies have found that ncRNAs are associated with the occurrence and development of GBM, and there is a complex regulatory network among ncRNAs, which can regulate cell proliferation, migration, apoptosis and differentiation, thus provide a basis for the development of highly specific diagnostic tools and therapeutic strategies in the future. The present review aimed to comprehensively describe the biogenesis, general features and functions of regulatory ncRNAs in GBM, and to interpret the potential biological functions of these ncRNAs in GBM as well as their impact on clinical diagnosis, treatment and prognosis and discusses the potential mechanisms of these RNA subtypes leading to cancer in order to contribute to the better design of personalized GBM therapies in the future.
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Affiliation(s)
- Lirui Dai
- Department of NeurosurgeryThe Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou UniversityZhengzhouChina,Institute of Neuroscience, Zhengzhou UniversityZhengzhouChina,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment ResearchZhengzhouHenanChina
| | - Wulong Liang
- Department of NeurosurgeryThe Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou UniversityZhengzhouChina,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment ResearchZhengzhouHenanChina
| | - Zimin Shi
- Department of NeurosurgeryThe Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou UniversityZhengzhouChina,Institute of Neuroscience, Zhengzhou UniversityZhengzhouChina,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment ResearchZhengzhouHenanChina
| | - Xiang Li
- Department of NeurosurgeryThe Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou UniversityZhengzhouChina,Institute of Neuroscience, Zhengzhou UniversityZhengzhouChina,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment ResearchZhengzhouHenanChina
| | - Shaolong Zhou
- Department of NeurosurgeryThe Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou UniversityZhengzhouChina,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment ResearchZhengzhouHenanChina
| | - Weihua Hu
- Department of NeurosurgeryThe Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou UniversityZhengzhouChina,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment ResearchZhengzhouHenanChina
| | - Zhuo Yang
- Department of NeurosurgeryThe Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou UniversityZhengzhouChina,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment ResearchZhengzhouHenanChina
| | - Xinjun Wang
- Department of NeurosurgeryThe Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou UniversityZhengzhouChina,Institute of Neuroscience, Zhengzhou UniversityZhengzhouChina,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment ResearchZhengzhouHenanChina
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8
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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.
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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,
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9
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Stavast CJ, van Zuijen I, Erkeland SJ. MicroRNA-139, an Emerging Gate-Keeper in Various Types of Cancer. Cells 2022; 11:cells11050769. [PMID: 35269391 PMCID: PMC8909004 DOI: 10.3390/cells11050769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 02/17/2022] [Accepted: 02/19/2022] [Indexed: 11/25/2022] Open
Abstract
Mounting data show that MIR139 is commonly silenced in solid cancer and hematological malignancies. MIR139 acts as a critical tumor suppressor by tuning the cellular response to different types of stress, including DNA damage, and by repressing oncogenic signaling pathways. Recently, novel insights into the mechanism of MIR139 silencing in tumor cells have been described. These include epigenetic silencing, inhibition of POL-II transcriptional activity on gene regulatory elements, enhanced expression of competing RNAs and post-transcriptional regulation by the microprocessor complex. Some of these MIR139-silencing mechanisms have been demonstrated in different types of cancer, suggesting that these are more general oncogenic events. Reactivation of MIR139 expression in tumor cells causes inhibition of tumor cell expansion and induction of cell death by the repression of oncogenic mRNA targets. In this review, we discuss the different aspects of MIR139 as a tumor suppressor gene and give an overview on different transcriptional mechanisms regulating MIR139 in oncogenic stress and across different types of cancer. The novel insights into the expression regulation and the tumor-suppressing activities of MIR139 may pave the way to new treatment options for cancer.
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10
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Jungers CF, Djuranovic S. Modulation of miRISC-Mediated Gene Silencing in Eukaryotes. Front Mol Biosci 2022; 9:832916. [PMID: 35237661 PMCID: PMC8882679 DOI: 10.3389/fmolb.2022.832916] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/18/2022] [Indexed: 11/13/2022] Open
Abstract
Gene expression is regulated at multiple levels in eukaryotic cells. Regulation at the post-transcriptional level is modulated by various trans-acting factors that bind to specific sequences in the messenger RNA (mRNA). The binding of different trans factors influences various aspects of the mRNA such as degradation rate, translation efficiency, splicing, localization, etc. MicroRNAs (miRNAs) are short endogenous ncRNAs that combine with the Argonaute to form the microRNA-induced silencing complex (miRISC), which uses base-pair complementation to silence the target transcript. RNA-binding proteins (RBPs) contribute to post-transcriptional control by influencing the mRNA stability and translation upon binding to cis-elements within the mRNA transcript. RBPs have been shown to impact gene expression through influencing the miRISC biogenesis, composition, or miRISC-mRNA target interaction. While there is clear evidence that those interactions between RBPs, miRNAs, miRISC and target mRNAs influence the efficiency of miRISC-mediated gene silencing, the exact mechanism for most of them remains unclear. This review summarizes our current knowledge on gene expression regulation through interactions of miRNAs and RBPs.
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11
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Jauhari A, Singh T, Yadav S. Neurodevelopmental Disorders and Neurotoxicity: MicroRNA in Focus. J Chem Neuroanat 2022; 120:102072. [DOI: 10.1016/j.jchemneu.2022.102072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 01/16/2022] [Accepted: 01/17/2022] [Indexed: 10/19/2022]
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12
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Morris C, Cluet D, Ricci EP. Ribosome dynamics and mRNA turnover, a complex relationship under constant cellular scrutiny. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1658. [PMID: 33949788 PMCID: PMC8519046 DOI: 10.1002/wrna.1658] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/26/2021] [Accepted: 03/26/2021] [Indexed: 12/01/2022]
Abstract
Eukaryotic gene expression is closely regulated by translation and turnover of mRNAs. Recent advances highlight the importance of translation in the control of mRNA degradation, both for aberrant and apparently normal mRNAs. During translation, the information contained in mRNAs is decoded by ribosomes, one codon at a time, and tRNAs, by specifically recognizing codons, translate the nucleotide code into amino acids. Such a decoding step does not process regularly, with various obstacles that can hinder ribosome progression, then leading to ribosome stalling or collisions. The progression of ribosomes is constantly monitored by the cell which has evolved several translation-dependent mRNA surveillance pathways, including nonsense-mediated decay (NMD), no-go decay (NGD), and non-stop decay (NSD), to degrade certain problematic mRNAs and the incomplete protein products. Recent progress in sequencing and ribosome profiling has made it possible to discover new mechanisms controlling ribosome dynamics, with numerous crosstalks between translation and mRNA decay. We discuss here various translation features critical for mRNA decay, with particular focus on current insights from the complexity of the genetic code and also the emerging role for the ribosome as a regulatory hub orchestrating mRNA decay, quality control, and stress signaling. Even if the interplay between mRNA translation and degradation is no longer to be demonstrated, a better understanding of their precise coordination is worthy of further investigation. This article is categorized under: RNA Turnover and Surveillance > Regulation of RNA Stability Translation > Translation Regulation RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Christelle Morris
- Laboratory of Biology and Modeling of the CellUniversité de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, Inserm U1293LyonFrance
| | - David Cluet
- Laboratory of Biology and Modeling of the CellUniversité de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, Inserm U1293LyonFrance
| | - Emiliano P. Ricci
- Laboratory of Biology and Modeling of the CellUniversité de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, Inserm U1293LyonFrance
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13
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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; 10:70948. [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] [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.
