201
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Kubota N, Suyama M. Mapping of promoter usage QTL using RNA-seq data reveals their contributions to complex traits. PLoS Comput Biol 2022; 18:e1010436. [PMID: 36037215 PMCID: PMC9462676 DOI: 10.1371/journal.pcbi.1010436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 09/09/2022] [Accepted: 07/25/2022] [Indexed: 11/18/2022] Open
Abstract
Genomic variations are associated with gene expression levels, which are called expression quantitative trait loci (eQTL). Most eQTL may affect the total gene expression levels by regulating transcriptional activities of a specific promoter. However, the direct exploration of genomic loci associated with promoter activities using RNA-seq data has been challenging because eQTL analyses treat the total expression levels estimated by summing those of all isoforms transcribed from distinct promoters. Here we propose a new method for identifying genomic loci associated with promoter activities, called promoter usage quantitative trait loci (puQTL), using conventional RNA-seq data. By leveraging public RNA-seq datasets from the lymphoblastoid cell lines of 438 individuals from the GEUVADIS project, we obtained promoter activity estimates and mapped 2,592 puQTL at the 10% FDR level. The results of puQTL mapping enabled us to interpret the manner in which genomic variations regulate gene expression. We found that 310 puQTL genes (16.1%) were not detected by eQTL analysis, suggesting that our pipeline can identify novel variant-gene associations. Furthermore, we identified genomic loci associated with the activity of "hidden" promoters, which the standard eQTL studies have ignored. We found that most puQTL signals were concordant with at least one genome-wide association study (GWAS) signal, enabling novel interpretations of the molecular mechanisms of complex traits. Our results emphasize the importance of the re-analysis of public RNA-seq datasets to obtain novel insights into gene regulation by genomic variations and their contributions to complex traits.
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Affiliation(s)
- Naoto Kubota
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Mikita Suyama
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
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202
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Edwards DK, Carfi A. Messenger ribonucleic acid vaccines against infectious diseases: current concepts and future prospects. Curr Opin Immunol 2022; 77:102214. [PMID: 35671599 PMCID: PMC9612403 DOI: 10.1016/j.coi.2022.102214] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/26/2022] [Accepted: 04/29/2022] [Indexed: 01/06/2023]
Abstract
Over the past two decades, scientific and technological advancements have revealed messenger ribonucleic acid (mRNA)-based vaccines as a well-tolerated and effective platform to combat infectious disease. The potential of mRNA-based vaccines was epitomized during the severe acute respiratory syndrome coronavirus 2 pandemic, wherein mRNA-based vaccines were rapidly developed and found highly efficacious with an acceptable safety profile. These properties together with the capability to quickly address pathogens of pandemic potential, pathogens with complex antigens, and multiple pathogens within a single vaccine have revitalized the field, and multiple mRNA-based vaccines have now entered clinical development. This review summarizes current mRNA-based vaccine technology, perspectives on ongoing clinical studies, and future prospects for the field.
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Affiliation(s)
| | - Andrea Carfi
- Moderna, Inc., 200 Technology Square, Cambridge, MA, USA.
