1
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Eisenhut P, Marx N, Borsi G, Papež M, Ruggeri C, Baumann M, Borth N. Corrigendum to "Manipulating gene expression levels in mammalian cell factories: An outline of synthetic molecular toolboxes to achieve multiplexed control" [New Biotechnol 79 (2024) 1-19]. N Biotechnol 2024; 84:30-36. [PMID: 39332183 DOI: 10.1016/j.nbt.2024.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2024]
Affiliation(s)
- Peter Eisenhut
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria
| | - Nicolas Marx
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria.
| | - Giulia Borsi
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Maja Papež
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria; BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Caterina Ruggeri
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Martina Baumann
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria
| | - Nicole Borth
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria; BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria.
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2
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Bubenik JL, Scotti MM, Swanson MS. Therapeutic targeting of RNA for neurological and neuromuscular disease. Genes Dev 2024; 38:698-717. [PMID: 39142832 PMCID: PMC11444190 DOI: 10.1101/gad.351612.124] [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] [Indexed: 08/16/2024]
Abstract
Neurological and neuromuscular diseases resulting from familial, sporadic, or de novo mutations have devasting personal, familial, and societal impacts. As the initial product of DNA transcription, RNA transcripts and their associated ribonucleoprotein complexes provide attractive targets for modulation by increasing wild-type or blocking mutant allele expression, thus relieving downstream pathological consequences. Therefore, it is unsurprising that many existing and under-development therapeutics have focused on targeting disease-associated RNA transcripts as a frontline drug strategy for these genetic disorders. This review focuses on the current range of RNA targeting modalities using examples of both dominant and recessive neurological and neuromuscular diseases.
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Affiliation(s)
- Jodi L Bubenik
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics, the Genetics Institute, University of Florida, Gainesville, Florida 32610, USA
| | - Marina M Scotti
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics, the Genetics Institute, University of Florida, Gainesville, Florida 32610, USA
| | - Maurice S Swanson
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics, the Genetics Institute, University of Florida, Gainesville, Florida 32610, USA
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3
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Coan M, Haefliger S, Ounzain S, Johnson R. Targeting and engineering long non-coding RNAs for cancer therapy. Nat Rev Genet 2024; 25:578-595. [PMID: 38424237 DOI: 10.1038/s41576-024-00693-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2024] [Indexed: 03/02/2024]
Abstract
RNA therapeutics (RNATx) aim to treat diseases, including cancer, by targeting or employing RNA molecules for therapeutic purposes. Amongst the most promising targets are long non-coding RNAs (lncRNAs), which regulate oncogenic molecular networks in a cell type-restricted manner. lncRNAs are distinct from protein-coding genes in important ways that increase their therapeutic potential yet also present hurdles to conventional clinical development. Advances in genome editing, oligonucleotide chemistry, multi-omics and RNA engineering are paving the way for efficient and cost-effective lncRNA-focused drug discovery pipelines. In this Review, we present the emerging field of lncRNA therapeutics for oncology, with emphasis on the unique strengths and challenges of lncRNAs within the broader RNATx framework. We outline the necessary steps for lncRNA therapeutics to deliver effective, durable, tolerable and personalized treatments for cancer.
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Affiliation(s)
- Michela Coan
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Dublin, Ireland
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Simon Haefliger
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | | | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland.
- Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Dublin, Ireland.
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
- Department for BioMedical Research, University of Bern, Bern, Switzerland.
- FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, Dublin, Ireland.
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4
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Sharma H, Valentine MNZ, Toki N, Sueki HN, Gustincich S, Takahashi H, Carninci P. Decryption of sequence, structure, and functional features of SINE repeat elements in SINEUP non-coding RNA-mediated post-transcriptional gene regulation. Nat Commun 2024; 15:1400. [PMID: 38383605 PMCID: PMC10881587 DOI: 10.1038/s41467-024-45517-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/26/2024] [Indexed: 02/23/2024] Open
Abstract
RNA structure folding largely influences RNA regulation by providing flexibility and functional diversity. In silico and in vitro analyses are limited in their ability to capture the intricate relationships between dynamic RNA structure and RNA functional diversity present in the cell. Here, we investigate sequence, structure and functional features of mouse and human SINE-transcribed retrotransposons embedded in SINEUPs long non-coding RNAs, which positively regulate target gene expression post-transcriptionally. In-cell secondary structure probing reveals that functional SINEs-derived RNAs contain conserved short structure motifs essential for SINEUP-induced translation enhancement. We show that SINE RNA structure dynamically changes between the nucleus and cytoplasm and is associated with compartment-specific binding to RBP and related functions. Moreover, RNA-RNA interaction analysis shows that the SINE-derived RNAs interact directly with ribosomal RNAs, suggesting a mechanism of translation regulation. We further predict the architecture of 18 SINE RNAs in three dimensions guided by experimental secondary structure data. Overall, we demonstrate that the conservation of short key features involved in interactions with RBPs and ribosomal RNA drives the convergent function of evolutionarily distant SINE-transcribed RNAs.
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Affiliation(s)
- Harshita Sharma
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Matthew N Z Valentine
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Naoko Toki
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Hiromi Nishiyori Sueki
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | | | - Hazuki Takahashi
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.
| | - Piero Carninci
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.
- Human Technopole, Milan, 20157, Italy.
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5
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Fukuda K. The role of transposable elements in human evolution and methods for their functional analysis: current status and future perspectives. Genes Genet Syst 2024; 98:289-304. [PMID: 37866889 DOI: 10.1266/ggs.23-00140] [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] [Indexed: 10/24/2023] Open
Abstract
Transposable elements (TEs) are mobile DNA sequences that can insert themselves into various locations within the genome, causing mutations that may provide advantages or disadvantages to individuals and species. The insertion of TEs can result in genetic variation that may affect a wide range of human traits including genetic disorders. Understanding the role of TEs in human biology is crucial for both evolutionary and medical research. This review discusses the involvement of TEs in human traits and disease susceptibility, as well as methods for functional analysis of TEs.
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Affiliation(s)
- Kei Fukuda
- Integrative Genomics Unit, The University of Melbourne
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6
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Cao Y, Liu H, Lu SS, Jones KA, Govind AP, Jeyifous O, Simmons CQ, Tabatabaei N, Green WN, Holder JL, Tahmasebi S, George AL, Dickinson BC. RNA-based translation activators for targeted gene upregulation. Nat Commun 2023; 14:6827. [PMID: 37884512 PMCID: PMC10603104 DOI: 10.1038/s41467-023-42252-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/04/2023] [Indexed: 10/28/2023] Open
Abstract
Technologies capable of programmable translation activation offer strategies to develop therapeutics for diseases caused by insufficient gene expression. Here, we present "translation-activating RNAs" (taRNAs), a bifunctional RNA-based molecular technology that binds to a specific mRNA of interest and directly upregulates its translation. taRNAs are constructed from a variety of viral or mammalian RNA internal ribosome entry sites (IRESs) and upregulate translation for a suite of target mRNAs. We minimize the taRNA scaffold to 94 nucleotides, identify two translation initiation factor proteins responsible for taRNA activity, and validate the technology by amplifying SYNGAP1 expression, a haploinsufficiency disease target, in patient-derived cells. Finally, taRNAs are suitable for delivery as RNA molecules by lipid nanoparticles (LNPs) to cell lines, primary neurons, and mouse liver in vivo. taRNAs provide a general and compact nucleic acid-based technology to upregulate protein production from endogenous mRNAs, and may open up possibilities for therapeutic RNA research.
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Affiliation(s)
- Yang Cao
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Huachun Liu
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Shannon S Lu
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Krysten A Jones
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Anitha P Govind
- Department of Neurobiology, The University of Chicago, Chicago, IL, USA
| | - Okunola Jeyifous
- Department of Neurobiology, The University of Chicago, Chicago, IL, USA
| | - Christine Q Simmons
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Negar Tabatabaei
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL, USA
| | - William N Green
- Department of Neurobiology, The University of Chicago, Chicago, IL, USA
| | - Jimmy L Holder
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Soroush Tahmasebi
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL, USA
| | - Alfred L George
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Bryan C Dickinson
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
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7
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Tokunaga M, Imamura T. Emerging concepts involving inhibitory and activating RNA functionalization towards the understanding of microcephaly phenotypes and brain diseases in humans. Front Cell Dev Biol 2023; 11:1168072. [PMID: 37408531 PMCID: PMC10318543 DOI: 10.3389/fcell.2023.1168072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/12/2023] [Indexed: 07/07/2023] Open
Abstract
Microcephaly is characterized as a small head circumference, and is often accompanied by developmental disorders. Several candidate risk genes for this disease have been described, and mutations in non-coding regions are occasionally found in patients with microcephaly. Various non-coding RNAs (ncRNAs), such as microRNAs (miRNAs), SINEUPs, telomerase RNA component (TERC), and promoter-associated lncRNAs (pancRNAs) are now being characterized. These ncRNAs regulate gene expression, enzyme activity, telomere length, and chromatin structure through RNA binding proteins (RBPs)-RNA interaction. Elucidating the potential roles of ncRNA-protein coordination in microcephaly pathogenesis might contribute to its prevention or recovery. Here, we introduce several syndromes whose clinical features include microcephaly. In particular, we focus on syndromes for which ncRNAs or genes that interact with ncRNAs may play roles. We discuss the possibility that the huge ncRNA field will provide possible new therapeutic approaches for microcephaly and also reveal clues about the factors enabling the evolutionary acquisition of the human-specific "large brain."
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8
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Pierattini B, D’Agostino S, Bon C, Peruzzo O, Alendar A, Codino A, Ros G, Persichetti F, Sanges R, Carninci P, Santoro C, Espinoza S, Valentini P, Pandolfini L, Gustincich S. SINEUP non-coding RNA activity depends on specific N6-methyladenosine nucleotides. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 32:402-414. [PMID: 37187707 PMCID: PMC10176434 DOI: 10.1016/j.omtn.2023.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/04/2023] [Indexed: 05/17/2023]
Abstract
SINEUPs are natural and synthetic antisense long non-coding RNAs (lncRNAs) selectively enhancing target mRNAs translation by increasing their association with polysomes. This activity requires two RNA domains: an embedded inverted SINEB2 element acting as effector domain, and an antisense region, the binding domain, conferring target selectivity. SINEUP technology presents several advantages to treat genetic (haploinsufficiencies) and complex diseases restoring the physiological activity of diseased genes and of compensatory pathways. To streamline these applications to the clinic, a better understanding of the mechanism of action is needed. Here we show that natural mouse SINEUP AS Uchl1 and synthetic human miniSINEUP-DJ-1 are N6-methyladenosine (m6A) modified by METTL3 enzyme. Then, we map m6A-modified sites along SINEUP sequence with Nanopore direct RNA sequencing and a reverse transcription assay. We report that m6A removal from SINEUP RNA causes the depletion of endogenous target mRNA from actively translating polysomes, without altering SINEUP enrichment in ribosomal subunit-associated fractions. These results prove that SINEUP activity requires an m6A-dependent step to enhance translation of target mRNAs, providing a new mechanism for m6A translation regulation and strengthening our knowledge of SINEUP-specific mode of action. Altogether these new findings pave the way to a more effective therapeutic application of this well-defined class of lncRNAs.
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Affiliation(s)
- Bianca Pierattini
- Area of Neuroscience, International School for Advanced Studies (SISSA), Trieste, Italy
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Sabrina D’Agostino
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Carlotta Bon
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Omar Peruzzo
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Andrej Alendar
- The Gurdon Institute and Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Azzurra Codino
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Gloria Ros
- Department of Health Sciences and Research Center on Autoimmune and Allergic Diseases (CAAD), University of Piemonte Orientale (UPO), Novara, Italy
| | - Francesca Persichetti
- Department of Health Sciences and Research Center on Autoimmune and Allergic Diseases (CAAD), University of Piemonte Orientale (UPO), Novara, Italy
| | - Remo Sanges
- Area of Neuroscience, International School for Advanced Studies (SISSA), Trieste, Italy
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences (IMS), Yokohama 230-0045, Japan
- Human Technopole, 20157 Milan, Italy
| | - Claudio Santoro
- Department of Health Sciences and Research Center on Autoimmune and Allergic Diseases (CAAD), University of Piemonte Orientale (UPO), Novara, Italy
| | - Stefano Espinoza
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
- Department of Health Sciences and Research Center on Autoimmune and Allergic Diseases (CAAD), University of Piemonte Orientale (UPO), Novara, Italy
| | - Paola Valentini
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
- Corresponding author: Paola Valentini, Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), via Melen 83, 16152 Genova, Italy.
| | - Luca Pandolfini
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
- Corresponding author: Luca Pandolfini, Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), via Melen 83, 16152 Genova, Italy.
| | - Stefano Gustincich
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
- Corresponding author: Stefano Gustincich, Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), via Melen 83, 16152 Genova, Italy.