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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
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14
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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.
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15
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Forbes TA, Brown BD, Lai C. Therapeutic RNA interference: A novel approach to the treatment of primary hyperoxaluria. Br J Clin Pharmacol 2021; 88:2525-2538. [PMID: 34022071 PMCID: PMC9291495 DOI: 10.1111/bcp.14925] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 04/19/2021] [Accepted: 05/08/2021] [Indexed: 12/13/2022] Open
Abstract
RNA interference (RNAi) is a natural biological pathway that inhibits gene expression by targeted degradation or translational inhibition of cytoplasmic mRNA by the RNA induced silencing complex. RNAi has long been exploited in laboratory research to study the biological consequences of the reduced expression of a gene of interest. More recently RNAi has been demonstrated as a therapeutic avenue for rare metabolic diseases. This review presents an overview of the cellular RNAi machinery as well as therapeutic RNAi design and delivery. As a clinical example we present primary hyperoxaluria, an ultrarare inherited disease of increased hepatic oxalate production which leads to recurrent calcium oxalate kidney stones. In the most common form of the disease (Type 1), end‐stage kidney disease occurs in childhood or young adulthood, often necessitating combined kidney and liver transplantation. In this context we discuss nedosiran (Dicerna Pharmaceuticals, Inc.) and lumasiran (Alnylam Pharmaceuticals), which are both novel RNAi therapies for primary hyperoxaluria that selectively reduce hepatic expression of lactate dehydrogenase and glycolate oxidase respectively, reducing hepatic oxalate production and urinary oxalate levels. Finally, we consider future optimizations advances in RNAi therapies.
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Affiliation(s)
- Thomas A Forbes
- Royal Children's Hospital, Parkville, Victoria, Australia.,Murdoch Children's Research Institute, Parkville, Victoria, Australia.,University of Melbourne, Parkville, Victoria, Australia
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16
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Munakata F, Suzawa M, Ui-Tei K. Identification of Phosphorylated Amino Acids in Human TNRC6A C-Terminal Region and Their Effects on the Interaction with the CCR4-NOT Complex. Genes (Basel) 2021; 12:genes12020271. [PMID: 33668648 PMCID: PMC7917804 DOI: 10.3390/genes12020271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 02/08/2021] [Accepted: 02/11/2021] [Indexed: 12/21/2022] Open
Abstract
Human GW182 family proteins have Argonaute (AGO)-binding domains in their N-terminal regions and silencing domains, which interact with RNA silencing-related proteins, in their C-terminal regions. Thus, they function as scaffold proteins between the AGO protein and RNA silencing-related proteins, such as carbon catabolite repressor4-negative on TATA (CCR4-NOT) or poly(A)-binding protein (PABP). Our mass spectrometry analysis and the phosphorylation data registered in PhosphoSitePlus, a post-translational modification database, suggested that the C-terminal region of a human GW182 family protein, TNRC6A, has at least four possible phosphorylation sites, which are located near the region interacting with the CCR4-NOT complex. Among them, two serine residues at amino acid positions 1332 and 1346 (S1332 and S1346) were certainly phosphorylated in human HeLa cells, but other two serine residues (S1616 and S1691) were not phosphorylated. Furthermore, it was revealed that the phosphorylation patterns of TNRC6A affect the interaction with the CCR4-NOT complex. When S1332 and S1346 were dephosphorylated, the interactions of TNRC6A with the CCR4-NOT complex were enhanced, and when S1616 and S1691 were phosphorylated, such interaction was suppressed. Thus, phosphorylation of TNRC6A was considered to regulate the interaction with RNA silencing-related factors that may affect RNA silencing activity.
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Affiliation(s)
- Fusako Munakata
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan; (F.M.); (M.S.)
| | - Masataka Suzawa
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan; (F.M.); (M.S.)
| | - Kumiko Ui-Tei
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan; (F.M.); (M.S.)
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8561, Japan
- Correspondence: ; Tel.: +81-3-5841-3044
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17
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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.
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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
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18
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Guo ZZ, Ma ZJ, He YZ, Jiang W, Xia Y, Pan CF, Wei K, Shi YJ, Chen L, Chen YJ. miR-550a-5p Functions as a Tumor Promoter by Targeting LIMD1 in Lung Adenocarcinoma. Front Oncol 2020; 10:570733. [PMID: 33194664 PMCID: PMC7655921 DOI: 10.3389/fonc.2020.570733] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 09/14/2020] [Indexed: 12/21/2022] Open
Abstract
Lung adenocarcinoma accounts for half of all lung cancer cases in most countries. Mounting evidence has demonstrated that microRNAs play important roles in cancer progression, and some of them can be identified as potential biomarkers. This study aimed to explore the role of miR-550a-5p, a lung adenocarcinoma-associated mature microRNA screened out from the TCGA database via R-studio and Perl, with abundant expression in samples and with 5-year survival prognosis difference, as well as having not been studied in lung cancer yet. Potential target genes were predicted by the online database. Gene ontology enrichment, pathway enrichment, protein–protein interaction network, and hub genes–microRNA network were constructed by FunRich, STRING database, and Cytoscape. Then, LIMD1, a known tumor suppressor gene reported by multiple articles, was found to have a negative correlation with miR-550a-5p. The expression of miR-550a-5p was up-regulated in tumor samples and tumor-associated cell lines. Its high expression was also correlated with tumor size. Cell line A549 treated with miR-550a-5p overexpression promoted tumor proliferation, while H1299 treated with miR-550a-5p knockdown showed the opposite result. Mechanically, miR-550a-5p negatively regulated LIMD1 by directly binding to its 3′-UTR validated by dual luciferase assay. In summary, a new potential prognostic and therapeutic biomarker, miR-550a-5p, has been identified by bioinformatics analysis and experimental validation in vitro and in vivo, which promotes lung adenocarcinoma by silencing a known suppressor oncogene LIMD1.