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203
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Ray S, Dandpat SS, Chatterjee S, Walter NG. Precise tuning of bacterial translation initiation by non-equilibrium 5'-UTR unfolding observed in single mRNAs. Nucleic Acids Res 2022; 50:8818-8833. [PMID: 35892287 PMCID: PMC9410914 DOI: 10.1093/nar/gkac635] [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: 12/16/2021] [Revised: 06/15/2022] [Accepted: 07/14/2022] [Indexed: 11/21/2022] Open
Abstract
Noncoding, structured 5′-untranslated regions (5′-UTRs) of bacterial messenger RNAs (mRNAs) can control translation efficiency by forming structures that either recruit or repel the ribosome. Here we exploit a 5′-UTR embedded preQ1-sensing, pseudoknotted translational riboswitch to probe how binding of a small ligand controls recruitment of the bacterial ribosome to the partially overlapping Shine-Dalgarno (SD) sequence. Combining single-molecule fluorescence microscopy with mutational analyses, we find that the stability of 30S ribosomal subunit binding is inversely correlated with the free energy needed to unfold the 5′-UTR during mRNA accommodation into the mRNA binding cleft. Ligand binding to the riboswitch stabilizes the structure to both antagonize 30S recruitment and accelerate 30S dissociation. Proximity of the 5′-UTR and stability of the SD:anti-SD interaction both play important roles in modulating the initial 30S-mRNA interaction. Finally, depletion of small ribosomal subunit protein S1, known to help resolve structured 5′-UTRs, further increases the energetic penalty for mRNA accommodation. The resulting model of rapid standby site exploration followed by gated non-equilibrium unfolding of the 5′-UTR during accommodation provides a mechanistic understanding of how translation efficiency is governed by riboswitches and other dynamic structure motifs embedded upstream of the translation initiation site of bacterial mRNAs.
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Affiliation(s)
- Sujay Ray
- Single-Molecule Analysis Group, Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shiba S Dandpat
- Single-Molecule Analysis Group, Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Surajit Chatterjee
- Single-Molecule Analysis Group, Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nils G Walter
- Single-Molecule Analysis Group, Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
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204
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Miyoshi K, Hagita H, Horiguchi T, Tanimura A, Noma T. Redefining GBA gene structure unveils the ability of Cap-independent, IRES-dependent gene regulation. Commun Biol 2022; 5:639. [PMID: 35831491 PMCID: PMC9279297 DOI: 10.1038/s42003-022-03577-5] [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: 03/10/2020] [Accepted: 06/10/2022] [Indexed: 11/09/2022] Open
Abstract
Glucosylceramide is the primary molecule of glycosphingolipids, and its metabolic regulation is crucial for life. Defects in the catabolizing enzyme, glucocerebrosidase (GCase), cause a lysosomal storage disorder known as Gaucher disease. However, the genetic regulation of GCase has not been fully understood. Here we show the redefined structure of the GCase coding gene (GBA), and clarify the regulatory mechanisms of its transcription and translation. First, alternative uses of the two GBA gene promoters were identified in fibroblasts and HL60-derived macrophages. Intriguingly, both GBA transcripts and GCase activities were induced in macrophages but not in neutrophils. Second, we observed cap-independent translation occurs via unique internal ribosome entry site activities in first promoter-driven GBA transcripts. Third, the reciprocal expression was observed in GBA and miR22-3p versus GBAP1 transcripts before and after HL60-induced macrophage differentiation. Nevertheless, these findings clearly demonstrate novel cell-type-specific GBA gene expression regulatory mechanisms, providing new insights into GCase biology. The cell type-specific expression of the glucocerebrosidase gene, associated with the lysosomal storage disorder called Gaucher disease, is linked to cis- and trans-regulatory transcriptional and translational mechanisms.
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Affiliation(s)
- Keiko Miyoshi
- Department of Oral Bioscience, Tokushima University Graduate School of Biomedical Sciences, Tokushima, 770-8504, Japan.