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9
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Cao C, Li A, Xu C, Wu B, Liu J, Liu Y. Enhancement of protein translation by CRISPR/dCasRx coupled with SINEB2 repeat of noncoding RNAs. Nucleic Acids Res 2023; 51:e33. [PMID: 36715335 PMCID: PMC10085674 DOI: 10.1093/nar/gkad010] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 12/23/2022] [Accepted: 01/04/2023] [Indexed: 01/31/2023] Open
Abstract
The use of new long noncoding RNAs (lncRNAs) as biotechnological or therapeutic tools is still in its infancy, despite recent efforts to uncover their involvement in various biological processes including mRNA translation. An important question is whether lncRNA functional elements can be used to target translation of mRNAs of interest by incorporating the RNA-targeting CRISPR tools. The CRISPR/dCasRx-SINEB2 technology was developed in this research by coupling the sgRNA of a catalytically inactive Type VI-D Cas13 enzyme (CasRx) to an integrated SINEB2 domain of uchl1 lncRNA that promotes the translation of targeted mRNA. It has been demonstrated to be effective and adaptable in selectively increasing the expression of a variety of exogenous and endogenous proteins with a variety of functions with minimal off-target effects. dCasRx-SINEB2 is currently the sole CRISPR-related technique for translational control of gene expression, and works just as well or even better than the traditional RNAe tool under comparable conditions. Additionally, human cancer cells can be prevented from proliferating and migrating both in vitro and in vivo by dCasRx-SINEB2-targeted mRNA translation of transcripts encoding for antitumor proteins, including PTEN and P53. The present study provides an innovative protein enhancement method that will have several applications in biopharmaceuticals production and cancer research.
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Affiliation(s)
- Congcong Cao
- Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen University, Shenzhen 518035, China.,Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Aolin Li
- Department of Urology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen 518035, China
| | - Chaojie Xu
- Department of Urology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Baorui Wu
- Department of Urology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230000, China
| | - Jun Liu
- Urology and Lithotripsy Center, Peking University People's Hospital, Beijing 100034, China.,Peking University Applied Lithotripsy Institute, Peking University, Beijing 100034, China
| | - Yuchen Liu
- Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen University, Shenzhen 518035, China.,Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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10
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Park J, Tucci A, Cipriani V, Demidov G, Rocca C, Senderek J, Butryn M, Velic A, Lam T, Galanaki E, Cali E, Vestito L, Maroofian R, Deininger N, Rautenberg M, Admard J, Hahn GA, Bartels C, van Os NJH, Horvath R, Chinnery PF, Tiet MY, Hewamadduma C, Hadjivassiliou M, Tofaris GK, Wood NW, Hayer SN, Bender F, Menden B, Cordts I, Klein K, Nguyen HP, Krauss JK, Blahak C, Strom TM, Sturm M, van de Warrenburg B, Lerche H, Maček B, Synofzik M, Ossowski S, Timmann D, Wolf ME, Smedley D, Riess O, Schöls L, Houlden H, Haack TB, Hengel H. Heterozygous UCHL1 loss-of-function variants cause a neurodegenerative disorder with spasticity, ataxia, neuropathy, and optic atrophy. Genet Med 2022; 24:2079-2090. [PMID: 35986737 DOI: 10.1016/j.gim.2022.07.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 07/03/2022] [Accepted: 07/03/2022] [Indexed: 10/15/2022] Open
Abstract
PURPOSE Biallelic variants in UCHL1 have been associated with a progressive early-onset neurodegenerative disorder, autosomal recessive spastic paraplegia type 79. In this study, we investigated heterozygous UCHL1 variants on the basis of results from cohort-based burden analyses. METHODS Gene-burden analyses were performed on exome and genome data of independent cohorts of patients with hereditary ataxia and spastic paraplegia from Germany and the United Kingdom in a total of 3169 patients and 33,141 controls. Clinical data of affected individuals and additional independent families were collected and evaluated. Patients' fibroblasts were used to perform mass spectrometry-based proteomics. RESULTS UCHL1 was prioritized in both independent cohorts as a candidate gene for an autosomal dominant disorder. We identified a total of 34 cases from 18 unrelated families, carrying 13 heterozygous loss-of-function variants (15 families) and an inframe insertion (3 families). Affected individuals mainly presented with spasticity (24/31), ataxia (28/31), neuropathy (11/21), and optic atrophy (9/17). The mass spectrometry-based proteomics showed approximately 50% reduction of UCHL1 expression in patients' fibroblasts. CONCLUSION Our bioinformatic analysis, in-depth clinical and genetic workup, and functional studies established haploinsufficiency of UCHL1 as a novel disease mechanism in spastic ataxia.
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Affiliation(s)
- Joohyun Park
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Arianna Tucci
- William Harvey Research Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Valentina Cipriani
- William Harvey Research Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom; UCL Institute of Ophthalmology, University College London, London, United Kingdom; Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom; UCL Genetics Institute, University College London, London, United Kingdom
| | - German Demidov
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Clarissa Rocca
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Jan Senderek
- Department of Neurology, Friedrich-Baur-Institute, University Hospital, Ludwig-Maximilian University Munich, Munich, Germany
| | - Michaela Butryn
- German Center for Neurodegenerative Diseases (DZNE), Magdeburg, Germany
| | - Ana Velic
- Proteome Center Tübingen, University of Tübingen, Tübingen, Germany
| | - Tanya Lam
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom; St George's Hospital NHS Trust, London, United Kingdom
| | - Evangelia Galanaki
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Elisa Cali
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Letizia Vestito
- William Harvey Research Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Reza Maroofian
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Natalie Deininger
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Maren Rautenberg
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Jakob Admard
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Gesa-Astrid Hahn
- CeGaT GmbH, Center for Genomics and Transcriptomics, Tübingen, Germany
| | - Claudius Bartels
- Department of Neurology, Otto-von-Guericke University, Magdeburg, Germany
| | - Nienke J H van Os
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Center of Expertise for Parkinson and Movement Disorders, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rita Horvath
- Department of Clinical Neurosciences, John Van Geest Centre for Brain Repair, University of Cambridge, Cambridge, United Kingdom
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, John Van Geest Centre for Brain Repair, University of Cambridge, Cambridge, United Kingdom; MRC Mitochondrial Biology Unit & Department of Clinical Neurosciences, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - May Yung Tiet
- Department of Clinical Neurosciences, John Van Geest Centre for Brain Repair, University of Cambridge, Cambridge, United Kingdom
| | - Channa Hewamadduma
- Sheffield Institute for Translational Neurosciences (SITraN), The University of Sheffield, Sheffield, United Kingdom; Royal Hallamshire Hospital, Sheffield Teaching Hospitals Foundation Trust, Sheffield, United Kingdom
| | - Marios Hadjivassiliou
- Royal Hallamshire Hospital, Sheffield Teaching Hospitals Foundation Trust, Sheffield, United Kingdom; Academic Department of Neurosciences, Sheffield Teaching Hospitals NHS Trust and The University of Sheffield, Sheffield, United Kingdom
| | - George K Tofaris
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Nicholas W Wood
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Stefanie N Hayer
- Department of Neurodegenerative Diseases, Center for Neurology and Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany; German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Friedemann Bender
- Department of Neurodegenerative Diseases, Center for Neurology and Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany; German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Benita Menden
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Isabell Cordts
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany; Department of Neurology, Klinikum rechts der Isar, Technical University Munich (TUM), Munich, Germany
| | - Katrin Klein
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Huu Phuc Nguyen
- Department of Human Genetics, Medical Faculty, Ruhr University Bochum, Bochum, Germany
| | - Joachim K Krauss
- Department of Neurosurgery, Hannover Medical School, Hannover, Germany
| | - Christian Blahak
- Department of Neurology, Ortenau Klinikum Lahr-Ettenheim, Lahr, Germany; Department of Neurology, Universitätsmedizin Mannheim, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Tim M Strom
- Institute of Human Genetics, Technische Universität München, Munich, Germany; Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Bart van de Warrenburg
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Center of Expertise for Parkinson and Movement Disorders, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Holger Lerche
- Department of Neurology and Epileptology, Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Boris Maček
- Proteome Center Tübingen, University of Tübingen, Tübingen, Germany
| | - Matthis Synofzik
- Department of Neurodegenerative Diseases, Center for Neurology and Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany; German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Dagmar Timmann
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences (C-TNBS), Essen University Hospital, University of Duisburg-Essen, Essen, Germany
| | - Marc E Wolf
- Department of Neurology, Universitätsmedizin Mannheim, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany; Department of Neurology, Klinikum Stuttgart, Stuttgart, Germany
| | - Damian Smedley
- William Harvey Research Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany; Center for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Ludger Schöls
- Department of Neurodegenerative Diseases, Center for Neurology and Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany; German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany; Center for Rare Diseases, University of Tübingen, Tübingen, Germany.
| | - Henry Houlden
- William Harvey Research Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom.
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany; Center for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Holger Hengel
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany; Department of Neurodegenerative Diseases, Center for Neurology and Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany; German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
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11
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CCIVR facilitates comprehensive identification of cis-natural antisense transcripts with their structural characteristics and expression profiles. Sci Rep 2022; 12:15525. [PMID: 36109624 PMCID: PMC9477841 DOI: 10.1038/s41598-022-19782-5] [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: 06/14/2022] [Accepted: 09/05/2022] [Indexed: 11/23/2022] Open
Abstract
Cis-natural antisense transcripts (cis-NATs) are transcribed from the same genomic locus as their partner gene but from the opposite DNA strand and overlap with the partner gene transcript. Here, we developed a simple and convenient program termed CCIVR (comprehensive cis-NATs identifier via RNA-seq data) that comprehensively identifies all kinds of cis-NATs based on genome annotation with expression data obtained from RNA-seq. Using CCIVR with genome databases, we demonstrated total cis-NAT pairs from 11 model organisms. CCIVR analysis with RNA-seq data from parthenogenetic and androgenetic embryonic stem cells identified well-known imprinted cis-NAT pair, KCNQ1/KCNQ1OT1, ensuring the availability of CCIVR. Finally, CCIVR identified cis-NAT pairs that demonstrate inversely correlated expression upon TGFβ stimulation including cis-NATs that functionally repress their partner genes by introducing epigenetic alteration in the promoters of partner genes. Thus, CCIVR facilitates the investigation of structural characteristics and functions of cis-NATs in numerous processes in various species.
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12
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The role of lncRNA-mediated ceRNA regulatory networks in pancreatic cancer. Cell Death Dis 2022; 8:287. [PMID: 35697671 PMCID: PMC9192730 DOI: 10.1038/s41420-022-01061-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/05/2022] [Accepted: 05/09/2022] [Indexed: 12/12/2022]
Abstract
Non-coding RNAs (ncRNAs), which occupy the vast majority of human transcripts are known for their inability to encode proteins. NcRNAs consist of a diverse range of RNA species, including long non-coding RNAs (lncRNAs), which have significant meaning for epigenetic modification, post-transcriptional regulation of target genes, molecular interference, etc. The dysregulation of ncRNAs will mediate the pathogenesis of diverse human diseases, like cancer. Pancreatic cancer, as one of the most lethal malignancies in the digestive system that is hard to make a definite diagnosis at an early clinicopathological stage with a miserable prognosis. Therefore, the identification of potential and clinically applicable biomarker is momentous to improve the overall survival rate and positively ameliorate the prognosis of patients with pancreatic carcinoma. LncRNAs as one kind of ncRNAs exert multitudinous biological functions, and act as molecular sponges, relying on microRNA response elements (MREs) to competitively target microRNAs (miRNAs), thereby attenuating the degradation or inhibition of miRNAs to their own downstream protein-coding target genes, also thus regulating the initiation and progression of neoplasms. LncRNAs, which emerge aforementioned function are called competing endogenous RNAs (ceRNAs). Consequently, abundant research of lncRNAs as potential biomarkers is of critical significance for the molecular diagnosis, targeted therapy, as well as prognosis monitoring of pancreatic cancer.
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13
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Petrosino G, Ponte G, Volpe M, Zarrella I, Ansaloni F, Langella C, Di Cristina G, Finaurini S, Russo MT, Basu S, Musacchia F, Ristoratore F, Pavlinic D, Benes V, Ferrante MI, Albertin C, Simakov O, Gustincich S, Fiorito G, Sanges R. Identification of LINE retrotransposons and long non-coding RNAs expressed in the octopus brain. BMC Biol 2022; 20:116. [PMID: 35581640 PMCID: PMC9115989 DOI: 10.1186/s12915-022-01303-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 04/21/2022] [Indexed: 01/07/2023] Open
Abstract
Background Transposable elements (TEs) widely contribute to the evolution of genomes allowing genomic innovations, generating germinal and somatic heterogeneity, and giving birth to long non-coding RNAs (lncRNAs). These features have been associated to the evolution, functioning, and complexity of the nervous system at such a level that somatic retrotransposition of long interspersed element (LINE) L1 has been proposed to be associated to human cognition. Among invertebrates, octopuses are fascinating animals whose nervous system reaches a high level of complexity achieving sophisticated cognitive abilities. The sequencing of the genome of the Octopus bimaculoides revealed a striking expansion of TEs which were proposed to have contributed to the evolution of its complex nervous system. We recently found a similar expansion also in the genome of Octopus vulgaris. However, a specific search for the existence and the transcription of full-length transpositionally competent TEs has not been performed in this genus. Results Here, we report the identification of LINE elements competent for retrotransposition in Octopus vulgaris and Octopus bimaculoides and show evidence suggesting that they might be transcribed and determine germline and somatic polymorphisms especially in the brain. Transcription and translation measured for one of these elements resulted in specific signals in neurons belonging to areas associated with behavioral plasticity. We also report the transcription of thousands of lncRNAs and the pervasive inclusion of TE fragments in the transcriptomes of both Octopus species, further testifying the crucial activity of TEs in the evolution of the octopus genomes. Conclusions The neural transcriptome of the octopus shows the transcription of thousands of putative lncRNAs and of a full-length LINE element belonging to the RTE class. We speculate that a convergent evolutionary process involving retrotransposons activity in the brain has been important for the evolution of sophisticated cognitive abilities in this genus. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01303-5.