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Affiliation(s)
- Zi-Zhang Guo
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zi-Jian Ma
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yao-Zhou He
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wei Jiang
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yang Xia
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chun-Feng Pan
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ke Wei
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yi-Jun Shi
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Liang Chen
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yi-Jiang Chen
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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19
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Mattijssen S, Iben JR, Li T, Coon SL, Maraia RJ. Single molecule poly(A) tail-seq shows LARP4 opposes deadenylation throughout mRNA lifespan with most impact on short tails. eLife 2020; 9:e59186. [PMID: 32744499 PMCID: PMC7413741 DOI: 10.7554/elife.59186] [Citation(s) in RCA: 21] [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: 06/02/2020] [Accepted: 08/02/2020] [Indexed: 12/22/2022] Open
Abstract
La-related protein 4 (LARP4) directly binds both poly(A) and poly(A)-binding protein (PABP). LARP4 was shown to promote poly(A) tail (PAT) lengthening and stabilization of individual mRNAs presumably by protection from deadenylation (Mattijssen et al., 2017). We developed a nucleotide resolution transcriptome-wide, single molecule SM-PAT-seq method. This revealed LARP4 effects on a wide range of PAT lengths for human mRNAs and mouse mRNAs from LARP4 knockout (KO) and control cells. LARP4 effects are clear on long PAT mRNAs but become more prominent at 30-75 nucleotides. We also analyzed time courses of PAT decay transcriptome-wide and for ~200 immune response mRNAs. This demonstrated accelerated deadenylation in KO cells on PATs < 75 nucleotides and phasing consistent with greater PABP dissociation in the absence of LARP4. Thus, LARP4 shapes PAT profiles throughout mRNA lifespan with impact on mRNA decay at short lengths known to sensitize PABP dissociation in response to deadenylation machinery.
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Affiliation(s)
- Sandy Mattijssen
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - James R Iben
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - Tianwei Li
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - Steven L Coon
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - Richard J Maraia
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
- Commissioned Corps, U.S. Public Health ServiceRockvilleUnited States
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20
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Artificial miRNAs targeting CAG repeat expansion in ORFs cause rapid deadenylation and translation inhibition of mutant transcripts. Cell Mol Life Sci 2020; 78:1577-1596. [PMID: 32696070 PMCID: PMC7904544 DOI: 10.1007/s00018-020-03596-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 07/01/2020] [Accepted: 07/09/2020] [Indexed: 02/07/2023]
Abstract
Polyglutamine (polyQ) diseases are incurable neurological disorders caused by CAG repeat expansion in the open reading frames (ORFs) of specific genes. This type of mutation in the HTT gene is responsible for Huntington’s disease (HD). CAG repeat-targeting artificial miRNAs (art-miRNAs) were shown as attractive therapeutic approach for polyQ disorders as they caused allele-selective decrease in the level of mutant proteins. Here, using polyQ disease models, we aimed to demonstrate how miRNA-based gene expression regulation is dependent on target sequence features. We show that the silencing efficiency and selectivity of art-miRNAs is influenced by the localization of the CAG repeat tract within transcript and the specific sequence context. Furthermore, we aimed to reveal the events leading to downregulation of mutant polyQ proteins and found very rapid activation of translational repression and HTT transcript deadenylation. Slicer-activity of AGO2 was dispensable in this process, as determined in AGO2 knockout cells generated with CRISPR-Cas9 technology. We also showed highly allele-selective downregulation of huntingtin in human HD neural progenitors (NPs). Taken together, art-miRNA activity may serve as a model of the cooperative activity and targeting of ORF regions by endogenous miRNAs.
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21
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Dexheimer PJ, Cochella L. MicroRNAs: From Mechanism to Organism. Front Cell Dev Biol 2020; 8:409. [PMID: 32582699 PMCID: PMC7283388 DOI: 10.3389/fcell.2020.00409] [Citation(s) in RCA: 183] [Impact Index Per Article: 45.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/04/2020] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are short, regulatory RNAs that act as post-transcriptional repressors of gene expression in diverse biological contexts. The emergence of small RNA-mediated gene silencing preceded the onset of multicellularity and was followed by a drastic expansion of the miRNA repertoire in conjunction with the evolution of complexity in the plant and animal kingdoms. Along this process, miRNAs became an essential feature of animal development, as no higher metazoan lineage tolerated loss of miRNAs or their associated protein machinery. In fact, ablation of the miRNA biogenesis machinery or the effector silencing factors results in severe embryogenesis defects in every animal studied. In this review, we summarize recent mechanistic insight into miRNA biogenesis and function, while emphasizing features that have enabled multicellular organisms to harness the potential of this broad class of repressors. We first discuss how different mechanisms of regulation of miRNA biogenesis are used, not only to generate spatio-temporal specificity of miRNA production within an animal, but also to achieve the necessary levels and dynamics of expression. We then explore how evolution of the mechanism for small RNA-mediated repression resulted in a diversity of silencing complexes that cause different molecular effects on their targets. Multicellular organisms have taken advantage of this variability in the outcome of miRNA-mediated repression, with differential use in particular cell types or even distinct subcellular compartments. Finally, we present an overview of how the animal miRNA repertoire has evolved and diversified, emphasizing the emergence of miRNA families and the biological implications of miRNA sequence diversification. Overall, focusing on selected animal models and through the lens of evolution, we highlight canonical mechanisms in miRNA biology and their variations, providing updated insight that will ultimately help us understand the contribution of miRNAs to the development and physiology of multicellular organisms.
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Affiliation(s)
- Philipp J Dexheimer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Luisa Cochella
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
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22
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Mei J, Hao L, Wang H, Xu R, Liu Y, Zhu Y, Liu C. Systematic characterization of non-coding RNAs in triple-negative breast cancer. Cell Prolif 2020; 53:e12801. [PMID: 32249490 PMCID: PMC7260065 DOI: 10.1111/cpr.12801] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/03/2020] [Accepted: 03/11/2020] [Indexed: 12/17/2022] Open
Abstract
Triple‐negative breast cancer (TNBC) is one of the most aggressive subtypes of breast cancer with negativity for oestrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor (HER2). Non‐coding RNAs (ncRNAs) make up most of the transcriptome and are widely present in eukaryotic cells. In recent years, emerging evidence suggests that ncRNAs, mainly microRNAs (miRNAs), long ncRNAs (lncRNAs) and circular RNAs (circRNAs), play prominent roles in the tumorigenesis and development of TNBC, but the functions of most ncRNAs have not been fully described. In this review, we systematically elucidate the general characteristics and biogenesis of miRNAs, lncRNAs and circRNAs, discuss the emerging functions of these ncRNAs in TNBC and present future perspectives in clinical practice.
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Affiliation(s)
- Jie Mei
- Department of Oncology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, China
| | - Leiyu Hao
- Department of Physiology, Nanjing Medical University, Nanjing, China
| | - Huiyu Wang
- Department of Oncology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, China
| | - Rui Xu
- Department of Physiology, Nanjing Medical University, Nanjing, China
| | - Yan Liu
- Department of Physiology, Nanjing Medical University, Nanjing, China
| | - Yichao Zhu
- Department of Physiology, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Chaoying Liu
- Department of Oncology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, China
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23
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Zaporozhchenko IA, Rykova EY, Laktionov PP. The Fundamentals of miRNA Biology: Structure, Biogenesis, and Regulatory Functions. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s106816202001015x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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24
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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: 25] [Impact Index Per Article: 6.3] [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.