| | - Hiroko Hagita
- Department of Oral Bioscience, Tokushima University Graduate School of Biomedical Sciences, Tokushima, 770-8504, Japan
| | - Taigo Horiguchi
- Department of Oral Bioscience, Tokushima University Graduate School of Biomedical Sciences, Tokushima, 770-8504, Japan
| | - Ayako Tanimura
- Division of Food & Health Sciences, Department of Environmental and Symbiotic Sciences, Faculty of Environmental and Symbiotic Sciences, Prefectural University of Kumamoto, Kumamoto, 862-8502, Japan
| | - Takafumi Noma
- Department of Nutrition and Health Promotion, Faculty of Human Life Studies, Hiroshima Jogakuin University, 4-13-1 Ushita-higashi, Higashi-ku, Hiroshima, 732-0063, Japan
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205
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Bhat VD, Jayaraj J, Babu K. RNA and neuronal function: the importance of post-transcriptional regulation. OXFORD OPEN NEUROSCIENCE 2022; 1:kvac011. [PMID: 38596700 PMCID: PMC10913846 DOI: 10.1093/oons/kvac011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/03/2022] [Accepted: 05/28/2022] [Indexed: 04/11/2024]
Abstract
The brain represents an organ with a particularly high diversity of genes that undergo post-transcriptional gene regulation through multiple mechanisms that affect RNA metabolism and, consequently, brain function. This vast regulatory process in the brain allows for a tight spatiotemporal control over protein expression, a necessary factor due to the unique morphologies of neurons. The numerous mechanisms of post-transcriptional regulation or translational control of gene expression in the brain include alternative splicing, RNA editing, mRNA stability and transport. A large number of trans-elements such as RNA-binding proteins and micro RNAs bind to specific cis-elements on transcripts to dictate the fate of mRNAs including its stability, localization, activation and degradation. Several trans-elements are exemplary regulators of translation, employing multiple cofactors and regulatory machinery so as to influence mRNA fate. Networks of regulatory trans-elements exert control over key neuronal processes such as neurogenesis, synaptic transmission and plasticity. Perturbations in these networks may directly or indirectly cause neuropsychiatric and neurodegenerative disorders. We will be reviewing multiple mechanisms of gene regulation by trans-elements occurring specifically in neurons.
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Affiliation(s)
- Vandita D Bhat
- Centre for Neuroscience, Indian Institute of Science, CV Raman Road, Bangalore 560012, Karnataka, India
| | - Jagannath Jayaraj
- Centre for Neuroscience, Indian Institute of Science, CV Raman Road, Bangalore 560012, Karnataka, India
| | - Kavita Babu
- Centre for Neuroscience, Indian Institute of Science, CV Raman Road, Bangalore 560012, Karnataka, India
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206
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Reixachs‐Solé M, Eyras E. Uncovering the impacts of alternative splicing on the proteome with current omics techniques. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1707. [PMID: 34979593 PMCID: PMC9542554 DOI: 10.1002/wrna.1707] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/27/2021] [Accepted: 11/29/2021] [Indexed: 12/15/2022]
Abstract
The high-throughput sequencing of cellular RNAs has underscored a broad effect of isoform diversification through alternative splicing on the transcriptome. Moreover, the differential production of transcript isoforms from gene loci has been recognized as a critical mechanism in cell differentiation, organismal development, and disease. Yet, the extent of the impact of alternative splicing on protein production and cellular function remains a matter of debate. Multiple experimental and computational approaches have been developed in recent years to address this question. These studies have unveiled how molecular changes at different steps in the RNA processing pathway can lead to differences in protein production and have functional effects. New and emerging experimental technologies open exciting new opportunities to develop new methods to fully establish the connection between messenger RNA expression and protein production and to further investigate how RNA variation impacts the proteome and cell function. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing Translation > Regulation RNA Evolution and Genomics > Computational Analyses of RNA.
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Affiliation(s)
- Marina Reixachs‐Solé
- The John Curtin School of Medical ResearchAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
- EMBL Australia Partner Laboratory Network and the Australian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Eduardo Eyras
- The John Curtin School of Medical ResearchAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
- EMBL Australia Partner Laboratory Network and the Australian National UniversityCanberraAustralian Capital TerritoryAustralia
- Catalan Institution for Research and Advanced StudiesBarcelonaSpain
- Hospital del Mar Medical Research Institute (IMIM)BarcelonaSpain
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207
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Simple synthesis of massively parallel RNA microarrays via enzymatic conversion from DNA microarrays. Nat Commun 2022; 13:3772. [PMID: 35773271 PMCID: PMC9246885 DOI: 10.1038/s41467-022-31370-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 06/14/2022] [Indexed: 11/20/2022] Open
Abstract
RNA catalytic and binding interactions with proteins and small molecules are fundamental elements of cellular life processes as well as the basis for RNA therapeutics and molecular engineering. In the absence of quantitative predictive capacity for such bioaffinity interactions, high throughput experimental approaches are needed to sufficiently sample RNA sequence space. Here we report on a simple and highly accessible approach to convert commercially available customized DNA microarrays of any complexity and density to RNA microarrays via a T7 RNA polymerase-mediated extension of photocrosslinked methyl RNA primers and subsequent degradation of the DNA templates. RNA microarrays have many potential applications, but are difficult to produce. Here, the AUs present a method for converting commercial, customizable DNA microarrays into RNA microarrays using an accessible three-step process involving primer photocrosslinking, extension, and template degradation.