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Affiliation(s)
- Giuseppe Petrosino
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, SZN, 80121, Naples, Italy.,Institute of Molecular Biology (IMB), Mainz, Germany
| | - Giovanna Ponte
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, SZN, 80121, Naples, Italy
| | - Massimiliano Volpe
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, SZN, 80121, Naples, Italy.,Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Via Enrico Melen 83, 16152, Genova, Italy.,Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Ilaria Zarrella
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, SZN, 80121, Naples, Italy
| | - Federico Ansaloni
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Via Enrico Melen 83, 16152, Genova, Italy
| | - Concetta Langella
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, SZN, 80121, Naples, Italy
| | - Giulia Di Cristina
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, SZN, 80121, Naples, Italy.,Institute of Zoology, University of Cologne, Cologne, Germany
| | - Sara Finaurini
- Neurobiology Sector, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136, Trieste, Italy
| | - Monia T Russo
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, SZN, 80121, Naples, Italy
| | - Swaraj Basu
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, SZN, 80121, Naples, Italy.,Strand Life Sciences, Bengaluru, India
| | - Francesco Musacchia
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, SZN, 80121, Naples, Italy
| | - Filomena Ristoratore
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, SZN, 80121, Naples, Italy
| | - Dinko Pavlinic
- Scientific Core Facilities & Technologies, GeneCore, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany.,Institute of Molecular and Clinical Ophthalmology, Basel, Switzerland
| | - Vladimir Benes
- Scientific Core Facilities & Technologies, GeneCore, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Maria I Ferrante
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, SZN, 80121, Naples, Italy
| | | | - Oleg Simakov
- Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 9040495, Japan.,Department of Molecular Evolution and Development, Wien University, Althanstraße 14 (UZA I), 1090, Wien, Austria
| | - Stefano Gustincich
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Via Enrico Melen 83, 16152, Genova, Italy.,Neurobiology Sector, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136, Trieste, Italy
| | - Graziano Fiorito
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, SZN, 80121, Naples, Italy.
| | - Remo Sanges
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, SZN, 80121, Naples, Italy. .,Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Via Enrico Melen 83, 16152, Genova, Italy. .,Neurobiology Sector, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136, Trieste, Italy.
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14
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Valentini P, Pierattini B, Zacco E, Mangoni D, Espinoza S, Webster NA, Andrews B, Carninci P, Tartaglia GG, Pandolfini L, Gustincich S. Towards SINEUP-based therapeutics: Design of an in vitro synthesized SINEUP RNA. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:1092-1102. [PMID: 35228902 PMCID: PMC8857549 DOI: 10.1016/j.omtn.2022.01.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 01/28/2022] [Indexed: 12/28/2022]
Abstract
SINEUPs are a novel class of natural and synthetic non-coding antisense RNA molecules able to increase the translation of a target mRNA. They present a modular organization comprising an unstructured antisense target-specific domain, which sets the specificity of each individual SINEUP, and a structured effector domain, which is responsible for the translation enhancement. In order to design a fully functional in vitro transcribed SINEUP for therapeutics applications, SINEUP RNAs were synthesized in vitro with a variety of chemical modifications and screened for their activity on endogenous target mRNA upon transfection. Three combinations of modified ribonucleotides-2'O methyl-ATP (Am), N6 methyl-ATP (m6A), and pseudo-UTP (ψ)-conferred SINEUP activity to naked RNA. The best combination tested in this study was fully modified with m6A and ψ. Aside from functionality, this combination conferred improved stability upon transfection and higher thermal stability. Common structural determinants of activity were identified by circular dichroisms, defining a core functional structure that is achieved with different combinations of modifications.
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Affiliation(s)
- Paola Valentini
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), 16152 Genova, Italy
| | - Bianca Pierattini
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), 16152 Genova, Italy
- Area of Neuroscience, International School for Advanced Studies (SISSA), 34136 Trieste, Italy
| | - Elsa Zacco
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), 16152 Genova, Italy
| | - Damiano Mangoni
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), 16152 Genova, Italy
| | - Stefano Espinoza
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), 16152 Genova, Italy
| | - Natalie A. Webster
- STORM Therapeutics, Babraham Research Campus, Moneta Building, Cambridge, CB22 3AT, UK
| | - Byron Andrews
- STORM Therapeutics, Babraham Research Campus, Moneta Building, Cambridge, CB22 3AT, UK
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | | | - Luca Pandolfini
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), 16152 Genova, Italy
| | - Stefano Gustincich
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), 16152 Genova, Italy
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15
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Zambrano N, Froechlich G, Lazarevic D, Passariello M, Nicosia A, De Lorenzo C, Morelli MJ, Sasso E. High-Throughput Monoclonal Antibody Discovery from Phage Libraries: Challenging the Current Preclinical Pipeline to Keep the Pace with the Increasing mAb Demand. Cancers (Basel) 2022; 14:cancers14051325. [PMID: 35267633 PMCID: PMC8909429 DOI: 10.3390/cancers14051325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/25/2022] [Accepted: 03/02/2022] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Monoclonal antibodies are increasingly used for a broad range of diseases. Rising demand must face with time time-consuming and laborious processes to isolate novel monoclonal antibodies. Next-generation sequencing coupled to phage display provides timely and sustainable high throughput selection strategy to rapidly access novel target. Here, we describe the current NGS-guided strategies to identify potential binders from enriched sub-libraires by applying a user-friendly informatic pipeline to identify and discard false positive clones. Rescue step and strategies to boost mAb yield are also discussed to improve the limiting selection and screening steps. Abstract Monoclonal antibodies are among the most powerful therapeutics in modern medicine. Since the approval of the first therapeutic antibody in 1986, monoclonal antibodies keep holding great expectations for application in a range of clinical indications, highlighting the need to provide timely and sustainable access to powerful screening options. However, their application in the past has been limited by time-consuming and expensive steps of discovery and production. The screening of antibody repertoires is a laborious step; however, the implementation of next-generation sequencing-guided screening of single-chain antibody fragments has now largely overcome this issue. This review provides a detailed overview of the current strategies for the identification of monoclonal antibodies from phage display-based libraries. We also discuss the challenges and the possible solutions to improve the limiting selection and screening steps, in order to keep pace with the increasing demand for monoclonal antibodies.
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Affiliation(s)
- Nicola Zambrano
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Degli Studi di Napoli Federico II, Via Pansini 5, 80131 Napoli, Italy; (G.F.); (M.P.); (A.N.); (C.D.L.)
- CEINGE—Biotecnologie Avanzate s.c. a.r.l., Via Gaetano Salvatore 486, 80145 Naples, Italy
- Correspondence: (N.Z.); (E.S.)
| | - Guendalina Froechlich
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Degli Studi di Napoli Federico II, Via Pansini 5, 80131 Napoli, Italy; (G.F.); (M.P.); (A.N.); (C.D.L.)
- CEINGE—Biotecnologie Avanzate s.c. a.r.l., Via Gaetano Salvatore 486, 80145 Naples, Italy
| | - Dejan Lazarevic
- Center for Omics Sciences Ospedale San Raffaele, Via Olgettina 58, 20132 Milano, Italy; (D.L.); (M.J.M.)
| | - Margherita Passariello
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Degli Studi di Napoli Federico II, Via Pansini 5, 80131 Napoli, Italy; (G.F.); (M.P.); (A.N.); (C.D.L.)
- CEINGE—Biotecnologie Avanzate s.c. a.r.l., Via Gaetano Salvatore 486, 80145 Naples, Italy
| | - Alfredo Nicosia
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Degli Studi di Napoli Federico II, Via Pansini 5, 80131 Napoli, Italy; (G.F.); (M.P.); (A.N.); (C.D.L.)
- CEINGE—Biotecnologie Avanzate s.c. a.r.l., Via Gaetano Salvatore 486, 80145 Naples, Italy
| | - Claudia De Lorenzo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Degli Studi di Napoli Federico II, Via Pansini 5, 80131 Napoli, Italy; (G.F.); (M.P.); (A.N.); (C.D.L.)
- CEINGE—Biotecnologie Avanzate s.c. a.r.l., Via Gaetano Salvatore 486, 80145 Naples, Italy
| | - Marco J. Morelli
- Center for Omics Sciences Ospedale San Raffaele, Via Olgettina 58, 20132 Milano, Italy; (D.L.); (M.J.M.)
| | - Emanuele Sasso
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Degli Studi di Napoli Federico II, Via Pansini 5, 80131 Napoli, Italy; (G.F.); (M.P.); (A.N.); (C.D.L.)
- CEINGE—Biotecnologie Avanzate s.c. a.r.l., Via Gaetano Salvatore 486, 80145 Naples, Italy
- Correspondence: (N.Z.); (E.S.)
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16
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Zhu YS, Zhu J. Molecular and cellular functions of long non-coding RNAs in prostate and breast cancer. Adv Clin Chem 2022; 106:91-179. [PMID: 35152976 DOI: 10.1016/bs.acc.2021.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Long noncoding RNAs (lncRNAs) are defined as noncoding RNA transcripts with a length greater than 200 nucleotides. Research over the last decade has made great strides in our understanding of lncRNAs, especially in the biology of their role in cancer. In this article, we will briefly discuss the biogenesis and characteristics of lncRNAs, then review their molecular and cellular functions in cancer by using prostate and breast cancer as examples. LncRNAs are abundant, diverse, and evolutionarily, less conserved than protein-coding genes. They are often expressed in a tumor and cell-specific manner. As a key epigenetic factor, lncRNAs can use a wide variety of molecular mechanisms to regulate gene expression at each step of the genetic information flow pathway. LncRNAs display widespread effects on cell behavior, tumor growth, and metastasis. They act intracellularly and extracellularly in an autocrine, paracrine and endocrine fashion. Increased understanding of lncRNA's role in cancer has facilitated the development of novel biomarkers for cancer diagnosis, led to greater understanding of cancer prognosis, enabled better prediction of therapeutic responses, and promoted identification of potential targets for cancer therapy.
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Affiliation(s)
- Yuan-Shan Zhu
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Clinical and Translational Science Center, Weill Cornell Medicine, New York, NY, United States.
| | - Jifeng Zhu
- Clinical and Translational Science Center, Weill Cornell Medicine, New York, NY, United States
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17
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Arnoldi M, Zarantonello G, Espinoza S, Gustincich S, Di Leva F, Biagioli M. Design and Delivery of SINEUP: A New Modular Tool to Increase Protein Translation. Methods Mol Biol 2022; 2434:63-87. [PMID: 35213010 PMCID: PMC9703201 DOI: 10.1007/978-1-0716-2010-6_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
SINEUP is a new class of long non-coding RNAs (lncRNAs) which contain an inverted Short Interspersed Nuclear Element (SINE) B2 element (invSINEB2) necessary to specifically upregulate target gene translation. Originally identified in the mouse AS-Uchl1 (antisense Ubiquitin carboxyl-terminal esterase L1) locus, natural SINEUP molecules are oriented head to head to their sense protein coding, target gene (Uchl1, in this example). Peculiarly, SINEUP is able to augment, in a specific and controlled way, the expression of the target protein, with no alteration of target mRNA levels. SINEUP is characterized by a modular structure with the Binding Domain (BD) providing specificity to the target transcript and an effector domain (ED)-containing the invSINEB2 element-able to promote the loading to the heavy polysomes of the target mRNA. Since the understanding of its modular structure in the endogenous AS-Uchl1 ncRNA, synthetic SINEUP molecules have been developed by creating a specific BD for the gene of interest and placing it upstream the invSINEB2 ED. Synthetic SINEUP is thus a novel molecular tool that potentially may be used for any industrial or biomedical application to enhance protein production, also as possible therapeutic strategy in haploinsufficiency-driven disorders.Here, we describe a detailed protocol to (1) design a specific BD directed to a gene of interest and (2) assemble and clone it with the ED to obtain a functional SINEUP molecule. Then, we provide guidelines to efficiently deliver SINEUP into mammalian cells and evaluate its ability to effectively upregulate target protein translation.
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Affiliation(s)
- Michele Arnoldi
- Neuroepigenetics Laboratory, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Giulia Zarantonello
- Neuroepigenetics Laboratory, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Stefano Espinoza
- Central RNA Laboratory, Istituto Italiano di Tecnologia, Genova, Italy
| | - Stefano Gustincich
- Central RNA Laboratory, Istituto Italiano di Tecnologia, Genova, Italy
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Francesca Di Leva
- Neuroepigenetics Laboratory, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy.
- Institute for Biomedicine, Eurac Research, Bolzano, Italy.
| | - Marta Biagioli
- Neuroepigenetics Laboratory, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy.
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18
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Zarantonello G, Arnoldi M, Filosi M, Tebaldi T, Spirito G, Barbieri A, Gustincich S, Sanges R, Domenici E, Di Leva F, Biagioli M. Natural SINEUP RNAs in Autism Spectrum Disorders: RAB11B-AS1 Dysregulation in a Neuronal CHD8 Suppression Model Leads to RAB11B Protein Increase. Front Genet 2021; 12:745229. [PMID: 34880900 PMCID: PMC8647803 DOI: 10.3389/fgene.2021.745229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/20/2021] [Indexed: 11/26/2022] Open
Abstract
CHD8 represents one of the highest confidence genetic risk factors implied in Autism Spectrum Disorders, with most mutations leading to CHD8 haploinsufficiency and the insurgence of specific phenotypes, such as macrocephaly, facial dysmorphisms, intellectual disability, and gastrointestinal complaints. While extensive studies have been conducted on the possible consequences of CHD8 suppression and protein coding RNAs dysregulation during neuronal development, the effects of transcriptional changes of long non-coding RNAs (lncRNAs) remain unclear. In this study, we focused on a peculiar class of natural antisense lncRNAs, SINEUPs, that enhance translation of a target mRNA through the activity of two RNA domains, an embedded transposable element sequence and an antisense region. By looking at dysregulated transcripts following CHD8 knock down (KD), we first identified RAB11B-AS1 as a potential SINEUP RNA for its domain configuration. Then we demonstrated that such lncRNA is able to increase endogenous RAB11B protein amounts without affecting its transcriptional levels. RAB11B has a pivotal role in vesicular trafficking, and mutations on this gene correlate with intellectual disability and microcephaly. Thus, our study discloses an additional layer of molecular regulation which is altered by CHD8 suppression. This represents the first experimental confirmation that naturally occurring SINEUP could be involved in ASD pathogenesis and underscores the importance of dysregulation of functional lncRNAs in neurodevelopment.
