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Rinaldi S, Moroni E, Rozza R, Magistrato A. Frontiers and Challenges of Computing ncRNAs Biogenesis, Function and Modulation. J Chem Theory Comput 2024; 20:993-1018. [PMID: 38287883 DOI: 10.1021/acs.jctc.3c01239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
Non-coding RNAs (ncRNAs), generated from nonprotein coding DNA sequences, constitute 98-99% of the human genome. Non-coding RNAs encompass diverse functional classes, including microRNAs, small interfering RNAs, PIWI-interacting RNAs, small nuclear RNAs, small nucleolar RNAs, and long non-coding RNAs. With critical involvement in gene expression and regulation across various biological and physiopathological contexts, such as neuronal disorders, immune responses, cardiovascular diseases, and cancer, non-coding RNAs are emerging as disease biomarkers and therapeutic targets. In this review, after providing an overview of non-coding RNAs' role in cell homeostasis, we illustrate the potential and the challenges of state-of-the-art computational methods exploited to study non-coding RNAs biogenesis, function, and modulation. This can be done by directly targeting them with small molecules or by altering their expression by targeting the cellular engines underlying their biosynthesis. Drawing from applications, also taken from our work, we showcase the significance and role of computer simulations in uncovering fundamental facets of ncRNA mechanisms and modulation. This information may set the basis to advance gene modulation tools and therapeutic strategies to address unmet medical needs.
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Affiliation(s)
- Silvia Rinaldi
- National Research Council of Italy (CNR) - Institute of Chemistry of OrganoMetallic Compounds (ICCOM), c/o Area di Ricerca CNR di Firenze Via Madonna del Piano 10, 50019 Sesto Fiorentino, Florence, Italy
| | - Elisabetta Moroni
- National Research Council of Italy (CNR) - Institute of Chemical Sciences and Technologies (SCITEC), via Mario Bianco 9, 20131 Milano, Italy
| | - Riccardo Rozza
- National Research Council of Italy (CNR) - Institute of Material Foundry (IOM) c/o International School for Advanced Studies (SISSA), Via Bonomea, 265, 34136 Trieste, Italy
| | - Alessandra Magistrato
- National Research Council of Italy (CNR) - Institute of Material Foundry (IOM) c/o International School for Advanced Studies (SISSA), Via Bonomea, 265, 34136 Trieste, Italy
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2
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Li H, You C, Yoshikawa M, Yang X, Gu H, Li C, Cui J, Chen X, Ye N, Zhang J, Wang G. A spontaneous thermo-sensitive female sterility mutation in rice enables fully mechanized hybrid breeding. Cell Res 2022; 32:931-945. [PMID: 36068348 PMCID: PMC9525692 DOI: 10.1038/s41422-022-00711-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 08/08/2022] [Indexed: 11/08/2022] Open
Abstract
Male sterility enables hybrid crop breeding to increase yields and has been extensively studied. But thermo-sensitive female sterility, which is an ideal property that may enable full mechanization in hybrid rice breeding, has rarely been investigated due to the absence of such germplasm. Here we identify the spontaneous thermo-sensitive female sterility 1 (tfs1) mutation that confers complete sterility under regular/high temperature and partial fertility under low temperature as a point mutation in ARGONAUTE7 (AGO7). AGO7 associates with miR390 to form an RNA-Induced Silencing Complex (RISC), which triggers the biogenesis of small interfering RNAs (siRNAs) from TRANS-ACTING3 (TAS3) loci by recruiting SUPPRESSOR OF GENE SILENCING (SGS3) and RNA-DEPENDENT RNA POLYMERASE6 (RDR6) to TAS3 transcripts. These siRNAs are known as tasiR-ARFs as they act in trans to repress auxin response factor genes. The mutant TFS1 (mTFS1) protein is compromised in its ability to load the miR390/miR390* duplex and eject miR390* during RISC formation. Furthermore, tasiR-ARF levels are reduced in tfs1 due to the deficiency in RDR6 but not SGS3 recruitment by mTFS1 RISC under regular/high temperature, while low temperature partially restores mTFS1 function in RDR6 recruitment and tasiR-ARF biogenesis. A miR390 mutant also exhibits female sterility, suggesting that female fertility is controlled by the miR390-AGO7 module. Notably, the tfs1 allele introduced into various elite rice cultivars endows thermo-sensitive female sterility. Moreover, field trials confirm the utility of tfs1 as a restorer line in fully mechanized hybrid rice breeding.