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208
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Katsoula G, Steinberg J, Tuerlings M, Coutinho de Almeida R, Southam L, Swift D, Meulenbelt I, Wilkinson JM, Zeggini E. A molecular map of long non-coding RNA expression, isoform switching and alternative splicing in osteoarthritis. Hum Mol Genet 2022; 31:2090-2105. [PMID: 35088088 PMCID: PMC9239745 DOI: 10.1093/hmg/ddac017] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/22/2021] [Accepted: 01/10/2022] [Indexed: 11/30/2022] Open
Abstract
Osteoarthritis is a prevalent joint disease and a major cause of disability worldwide with no curative therapy. Development of disease-modifying therapies requires a better understanding of the molecular mechanisms underpinning disease. A hallmark of osteoarthritis is cartilage degradation. To define molecular events characterizing osteoarthritis at the whole transcriptome level, we performed deep RNA sequencing in paired samples of low- and high-osteoarthritis grade knee cartilage derived from 124 patients undergoing total joint replacement. We detected differential expression between low- and high-osteoarthritis grade articular cartilage for 365 genes and identified a 38-gene signature in osteoarthritis cartilage by replicating our findings in an independent dataset. We also found differential expression for 25 novel long non-coding RNA genes (lncRNAs) and identified potential lncRNA interactions with RNA-binding proteins in osteoarthritis. We assessed alterations in the relative usage of individual gene transcripts and identified differential transcript usage for 82 genes, including ABI3BP, coding for an extracellular matrix protein, AKT1S1, a negative regulator of the mTOR pathway and TPRM4, coding for a transient receptor potential channel. We further assessed genome-wide differential splicing, for the first time in osteoarthritis, and detected differential splicing for 209 genes, which were enriched for extracellular matrix, proteoglycans and integrin surface interactions terms. In the largest study of its kind in osteoarthritis, we find that isoform and splicing changes, in addition to extensive differences in both coding and non-coding sequence expression, are associated with disease and demonstrate a novel layer of genomic complexity to osteoarthritis pathogenesis.
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Affiliation(s)
- Georgia Katsoula
- Technical University of Munich (TUM), School of Medicine, Munich 81675, Germany
- Institute of Translational Genomics, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Julia Steinberg
- Institute of Translational Genomics, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg 85764, Germany
- Daffodil Centre, University of Sydney, a joint venture with Cancer Council NSW, Sydney, NSW 1340, Australia
| | - Margo Tuerlings
- Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden 2333 ZC, The Netherlands
| | - Rodrigo Coutinho de Almeida
- Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden 2333 ZC, The Netherlands
| | - Lorraine Southam
- Institute of Translational Genomics, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Diane Swift
- Department of Oncology and Metabolism, University of Sheffield, Metabolic Bone Unit, Sorby Wing Northern General Hospital Sheffield, Sheffield, S5 7AU, UK
| | - Ingrid Meulenbelt
- Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden 2333 ZC, The Netherlands
| | - J Mark Wilkinson
- Department of Oncology and Metabolism, University of Sheffield, Metabolic Bone Unit, Sorby Wing Northern General Hospital Sheffield, Sheffield, S5 7AU, UK
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg 85764, Germany
- Technical University of Munich (TUM) and Klinikum Rechts der Isar, TUM School of Medicine, Munich 81675, Germany
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209
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Basu I, Gorai B, Chandran T, Maiti PK, Hussain T. Selection of start codon during mRNA scanning in eukaryotic translation initiation. Commun Biol 2022; 5:587. [PMID: 35705698 PMCID: PMC9200866 DOI: 10.1038/s42003-022-03534-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 05/25/2022] [Indexed: 11/24/2022] Open