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Affiliation(s)
- Giulia Zarantonello
- Laboratory of Neuroepigenetics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Michele Arnoldi
- Laboratory of Neuroepigenetics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Michele Filosi
- Laboratory of Neurogenomic Biomarkers, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Toma Tebaldi
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, United States.,Laboratory of RNA and Disease Data Science, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Giovanni Spirito
- Laboratory of Computational Genomics, Area of Neuroscience, International School of Advanced Studies (SISSA), Trieste, Italy.,Central RNA Laboratory, Italian Institute of Technology (IIT), Genova, Italy
| | - Anna Barbieri
- Laboratory of Neuroepigenetics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Stefano Gustincich
- Central RNA Laboratory, Italian Institute of Technology (IIT), Genova, Italy
| | - Remo Sanges
- Laboratory of Computational Genomics, Area of Neuroscience, International School of Advanced Studies (SISSA), Trieste, Italy.,Central RNA Laboratory, Italian Institute of Technology (IIT), Genova, Italy
| | - Enrico Domenici
- Laboratory of Neurogenomic Biomarkers, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy.,Fondazione The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto, Italy
| | - Francesca Di Leva
- Laboratory of Neuroepigenetics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Marta Biagioli
- Laboratory of Neuroepigenetics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
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19
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Lagarrigue S, Lorthiois M, Degalez F, Gilot D, Derrien T. LncRNAs in domesticated animals: from dog to livestock species. Mamm Genome 2021; 33:248-270. [PMID: 34773482 PMCID: PMC9114084 DOI: 10.1007/s00335-021-09928-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/19/2021] [Indexed: 11/29/2022]
Abstract
Animal genomes are pervasively transcribed into multiple RNA molecules, of which many will not be translated into proteins. One major component of this transcribed non-coding genome is the long non-coding RNAs (lncRNAs), which are defined as transcripts longer than 200 nucleotides with low coding-potential capabilities. Domestic animals constitute a unique resource for studying the genetic and epigenetic basis of phenotypic variations involving protein-coding and non-coding RNAs, such as lncRNAs. This review presents the current knowledge regarding transcriptome-based catalogues of lncRNAs in major domesticated animals (pets and livestock species), covering a broad phylogenetic scale (from dogs to chicken), and in comparison with human and mouse lncRNA catalogues. Furthermore, we describe different methods to extract known or discover novel lncRNAs and explore comparative genomics approaches to strengthen the annotation of lncRNAs. We then detail different strategies contributing to a better understanding of lncRNA functions, from genetic studies such as GWAS to molecular biology experiments and give some case examples in domestic animals. Finally, we discuss the limitations of current lncRNA annotations and suggest research directions to improve them and their functional characterisation.
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Affiliation(s)
| | - Matthias Lorthiois
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, 2 av Prof Leon Bernard, F-35000, Rennes, France
| | - Fabien Degalez
- INRAE, INSTITUT AGRO, PEGASE UMR 1348, 35590, Saint-Gilles, France
| | - David Gilot
- CLCC Eugène Marquis, INSERM, Université Rennes, UMR_S 1242, 35000, Rennes, France
| | - Thomas Derrien
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, 2 av Prof Leon Bernard, F-35000, Rennes, France.
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20
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SINEUPs: a novel toolbox for RNA therapeutics. Essays Biochem 2021; 65:775-789. [PMID: 34623427 PMCID: PMC8564737 DOI: 10.1042/ebc20200114] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 07/22/2021] [Accepted: 08/23/2021] [Indexed: 12/17/2022]
Abstract
RNA molecules have emerged as a new class of promising therapeutics to expand the range of druggable targets in the genome. In addition to ‘canonical’ protein-coding mRNAs, the emerging richness of sense and antisense long non-coding RNAs (lncRNAs) provides a new reservoir of molecular tools for RNA-based drugs. LncRNAs are composed of modular structural domains with specific activities involving the recruitment of protein cofactors or directly interacting with nucleic acids. A single therapeutic RNA transcript can then be assembled combining domains with defined secondary structures and functions, and antisense sequences specific for the RNA/DNA target of interest. As the first representative molecules of this new pharmacology, we have identified SINEUPs, a new functional class of natural antisense lncRNAs that increase the translation of partially overlapping mRNAs. Their activity is based on the combination of two domains: an embedded mouse inverted SINEB2 element that enhances mRNA translation (effector domain) and an overlapping antisense region that provides specificity for the target sense transcript (binding domain). By genetic engineering, synthetic SINEUPs can potentially target any mRNA of interest increasing translation and therefore the endogenous level of the encoded protein. In this review, we describe the state-of-the-art knowledge of SINEUPs and discuss recent publications showing their potential application in diseases where a physiological increase of endogenous protein expression can be therapeutic.
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21
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Functional annotation of lncRNA in high-throughput screening. Essays Biochem 2021; 65:761-773. [PMID: 33835127 PMCID: PMC8564734 DOI: 10.1042/ebc20200061] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/25/2021] [Accepted: 03/15/2021] [Indexed: 12/17/2022]
Abstract
Recent efforts on the characterization of long non-coding RNAs (lncRNAs) revealed their functional roles in modulating diverse cellular processes. These include pluripotency maintenance, lineage commitment, carcinogenesis, and pathogenesis of various diseases. By interacting with DNA, RNA and protein, lncRNAs mediate multifaceted mechanisms to regulate transcription, RNA processing, RNA interference and translation. Of more than 173000 discovered lncRNAs, the majority remain functionally unknown. The cell type-specific expression and localization of the lncRNA also suggest potential distinct functions of lncRNAs across different cell types. This highlights the niche of identifying functional lncRNAs in different biological processes and diseases through high-throughput (HTP) screening. This review summarizes the current work performed and perspectives on HTP screening of functional lncRNAs where different technologies, platforms, cellular responses and the downstream analyses are discussed. We hope to provide a better picture in applying different technologies to facilitate functional annotation of lncRNA efficiently.
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22
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Fogeron ML, Lecoq L, Cole L, Harbers M, Böckmann A. Easy Synthesis of Complex Biomolecular Assemblies: Wheat Germ Cell-Free Protein Expression in Structural Biology. Front Mol Biosci 2021; 8:639587. [PMID: 33842544 PMCID: PMC8027086 DOI: 10.3389/fmolb.2021.639587] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 01/20/2021] [Indexed: 12/18/2022] Open
Abstract
Cell-free protein synthesis (CFPS) systems are gaining more importance as universal tools for basic research, applied sciences, and product development with new technologies emerging for their application. Huge progress was made in the field of synthetic biology using CFPS to develop new proteins for technical applications and therapy. Out of the available CFPS systems, wheat germ cell-free protein synthesis (WG-CFPS) merges the highest yields with the use of a eukaryotic ribosome, making it an excellent approach for the synthesis of complex eukaryotic proteins including, for example, protein complexes and membrane proteins. Separating the translation reaction from other cellular processes, CFPS offers a flexible means to adapt translation reactions to protein needs. There is a large demand for such potent, easy-to-use, rapid protein expression systems, which are optimally serving protein requirements to drive biochemical and structural biology research. We summarize here a general workflow for a wheat germ system providing examples from the literature, as well as applications used for our own studies in structural biology. With this review, we want to highlight the tremendous potential of the rapidly evolving and highly versatile CFPS systems, making them more widely used as common tools to recombinantly prepare particularly challenging recombinant eukaryotic proteins.
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Affiliation(s)
- Marie-Laure Fogeron
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Laura Cole
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Matthias Harbers
- CellFree Sciences, Yokohama, Japan
- RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
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23
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Ho JJD, Man JHS, Schatz JH, Marsden PA. Translational remodeling by RNA-binding proteins and noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1647. [PMID: 33694288 DOI: 10.1002/wrna.1647] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/14/2022]
Abstract
Responsible for generating the proteome that controls phenotype, translation is the ultimate convergence point for myriad upstream signals that influence gene expression. System-wide adaptive translational reprogramming has recently emerged as a pillar of cellular adaptation. As classic regulators of mRNA stability and translation efficiency, foundational studies established the concept of collaboration and competition between RNA-binding proteins (RBPs) and noncoding RNAs (ncRNAs) on individual mRNAs. Fresh conceptual innovations now highlight stress-activated, evolutionarily conserved RBP networks and ncRNAs that increase the translation efficiency of populations of transcripts encoding proteins that participate in a common cellular process. The discovery of post-transcriptional functions for long noncoding RNAs (lncRNAs) was particularly intriguing given their cell-type-specificity and historical definition as nuclear-functioning epigenetic regulators. The convergence of RBPs, lncRNAs, and microRNAs on functionally related mRNAs to enable adaptive protein synthesis is a newer biological paradigm that highlights their role as "translatome (protein output) remodelers" and reinvigorates the paradigm of "RNA operons." Together, these concepts modernize our understanding of cellular stress adaptation and strategies for therapeutic development. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Translation > Translation Regulation Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- J J David Ho
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida, USA.,Division of Hematology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Jeffrey H S Man
- Keenan Research Centre, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada.,Department of Respirology, University Health Network, Latner Thoracic Research Laboratories, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan H Schatz
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida, USA.,Division of Hematology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Philip A Marsden
- Keenan Research Centre, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada
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24
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Etchegaray E, Naville M, Volff JN, Haftek-Terreau Z. Transposable element-derived sequences in vertebrate development. Mob DNA 2021; 12:1. [PMID: 33407840 PMCID: PMC7786948 DOI: 10.1186/s13100-020-00229-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 12/15/2020] [Indexed: 12/14/2022] Open
Abstract
Transposable elements (TEs) are major components of all vertebrate genomes that can cause deleterious insertions and genomic instability. However, depending on the specific genomic context of their insertion site, TE sequences can sometimes get positively selected, leading to what are called "exaptation" events. TE sequence exaptation constitutes an important source of novelties for gene, genome and organism evolution, giving rise to new regulatory sequences, protein-coding exons/genes and non-coding RNAs, which can play various roles beneficial to the host. In this review, we focus on the development of vertebrates, which present many derived traits such as bones, adaptive immunity and a complex brain. We illustrate how TE-derived sequences have given rise to developmental innovations in vertebrates and how they thereby contributed to the evolutionary success of this lineage.
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Affiliation(s)
- Ema Etchegaray
- Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364, Lyon, France.
| | - Magali Naville
- Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364, Lyon, France
| | - Jean-Nicolas Volff
- Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364, Lyon, France
| | - Zofia Haftek-Terreau
- Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364, Lyon, France
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25
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Toki N, Takahashi H, Sharma H, Valentine MNZ, Rahman FUM, Zucchelli S, Gustincich S, Carninci P. SINEUP long non-coding RNA acts via PTBP1 and HNRNPK to promote translational initiation assemblies. Nucleic Acids Res 2020; 48:11626-11644. [PMID: 33130894 PMCID: PMC7672464 DOI: 10.1093/nar/gkaa814] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 08/26/2020] [Accepted: 09/23/2020] [Indexed: 12/14/2022] Open
Abstract
SINEUPs are long non-coding RNAs (lncRNAs) that contain a SINE element, and which up-regulate the translation of target mRNA. They have been studied in a wide range of applications, as both biological and therapeutic tools, although the underpinning molecular mechanism is unclear. Here, we focused on the sub-cellular distribution of target mRNAs and SINEUP RNAs, performing co-transfection of expression vectors for these transcripts into human embryonic kidney cells (HEK293T/17), to investigate the network of translational regulation. The results showed that co-localization of target mRNAs and SINEUP RNAs in the cytoplasm was a key phenomenon. We identified PTBP1 and HNRNPK as essential RNA binding proteins. These proteins contributed to SINEUP RNA sub-cellular distribution and to assembly of translational initiation complexes, leading to enhanced target mRNA translation. These findings will promote a better understanding of the mechanisms employed by regulatory RNAs implicated in efficient protein translation.
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Affiliation(s)
- Naoko Toki
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045 Japan
- Functional Genomics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Hazuki Takahashi
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045 Japan
- Functional Genomics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Harshita Sharma
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045 Japan
| | - Matthew N Z Valentine
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045 Japan
| | - Ferdous-Ur M Rahman
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045 Japan
| | - Silvia Zucchelli
- Department of Health Sciences, Center for Autoimmune and Allergic Diseases (CAAD) and Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), University of Piemonte Orientale, Novara, Italy
| | - Stefano Gustincich
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Genova, Italy
| | - Piero Carninci
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045 Japan
- Functional Genomics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
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26
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Toki N, Takahashi H, Zucchelli S, Gustincich S, Carninci P. Synthetic in vitro transcribed lncRNAs (SINEUPs) with chemical modifications enhance target mRNA translation. FEBS Lett 2020; 594:4357-4369. [PMID: 33012004 DOI: 10.1002/1873-3468.13928] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 08/24/2020] [Accepted: 08/24/2020] [Indexed: 01/14/2023]
Abstract
Chemically modified mRNAs are extensively studied with a view toward their clinical application. In particular, long noncoding RNAs (lncRNAs) containing SINE elements, which enhance the translation of their target mRNAs (i.e., SINEUPs), have potential as RNA therapies for various diseases, such as haploinsufficiencies. To establish a SINEUP-based system for efficient protein expression, we directly transfected chemically modified in vitro transcribed (mIVT) SINEUP RNAs to examine their effects on target mRNA translation. mIVT SINEUP RNAs enhanced translation of EGFP mRNA and endogenous target Sox9 mRNA in both cultured cells and a cell-free translation system. Our findings reveal the functional role of RNA modifications in SINEUPs and suggest several broad clinical applications of such an RNA regulatory system.