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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.
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25
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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.
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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,
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26
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Nowosad K, Hordyjewska-Kowalczyk E, Tylzanowski P. Mutations in gene regulatory elements linked to human limb malformations. J Med Genet 2019; 57:361-370. [PMID: 31857429 DOI: 10.1136/jmedgenet-2019-106369] [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: 06/12/2019] [Revised: 10/09/2019] [Accepted: 11/03/2019] [Indexed: 01/08/2023]
Abstract
Most of the human genome has a regulatory function in gene expression. The technological progress made in recent years permitted the revision of old and discovery of new mutations outside of the protein-coding regions that do affect human limb morphology. Steadily increasing discovery rate of such mutations suggests that until now the largely neglected part of the genome rises to its well-deserved prominence. In this review, we describe the recent technological advances permitting this unprecedented advance in identifying non-coding mutations. We especially focus on the mutations in cis-regulatory elements such as enhancers, and trans-regulatory elements such as miRNA and long non-coding RNA, linked to hereditary or inborn limb defects. We also discuss the role of chromatin organisation and enhancer-promoter interactions in the aetiology of limb malformations.
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Affiliation(s)
- Karol Nowosad
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Lublin, Poland.,The Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Ewa Hordyjewska-Kowalczyk
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Lublin, Poland.,The Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Przemko Tylzanowski
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Lublin, Poland .,Department of Development and Regeneration, Skeletal Biology and Engineering Research Center, University of Leuven, Leuven, Belgium
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27
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Hanet A, Räsch F, Weber R, Ruscica V, Fauser M, Raisch T, Kuzuoğlu-Öztürk D, Chang CT, Bhandari D, Igreja C, Wohlbold L. HELZ directly interacts with CCR4-NOT and causes decay of bound mRNAs. Life Sci Alliance 2019; 2:2/5/e201900405. [PMID: 31570513 PMCID: PMC6769256 DOI: 10.26508/lsa.201900405] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 09/13/2019] [Accepted: 09/13/2019] [Indexed: 12/11/2022] Open
Abstract
The putative UPF1-like SF1 helicase HELZ directly interacts with the CCR4–NOT deadenylase complex to induce translational repression and 5′-to-3′ decay of bound mRNAs. Eukaryotic superfamily (SF) 1 helicases have been implicated in various aspects of RNA metabolism, including transcription, processing, translation, and degradation. Nevertheless, until now, most human SF1 helicases remain poorly understood. Here, we have functionally and biochemically characterized the role of a putative SF1 helicase termed “helicase with zinc-finger,” or HELZ. We discovered that HELZ associates with various mRNA decay factors, including components of the carbon catabolite repressor 4-negative on TATA box (CCR4–NOT) deadenylase complex in human and Drosophila melanogaster cells. The interaction between HELZ and the CCR4–NOT complex is direct and mediated by extended low-complexity regions in the C-terminal part of the protein. We further reveal that HELZ requires the deadenylase complex to mediate translational repression and decapping-dependent mRNA decay. Finally, transcriptome-wide analysis of Helz-null cells suggests that HELZ has a role in the regulation of the expression of genes associated with the development of the nervous system.
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Affiliation(s)
- Aoife Hanet
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Felix Räsch
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Ramona Weber
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Vincenzo Ruscica
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Maria Fauser
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Tobias Raisch
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany.,Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Duygu Kuzuoğlu-Öztürk
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany.,Helen Diller Family Cancer Research, University of California San Francisco, San Francisco, CA, USA
| | - Chung-Te Chang
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Dipankar Bhandari
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Cátia Igreja
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Lara Wohlbold
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
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28
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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.
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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
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29
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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.
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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
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30
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Suzuki T, Kikuguchi C, Nishijima S, Nagashima T, Takahashi A, Okada M, Yamamoto T. Postnatal liver functional maturation requires Cnot complex-mediated decay of mRNAs encoding cell cycle and immature liver genes. Development 2019; 146:dev.168146. [PMID: 30733279 PMCID: PMC6398447 DOI: 10.1242/dev.168146] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 01/21/2019] [Indexed: 12/22/2022]
Abstract
Liver development involves dramatic gene expression changes mediated by transcriptional and post-transcriptional control. Here, we show that the Cnot deadenylase complex plays a crucial role in liver functional maturation. The Cnot3 gene encodes an essential subunit of the Cnot complex. Mice lacking Cnot3 in liver have reduced body and liver masses, and they display anemia and severe liver damage. Histological analyses indicate that Cnot3-deficient (Cnot3−/−) hepatocytes are irregular in size and morphology, resulting in formation of abnormal sinusoids. We observe hepatocyte death, increased abundance of mitotic and mononucleate hepatocytes, and inflammation. Cnot3−/− livers show increased expression of immune response-related, cell cycle-regulating and immature liver genes, while many genes relevant to liver functions, such as oxidation-reduction, lipid metabolism and mitochondrial function, decrease, indicating impaired liver functional maturation. Highly expressed mRNAs possess elongated poly(A) tails and are stabilized in Cnot3−/− livers, concomitant with an increase of the proteins they encode. In contrast, transcription of liver function-related mRNAs was lower in Cnot3−/− livers. We detect efficient suppression of Cnot3 protein postnatally, demonstrating the crucial contribution of mRNA decay to postnatal liver functional maturation. Summary: Regulation of both mRNA transcription and stability plays a crucial role in postnatal liver development; in particular, Cnot complex-mediated mRNA decay is essential for postnatal liver functional maturation.