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Affiliation(s)
- Haoxuan Li
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Agriculture, Hunan Agricultural University, Changsha, Hunan, China
| | - Chenjiang You
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Manabu Yoshikawa
- Division of Plant and Microbial Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 2-1-2 Kannondai Tsukuba, Ibaraki, Japan
| | - Xiaoyu Yang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong, China
| | - Haiyong Gu
- The Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Chuanguo Li
- The Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Jie Cui
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA.
| | - Nenghui Ye
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Agriculture, Hunan Agricultural University, Changsha, Hunan, China.
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, Hong Kong, China.
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China.
| | - Guanqun Wang
- Department of Biology, Hong Kong Baptist University, Hong Kong, China.
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China.
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3
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Peng H, Wang M, Wang N, Yang C, Guo W, Li G, Huang S, Wei D, Liu D. Different N-Glycosylation Sites Reduce the Activity of Recombinant DSPAα2. Curr Issues Mol Biol 2022; 44:3930-3947. [PMID: 36135182 PMCID: PMC9497888 DOI: 10.3390/cimb44090270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/28/2022] [Accepted: 08/29/2022] [Indexed: 12/01/2022] Open
Abstract
Bat plasminogen activators α2 (DSPAα2) has extremely high medicinal value as a powerful natural thrombolytic protein. However, wild-type DSPAα2 has two N-glycosylation sites (N185 and N398) and its non-human classes of high-mannose-type N-glycans may cause immune responses in vivo. By mutating the N-glycosylation sites, we aimed to study the effect of its N-glycan chain on plasminogen activation, fibrin sensitivity, and to observe the physicochemical properties of DSPAα2. A logical structure design was performed in this study. Four single mutants and one double mutant were constructed and expressed in Pichia pastoris. When the N398 site was eliminated, the plasminogen activator in the mutants had their activities reduced to ~40%. When the N185 site was inactivated, there was a weak decrease in the plasminogen activation of its mutant, while the fibrin sensitivity significantly decreased by ~10-fold. Neither N-glycosylation nor deglycosylation mutations changed the pH resistance or heat resistance of DSPAα2. This study confirms that N-glycosylation affects the biochemical function of DSPAα2, which provides a reference for subsequent applications of DSPAα2.
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Affiliation(s)
- Huakang Peng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Mengqi Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Nan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Caifeng Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wenfang Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Gangqiang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Sumei Huang
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Di Wei
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Dehu Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Correspondence:
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4
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Gan HH, Twaddle A, Marchand B, Gunsalus KC. Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. J Mol Biol 2021; 433:167051. [PMID: 33992693 PMCID: PMC8118711 DOI: 10.1016/j.jmb.2021.167051] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/06/2021] [Accepted: 05/08/2021] [Indexed: 12/16/2022]
Abstract
The COVID-19 pandemic has triggered concerns about the emergence of more infectious and pathogenic viral strains. As a public health measure, efficient screening methods are needed to determine the functional effects of new sequence variants. Here we show that structural modeling of SARS-CoV-2 Spike protein binding to the human ACE2 receptor, the first step in host-cell entry, predicts many novel variant combinations with enhanced binding affinities. By focusing on natural variants at the Spike-hACE2 interface and assessing over 700 mutant complexes, our analysis reveals that high-affinity Spike mutations (including N440K, S443A, G476S, E484R, G502P) tend to cluster near known human ACE2 recognition sites (K31 and K353). These Spike regions are structurally flexible, allowing certain mutations to optimize interface interaction energies. Although most human ACE2 variants tend to weaken binding affinity, they can interact with Spike mutations to generate high-affinity double mutant complexes, suggesting variation in individual susceptibility to infection. Applying structural analysis to highly transmissible variants, we find that circulating point mutations S477N, E484K and N501Y form high-affinity complexes (~40% more than wild-type). By combining predicted affinities and available antibody escape data, we show that fast-spreading viral variants exploit combinatorial mutations possessing both enhanced affinity and antibody resistance, including S477N/E484K, E484K/N501Y and K417T/E484K/N501Y. Thus, three-dimensional modeling of the Spike/hACE2 complex predicts changes in structure and binding affinity that correlate with transmissibility and therefore can help inform future intervention strategies.