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Affiliation(s)
- Naoko Toki
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Functional Genomics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Hazuki Takahashi
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Functional Genomics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Silvia Zucchelli
- Department of Health Sciences, Center for Autoimmune and Allergic Diseases (CAAD) and Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), University of Piemonte Orientale (UPO), Novara, Italy
| | - Stefano Gustincich
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia (IIT), Genova, Italy.,Area of Neuroscience, International School for Advanced Studies (SISSA), Trieste, Italy
| | - Piero Carninci
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Functional Genomics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
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27
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Hoseinpoor R, Kazemi B, Rajabibazl M, Rahimpour A. Improving the expression of anti-IL-2Rα monoclonal antibody in the CHO cells through optimization of the expression vector and translation efficiency. J Biotechnol 2020; 324:112-120. [PMID: 33007349 DOI: 10.1016/j.jbiotec.2020.09.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 08/21/2020] [Accepted: 09/08/2020] [Indexed: 12/17/2022]
Abstract
The growing need for monoclonal antibodies (mAbs) necessitates the development of novel and efficient production approaches. Regulatory elements like ubiquitous chromatin-opening elements (UCOEs) have been employed for improvement of the mAb expression in the Chinese hamster ovary (CHO) cells. SINEUPs are a class of long non-coding RNAs, which can improve the translation of partly overlapping mRNAs. A combination of these two elements might lead to higher production of mAbs. Therefore, the current study was conducted to investigate the effects of SINEUPs and A2UCOE on the expression of an IgG1 in the CHO-K1 cells. Hence, after constructing the mAb, mAb-SINEUP, and mAb-UCOE vectors, four stable cell pools were generated through combining the above vectors. According to the expression analysis, antibody yields were higher in the mAb-SINEUP and mAb-UCOE cell pools compared to the mAb cells. In addition, the cells possessing both SINEUP and UCOE elements provided the best expression. Persistent mAb expression was observed for over 2 months in these cells, whilst the expression was decreased in the mAb pool. SINEUP and UCOE positively influenced the stable mAb expression. It can be concluded that the SINEUP and UCOE enhance the antibody stability and expression level separately and their combination improves the mAb production in the CHO cells.
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Affiliation(s)
- Reyhaneh Hoseinpoor
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bahram Kazemi
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoumeh Rajabibazl
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Azam Rahimpour
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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28
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Ohyama T, Takahashi H, Sharma H, Yamazaki T, Gustincich S, Ishii Y, Carninci P. An NMR-based approach reveals the core structure of the functional domain of SINEUP lncRNAs. Nucleic Acids Res 2020; 48:9346-9360. [PMID: 32697302 PMCID: PMC7498343 DOI: 10.1093/nar/gkaa598] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 06/30/2020] [Accepted: 07/06/2020] [Indexed: 02/06/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are attracting widespread attention for their emerging regulatory, transcriptional, epigenetic, structural and various other functions. Comprehensive transcriptome analysis has revealed that retrotransposon elements (REs) are transcribed and enriched in lncRNA sequences. However, the functions of lncRNAs and the molecular roles of the embedded REs are largely unknown. The secondary and tertiary structures of lncRNAs and their embedded REs are likely to have essential functional roles, but experimental determination and reliable computational prediction of large RNA structures have been extremely challenging. We report here the nuclear magnetic resonance (NMR)-based secondary structure determination of the 167-nt inverted short interspersed nuclear element (SINE) B2, which is embedded in antisense Uchl1 lncRNA and upregulates the translation of sense Uchl1 mRNAs. By using NMR 'fingerprints' as a sensitive probe in the domain survey, we successfully divided the full-length inverted SINE B2 into minimal units made of two discrete structured domains and one dynamic domain without altering their original structures after careful boundary adjustments. This approach allowed us to identify a structured domain in nucleotides 31-119 of the inverted SINE B2. This approach will be applicable to determining the structures of other regulatory lncRNAs.
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Affiliation(s)
- Takako Ohyama
- NMR Division, RIKEN SPring-8 Center (RSC), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Hazuki Takahashi
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Harshita Sharma
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Toshio Yamazaki
- NMR Division, RIKEN SPring-8 Center (RSC), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Stefano Gustincich
- Central RNA Laboratory, Instituto Italiano di Tecnologia (IIT), 16163 Genova, Italy
| | - Yoshitaka Ishii
- NMR Division, RIKEN SPring-8 Center (RSC), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Piero Carninci
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
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29
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LncRNA DLG2-AS1 as a Novel Biomarker in Lung Adenocarcinoma. Cancers (Basel) 2020; 12:cancers12082080. [PMID: 32731343 PMCID: PMC7463504 DOI: 10.3390/cancers12082080] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 07/24/2020] [Indexed: 12/23/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are a heterogeneous class of non-coding RNAs whose biological roles are still poorly understood. LncRNAs serve as gene expression regulators, frequently interacting with epigenetic factors to shape the outcomes of crucial biological processes, and playing roles in different pathologies including cancer. Over the last years, growing scientific evidence supports the key role of some lncRNAs in tumor development and proposes them as valuable biomarkers for the clinic. In this study, we aimed to characterize lncRNAs whose expression is altered in tumor samples from patients with lung adenocarcinoma (LUAD) compared to adjacent normal tissue samples. On an RT-qPCR survey of 90 cancer-related lncRNAs, we found one lncRNA, DLG2-AS1, which was consistently downregulated in 70 LUAD patients. To gain insight into its biological function, DLG2-AS1 was cloned and successfully re-expressed in LUAD cancer cell lines. We determined that DLG2-AS1 is not a cis-regulatory element of its overlapping gene DLG2, as their transcription levels were not correlated, nor did DLG2-AS1 restoration modify the expression of DLG2 protein. Furthermore, after generating a receiver operating curve (ROC) and calculating the area under curve (AUC), we found that DLG2-AS1 expression showed high sensitivity and specificity (AUC = 0.726) for the classification of LUAD and normal samples, determining its value as a potential lung cancer biomarker.
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30
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Salvatori B, Biscarini S, Morlando M. Non-coding RNAs in Nervous System Development and Disease. Front Cell Dev Biol 2020; 8:273. [PMID: 32435641 PMCID: PMC7218086 DOI: 10.3389/fcell.2020.00273] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/31/2020] [Indexed: 12/13/2022] Open
Abstract
The rapid advance of RNA sequencing technologies contributed to a deep understanding of transcriptome composition and has allowed the discovery of a large number of non-coding RNAs (ncRNAs). The ability of these RNA molecules to be engaged in intricate and dynamic interactions with proteins and nucleic acids led to a great expansion of gene expression regulation mechanisms. By this matter, ncRNAs contribute to the increase in regulatory complexity that becomes highly specific between tissues and cell types. Among the ncRNAs, long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) are especially abundant in nervous system and have been shown to be implicated in its development, plasticity and aging as well as in neurological disorders. This review provides an overview of how these two diverse classes of ncRNAs control cellular processes during nervous system development, physiology, and disease conditions with particular emphasis on neurodegenerative disorders. The use of ncRNAs as biomarkers, tools, or targets for therapeutic intervention in neurodegeneration are also discussed.
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Affiliation(s)
- Beatrice Salvatori
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Silvia Biscarini
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Mariangela Morlando
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, Perugia, Italy
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31
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Reißer S, Zucchelli S, Gustincich S, Bussi G. Conformational ensembles of an RNA hairpin using molecular dynamics and sparse NMR data. Nucleic Acids Res 2020; 48:1164-1174. [PMID: 31889193 PMCID: PMC7026608 DOI: 10.1093/nar/gkz1184] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 12/05/2019] [Accepted: 12/09/2019] [Indexed: 01/12/2023] Open
Abstract
Solution nuclear magnetic resonance (NMR) experiments allow RNA dynamics to be determined in an aqueous environment. However, when a limited number of peaks are assigned, it is difficult to obtain structural information. We here show a protocol based on the combination of experimental data (Nuclear Overhauser Effect, NOE) and molecular dynamics simulations with enhanced sampling methods. This protocol allows to (a) obtain a maximum entropy ensemble compatible with NMR restraints and (b) obtain a minimal set of metastable conformations compatible with the experimental data (maximum parsimony). The method is applied to a hairpin of 29 nt from an inverted SINEB2, which is part of the SINEUP family and has been shown to enhance protein translation. A clustering procedure is introduced where the annotation of base-base interactions and glycosidic bond angles is used as a metric. By reweighting the contributions of the clusters, minimal sets of four conformations could be found which are compatible with the experimental data. A motif search on the structural database showed that some identified low-population states are present in experimental structures of other RNA transcripts. The introduced method can be applied to characterize RNA dynamics in systems where a limited amount of NMR information is available.
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Affiliation(s)
- Sabine Reißer
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy
| | - Silvia Zucchelli
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy
- Department of Health Sciences, Center for Autoimmune and Allergic Diseases (CAAD) and Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), University of Piemonte Orientale, Novara, Italy
| | - Stefano Gustincich
- Central RNA Laboratory and Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia (IIT), 16163 Genova, Italy
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy
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A Single Cell but Many Different Transcripts: A Journey into the World of Long Non-Coding RNAs. Int J Mol Sci 2020; 21:ijms21010302. [PMID: 31906285 PMCID: PMC6982300 DOI: 10.3390/ijms21010302] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/17/2019] [Accepted: 12/23/2019] [Indexed: 02/07/2023] Open
Abstract
In late 2012 it was evidenced that most of the human genome is transcribed but only a small percentage of the transcripts are translated. This observation supported the importance of non-coding RNAs and it was confirmed in several organisms. The most abundant non-translated transcripts are long non-coding RNAs (lncRNAs). In contrast to protein-coding RNAs, they show a more cell-specific expression. To understand the function of lncRNAs, it is fundamental to investigate in which cells they are preferentially expressed and to detect their subcellular localization. Recent improvements of techniques that localize single RNA molecules in tissues like single-cell RNA sequencing and fluorescence amplification methods have given a considerable boost in the knowledge of the lncRNA functions. In recent years, single-cell transcription variability was associated with non-coding RNA expression, revealing this class of RNAs as important transcripts in the cell lineage specification. The purpose of this review is to collect updated information about lncRNA classification and new findings on their function derived from single-cell analysis. We also retained useful for all researchers to describe the methods available for single-cell analysis and the databases collecting single-cell and lncRNA data. Tables are included to schematize, describe, and compare exposed concepts.
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Lyu Y, Bai L, Qin C. Long noncoding RNAs in neurodevelopment and Parkinson's disease. Animal Model Exp Med 2019; 2:239-251. [PMID: 31942556 PMCID: PMC6930994 DOI: 10.1002/ame2.12093] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 11/12/2019] [Accepted: 11/20/2019] [Indexed: 12/16/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are RNA molecules comprising more than 200 nucleotides, which are not translated into proteins. Many studies have shown that lncRNAs are involved in regulating a variety of biological processes, including immune, cancer, stress, development and differentiation at the transcriptional, epigenetic or post-transcriptional levels. Here, we review the role of lncRNAs in the process of neurodevelopment, neural differentiation, synaptic function, and pathogenesis of Parkinson's disease (PD). These pathomechanisms include protein misfolding and aggregation, disordered protein degradation, mitochondrial dysfunction, oxidative stress, autophagy, apoptosis, and neuroinflammation. This information will provide the basis of lncRNA-based disease diagnosis and drug treatment for PD.
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Affiliation(s)
- Ying Lyu
- Institute of Medical Laboratory Animal ScienceChinese Academy of Medical Sciences & Comparative Medical CenterPeking Union Medical CollegeBeijingChina
| | - Lin Bai
- Institute of Medical Laboratory Animal ScienceChinese Academy of Medical Sciences & Comparative Medical CenterPeking Union Medical CollegeBeijingChina
| | - Chuan Qin
- Institute of Medical Laboratory Animal ScienceChinese Academy of Medical Sciences & Comparative Medical CenterPeking Union Medical CollegeBeijingChina
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34
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Bon C, Luffarelli R, Russo R, Fortuni S, Pierattini B, Santulli C, Fimiani C, Persichetti F, Cotella D, Mallamaci A, Santoro C, Carninci P, Espinoza S, Testi R, Zucchelli S, Condò I, Gustincich S. SINEUP non-coding RNAs rescue defective frataxin expression and activity in a cellular model of Friedreich's Ataxia. Nucleic Acids Res 2019; 47:10728-10743. [PMID: 31584077 PMCID: PMC6847766 DOI: 10.1093/nar/gkz798] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 08/08/2019] [Accepted: 09/28/2019] [Indexed: 12/16/2022] Open
Abstract
Friedreich's ataxia (FRDA) is an untreatable disorder with neuro- and cardio-degenerative progression. This monogenic disease is caused by the hyper-expansion of naturally occurring GAA repeats in the first intron of the FXN gene, encoding for frataxin, a protein implicated in the biogenesis of iron-sulfur clusters. As the genetic defect interferes with FXN transcription, FRDA patients express a normal frataxin protein but at insufficient levels. Thus, current therapeutic strategies are mostly aimed to restore physiological FXN expression. We have previously described SINEUPs, natural and synthetic antisense long non-coding RNAs, which promote translation of partially overlapping mRNAs through the activity of an embedded SINEB2 domain. Here, by in vitro screening, we have identified a number of SINEUPs targeting human FXN mRNA and capable to up-regulate frataxin protein to physiological amounts acting at the post-transcriptional level. Furthermore, FXN-specific SINEUPs promote the recovery of disease-associated mitochondrial aconitase defects in FRDA-derived cells. In summary, we provide evidence that SINEUPs may be the first gene-specific therapeutic approach to activate FXN translation in FRDA and, more broadly, a novel scalable platform to develop new RNA-based therapies for haploinsufficient diseases.