Abstract
Accurate and high-speed scanning and subsequent selection of the correct start codon are important events in protein synthesis. Eukaryotic mRNAs have long 5′ UTRs that are inspected for the presence of a start codon by the ribosomal 48S pre-initiation complex (PIC). However, the conformational state of the 48S PIC required for inspecting every codon is not clearly understood. Here, atomistic molecular dynamics (MD) simulations and energy calculations suggest that the scanning conformation of 48S PIC may reject all but 4 (GUG, CUG, UUG and ACG) of the 63 non-AUG codons, and initiation factor eIF1 is crucial for this discrimination. We provide insights into the possible role of initiation factors eIF1, eIF1A, eIF2α and eIF2β in scanning. Overall, the study highlights how the scanning conformation of ribosomal 48S PIC acts as a coarse selectivity checkpoint for start codon selection and scans long 5′ UTRs in eukaryotic mRNAs with accuracy and high speed. Molecular simulations of start codon selection by the eukaryotic ribosome during mRNA scanning provide further insight into high speed of scanning and how initiation factors contribute toward codon-anticodon-ribosome network stability.
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Affiliation(s)
- Ipsita Basu
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, 560012, India
| | - Biswajit Gorai
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, 560012, India.,Department of Chemical Engineering, University of New Hampshire, Durham, NH-03824, USA
| | - Thyageshwar Chandran
- Department of Molecular Reproduction, Development and Genetics, Division of Biological Sciences, Indian Institute of Science, Bangalore, 560012, India.,Department of Biotechnology, National Institute of Technology-Warangal, Telangana, 506004, India
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, 560012, India.
| | - Tanweer Hussain
- Department of Molecular Reproduction, Development and Genetics, Division of Biological Sciences, Indian Institute of Science, Bangalore, 560012, India.
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210
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Friedrich D, Marintchev A, Arthanari H. The metaphorical swiss army knife: The multitude and diverse roles of HEAT domains in eukaryotic translation initiation. Nucleic Acids Res 2022; 50:5424-5442. [PMID: 35552740 PMCID: PMC9177959 DOI: 10.1093/nar/gkac342] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/20/2022] [Accepted: 04/22/2022] [Indexed: 11/24/2022] Open
Abstract
Biomolecular associations forged by specific interaction among structural scaffolds are fundamental to the control and regulation of cell processes. One such structural architecture, characterized by HEAT repeats, is involved in a multitude of cellular processes, including intracellular transport, signaling, and protein synthesis. Here, we review the multitude and versatility of HEAT domains in the regulation of mRNA translation initiation. Structural and cellular biology approaches, as well as several biophysical studies, have revealed that a number of HEAT domain-mediated interactions with a host of protein factors and RNAs coordinate translation initiation. We describe the basic structural architecture of HEAT domains and briefly introduce examples of the cellular processes they dictate, including nuclear transport by importin and RNA degradation. We then focus on proteins in the translation initiation system featuring HEAT domains, specifically the HEAT domains of eIF4G, DAP5, eIF5, and eIF2Bϵ. Comparative analysis of their remarkably versatile interactions, including protein-protein and protein-RNA recognition, reveal the functional importance of flexible regions within these HEAT domains. Here we outline how HEAT domains orchestrate fundamental aspects of translation initiation and highlight open mechanistic questions in the area.