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Affiliation(s)
- Toru Suzuki
- Laboratory for Immunogenetics, Center for Integrative Medical Sciences, RIKEN, 1-7-22, Suehiro-cho, Yokohama 230-0045, Japan
| | - Chisato Kikuguchi
- Laboratory for Immunogenetics, Center for Integrative Medical Sciences, RIKEN, 1-7-22, Suehiro-cho, Yokohama 230-0045, Japan
| | - Saori Nishijima
- Cell Signal Unit, Okinawa Institute of Science and Technology, 1919-1 Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Takeshi Nagashima
- Division of Cell Proliferation, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Akinori Takahashi
- Cell Signal Unit, Okinawa Institute of Science and Technology, 1919-1 Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Mariko Okada
- Laboratory for Integrated Cellular Systems, Center for Integrative Medical Sciences, RIKEN, 1-7-22, Suehiro-cho, Yokohama 230-0045, Japan.,Laboratory for Cell Systems, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tadashi Yamamoto
- Laboratory for Immunogenetics, Center for Integrative Medical Sciences, RIKEN, 1-7-22, Suehiro-cho, Yokohama 230-0045, Japan .,Cell Signal Unit, Okinawa Institute of Science and Technology, 1919-1 Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
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31
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Mayya VK, Duchaine TF. Ciphers and Executioners: How 3'-Untranslated Regions Determine the Fate of Messenger RNAs. Front Genet 2019; 10:6. [PMID: 30740123 PMCID: PMC6357968 DOI: 10.3389/fgene.2019.00006] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 01/07/2019] [Indexed: 12/29/2022] Open
Abstract
The sequences and structures of 3'-untranslated regions (3'UTRs) of messenger RNAs govern their stability, localization, and expression. 3'UTR regulatory elements are recognized by a wide variety of trans-acting factors that include microRNAs (miRNAs), their associated machinery, and RNA-binding proteins (RBPs). In turn, these factors instigate common mechanistic strategies to execute the regulatory programs encoded by 3'UTRs. Here, we review classes of factors that recognize 3'UTR regulatory elements and the effector machineries they guide toward mRNAs to dictate their expression and fate. We outline illustrative examples of competitive, cooperative, and coordinated interplay such as mRNA localization and localized translation. We further review the recent advances in the study of mRNP granules and phase transition, and their possible significance for the functions of 3'UTRs. Finally, we highlight some of the most recent strategies aimed at deciphering the complexity of the regulatory codes of 3'UTRs, and identify some of the important remaining challenges.
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Affiliation(s)
| | - Thomas F. Duchaine
- Goodman Cancer Research Centre and Department of Biochemistry, McGill University, Montreal, QC, Canada
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32
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Rotavirus Induces Formation of Remodeled Stress Granules and P Bodies and Their Sequestration in Viroplasms To Promote Progeny Virus Production. J Virol 2018; 92:JVI.01363-18. [PMID: 30258011 DOI: 10.1128/jvi.01363-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 09/20/2018] [Indexed: 02/06/2023] Open
Abstract
Rotavirus replicates in unique virus-induced cytoplasmic inclusion bodies called viroplasms (VMs), the composition and structure of which have yet to be understood. Based on the analysis of a few proteins, earlier studies reported that rotavirus infection inhibits stress granule (SG) formation and disrupts P bodies (PBs). However, the recent demonstration that rotavirus infection induces cytoplasmic relocalization and colocalization with VMs of several nuclear hnRNPs and AU-rich element-binding proteins (ARE-BPs), which are known components of SGs and PBs, suggested the possibility of rotavirus-induced remodeling of SGs and PBs, prompting us to analyze a large number of the SG and PB components to understand the status of SGs and PBs in rotavirus-infected cells. Here we demonstrate that rotavirus infection induces molecular triage by selective exclusion of a few proteins of SGs (G3BP1 and ZBP1) and PBs (DDX6, EDC4, and Pan3) and sequestration of the remodeled/atypical cellular organelles, containing the majority of their components, in the VM. The punctate SG and PB structures are seen at about 4 h postinfection (hpi), coinciding with the appearance of small VMs, many of which fuse to form mature large VMs with progression of infection. By use of small interfering RNA (siRNA)-mediated knockdown and/or ectopic overexpression, the majority of the SG and PB components, except for ADAR1, were observed to inhibit viral protein expression and virus growth. In conclusion, this study demonstrates that VMs are highly complex supramolecular structures and that rotavirus employs a novel strategy of sequestration in the VM and harnessing of the remodeled cellular RNA recycling bins to promote its growth.IMPORTANCE Rotavirus is known to replicate in specialized virus-induced cytoplasmic inclusion bodies called viroplasms (VMs), but the composition and structure of VMs are not yet understood. Here we demonstrate that rotavirus interferes with normal SG and PB assembly but promotes formation of atypical SG-PB structures by selective exclusion of a few components and employs a novel strategy of sequestration of the remodeled SG-PB granules in the VMs to promote virus growth by modulating their negative influence on virus infection. Rotavirus VMs appear to be complex supramolecular structures formed by the union of the triad of viral replication complexes and remodeled SGs and PBs, as well as other host factors, and designed to promote productive virus infection. These observations have implications for the planning of future research with the aim of understanding the structure of the VM, the mechanism of morphogenesis of the virus, and the detailed roles of host proteins in rotavirus biology.
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33
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Li Z, Xu R, Li N. MicroRNAs from plants to animals, do they define a new messenger for communication? Nutr Metab (Lond) 2018; 15:68. [PMID: 30302122 PMCID: PMC6167836 DOI: 10.1186/s12986-018-0305-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 09/21/2018] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs), a class of single-stranded non-coding RNA of about 22 nucleotides, are potent regulators of gene expression existing in both plants and animals. Recent studies showed that plant miRNAs could enter mammalian bloodstream via gastrointestinal tract, through which access a variety of tissues and cells of recipients to exert therapeutic effects. This intriguing phenomenon indicates that miRNAs of diet/plant origin may act as a new class of bioactive ingredients communicating with mammalian systems. In this review, in order to pinpoint the reason underlying discrepancies of miRNAs transmission from diet/plant to animals, the pathways that generate miRNAs and machineries involved in the functions of miRNAs in both kingdoms were outlined and compared. Then, the current controversies concerning cross-kingdom regulations and the potential mechanisms responsible for absorption and transfer of diet/plant-derived miRNAs were interpreted. Furthermore, the hormone-like action of miRNAs and the intricate interplay between miRNAs and hormones were implicated. Finally, how these findings may impact nutrition and medicine were briefly discussed.
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Affiliation(s)
- Zhiqing Li
- 1State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Tsinghua University, Beijing, 100005 People's Republic of China
| | - Ruodan Xu
- 2Institute of Basic Theory for Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700 People's Republic of China.,3Department of Engineering, Aarhus University, 8000 Aarhus, Denmark
| | - Ning Li
- 2Institute of Basic Theory for Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700 People's Republic of China
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34
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Shi JX, Li JS, Hu R, Zhao XC, Liang CC, Li XM, Wang H, Shi Y, Su X. CNOT1 is involved in TTP‑mediated ICAM‑1 and IL‑8 mRNA decay. Mol Med Rep 2018; 18:2321-2327. [PMID: 29956766 DOI: 10.3892/mmr.2018.9213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 05/21/2018] [Indexed: 11/06/2022] Open
Abstract
Subunit 1 is the scaffold protein of the carbon catabolite repressor protein 4 (CCR4)‑negative on TATA (NOT) complex (CNOT1). In our previous study, it was reported that tristetraprolin (TTP) could recruit subunit 7 of the CCR4‑NOT complex (CNOT7) to induce the degradation of intercellular adhesion molecule‑1 (ICAM‑1) and interleukin‑8 (IL‑8) mRNA in human pulmonary microvascular endothelial cells (HPMECs). It was additionally demonstrated that TTP, CNOT7 and CNOT1 formed a complex in HPMECs. However, whether CNOT1 is involved in TTP‑mediated ICAM‑1 and IL‑8 mRNA decay remains unclear. The present study demonstrated that CNOT1 knockdown improved ICAM‑1 and IL‑8 mRNA stabilization and protein expression levels. The immunofluorescence results demonstrated that CNOT1, CNOT7 and TTP are co‑localized in the cytoplasm. CNOT1 silencing abolished CNOT7 and TTP coimmunoprecipitation. However, CNOT7 silencing did not influence CNOT1 and TTP coimmunoprecipitation, and TTP silencing additionally did not influence CNOT1 and CNOT7 coimmunoprecipitation. These results together with the authors' previous study, have identified that CNOT1 provides a platform for the recruitment of TTP and CNOT7, and is involved in TTP‑mediated ICAM‑1 and IL‑8 mRNA decay.