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Affiliation(s)
- Carlotta Bon
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
- Area of Neuroscience, International School for Advanced Studies (SISSA), Italy
| | - Riccardo Luffarelli
- Department of Biomedicine and Prevention, Laboratory of Signal Transduction, University of Rome Tor Vergata, Rome, Italy
| | - Roberta Russo
- Area of Neuroscience, International School for Advanced Studies (SISSA), Italy
| | - Silvia Fortuni
- Department of Biomedicine and Prevention, Laboratory of Signal Transduction, University of Rome Tor Vergata, Rome, Italy
| | - Bianca Pierattini
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
- Area of Neuroscience, International School for Advanced Studies (SISSA), Italy
| | - Chiara Santulli
- Area of Neuroscience, International School for Advanced Studies (SISSA), Italy
| | - Cristina Fimiani
- Area of Neuroscience, International School for Advanced Studies (SISSA), Italy
| | - Francesca Persichetti
- Department of Health Sciences and Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), University of Piemonte Orientale (UPO), Novara, Italy
| | - Diego Cotella
- Department of Health Sciences and Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), University of Piemonte Orientale (UPO), Novara, Italy
| | - Antonello Mallamaci
- Area of Neuroscience, International School for Advanced Studies (SISSA), Italy
| | - Claudio Santoro
- Department of Health Sciences and Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), University of Piemonte Orientale (UPO), Novara, Italy
| | - Piero Carninci
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa, Japan
| | - Stefano Espinoza
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Roberto Testi
- Department of Biomedicine and Prevention, Laboratory of Signal Transduction, University of Rome Tor Vergata, Rome, Italy
| | - Silvia Zucchelli
- Area of Neuroscience, International School for Advanced Studies (SISSA), Italy
- Department of Health Sciences and Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), University of Piemonte Orientale (UPO), Novara, Italy
| | - Ivano Condò
- Department of Biomedicine and Prevention, Laboratory of Signal Transduction, University of Rome Tor Vergata, Rome, Italy
| | - Stefano Gustincich
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
- Area of Neuroscience, International School for Advanced Studies (SISSA), Italy
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35
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Fasolo F, Patrucco L, Volpe M, Bon C, Peano C, Mignone F, Carninci P, Persichetti F, Santoro C, Zucchelli S, Sblattero D, Sanges R, Cotella D, Gustincich S. The RNA-binding protein ILF3 binds to transposable element sequences in SINEUP lncRNAs. FASEB J 2019; 33:13572-13589. [PMID: 31570000 PMCID: PMC6894054 DOI: 10.1096/fj.201901618rr] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Transposable elements (TEs) compose about half of the mammalian genome and, as embedded sequences, up to 40% of long noncoding RNA (lncRNA) transcripts. Embedded TEs may represent functional domains within lncRNAs, providing a structured RNA platform for protein interaction. Here we show the interactome profile of the mouse inverted short interspersed nuclear element (SINE) of subfamily B2 (invSINEB2) alone and embedded in antisense (AS) ubiquitin C-terminal hydrolase L1 (Uchl1), an lncRNA that is AS to Uchl1 gene. AS Uchl1 is the representative member of a functional class of AS lncRNAs, named SINEUPs, in which the invSINEB2 acts as effector domain (ED)-enhancing translation of sense protein-coding mRNAs. By using RNA-interacting domainome technology, we identify the IL enhancer-binding factor 3 (ILF3) as a protein partner of AS Uchl1 RNA. We determine that this interaction is mediated by the RNA-binding motif 2 of ILF3 and the invSINEB2. Furthermore, we show that ILF3 is able to bind a free right Arthrobacter luteus (Alu) monomer sequence, the embedded TE acting as ED in human SINEUPs. Bioinformatic analysis of Encyclopedia of DNA Elements-enhanced cross-linking immunoprecipitation data reveals that ILF3 binds transcribed human SINE sequences at transcriptome-wide levels. We then demonstrate that the embedded TEs modulate AS Uchl1 RNA nuclear localization to an extent moderately influenced by ILF3. This work unveils the existence of a specific interaction between embedded TEs and an RNA-binding protein, strengthening the model of TEs as functional modules in lncRNAs.-Fasolo, F., Patrucco, L., Volpe, M., Bon, C., Peano, C., Mignone, F., Carninci, P., Persichetti, F., Santoro, C., Zucchelli, S., Sblattero, D., Sanges, R., Cotella, D., Gustincich, S. The RNA-binding protein ILF3 binds to transposable element sequences in SINEUP lncRNAs.
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Affiliation(s)
- Francesca Fasolo
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Laura Patrucco
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | - Massimiliano Volpe
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy.,Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Carlotta Bon
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy.,Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Clelia Peano
- Institute of Genetic and Biomedical Research (IRGB), National Research Council (CNR), Milan, Italy.,Humanitas Clinical and Research Center, Rozzano, Italy
| | - Flavio Mignone
- Department of Sciences and Innovation, Università del Piemonte Orientale, Alessandria, Italy
| | - Piero Carninci
- Division of Genomic Technologies, Riken Center for Life Science Technologies, Yokohama, Japan
| | | | - Claudio Santoro
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | - Silvia Zucchelli
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy.,Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | | | - Remo Sanges
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy.,Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy.,Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Diego Cotella
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | - Stefano Gustincich
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy.,Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
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36
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Espinoza S, Scarpato M, Damiani D, Managò F, Mereu M, Contestabile A, Peruzzo O, Carninci P, Santoro C, Papaleo F, Mingozzi F, Ronzitti G, Zucchelli S, Gustincich S. SINEUP Non-coding RNA Targeting GDNF Rescues Motor Deficits and Neurodegeneration in a Mouse Model of Parkinson's Disease. Mol Ther 2019; 28:642-652. [PMID: 31495777 PMCID: PMC7000958 DOI: 10.1016/j.ymthe.2019.08.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 08/02/2019] [Accepted: 08/12/2019] [Indexed: 02/06/2023] Open
Abstract
Glial cell-derived neurotrophic factor (GDNF) has a potent action in promoting the survival of dopamine (DA) neurons. Several studies indicate that increasing GDNF levels may be beneficial for the treatment of Parkinson’s disease (PD) by reducing neurodegeneration of DA neurons. Despite a plethora of preclinical studies showing GDNF efficacy in PD animal models, its application in humans remains questionable for its poor efficacy and side effects due to its uncontrolled, ectopic expression. Here we took advantage of SINEUPs, a new class of antisense long non-coding RNA, that promote translation of partially overlapping sense protein-coding mRNAs with no effects on their mRNA levels. By synthesizing a SINEUP targeting Gdnf mRNA, we were able to increase endogenous GDNF protein levels by about 2-fold. Adeno-associated virus (AAV)9-mediated delivery in the striatum of wild-type (WT) mice led to an increase of endogenous GDNF protein for at least 6 months and the potentiation of the DA system’s functions while showing no side effects. Furthermore, SINEUP-GDNF was able to ameliorate motor deficits and neurodegeneration of DA neurons in a PD neurochemical mouse model. Our data indicate that SINEUP-GDNF could represent a new strategy to increase endogenous GDNF protein levels in a more physiological manner for therapeutic treatments of PD.
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Affiliation(s)
- Stefano Espinoza
- Central RNA Laboratory and Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia (IIT), 16263 Genova, Italy
| | - Margherita Scarpato
- Central RNA Laboratory and Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia (IIT), 16263 Genova, Italy
| | - Devid Damiani
- Central RNA Laboratory and Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia (IIT), 16263 Genova, Italy
| | - Francesca Managò
- Central RNA Laboratory and Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia (IIT), 16263 Genova, Italy
| | - Maddalena Mereu
- Central RNA Laboratory and Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia (IIT), 16263 Genova, Italy; Dipartimento di Scienze del Farmaco, Universita' degli Studi di Padova, Largo Meneghetti 2, 35131 Padova, Italy
| | - Andrea Contestabile
- Central RNA Laboratory and Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia (IIT), 16263 Genova, Italy
| | - Omar Peruzzo
- Central RNA Laboratory and Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia (IIT), 16263 Genova, Italy
| | - Piero Carninci
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa, Japan
| | - Claudio Santoro
- Department of Health Sciences and Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), University of Piemonte Orientale (UPO), 28100 Novara, Italy
| | - Francesco Papaleo
- Central RNA Laboratory and Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia (IIT), 16263 Genova, Italy
| | - Federico Mingozzi
- INTEGRARE, Genethon, Inserm, Univ Evry, Université Paris-Saclay, 91002 Evry, France
| | - Giuseppe Ronzitti
- INTEGRARE, Genethon, Inserm, Univ Evry, Université Paris-Saclay, 91002 Evry, France
| | - Silvia Zucchelli
- Department of Health Sciences and Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), University of Piemonte Orientale (UPO), 28100 Novara, Italy; Area of Neuroscience, Scuola Internazionale degli Studi Avanzati (SISSA), 34012 Trieste, Italy
| | - Stefano Gustincich
- Central RNA Laboratory and Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia (IIT), 16263 Genova, Italy.
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37
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Jin SH, Yao Y, Wu Q. RNA Enhancement by lncRNA Promotes Translation Through Recruitment of ILF3 and EIF4A1 to the Target Mammalian mRNAs. Mol Biol 2019. [DOI: 10.1134/s0026893319010047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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38
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Elkouris M, Kouroupi G, Vourvoukelis A, Papagiannakis N, Kaltezioti V, Matsas R, Stefanis L, Xilouri M, Politis PK. Long Non-coding RNAs Associated With Neurodegeneration-Linked Genes Are Reduced in Parkinson's Disease Patients. Front Cell Neurosci 2019; 13:58. [PMID: 30853899 PMCID: PMC6396023 DOI: 10.3389/fncel.2019.00058] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 02/05/2019] [Indexed: 11/13/2022] Open
Abstract
Transcriptome analysis has identified a plethora of long non-coding RNAs (lncRNAs) expressed in the human brain and associated with neurological diseases. However, whether lncRNAs expression levels correlate with Parkinson's disease (PD) pathogenesis remains unknown. Herein, we show that a number of lncRNA genes encompassing transcriptional units in close proximity to PD-linked protein-coding genes, including SNCA, LRRK2, PINK1, DJ-1, UCH-L1, MAPT and GBA1, are expressed in human dopaminergic cells and post-mortem material, such as cortex, Substantia Nigra and cerebellum. Interestingly, these lncRNAs are upregulated during neuronal differentiation of SH-SY5Y cells and of dopaminergic neurons generated from human fibroblast-derived induced pluripotent stem cells. Importantly, six lncRNAs are found under-expressed in the nigra and three in the cerebellum of PD patients compared to controls. Simultaneously, SNCA mRNA levels are increased in the nigra, while LRRK2 and PINK1 mRNA levels are decreased both in the nigra and the cerebellum of PD subjects compared to controls, indicating a possible correlation between the expression profile of the respective lncRNAs with their adjacent coding genes. Interestingly, all dysregulated lncRNAs are also detected in human peripheral blood mononuclear cells and four of them in exosomes derived from human cerebrospinal fluid, providing initial evidence for their potential use as diagnostic tools for PD. Our data raise the intriguing possibility that these lncRNAs may be involved in disease pathogenesis by regulating their neighboring PD-associated genes and may thus represent novel targets for the diagnosis and/or treatment of PD or related diseases.