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Affiliation(s)
- Hin Hark Gan
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, United States,Corresponding authors at: Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, United States (K.C. Gunsalus)
| | - Alan Twaddle
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, United States,NYU Abu Dhabi Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Benoit Marchand
- High-Performance Computing, Center for Research Computing, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Kristin C. Gunsalus
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, United States,NYU Abu Dhabi Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates,Corresponding authors at: Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, United States (K.C. Gunsalus)
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5
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Lessel D, Zeitler DM, Reijnders MRF, Kazantsev A, Hassani Nia F, Bartholomäus A, Martens V, Bruckmann A, Graus V, McConkie-Rosell A, McDonald M, Lozic B, Tan ES, Gerkes E, Johannsen J, Denecke J, Telegrafi A, Zonneveld-Huijssoon E, Lemmink HH, Cham BWM, Kovacevic T, Ramsdell L, Foss K, Le Duc D, Mitter D, Syrbe S, Merkenschlager A, Sinnema M, Panis B, Lazier J, Osmond M, Hartley T, Mortreux J, Busa T, Missirian C, Prasun P, Lüttgen S, Mannucci I, Lessel I, Schob C, Kindler S, Pappas J, Rabin R, Willemsen M, Gardeitchik T, Löhner K, Rump P, Dias KR, Evans CA, Andrews PI, Roscioli T, Brunner HG, Chijiwa C, Lewis MES, Jamra RA, Dyment DA, Boycott KM, Stegmann APA, Kubisch C, Tan EC, Mirzaa GM, McWalter K, Kleefstra T, Pfundt R, Ignatova Z, Meister G, Kreienkamp HJ. Germline AGO2 mutations impair RNA interference and human neurological development. Nat Commun 2020; 11:5797. [PMID: 33199684 PMCID: PMC7670403 DOI: 10.1038/s41467-020-19572-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 09/21/2020] [Indexed: 12/29/2022] Open
Abstract
ARGONAUTE-2 and associated miRNAs form the RNA-induced silencing complex (RISC), which targets mRNAs for translational silencing and degradation as part of the RNA interference pathway. Despite the essential nature of this process for cellular function, there is little information on the role of RISC components in human development and organ function. We identify 13 heterozygous mutations in AGO2 in 21 patients affected by disturbances in neurological development. Each of the identified single amino acid mutations result in impaired shRNA-mediated silencing. We observe either impaired RISC formation or increased binding of AGO2 to mRNA targets as mutation specific functional consequences. The latter is supported by decreased phosphorylation of a C-terminal serine cluster involved in mRNA target release, increased formation of dendritic P-bodies in neurons and global transcriptome alterations in patient-derived primary fibroblasts. Our data emphasize the importance of gene expression regulation through the dynamic AGO2-RNA association for human neuronal development.