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Affiliation(s)
- Jia-Xin Shi
- Department of Respiratory Medicine, The First People's Hospital of Lianyungang City, Lianyungang, Jiangsu 222002, P.R. China
| | - Jia-Shu Li
- Department of Respiratory Medicine, The First People's Hospital of Lianyungang City, Lianyungang, Jiangsu 222002, P.R. China
| | - Rong Hu
- Department of Respiratory Medicine, The First People's Hospital of Lianyungang City, Lianyungang, Jiangsu 222002, P.R. China
| | - Xin-Cheng Zhao
- Department of Respiratory Medicine, The First People's Hospital of Lianyungang City, Lianyungang, Jiangsu 222002, P.R. China
| | - Cheng-Cheng Liang
- Department of Respiratory Medicine, The First People's Hospital of Lianyungang City, Lianyungang, Jiangsu 222002, P.R. China
| | - Xiao-Min Li
- Department of Respiratory Medicine, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221004, P.R. China
| | - Hong Wang
- Department of Respiratory and Critical Care Medicine, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Yi Shi
- Department of Respiratory and Critical Care Medicine, Jinling Hospital, Nanjing, Jiangsu 210002, P.R. China
| | - Xin Su
- Department of Respiratory and Critical Care Medicine, Jinling Hospital, Nanjing, Jiangsu 210002, P.R. China
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35
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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.
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36
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Lima JF, Cerqueira L, Figueiredo C, Oliveira C, Azevedo NF. Anti-miRNA oligonucleotides: A comprehensive guide for design. RNA Biol 2018; 15:338-352. [PMID: 29570036 DOI: 10.1080/15476286.2018.1445959] [Citation(s) in RCA: 155] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
MicroRNAs (miRNAs) are small, non-coding RNA molecules that regulate gene expression post-transcriptionally. As a consequence of their function towards mRNA, miRNAs are widely associated with the pathogenesis of several human diseases, making miRNAs a target for new therapeutic strategies based on the control of their expression. Indeed, numerous works were published in the past decades showing the potential use of antisense oligonucleotides to target aberrant miRNAs (AMOs) involved in several human pathologies. New classes of chemical-modified-AMOs, including locked nucleic acid oligonucleotides, have recently proved their worth in silencing miRNAs. A correct design of a specific AMOs can help to improve their performance and potency towards the target miRNA by increasing for instance nuclease resistance and target affinity. This review outlines the technologies involved to suppress aberrant miRNAs. From the design strategies used in AMOs to its application in novel miRNA-based therapeutics and detection methodologies.
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Affiliation(s)
- Joana Filipa Lima
- a LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering , Faculty of Engineering of the University of Porto , R. Dr. Roberto Frias, Porto , Portugal.,b Biomode 2, S. A., INL - Avda. Mestre José Veiga s/n, Braga , Portugal.,c i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto , R. Alfredo Allen, Porto , Portugal.,d IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto , Rua Júlio Amaral de Carvalho, 45, Porto , Portugal
| | - Laura Cerqueira
- a LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering , Faculty of Engineering of the University of Porto , R. Dr. Roberto Frias, Porto , Portugal.,b Biomode 2, S. A., INL - Avda. Mestre José Veiga s/n, Braga , Portugal
| | - Ceu Figueiredo
- c i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto , R. Alfredo Allen, Porto , Portugal.,d IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto , Rua Júlio Amaral de Carvalho, 45, Porto , Portugal.,e FMUP, Faculty of Medicine of the University of Porto , Al. Prof. Hernâni Monteiro, Porto , Portugal
| | - Carla Oliveira
- c i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto , R. Alfredo Allen, Porto , Portugal.,d IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto , Rua Júlio Amaral de Carvalho, 45, Porto , Portugal.,e FMUP, Faculty of Medicine of the University of Porto , Al. Prof. Hernâni Monteiro, Porto , Portugal
| | - Nuno Filipe Azevedo
- a LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering , Faculty of Engineering of the University of Porto , R. Dr. Roberto Frias, Porto , Portugal
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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.
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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
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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.
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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
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39
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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: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [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.
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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.
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40
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Mengardi C, Limousin T, Ricci EP, Soto-Rifo R, Decimo D, Ohlmann T. microRNAs stimulate translation initiation mediated by HCV-like IRESes. Nucleic Acids Res 2017; 45:4810-4824. [PMID: 28077561 PMCID: PMC5416841 DOI: 10.1093/nar/gkw1345] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 12/22/2016] [Indexed: 01/04/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that control gene expression by recognizing and hybridizing to a specific sequence generally located in the 3΄ untranslated region (UTR) of targeted mRNAs. miRNA-induced inhibition of translation occurs during the initiation step, most probably at the level of ribosome scanning. In this process, the RNA-induced silencing complex interacts both with PABP and the 43S pre-initiation complex to disrupt scanning of the 40S ribosome. However, in some specific cases, miRNAs can stimulate translation. Although the mechanism of miRNA-mediated upregulation is unknown, it appears that the poly(A) tail and the lack of availability of the TNRC6 proteins are amongst major determinants. The genomic RNA of the Hepatitis C Virus is uncapped, non-polyadenylated and harbors a peculiar internal ribosome entry site (IRES) that binds the ribosome directly to the AUG codon. Thus, we have exploited the unique properties of the HCV IRES and other related IRESes (HCV-like) to study how translation initiation can be modulated by miRNAs on these elements. Here, we report that miRNA binding to the 3΄ UTR can stimulate translation of a reporter gene given that its expression is driven by an HCV-like IRES and that it lacks a poly(A) tail at its 3΄ extremity.