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Affiliation(s)
- Maximilianos Elkouris
- Center for Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Georgia Kouroupi
- Laboratory of Cellular and Molecular Neurobiology, Hellenic Pasteur InstituteAthens, Greece
| | - Alexios Vourvoukelis
- Center of Clinical Research, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Nikolaos Papagiannakis
- Center of Clinical Research, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
- First Department of Neurology, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Valeria Kaltezioti
- Center for Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Rebecca Matsas
- Laboratory of Cellular and Molecular Neurobiology, Hellenic Pasteur InstituteAthens, Greece
| | - Leonidas Stefanis
- Center of Clinical Research, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
- First Department of Neurology, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Maria Xilouri
- Center of Clinical Research, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Panagiotis K. Politis
- Center for Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
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Zucchelli S, Fedele S, Vatta P, Calligaris R, Heutink P, Rizzu P, Itoh M, Persichetti F, Santoro C, Kawaji H, Lassmann T, Hayashizaki Y, Carninci P, Forrest ARR, Gustincich S. Antisense Transcription in Loci Associated to Hereditary Neurodegenerative Diseases. Mol Neurobiol 2019; 56:5392-5415. [PMID: 30610612 PMCID: PMC6614138 DOI: 10.1007/s12035-018-1465-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 12/19/2018] [Indexed: 12/12/2022]
Abstract
Natural antisense transcripts are common features of mammalian genes providing additional regulatory layers of gene expression. A comprehensive description of antisense transcription in loci associated to familial neurodegenerative diseases may identify key players in gene regulation and provide tools for manipulating gene expression. We take advantage of the FANTOM5 sequencing datasets that represent the largest collection to date of genome-wide promoter usage in almost 2000 human samples. Transcription start sites (TSSs) are mapped at high resolution by the use of a modified protocol of cap analysis of gene expression (CAGE) for high-throughput single molecule next-generation sequencing with Helicos (hCAGE). Here we present the analysis of antisense transcription at 17 loci associated to hereditary Alzheimer’s disease, Frontotemporal Dementia, Parkinson’s disease, Amyotrophic Lateral Sclerosis, and Huntington’s disease. We focused our analysis on libraries derived from brain tissues and primary cells. We also screened libraries from total blood and blood cell populations in the quest for peripheral biomarkers of neurodegenerative diseases. We identified 63 robust promoters in antisense orientation to genes associated to familial neurodegeneration. When applying a less stringent cutoff, this number increases to over 400. A subset of these promoters represents alternative TSSs for 24 FANTOM5 annotated long noncoding RNA (lncRNA) genes, in antisense orientation to 13 of the loci analyzed here, while the remaining contribute to the expression of additional transcript variants. Intersection with GWAS studies, sample ontology, and dynamic expression reveals association to specific genetic traits as well as cell and tissue types, not limited to neurodegenerative diseases. Antisense transcription was validated for a subset of genes, including those encoding for Microtubule-Associated Protein Tau, α-synuclein, Parkinsonism-associated deglycase DJ-1, and Leucin-Rich Repeat Kinase 2. This work provides evidence for the existence of additional regulatory mechanisms of the expression of neurodegenerative disease-causing genes by previously not-annotated and/or not-validated antisense long noncoding RNAs.
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Affiliation(s)
- Silvia Zucchelli
- Area of Neuroscience, SISSA, Trieste, Italy
- Department of Health Sciences and Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), University of Piemonte Orientale (UPO), Novara, Italy
| | | | - Paolo Vatta
- Area of Neuroscience, SISSA, Trieste, Italy
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Raffaella Calligaris
- Area of Neuroscience, SISSA, Trieste, Italy
- Department of Medical, Surgical and Health Sciences, Clinical Neurology Unit, Cattinara University Hospital, Trieste, Italy
| | - Peter Heutink
- Section Medical Genomics, Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
- Genome Biology of Neurodegenerative Diseases, Deutsches Zentrum fur Neurodegenerative Erkrankungen (DZNE), Standort, Tübingen, Germany
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
- RIKEN Omics Science Center, Yokohama, Japan
| | - Patrizia Rizzu
- Section Medical Genomics, Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
- Applied Genomics for Neurodegenerative Diseases, Deutsches Zentrum fur Neurodegenerative Erkrankungen (DZNE), Standort, Tübingen, Germany
| | - Masayoshi Itoh
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
- RIKEN Omics Science Center, Yokohama, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wakō, Japan
| | - Francesca Persichetti
- Department of Health Sciences and Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), University of Piemonte Orientale (UPO), Novara, Italy
| | - Claudio Santoro
- Department of Health Sciences and Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), University of Piemonte Orientale (UPO), Novara, Italy
| | - Hideya Kawaji
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
- RIKEN Omics Science Center, Yokohama, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wakō, Japan
- Preventive Medicine and Applied Genomics Unit, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Timo Lassmann
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
- RIKEN Omics Science Center, Yokohama, Japan
- Telethon Kids Institute, The University of Western Australia, 100 Roberts Road, Subiaco, WA 6008 Australia
- Laboratory for Applied Computational Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yoshihide Hayashizaki
- RIKEN Omics Science Center, Yokohama, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wakō, Japan
| | - Piero Carninci
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
- RIKEN Omics Science Center, Yokohama, Japan
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Alistair R. R. Forrest
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
- RIKEN Omics Science Center, Yokohama, Japan
- Laboratory for Genome Information Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Stefano Gustincich
- Area of Neuroscience, SISSA, Trieste, Italy
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
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Sauvageau M. Diverging RNPs: Toward Understanding lncRNA-Protein Interactions and Functions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1203:285-312. [PMID: 31811638 DOI: 10.1007/978-3-030-31434-7_10] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
RNA-protein interactions are essential to a variety of biological processes. The realization that mammalian genomes are pervasively transcribed brought a tidal wave of tens of thousands of newly identified long noncoding RNAs (lncRNAs) and raised questions about their purpose in cells. The vast majority of lncRNAs have yet to be studied, and it remains to be determined to how many of these transcripts a function can be ascribed. However, results gleaned from studying a handful of these macromolecules have started to reveal common themes of biological function and mechanism of action involving intricate RNA-protein interactions. Some lncRNAs were shown to regulate the chromatin and transcription of distant and neighboring genes in the nucleus, while others regulate the translation or localization of proteins in the cytoplasm. Some lncRNAs were found to be crucial during development, while mutations and aberrant expression of others have been associated with several types of cancer and a plethora of diseases. Over the last few years, the establishment of new technologies has been key in providing the tools to decode the rules governing lncRNA-protein interactions and functions. This chapter will highlight the general characteristics of lncRNAs, their function, and their mode of action, with a special focus on protein interactions. It will also describe the methods at the disposition of scientists to help them cross this next frontier in our understanding of lncRNA biology.
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Affiliation(s)
- Martin Sauvageau
- Montreal Clinical Research Institute (IRCM), Montréal, QC, Canada. .,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, Canada.
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Blokhin I, Khorkova O, Hsiao J, Wahlestedt C. Developments in lncRNA drug discovery: where are we heading? Expert Opin Drug Discov 2018; 13:837-849. [PMID: 30078338 DOI: 10.1080/17460441.2018.1501024] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
INTRODUCTION The central dogma of molecular biology, which states that the only role of long RNA transcripts is to convey information from gene to protein, was brought into question in recent years due to discovery of the extensive presence and complex roles of long noncoding RNAs (lncRNAs). Furthermore, lncRNAs were found to be involved in pathogenesis of multiple diseases and thus represent a new class of therapeutic targets. Translational efforts in the lncRNA field have been augmented by progress in optimizing the chemistry and delivery platforms of lncRNA-targeting modalities, including oligonucleotide-based drugs and CRISPR-Cas9. Areas covered: This review covers the current advances in characterizing diversity and biological functions of lncRNA focusing on their therapeutic potential in selected therapeutic areas. Expert opinion: Due to accelerating parallel progress in lncRNA biology and lncRNA-compatible therapeutic modalities, it is likely that lncRNA-dependent mechanisms of pathogenesis will soon be targeted in various disorders, including neurological, psychiatric, cardiovascular, infectious diseases, and cancer. Significant efforts, however, are still required to better understand the biology of both lncRNAs and lncRNA-targeting drugs. Further work is needed in the areas of lncRNA nomenclature, database representation, intra/interfield communication, and education of the community at large.
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Affiliation(s)
- Ilya Blokhin
- a Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences , University of Miami Miller School of Medicine , Miami , FL , USA
| | | | | | - Claes Wahlestedt
- a Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences , University of Miami Miller School of Medicine , Miami , FL , USA
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Sasso E, Latino D, Froechlich G, Succoio M, Passariello M, De Lorenzo C, Nicosia A, Zambrano N. A long non-coding SINEUP RNA boosts semi-stable production of fully human monoclonal antibodies in HEK293E cells. MAbs 2018; 10:730-737. [PMID: 29658818 PMCID: PMC6150626 DOI: 10.1080/19420862.2018.1463945] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Use of monoclonal antibodies is emerging as a highly promising and fast-developing scenario for innovative treatment of viral, autoimmune and tumour diseases. The search for diagnostic and therapeutic antibodies currently depends on in vitro screening approaches, such as phage and yeast display technologies. Antibody production still represents a critical step for preclinical and clinical evaluations. Accordingly, improving production of monoclonal antibodies represents an opportunity, to facilitate downstream target validations. SINEUP RNAs are long non-coding transcripts, possessing the ability to enhance translation of selected mRNAs. We applied SINEUP technology to semi-stable production of monoclonal antibodies in HEK293E cells, which allows for episomal propagation of the expression vectors encoding the heavy and light chains of IgGs. Co-expression of SINEUP RNA with mRNAs encoding heavy and light chains of IgG4s was able to increase the production of different anti-CLDN1 antibodies up to three-fold. Improved production of monoclonal antibodies was achieved both in transiently transfected HEK293E cells and in cellular clones with stable expression of the SINEUP. Compared to antibody preparations obtained under standard conditions, the anti-CLDN1 IgG4s produced in the presence of the SINEUP transcript showed unaltered post-translational modifications, and retained the ability to recognize their target. We thus propose SINEUP technology as a valuable tool to enhance semi-stable antibody production in human cell lines.
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Affiliation(s)
- Emanuele Sasso
- a Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II , Napoli , Italy.,b CEINGE Biotecnologie Avanzate S.C.AR.L. , Napoli , Italy.,c Associazione Culturale DiSciMuS RFC , Casoria , NA , Italy
| | - Debora Latino
- a Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II , Napoli , Italy.,b CEINGE Biotecnologie Avanzate S.C.AR.L. , Napoli , Italy
| | - Guendalina Froechlich
- a Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II , Napoli , Italy.,b CEINGE Biotecnologie Avanzate S.C.AR.L. , Napoli , Italy
| | - Mariangela Succoio
- a Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II , Napoli , Italy.,b CEINGE Biotecnologie Avanzate S.C.AR.L. , Napoli , Italy.,c Associazione Culturale DiSciMuS RFC , Casoria , NA , Italy
| | - Margherita Passariello
- a Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II , Napoli , Italy.,b CEINGE Biotecnologie Avanzate S.C.AR.L. , Napoli , Italy
| | - Claudia De Lorenzo
- a Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II , Napoli , Italy.,b CEINGE Biotecnologie Avanzate S.C.AR.L. , Napoli , Italy
| | - Alfredo Nicosia
- a Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II , Napoli , Italy.,b CEINGE Biotecnologie Avanzate S.C.AR.L. , Napoli , Italy.,d ReiThera S.R.L. Roma , Italy
| | - Nicola Zambrano
- a Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II , Napoli , Italy.,b CEINGE Biotecnologie Avanzate S.C.AR.L. , Napoli , Italy.,c Associazione Culturale DiSciMuS RFC , Casoria , NA , Italy
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Structural determinants of the SINE B2 element embedded in the long non-coding RNA activator of translation AS Uchl1. Sci Rep 2018; 8:3189. [PMID: 29453387 PMCID: PMC5816658 DOI: 10.1038/s41598-017-14908-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 10/18/2017] [Indexed: 12/22/2022] Open
Abstract
Pervasive transcription of mammalian genomes leads to a previously underestimated level of complexity in gene regulatory networks. Recently, we have identified a new functional class of natural and synthetic antisense long non-coding RNAs (lncRNA) that increases translation of partially overlapping sense mRNAs. These molecules were named SINEUPs, as they require an embedded inverted SINE B2 element for their UP-regulation of translation. Mouse AS Uchl1 is the representative member of natural SINEUPs. It was originally discovered for its role in increasing translation of Uchl1 mRNA, a gene associated with neurodegenerative diseases. Here we present the secondary structure of the SINE B2 Transposable Element (TE) embedded in AS Uchl1. We find that specific structural regions, containing a short hairpin, are required for the ability of AS Uchl1 RNA to increase translation of its target mRNA. We also provide a high-resolution structure of the relevant hairpin, based on NMR observables. Our results highlight the importance of structural determinants in embedded TEs for their activity as functional domains in lncRNAs.
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Takahashi H, Kozhuharova A, Sharma H, Hirose M, Ohyama T, Fasolo F, Yamazaki T, Cotella D, Santoro C, Zucchelli S, Gustincich S, Carninci P. Identification of functional features of synthetic SINEUPs, antisense lncRNAs that specifically enhance protein translation. PLoS One 2018; 13:e0183229. [PMID: 29414979 PMCID: PMC5802440 DOI: 10.1371/journal.pone.0183229] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 08/01/2017] [Indexed: 12/26/2022] Open
Abstract
SINEUPs are antisense long noncoding RNAs, in which an embedded SINE B2 element UP-regulates translation of partially overlapping target sense mRNAs. SINEUPs contain two functional domains. First, the binding domain (BD) is located in the region antisense to the target, providing specific targeting to the overlapping mRNA. Second, the inverted SINE B2 represents the effector domain (ED) and enhances translation. To adapt SINEUP technology to a broader number of targets, we took advantage of a high-throughput, semi-automated imaging system to optimize synthetic SINEUP BD and ED design in HEK293T cell lines. Using SINEUP-GFP as a model SINEUP, we extensively screened variants of the BD to map features needed for optimal design. We found that most active SINEUPs overlap an AUG-Kozak sequence. Moreover, we report our screening of the inverted SINE B2 sequence to identify active sub-domains and map the length of the minimal active ED. Our synthetic SINEUP-GFP screening of both BDs and EDs constitutes a broad test with flexible applications to any target gene of interest.