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Affiliation(s)
- Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany.
| | - Daniela M Zeitler
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, Regensburg, Germany
| | - Margot R F Reijnders
- Department of Human Genetics, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Andriy Kazantsev
- Institute of Biochemistry & Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Fatemeh Hassani Nia
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Alexander Bartholomäus
- Institute of Biochemistry & Molecular Biology, University of Hamburg, Hamburg, Germany
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Victoria Martens
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Astrid Bruckmann
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, Regensburg, Germany
| | - Veronika Graus
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, Regensburg, Germany
| | - Allyn McConkie-Rosell
- Division of Medical Genetics, Department of Pediatrics, Duke University, Durham, NC, 27707, USA
| | - Marie McDonald
- Division of Medical Genetics, Department of Pediatrics, Duke University, Durham, NC, 27707, USA
| | - Bernarda Lozic
- University Hospital of Split, Split, Croatia
- University of Split School of Medicine, Split, Croatia
| | - Ee-Shien Tan
- Genetics Service, Department of Paediatrics, KK Women's & Children's Hospital, Singapore, Singapore
| | - Erica Gerkes
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jessika Johannsen
- Department of Pediatrics, University Medical Center Eppendorf, 20246, Hamburg, Germany
| | - Jonas Denecke
- Department of Pediatrics, University Medical Center Eppendorf, 20246, Hamburg, Germany
| | | | - Evelien Zonneveld-Huijssoon
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Henny H Lemmink
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Breana W M Cham
- Genetics Service, Department of Paediatrics, KK Women's & Children's Hospital, Singapore, Singapore
| | | | - Linda Ramsdell
- Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA, 98105, USA
| | - Kimberly Foss
- Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA, 98105, USA
| | - Diana Le Duc
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig, Germany
| | - Diana Mitter
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig, Germany
| | - Steffen Syrbe
- Department of General Paediatrics, Division of Pediatric Epileptology, Centre for Paediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Margje Sinnema
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Bianca Panis
- Department of Pediatrics, Zuyderland Medical Center, Heerlen and Sittard, 6419, the Netherlands
| | - Joanna Lazier
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Matthew Osmond
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Jeremie Mortreux
- Département de Génétique Médicale, CHU Timone Enfants, Assistance Publique - Hôpitaux de Marseille AP-HM, Marseille, France
- Aix Marseille Univ, INSERM, MMG, U1251, Marseille, France
| | - Tiffany Busa
- Département de Génétique Médicale, CHU Timone Enfants, Assistance Publique - Hôpitaux de Marseille AP-HM, Marseille, France
| | - Chantal Missirian
- Département de Génétique Médicale, CHU Timone Enfants, Assistance Publique - Hôpitaux de Marseille AP-HM, Marseille, France
- Aix Marseille Univ, INSERM, MMG, U1251, Marseille, France
| | - Pankaj Prasun
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Sabine Lüttgen
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Ilaria Mannucci
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Ivana Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Claudia Schob
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Stefan Kindler
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - John Pappas
- Department of Pediatrics, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Rachel Rabin
- Department of Pediatrics, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Marjolein Willemsen
- Department of Human Genetics, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands
| | - Thatjana Gardeitchik
- Department of Human Genetics, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands
| | - Katharina Löhner
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Patrick Rump
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Kerith-Rae Dias
- Neuroscience Research Australia (NeuRA), Prince of Wales Clinical School, University of New South Wales, Sydney, Australia
- NSW Health Pathology Randwick Genetics, Sydney, Australia
| | - Carey-Anne Evans
- Neuroscience Research Australia (NeuRA), Prince of Wales Clinical School, University of New South Wales, Sydney, Australia
- NSW Health Pathology Randwick Genetics, Sydney, Australia
| | - Peter Ian Andrews
- Department of Neurology, Sydney Children's Hospital, Sydney, Australia
- School of Women's and Children's Health, University of New South Wales, Sydney, Australia
| | - Tony Roscioli
- Neuroscience Research Australia (NeuRA), Prince of Wales Clinical School, University of New South Wales, Sydney, Australia
- Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, Australia
- New South Wales Health Pathology Genomics Laboratory Randwick, Sydney, Australia
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Chieko Chijiwa
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - M E Suzanne Lewis
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig, Germany
| | - David A Dyment
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Kym M Boycott
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Alexander P A Stegmann
- Department of Human Genetics, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Christian Kubisch
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Ene-Choo Tan
- Research Laboratory, KK Women's & Children's Hospital, Singapore, Singapore
| | - Ghayda M Mirzaa
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, 98195, US
| | | | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Zoya Ignatova
- Institute of Biochemistry & Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Gunter Meister
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, Regensburg, Germany
| | - Hans-Jürgen Kreienkamp
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany.