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Affiliation(s)
- Daniel Friedrich
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Assen Marintchev
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, MA, USA
| | - Haribabu Arthanari
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
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211
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Engineering nonphotosynthetic carbon fixation for production of bioplastics by methanogenic archaea. Proc Natl Acad Sci U S A 2022; 119:e2118638119. [PMID: 35639688 DOI: 10.1073/pnas.2118638119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SignificanceBiological carbon fixation provides opportunities to directly utilize CO2 to synthesize a broad range of value-added compounds, potentially displacing petroleum feedstock use in industry. Chemoautotrophs are particularly interesting as their carbon fixation can be driven chemically by renewable H2 in place of light, which can limit industrial fermentation of photosynthetic organisms. We describe the development of a methanogenic host, Methanococcus maripaludis, for metabolic engineering. Since redox cofactors used in upstream archaeal carbon fixation pathways are orthogonal to typical downstream biosynthetic pathways, it was necessary to engineer both NADH biosynthesis and turnover. In doing so, we are able to show that methanogenic archaea can, indeed, serve as a platform for the high-yield production of bioplastics and monomers from CO2 and H2.
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212
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Arango D, Sturgill D, Yang R, Kanai T, Bauer P, Roy J, Wang Z, Hosogane M, Schiffers S, Oberdoerffer S. Direct epitranscriptomic regulation of mammalian translation initiation through N4-acetylcytidine. Mol Cell 2022; 82:2797-2814.e11. [PMID: 35679869 PMCID: PMC9361928 DOI: 10.1016/j.molcel.2022.05.016] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 03/14/2022] [Accepted: 05/12/2022] [Indexed: 12/14/2022]
Abstract
mRNA function is influenced by modifications that modulate canonical nucleobase behavior. We show that a single modification mediates distinct impacts on mRNA translation in a position-dependent manner. Although cytidine acetylation (ac4C) within protein-coding sequences stimulates translation, ac4C within 5' UTRs impacts protein synthesis at the level of initiation. 5' UTR acetylation promotes initiation at upstream sequences, competitively inhibiting annotated start codons. Acetylation further directly impedes initiation at optimal AUG contexts: ac4C within AUG-flanking Kozak sequences reduced initiation in base-resolved transcriptome-wide HeLa results and in vitro utilizing substrates with site-specific ac4C incorporation. Cryo-EM of mammalian 80S initiation complexes revealed that ac4C in the -1 position adjacent to an AUG start codon disrupts an interaction between C and hypermodified t6A at nucleotide 37 of the initiator tRNA. These findings demonstrate the impact of RNA modifications on nucleobase function at a molecular level and introduce mRNA acetylation as a factor regulating translation in a location-specific manner.
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Affiliation(s)
- Daniel Arango
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - David Sturgill
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Renbin Yang
- Center for Molecular Microscopy, Frederick National Laboratory for Cancer Research, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD 21701, USA
| | - Tapan Kanai
- Center for Molecular Microscopy, Frederick National Laboratory for Cancer Research, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD 21701, USA
| | - Paulina Bauer
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jyoti Roy
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Ziqiu Wang
- Center for Molecular Microscopy, Frederick National Laboratory for Cancer Research, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD 21701, USA
| | - Masaki Hosogane
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sarah Schiffers
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Shalini Oberdoerffer
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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213
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Qureischi M, Mohr J, Arellano-Viera E, Knudsen SE, Vohidov F, Garitano-Trojaola A. mRNA-based therapies: Preclinical and clinical applications. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2022; 372:1-54. [PMID: 36064262 DOI: 10.1016/bs.ircmb.2022.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
At the fundamental level, messenger RNA (mRNA)-based therapeutics involves the delivery of in vitro-transcribed (IVT) mRNA into the cytoplasm of a target cell, where it is translated into the desired protein. IVT mRNA presents various advantages compared to DNA and recombinant protein-based approaches that make it ideal for a broad range of therapeutic applications. IVT mRNA, which is translated in the cytoplasm after transfection into cells, can encode virtually any target protein. Notably, it does not enter the nucleus, which avoids its integration into the genome and the risk of insertional mutagenesis. The large-scale production of IVT mRNA is less complex than production of recombinant proteins, and Good Manufacturing Practice-compliant mRNA production is easily scalable, ideally poising mRNA for not only off-the-shelf, but more personalized treatment approaches. IVT mRNA's safety profile, pharmacokinetics, and pharmacodynamics, including its inherent immunostimulatory capacity, can be optimized for different therapeutic applications by harnessing a wide array of optimized sequence elements, chemical modifications, purification techniques, and delivery methods. The value of IVT mRNA was recently proved during the COVID-19 pandemic when mRNA-based vaccines outperformed the efficacy of established technologies, and millions of doses were rapidly deployed. In this review, we will discuss chemical modifications of IVT mRNA and highlight numerous preclinical and clinical applications including vaccines for cancer and infectious diseases, cancer immunotherapy, protein replacement, gene editing, and cell reprogramming.