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Affiliation(s)
- Hazuki Takahashi
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa, Japan
| | - Ana Kozhuharova
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa, Japan
| | - Harshita Sharma
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa, Japan
| | - Masakazu Hirose
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa, Japan
| | - Takako Ohyama
- RIKEN Center for Life Science Technologies, Division of Structural and Synthetic Biology, Yokohama, Kanagawa, Japan
| | - Francesca Fasolo
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati, Trieste, Italy
| | - Toshio Yamazaki
- RIKEN Center for Life Science Technologies, Division of Structural and Synthetic Biology, Yokohama, Kanagawa, Japan
| | - Diego Cotella
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | - Claudio Santoro
- Department of Health Sciences & IRCAD, Università del Piemonte Orientale, Novara, Italy
| | - Silvia Zucchelli
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati, Trieste, Italy
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | - Stefano Gustincich
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati, Trieste, Italy
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Genova, Italy
| | - Piero Carninci
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa, Japan
- TransSINE Technologies, Yokohama, Kanagawa, Japan
- * E-mail:
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Jung J, Lee S, Cho HS, Park K, Ryu JW, Jung M, Kim J, Kim H, Kim DS. Bioinformatic analysis of regulation of natural antisense transcripts by transposable elements in human mRNA. Genomics 2018; 111:159-166. [PMID: 29366860 DOI: 10.1016/j.ygeno.2018.01.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 01/16/2018] [Accepted: 01/17/2018] [Indexed: 12/19/2022]
Abstract
Non-coding RNA is no longer considered to be "junk" DNA, based on evidence uncovered in recent decades. In particular, the important role played by natural antisense transcripts (NATs) in regulating the expression of genes is receiving increasing attention. However, the regulatory mechanisms of NATs remain incompletely understood. It is well-known that the insertion of transposable elements (TEs) can affect gene transcription. Using a bioinformatics approach, we identified NATs using human mRNA sequences from the UCSC Genome Browser Database. Our in silico analysis identified 1079 NATs and 700 sense-antisense gene pairs. We identified 179 NATs that showed evidence of having been affected by TEs during cellular gene expression. These findings may provide an understanding of the complex regulation mechanisms of NATs. If our understanding of NATs as modulators of gene expression is further enhanced, we can develop ways to control gene expression.
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Affiliation(s)
- Jaeeun Jung
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea; Department of Rare Disease Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Sugi Lee
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea; Department of Rare Disease Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Hyun-Soo Cho
- Department of Stem Cell Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Kunhyang Park
- Department of Core Facility Management Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Jea-Woon Ryu
- Department of Rare Disease Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Minah Jung
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea; Department of Rare Disease Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Jeongkil Kim
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea; Department of Rare Disease Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - HyeRan Kim
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea; Department of Plant Systems Engineering Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Dae-Soo Kim
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea; Department of Rare Disease Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea.
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Methods for Using Small Non-Coding RNAs to Improve Recombinant Protein Expression in Mammalian Cells. Genes (Basel) 2018; 9:genes9010025. [PMID: 29315258 PMCID: PMC5793178 DOI: 10.3390/genes9010025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 12/19/2017] [Accepted: 01/03/2018] [Indexed: 12/27/2022] Open
Abstract
The ability to produce recombinant proteins by utilizing different “cell factories” revolutionized the biotherapeutic and pharmaceutical industry. Chinese hamster ovary (CHO) cells are the dominant industrial producer, especially for antibodies. Human embryonic kidney cells (HEK), while not being as widely used as CHO cells, are used where CHO cells are unable to meet the needs for expression, such as growth factors. Therefore, improving recombinant protein expression from mammalian cells is a priority, and continuing effort is being devoted to this topic. Non-coding RNAs are RNA segments that are not translated into a protein and often have a regulatory role. Since their discovery, major progress has been made towards understanding their functions. Non-coding RNA has been investigated extensively in relation to disease, especially cancer, and recently they have also been used as a method for engineering cells to improve their protein expression capability. In this review, we provide information about methods used to identify non-coding RNAs with the potential of improving recombinant protein expression in mammalian cell lines.
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47
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Shapiro JA. Living Organisms Author Their Read-Write Genomes in Evolution. BIOLOGY 2017; 6:E42. [PMID: 29211049 PMCID: PMC5745447 DOI: 10.3390/biology6040042] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/17/2017] [Accepted: 11/28/2017] [Indexed: 12/18/2022]
Abstract
Evolutionary variations generating phenotypic adaptations and novel taxa resulted from complex cellular activities altering genome content and expression: (i) Symbiogenetic cell mergers producing the mitochondrion-bearing ancestor of eukaryotes and chloroplast-bearing ancestors of photosynthetic eukaryotes; (ii) interspecific hybridizations and genome doublings generating new species and adaptive radiations of higher plants and animals; and, (iii) interspecific horizontal DNA transfer encoding virtually all of the cellular functions between organisms and their viruses in all domains of life. Consequently, assuming that evolutionary processes occur in isolated genomes of individual species has become an unrealistic abstraction. Adaptive variations also involved natural genetic engineering of mobile DNA elements to rewire regulatory networks. In the most highly evolved organisms, biological complexity scales with "non-coding" DNA content more closely than with protein-coding capacity. Coincidentally, we have learned how so-called "non-coding" RNAs that are rich in repetitive mobile DNA sequences are key regulators of complex phenotypes. Both biotic and abiotic ecological challenges serve as triggers for episodes of elevated genome change. The intersections of cell activities, biosphere interactions, horizontal DNA transfers, and non-random Read-Write genome modifications by natural genetic engineering provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago GCIS W123B, 979 E. 57th Street, Chicago, IL 60637, USA.
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48
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Li PP, Sun X, Xia G, Arbez N, Paul S, Zhu S, Peng HB, Ross CA, Koeppen AH, Margolis RL, Pulst SM, Ashizawa T, Rudnicki DD. ATXN2-AS, a gene antisense to ATXN2, is associated with spinocerebellar ataxia type 2 and amyotrophic lateral sclerosis. Ann Neurol 2017; 80:600-15. [PMID: 27531668 DOI: 10.1002/ana.24761] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 08/10/2016] [Accepted: 08/12/2016] [Indexed: 01/10/2023]
Abstract
OBJECTIVE Spinocerebellar ataxia type 2 (SCA2) is a neurodegenerative disease caused by a CAG repeat expansion in the gene ataxin-2 (ATXN2). ATXN2 intermediate-length CAG expansions were identified as a risk factor for amyotrophic lateral sclerosis (ALS). The ATXN2 CAG repeat is translated into polyglutamine, and SCA2 pathogenesis has been thought to derive from ATXN2 protein containing an expanded polyglutamine tract. However, recent evidence of bidirectional transcription at multiple CAG/CTG disease loci has led us to test whether additional mechanisms of pathogenesis may contribute to SCA2. METHODS In this work, using human postmortem tissue, various cell models, and animal models, we provide the first evidence that an antisense transcript at the SCA2 locus contributes to SCA2 pathogenesis. RESULTS We demonstrate the expression of a transcript, containing the repeat as a CUG tract, derived from a gene (ATXN2-AS) directly antisense to ATXN2. ATXN2-AS transcripts with normal and expanded CUG repeats are expressed in human postmortem SCA2 brains, human SCA2 fibroblasts, induced SCA2 pluripotent stem cells, SCA2 neural stem cells, and lymphoblastoid lines containing an expanded ATXN2 allele associated with ALS. ATXN2-AS transcripts with a CUG repeat expansion are toxic in an SCA2 cell model and form RNA foci in SCA2 cerebellar Purkinje cells. Finally, we detected missplicing of amyloid beta precursor protein and N-methyl-D-aspartate receptor 1 in SCA2 brains, consistent with findings in other diseases characterized by RNA-mediated pathogenesis. INTERPRETATION These results suggest that ATXN2-AS has a role in SCA2 and possibly ALS pathogenesis, and may therefore provide a novel therapeutic target for these diseases. Ann Neurol 2016;80:600-615.
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Affiliation(s)
- Pan P Li
- Division of Neurobiology, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Xin Sun
- Division of Neurobiology, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD.,Research and Neurology Services, Veterans Affairs Medical Center, Albany, NY
| | - Guangbin Xia
- Department of Neurology, College of Medicine, and McKnight Brain Institute, University of Florida, Gainesville, FL
| | - Nicolas Arbez
- Division of Neurobiology, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Sharan Paul
- Department of Neurology, University of Utah, Salt Lake City, UT
| | - Shanshan Zhu
- Division of Neurobiology, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD
| | - H Benjamin Peng
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Christopher A Ross
- Division of Neurobiology, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD.,Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD.,Program of Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Arnulf H Koeppen
- Research and Neurology Services, Veterans Affairs Medical Center, Albany, NY.,Department of Neurology and Pathology, Albany Medical College, Albany, NY
| | - Russell L Margolis
- Division of Neurobiology, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD.,Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD.,Program of Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Stefan M Pulst
- Department of Neurology, University of Utah, Salt Lake City, UT
| | - Tetsuo Ashizawa
- Department of Neurology, College of Medicine, and McKnight Brain Institute, University of Florida, Gainesville, FL
| | - Dobrila D Rudnicki
- Division of Neurobiology, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD. .,Program of Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD.
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49
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Bonetti A, Carninci P. From bench to bedside: The long journey of long non-coding RNAs. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.coisb.2017.04.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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50
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Wucher V, Legeai F, Hédan B, Rizk G, Lagoutte L, Leeb T, Jagannathan V, Cadieu E, David A, Lohi H, Cirera S, Fredholm M, Botherel N, Leegwater PA, Le Béguec C, Fieten H, Johnson J, Alföldi J, André C, Lindblad-Toh K, Hitte C, Derrien T. FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome. Nucleic Acids Res 2017; 45:e57. [PMID: 28053114 PMCID: PMC5416892 DOI: 10.1093/nar/gkw1306] [Citation(s) in RCA: 192] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 12/13/2016] [Accepted: 12/14/2016] [Indexed: 12/13/2022] Open
Abstract
Whole transcriptome sequencing (RNA-seq) has become a standard for cataloguing and monitoring RNA populations. One of the main bottlenecks, however, is to correctly identify the different classes of RNAs among the plethora of reconstructed transcripts, particularly those that will be translated (mRNAs) from the class of long non-coding RNAs (lncRNAs). Here, we present FEELnc (FlExible Extraction of LncRNAs), an alignment-free program that accurately annotates lncRNAs based on a Random Forest model trained with general features such as multi k-mer frequencies and relaxed open reading frames. Benchmarking versus five state-of-the-art tools shows that FEELnc achieves similar or better classification performance on GENCODE and NONCODE data sets. The program also provides specific modules that enable the user to fine-tune classification accuracy, to formalize the annotation of lncRNA classes and to identify lncRNAs even in the absence of a training set of non-coding RNAs. We used FEELnc on a real data set comprising 20 canine RNA-seq samples produced by the European LUPA consortium to substantially expand the canine genome annotation to include 10 374 novel lncRNAs and 58 640 mRNA transcripts. FEELnc moves beyond conventional coding potential classifiers by providing a standardized and complete solution for annotating lncRNAs and is freely available at https://github.com/tderrien/FEELnc.
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Affiliation(s)
- Valentin Wucher
- Institut Génétique et Développement de Rennes, CNRS, UMR6290, University Rennes1, Rennes, Cedex 35043, France
| | - Fabrice Legeai
- IGEPP, BIPAA, INRA, Campus Beaulieu, Le Rheu 35653, France
- Institut National de Recherche en Informatique et en Automatique, Institut de Recherche en Informatique et Systèmes Aléatoires, Genscale, Campus Beaulieu, Rennes 35042, France
| | - Benoît Hédan
- Institut Génétique et Développement de Rennes, CNRS, UMR6290, University Rennes1, Rennes, Cedex 35043, France
| | - Guillaume Rizk
- Institut National de Recherche en Informatique et en Automatique, Institut de Recherche en Informatique et Systèmes Aléatoires, Genscale, Campus Beaulieu, Rennes 35042, France
| | - Lætitia Lagoutte
- Institut Génétique et Développement de Rennes, CNRS, UMR6290, University Rennes1, Rennes, Cedex 35043, France
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3001, Switzerland
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3001, Switzerland
| | - Edouard Cadieu
- Institut Génétique et Développement de Rennes, CNRS, UMR6290, University Rennes1, Rennes, Cedex 35043, France
| | - Audrey David
- IGEPP, BIPAA, INRA, Campus Beaulieu, Le Rheu 35653, France
| | - Hannes Lohi
- Department of Veterinary Biosciences and Research Programs Unit, Molecular Neurology, University of Helsinki, PO Box 63, Helsinki 00014, Finland
- The Folkhälsan Institute of Genetics, Helsinki 00014, Finland
| | - Susanna Cirera
- Department of Veterinary Clinical and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 1870, Denmark
| | - Merete Fredholm
- Department of Veterinary Clinical and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 1870, Denmark
| | - Nadine Botherel
- Institut Génétique et Développement de Rennes, CNRS, UMR6290, University Rennes1, Rennes, Cedex 35043, France
| | - Peter A.J. Leegwater
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht 3584CM, the Netherlands
| | - Céline Le Béguec
- Institut Génétique et Développement de Rennes, CNRS, UMR6290, University Rennes1, Rennes, Cedex 35043, France
| | - Hille Fieten
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht 3584CM, the Netherlands
| | - Jeremy Johnson
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jessica Alföldi
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Catherine André
- Institut Génétique et Développement de Rennes, CNRS, UMR6290, University Rennes1, Rennes, Cedex 35043, France
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala 751 23, Sweden
| | - Christophe Hitte
- Institut Génétique et Développement de Rennes, CNRS, UMR6290, University Rennes1, Rennes, Cedex 35043, France
| | - Thomas Derrien
- Institut Génétique et Développement de Rennes, CNRS, UMR6290, University Rennes1, Rennes, Cedex 35043, France
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