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6
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Chahal J, Gebert LF, Gan HH, Camacho E, Gunsalus KC, MacRae IJ, Sagan SM. miR-122 and Ago interactions with the HCV genome alter the structure of the viral 5' terminus. Nucleic Acids Res 2019; 47:5307-5324. [PMID: 30941417 PMCID: PMC6547439 DOI: 10.1093/nar/gkz194] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/11/2019] [Accepted: 03/20/2019] [Indexed: 12/12/2022] Open
Abstract
Hepatitis C virus (HCV) is a positive-sense RNA virus that interacts with the liver-specific microRNA, miR-122. miR-122 binds to two sites in the 5' untranslated region (UTR) and this interaction promotes HCV RNA accumulation, although the precise role of miR-122 in the HCV life cycle remains unclear. Using biophysical analyses and Selective 2' Hydroxyl Acylation analyzed by Primer Extension (SHAPE) we investigated miR-122 interactions with the 5' UTR. Our data suggests that miR-122 binding results in alteration of nucleotides 1-117 to suppress an alternative secondary structure and promote functional internal ribosomal entry site (IRES) formation. Furthermore, we demonstrate that two hAgo2:miR-122 complexes are able to bind to the HCV 5' terminus simultaneously and SHAPE analyses revealed further alterations to the structure of the 5' UTR to accommodate these complexes. Finally, we present a computational model of the hAgo2:miR-122:HCV RNA complex at the 5' terminus of the viral genome as well as hAgo2:miR-122 interactions with the IRES-40S complex that suggest hAgo2 is likely to form additional interactions with SLII which may further stabilize the HCV IRES. Taken together, our results support a model whereby hAgo2:miR-122 complexes alter the structure of the viral 5' terminus and promote formation of the HCV IRES.
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Affiliation(s)
- Jasmin Chahal
- Department of Microbiology & Immunology, McGill University, Montréal, QC H3G 1Y6, Canada
| | - Luca F R Gebert
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hin Hark Gan
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, USA
| | - Edna Camacho
- Department of Biochemistry, McGill University, Montréal, QC H3G 1Y6, Canada
| | - Kristin C Gunsalus
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, USA
- Division of Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Ian J MacRae
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Selena M Sagan
- Department of Microbiology & Immunology, McGill University, Montréal, QC H3G 1Y6, Canada
- Department of Biochemistry, McGill University, Montréal, QC H3G 1Y6, Canada
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7
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Abstract
Translational repression and degradation of transcripts by microRNAs (miRNAs) is mediated by a ribonucleoprotein complex called the miRNA-induced silencing complex (miRISC, or RISC). Advances in experimental determination of RISC structures have enabled detailed analysis and modeling of known miRNA targets, yet a full appreciation of the structural factors influencing target recognition remains a challenge, primarily because target recognition involves a combination of RNA-RNA and RNA-protein interactions that can vary greatly among different miRNA-target pairs. In this chapter, we review progress toward understanding the role of tertiary structure in miRNA target recognition using computational approaches to assemble RISC complexes at known targets and physics-based methods for computing target interactions. Using this framework to examine RISC structures and dynamics, we describe how the conformational flexibility of Argonautes plays an important role in accommodating the diversity of miRNA-target duplexes formed at canonical and noncanonical target sites. We then discuss applications of tertiary structure-based approaches to emerging topics, including the structural effects of SNPs in miRNA targets and cooperative interactions involving Argonaute-Argonaute complexes. We conclude by assessing the prospects for genome-scale modeling of RISC structures and modeling of higher-order Argonaute complexes associated with miRNA biogenesis, mRNA regulation, and other functions.