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214
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Tian C, Zhang Y, Li J, Wang Y. Benchmarking Intrinsic Promoters and Terminators for Plant Synthetic Biology Research. BIODESIGN RESEARCH 2022; 2022:9834989. [PMID: 37850139 PMCID: PMC10521690 DOI: 10.34133/2022/9834989] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 05/11/2022] [Indexed: 10/19/2023] Open
Abstract
The emerging plant synthetic metabolic engineering has been exhibiting great promise to produce either value-added metabolites or therapeutic proteins. However, promoters for plant pathway engineering are generally selected empirically. The quantitative characterization of plant-based promoters is essential for optimal control of gene expression in plant chassis. Here, we used N. benthamiana leaves and BY2 suspension cells to quantitatively characterize a library of plant promoters by transient expression of firefly/Renilla luciferase. We validated the dual-luciferase reporter system by examining the correlation between reporter protein and mRNA levels. In addition, we investigated the effects of terminator-promoter combinations on gene expression and found that the combinations of promoters and terminators resulted in a 326-fold difference between the strongest and weakest performance, as reflected in reporter gene expression. As a proof of concept, we used the quantitatively characterized promoters to engineer the betalain pathway in N. benthamiana. Seven selected plant promoters with different expression strengths were used orthogonally to express CYP76AD1 and DODA, resulting in a final betalain production range of 6.0-362.4 μg/g fresh weight. Our systematic approach not only demonstrates the various intensities of multiple promoter sequences in N. benthamiana and BY2 cells but also adds to the toolbox of plant promoters for plant engineering.
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Affiliation(s)
- Chenfei Tian
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yixin Zhang
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
| | - Jianhua Li
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yong Wang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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215
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Swaminathan J, Maegawa S, Shaik S, Sharma A, Bravo-Alegria J, Guo L, Xu L, Harmanci A, Gopalakrishnan V. Cross-Talk Between Histone Methyltransferases and Demethylases Regulate REST Transcription During Neurogenesis. Front Oncol 2022; 12:855167. [PMID: 35600406 PMCID: PMC9120943 DOI: 10.3389/fonc.2022.855167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/29/2022] [Indexed: 11/13/2022] Open
Abstract
The RE1 Silencing Transcription Factor (REST) is a major regulator of neurogenesis and brain development. Medulloblastoma (MB) is a pediatric brain cancer characterized by a blockade of neuronal specification. REST gene expression is aberrantly elevated in a subset of MBs that are driven by constitutive activation of sonic hedgehog (SHH) signaling in cerebellar granular progenitor cells (CGNPs), the cells of origin of this subgroup of tumors. To understand its transcriptional deregulation in MBs, we first studied control of Rest gene expression during neuronal differentiation of normal mouse CGNPs. Higher Rest expression was observed in proliferating CGNPs compared to differentiating neurons. Interestingly, two Rest isoforms were expressed in CGNPs, of which only one showed a significant reduction in expression during neurogenesis. In proliferating CGNPs, higher MLL4 and KDM7A activities opposed by the repressive polycomb repressive complex 2 (PRC2) and the G9A/G9A-like protein (GLP) complex function allowed Rest homeostasis. During differentiation, reduction in MLL4 enrichment on chromatin, in conjunction with an increase in PRC2/G9A/GLP/KDM7A activities promoted a decline in Rest expression. These findings suggest a lineage-context specific paradoxical role for KDM7A in the regulation of Rest expression in CGNPs. In human SHH-MBs (SHH-α and SHH-β) where elevated REST gene expression is associated with poor prognosis, up- or downregulation of KDM7A caused a significant worsening in patient survival. Our studies are the first to implicate KDM7A in REST regulation and in MB biology.