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Affiliation(s)
- Chloé Mengardi
- CIRI, International Center for Infectiology Research, Université de Lyon, 69364 Lyon, France.,INSERM, U1111, Lyon, France.,Ecole Normale Supérieure de Lyon, Lyon, France.,Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France.,CNRS, UMR5308, Lyon, France
| | - Taran Limousin
- CIRI, International Center for Infectiology Research, Université de Lyon, 69364 Lyon, France.,INSERM, U1111, Lyon, France.,Ecole Normale Supérieure de Lyon, Lyon, France.,Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France.,CNRS, UMR5308, Lyon, France
| | - Emiliano P Ricci
- CIRI, International Center for Infectiology Research, Université de Lyon, 69364 Lyon, France.,INSERM, U1111, Lyon, France.,Ecole Normale Supérieure de Lyon, Lyon, France.,Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France.,CNRS, UMR5308, Lyon, France
| | - Ricardo Soto-Rifo
- CIRI, International Center for Infectiology Research, Université de Lyon, 69364 Lyon, France.,INSERM, U1111, Lyon, France.,Ecole Normale Supérieure de Lyon, Lyon, France.,Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France.,CNRS, UMR5308, Lyon, France
| | - Didier Decimo
- CIRI, International Center for Infectiology Research, Université de Lyon, 69364 Lyon, France.,INSERM, U1111, Lyon, France.,Ecole Normale Supérieure de Lyon, Lyon, France.,Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France.,CNRS, UMR5308, Lyon, France
| | - Théophile Ohlmann
- CIRI, International Center for Infectiology Research, Université de Lyon, 69364 Lyon, France.,INSERM, U1111, Lyon, France.,Ecole Normale Supérieure de Lyon, Lyon, France.,Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France.,CNRS, UMR5308, Lyon, France
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41
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Fukao A, Fujiwara T. The coupled and uncoupled mechanisms by which trans-acting factors regulate mRNA stability and translation. J Biochem 2017; 161:309-314. [PMID: 28039391 DOI: 10.1093/jb/mvw086] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 10/11/2016] [Indexed: 12/25/2022] Open
Abstract
In mammals, spatiotemporal control of protein synthesis plays a key role in the post-transcriptional regulation of gene expression during cell proliferation, development and differentiation and RNA-binding proteins (RBPs) and microRNAs (miRNAs) are required for this phenomenon. RBPs and miRNAs control the levels of mRNA protein products by regulating mRNA stability and translation. Recent studies have shown that RBPs and miRNAs simultaneously regulate mRNA stability and translation, and that the differential functions of RBPs and miRNAs are dependent on their interaction partners. Here, we summarize the coupled- and uncoupled mechanisms by which trans-acting factors regulate mRNA stability and translation.
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42
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Paces J, Nic M, Novotny T, Svoboda P. Literature review of baseline information to support the risk assessment of RNAi‐based GM plants. ACTA ACUST UNITED AC 2017. [PMCID: PMC7163844 DOI: 10.2903/sp.efsa.2017.en-1246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Paces
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
| | | | | | - Petr Svoboda
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
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43
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Long non-coding RNA GAS5 controls human embryonic stem cell self-renewal by maintaining NODAL signalling. Nat Commun 2016; 7:13287. [PMID: 27811843 PMCID: PMC5097163 DOI: 10.1038/ncomms13287] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 09/16/2016] [Indexed: 12/18/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are known players in the regulatory circuitry of the self-renewal in human embryonic stem cells (hESCs). However, most hESC-specific lncRNAs remain uncharacterized. Here we demonstrate that growth-arrest-specific transcript 5 (GAS5), a known tumour suppressor and growth arrest-related lncRNA, is highly expressed and directly regulated by pluripotency factors OCT4 and SOX2 in hESCs. Phenotypic analysis shows that GAS5 knockdown significantly impairs hESC self-renewal, but its overexpression significantly promotes hESC self-renewal. Using RNA sequencing and functional analysis, we demonstrate that GAS5 maintains NODAL signalling by protecting NODAL expression from miRNA-mediated degradation. Therefore, we propose that the above pluripotency factors, GAS5 and NODAL form a feed-forward signalling loop that maintains hESC self-renewal. As this regulatory function of GAS5 is stem cell specific, our findings also indicate that the functions of lncRNAs may vary in different cell types due to competing endogenous mechanisms.
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44
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Coordinated Regulation of Cap-Dependent Translation and MicroRNA Function by Convergent Signaling Pathways. Mol Cell Biol 2016; 36:2360-73. [PMID: 27354062 DOI: 10.1128/mcb.01011-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 06/14/2016] [Indexed: 01/08/2023] Open
Abstract
Cell growth and proliferation require the coordinated activation of many cellular processes, including cap-dependent mRNA translation. MicroRNAs oppose cap-dependent translation and set thresholds for expression of target proteins. Emerging data suggest that microRNA function is enhanced by cellular activation due in part to induction of the RNA-induced silencing complex (RISC) scaffold protein GW182. In the current study, we demonstrate that increased expression of GW182 in activated or transformed immune cells results from effects of phosphoinositol 3-kinase-Akt-mechanistic target of rapamycin (PI3K-Akt-mTOR) and Jak-Stat-Pim signaling on the translation of GW182 mRNA. Both signaling pathways enhanced polysome occupancy and eukaryotic initiation factor 4E (eIF4E) binding to the 5' 7mG cap of GW182 mRNA. The effect of Jak-Stat-Pim signaling on polysome occupancy and expression of GW182 protein was greater than that of PI3K-Akt-mTOR signaling, likely resulting from enhanced eIF4A-dependent unwinding of G-quadruplexes in the 5' untranslated region of GW182 mRNA. Consistent with this, GW182 expression and microRNA function were reduced by inhibition of mTOR or Pim kinases, translation initiation complex assembly, or eIF4A function. Taken together, these data provide a mechanistic link between microRNA function and cap-dependent translation that allows activated immune cells to maintain microRNA-mediated repression of targets despite enhanced rates of protein synthesis.
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45
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Sarnow P, Sagan SM. Unraveling the Mysterious Interactions Between Hepatitis C Virus RNA and Liver-Specific MicroRNA-122. Annu Rev Virol 2016; 3:309-332. [PMID: 27578438 DOI: 10.1146/annurev-virology-110615-042409] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Many viruses encode or subvert cellular microRNAs (miRNAs) to aid in their gene expression, amplification strategies, or pathogenic signatures. miRNAs typically downregulate gene expression by binding to the 3' untranslated region of their mRNA targets. As a result, target mRNAs are translationally repressed and subsequently deadenylated and degraded. Curiously, hepatitis C virus (HCV), a member of the Flaviviridae family, recruits two molecules of liver-specific microRNA-122 (miR-122) to the 5' end of its genome. In contrast to the canonical activity of miRNAs, the interactions of miR-122 with the viral genome promote viral RNA accumulation in cultured cells and in animal models of HCV infection. Sequestration of miR-122 results in loss of viral RNA both in cell culture and in the livers of chronic HCV-infected patients. This review discusses the mechanisms by which miR-122 is thought to enhance viral RNA abundance and the consequences of miR-122-HCV interactions. We also describe preliminary findings from phase II clinical trials in patients treated with miR-122 antisense oligonucleotides.