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Affiliation(s)
- Hin Hark Gan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Kristin C Gunsalus
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA.
- Center for Genomics and Systems Biology, NYU Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates.
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8
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Recent Molecular Genetic Explorations of Caenorhabditis elegans MicroRNAs. Genetics 2018; 209:651-673. [PMID: 29967059 PMCID: PMC6028246 DOI: 10.1534/genetics.118.300291] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 04/30/2018] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs are small, noncoding RNAs that regulate gene expression at the post-transcriptional level in essentially all aspects of Caenorhabditis elegans biology. More than 140 genes that encode microRNAs in C. elegans regulate development, behavior, metabolism, and responses to physiological and environmental changes. Genetic analysis of C. elegans microRNA genes continues to enhance our fundamental understanding of how microRNAs are integrated into broader gene regulatory networks to control diverse biological processes, including growth, cell division, cell fate determination, behavior, longevity, and stress responses. As many of these microRNA sequences and the related processing machinery are conserved over nearly a billion years of animal phylogeny, the assignment of their functions via worm genetics may inform the functions of their orthologs in other animals, including humans. In vivo investigations are especially important for microRNAs because in silico extrapolation of their functions using mRNA target prediction programs can easily assign microRNAs to incorrect genetic pathways. At this mezzanine level of microRNA bioinformatic sophistication, genetic analysis continues to be the gold standard for pathway assignments.
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Flamand MN, Gan HH, Mayya VK, Gunsalus KC, Duchaine TF. A non-canonical site reveals the cooperative mechanisms of microRNA-mediated silencing. Nucleic Acids Res 2017; 45:7212-7225. [PMID: 28482037 PMCID: PMC5499589 DOI: 10.1093/nar/gkx340] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/18/2017] [Indexed: 01/08/2023] Open
Abstract
Although strong evidence supports the importance of their cooperative interactions, microRNA (miRNA)-binding sites are still largely investigated as functionally independent regulatory units. Here, a survey of alternative 3΄UTR isoforms implicates a non-canonical seedless site in cooperative miRNA-mediated silencing. While required for target mRNA deadenylation and silencing, this site is not sufficient on its own to physically recruit miRISC. Instead, it relies on facilitating interactions with a nearby canonical seed-pairing site to recruit the Argonaute complexes. We further show that cooperation between miRNA target sites is necessary for silencing in vivo in the C. elegans embryo, and for the recruitment of the Ccr4-Not effector complex. Using a structural model of cooperating miRISCs, we identified allosteric determinants of cooperative miRNA-mediated silencing that are required for both embryonic and larval miRNA functions. Our results delineate multiple cooperative mechanisms in miRNA-mediated silencing and further support the consideration of target site cooperation as a fundamental characteristic of miRNA function.