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Affiliation(s)
- Peter Sarnow
- Department of Microbiology and Immunology, Stanford University, Stanford, California 94305
| | - Selena M Sagan
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada;
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46
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Fukao A, Aoyama T, Fujiwara T. The molecular mechanism of translational control via the communication between the microRNA pathway and RNA-binding proteins. RNA Biol 2016; 12:922-6. [PMID: 26274611 DOI: 10.1080/15476286.2015.1073436] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
MicroRNAs (miRNAs) are evolutionarily conserved small noncoding RNAs found in most plants and animals. The miRNA pathway regulates posttranscriptional gene expression through the deadenylation and translation repression of target mRNAs. Recent studies revealed that the early step of translation initiation is the target of "pure" translation repression by the miRNA pathway. Moreover, particularly in animals, the miRNA pathway is required for neuronal development, differentiation, and plasticity. In addition, some functions of miRNAs are regulated by RNA-binding proteins (RBPs) in neuronal cells. This review summarizes new insights about the molecular mechanisms of pure translation repression by miRNA pathway and the communication between the miRNA pathway and RBPs in neuronal local translation.
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Affiliation(s)
- Akira Fukao
- a Laboratory of Biochemistry; Department of Pharmacy; Kinki University ; Higashi-Osaka , Japan
| | - Tomohiko Aoyama
- b Graduate School of Pharmaceutical Sciences; Nagoya City University ; Mizuho-ku, Nagoya , Japan
| | - Toshinobu Fujiwara
- a Laboratory of Biochemistry; Department of Pharmacy; Kinki University ; Higashi-Osaka , Japan
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47
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Azlan A, Dzaki N, Azzam G. Argonaute: The executor of small RNA function. J Genet Genomics 2016; 43:481-94. [PMID: 27569398 DOI: 10.1016/j.jgg.2016.06.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 05/08/2016] [Accepted: 06/17/2016] [Indexed: 01/06/2023]
Abstract
The discovery of small non-coding RNAs - microRNA (miRNA), short interfering RNA (siRNA) and PIWI-interacting RNA (piRNA) - represents one of the most exciting frontiers in biology specifically on the mechanism of gene regulation. In order to execute their functions, these small RNAs require physical interactions with their protein partners, the Argonaute (AGO) family proteins. Over the years, numerous studies have made tremendous progress on understanding the roles of AGO in gene silencing in various organisms. In this review, we summarize recent progress of AGO-mediated gene silencing and other cellular processes in which AGO proteins have been implicated with a particular focus on progress made in flies, humans and other model organisms as compliment.
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Affiliation(s)
- Azali Azlan
- School of Biological Sciences, Universiti Sains Malaysia, Penang 11800, Malaysia
| | - Najat Dzaki
- School of Biological Sciences, Universiti Sains Malaysia, Penang 11800, Malaysia
| | - Ghows Azzam
- School of Biological Sciences, Universiti Sains Malaysia, Penang 11800, Malaysia; Advance Medical and Dental Institute, Universiti Sains Malaysia, Penang 11800, Malaysia.
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48
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Cao DD, Li L, Chan WY. MicroRNAs: Key Regulators in the Central Nervous System and Their Implication in Neurological Diseases. Int J Mol Sci 2016; 17:E842. [PMID: 27240359 PMCID: PMC4926376 DOI: 10.3390/ijms17060842] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 05/20/2016] [Accepted: 05/23/2016] [Indexed: 01/03/2023] Open
Abstract
MicroRNAs (miRNAs) are a class of small, well-conserved noncoding RNAs that regulate gene expression post-transcriptionally. They have been demonstrated to regulate a lot of biological pathways and cellular functions. Many miRNAs are dynamically regulated during central nervous system (CNS) development and are spatially expressed in adult brain indicating their essential roles in neural development and function. In addition, accumulating evidence strongly suggests that dysfunction of miRNAs contributes to neurological diseases. These observations, together with their gene regulation property, implicated miRNAs to be the key regulators in the complex genetic network of the CNS. In this review, we first focus on the ways through which miRNAs exert the regulatory function and how miRNAs are regulated in the CNS. We then summarize recent findings that highlight the versatile roles of miRNAs in normal CNS physiology and their association with several types of neurological diseases. Subsequently we discuss the limitations of miRNAs research based on current studies as well as the potential therapeutic applications and challenges of miRNAs in neurological disorders. We endeavor to provide an updated description of the regulatory roles of miRNAs in normal CNS functions and pathogenesis of neurological diseases.
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Affiliation(s)
- Dan-Dan Cao
- Faculty of Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong-Chinese Academy of Sciences Guangzhou Institute of Biomedicine and Health Joint Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong 999077, SAR, China.
| | - Lu Li
- Faculty of Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong-Chinese Academy of Sciences Guangzhou Institute of Biomedicine and Health Joint Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong 999077, SAR, China.
| | - Wai-Yee Chan
- Faculty of Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong-Chinese Academy of Sciences Guangzhou Institute of Biomedicine and Health Joint Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong 999077, SAR, China.
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49
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Schober A, Weber C. Mechanisms of MicroRNAs in Atherosclerosis. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2016; 11:583-616. [DOI: 10.1146/annurev-pathol-012615-044135] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Andreas Schober
- Institute for Cardiovascular Prevention, Ludwig Maximilians University Munich, Munich 80336, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich 80336, Germany;
| | - Christian Weber
- Institute for Cardiovascular Prevention, Ludwig Maximilians University Munich, Munich 80336, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich 80336, Germany;
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50
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Kuzuoğlu-Öztürk D, Bhandari D, Huntzinger E, Fauser M, Helms S, Izaurralde E. miRISC and the CCR4-NOT complex silence mRNA targets independently of 43S ribosomal scanning. EMBO J 2016; 35:1186-203. [PMID: 27009120 PMCID: PMC4888236 DOI: 10.15252/embj.201592901] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 02/18/2016] [Indexed: 12/13/2022] Open
Abstract
miRNAs associate with Argonaute (AGO) proteins to silence the expression of mRNA targets by inhibiting translation and promoting deadenylation, decapping, and mRNA degradation. A current model for silencing suggests that AGOs mediate these effects through the sequential recruitment of GW182 proteins, the CCR4–NOT deadenylase complex and the translational repressor and decapping activator DDX6. An alternative model posits that AGOs repress translation by interfering with eIF4A function during 43S ribosomal scanning and that this mechanism is independent of GW182 and the CCR4–NOT complex in Drosophila melanogaster. Here, we show that miRNAs, AGOs, GW182, the CCR4–NOT complex, and DDX6/Me31B repress and degrade polyadenylated mRNA targets that are translated via scanning‐independent mechanisms in both human and Dm cells. This and additional observations indicate a common mechanism used by these proteins and miRNAs to mediate silencing. This mechanism does not require eIF4A function during ribosomal scanning.
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Affiliation(s)
- Duygu Kuzuoğlu-Öztürk
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Dipankar Bhandari
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Eric Huntzinger
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Maria Fauser
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Sigrun Helms
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Elisa Izaurralde
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
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