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Affiliation(s)
- Mathieu N Flamand
- Department of Biochemistry & Goodman Cancer Research Centre, McGill University, Montreal, Quebec H3G 1Y6 Canada
| | - Hin Hark Gan
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, USA
| | - Vinay K Mayya
- Department of Biochemistry & Goodman Cancer Research Centre, McGill University, Montreal, Quebec H3G 1Y6 Canada
| | - Kristin C Gunsalus
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, USA.,Division of Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Thomas F Duchaine
- Department of Biochemistry & Goodman Cancer Research Centre, McGill University, Montreal, Quebec H3G 1Y6 Canada
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Harikrishna S, Pradeepkumar PI. Probing the Binding Interactions between Chemically Modified siRNAs and Human Argonaute 2 Using Microsecond Molecular Dynamics Simulations. J Chem Inf Model 2017; 57:883-896. [DOI: 10.1021/acs.jcim.6b00773] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- S. Harikrishna
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai−400076, India
| | - P. I. Pradeepkumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai−400076, India
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MicroRNA-34 directly targets pair-rule genes and cytoskeleton component in the honey bee. Sci Rep 2017; 7:40884. [PMID: 28098233 PMCID: PMC5241629 DOI: 10.1038/srep40884] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 12/12/2016] [Indexed: 01/06/2023] Open
Abstract
MicroRNAs (miRNAs) are key regulators of developmental processes, such as cell fate determination and differentiation. Previous studies showed Dicer knockdown in honeybee embryos disrupt the processing of functional mature miRNAs and impairs embryo patterning. Here we investigated the expression profiles of miRNAs in honeybee embryogenesis and the role of the highly conserved miR-34-5p in the regulation of genes involved in insect segmentation. A total of 221 miRNAs were expressed in honey bee embryogenesis among which 97 mature miRNA sequences have not been observed before. Interestingly, we observed a switch in dominance between the 5-prime and 3-prime arm of some miRNAs in different embryonic stages; however, most miRNAs present one dominant arm across all stages of embryogenesis. Our genome-wide analysis of putative miRNA-target networks and functional pathways indicates miR-34-5p is one of the most conserved and connected miRNAs associated with the regulation of genes involved in embryonic patterning and development. In addition, we experimentally validated that miR-34-5p directly interacts to regulatory elements in the 3'-untranslated regions of pair-rule (even-skipped, hairy, fushi-tarazu transcription factor 1) and cytoskeleton (actin5C) genes. Our study suggests that miR-34-5p may regulate the expression of pair-rule and cytoskeleton genes during early development and control insect segmentation.
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Xu Y, Chen Y, Li D, Liu Q, Xuan Z, Li WH. TargetLink, a new method for identifying the endogenous target set of a specific microRNA in intact living cells. RNA Biol 2016; 14:259-274. [PMID: 27982722 DOI: 10.1080/15476286.2016.1270006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
MicroRNAs are small non-coding RNAs acting as posttranscriptional repressors of gene expression. Identifying mRNA targets of a given miRNA remains an outstanding challenge in the field. We have developed a new experimental approach, TargetLink, that applied locked nucleic acid (LNA) as the affinity probe to enrich target genes of a specific microRNA in intact cells. TargetLink also consists a rigorous and systematic data analysis pipeline to identify target genes by comparing LNA-enriched sequences between experimental and control samples. Using miR-21 as a test microRNA, we identified 12 target genes of miR-21 in a human colorectal cancer cell by this approach. The majority of the identified targets interacted with miR-21 via imperfect seed pairing. Target validation confirmed that miR-21 repressed the expression of the identified targets. The cellular abundance of the identified miR-21 target transcripts varied over a wide range, with some targets expressed at a rather low level, confirming that both abundant and rare transcripts are susceptible to regulation by microRNAs, and that TargetLink is an efficient approach for identifying the target set of a specific microRNA in intact cells. C20orf111, one of the novel targets identified by TargetLink, was found to reside in the nuclear speckle and to be reliably repressed by miR-21 through the interaction at its coding sequence.
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Affiliation(s)
- Yan Xu
- a Department of Cell Biology and of Biochemistry , University of Texas Southwestern Medical Center , Dallas , TX , USA
| | - Yan Chen
- a Department of Cell Biology and of Biochemistry , University of Texas Southwestern Medical Center , Dallas , TX , USA
| | - Daliang Li
- a Department of Cell Biology and of Biochemistry , University of Texas Southwestern Medical Center , Dallas , TX , USA
| | - Qing Liu
- a Department of Cell Biology and of Biochemistry , University of Texas Southwestern Medical Center , Dallas , TX , USA
| | - Zhenyu Xuan
- b Department of Biological Sciences , Center for Systems Biology, The University of Texas at Dallas , Richardson , TX , USA
| | - Wen-Hong Li
- a Department of Cell Biology and of Biochemistry , University of Texas Southwestern Medical Center , Dallas , TX , USA
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