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Affiliation(s)
- Jyothishmathi Swaminathan
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| | - Shinji Maegawa
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| | - Shavali Shaik
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| | - Ajay Sharma
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| | - Javiera Bravo-Alegria
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| | - Lei Guo
- Quantitative Biomedical Research Center, Department of Population & Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Lin Xu
- Quantitative Biomedical Research Center, Department of Population & Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Arif Harmanci
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center, Houston, TX, United States
| | - Vidya Gopalakrishnan
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
- Department of Molecular and Cellular Oncology, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
- Brain Tumor Center - University of Texas, MD Anderson Cancer Center, Houston, TX, United States
- Center for Cancer Epigenetics - University of Texas, MD Anderson Cancer Center, Houston, TX, United States
- MD Anderson-UTHealth Science Center Graduate School of Biomedical Sciences, Houston, TX, United States
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216
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Liu J, Huang T, Chen W, Ding C, Zhao T, Zhao X, Cai B, Zhang Y, Li S, Zhang L, Xue M, He X, Ge W, Zhou C, Xu Y, Zhang R. Developmental mRNA m 5C landscape and regulatory innovations of massive m 5C modification of maternal mRNAs in animals. Nat Commun 2022; 13:2484. [PMID: 35513466 PMCID: PMC9072368 DOI: 10.1038/s41467-022-30210-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 04/06/2022] [Indexed: 11/09/2022] Open
Abstract
m5C is one of the longest-known RNA modifications, however, its developmental dynamics, functions, and evolution in mRNAs remain largely unknown. Here, we generate quantitative mRNA m5C maps at different stages of development in 6 vertebrate and invertebrate species and find convergent and unexpected massive methylation of maternal mRNAs mediated by NSUN2 and NSUN6. Using Drosophila as a model, we reveal that embryos lacking maternal mRNA m5C undergo cell cycle delays and fail to timely initiate maternal-to-zygotic transition, implying the functional importance of maternal mRNA m5C. From invertebrates to the lineage leading to humans, two waves of m5C regulatory innovations are observed: higher animals gain cis-directed NSUN2-mediated m5C sites at the 5' end of the mRNAs, accompanied by the emergence of more structured 5'UTR regions; humans gain thousands of trans-directed NSUN6-mediated m5C sites enriched in genes regulating the mitotic cell cycle. Collectively, our studies highlight the existence and regulatory innovations of a mechanism of early embryonic development and provide key resources for elucidating the role of mRNA m5C in biology and disease. mRNAs are known to be decorated with m5C at a low-to-medium level. Here, the authors generate atlases of mRNA m5C during animal development in 6 species and identify convergent and unexpected massive methylation of maternal mRNAs by NSUN2 and NSUN6.
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Affiliation(s)
- Jianheng Liu
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Tao Huang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Wanying Chen
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Chenhui Ding
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Center for Reproductive Medicine and Department of Gynecology & Obstetrics, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China
| | - Tianxuan Zhao
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Xueni Zhao
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Bing Cai
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Center for Reproductive Medicine and Department of Gynecology & Obstetrics, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China
| | - Yusen Zhang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Song Li
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Center for Reproductive Medicine and Department of Gynecology & Obstetrics, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China
| | - Ling Zhang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Maoguang Xue
- Division of Human Reproduction and Developmental Genetics, Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China.,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China
| | - Xiuju He
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Wanzhong Ge
- Division of Human Reproduction and Developmental Genetics, Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China. .,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China. .,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Canquan Zhou
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Center for Reproductive Medicine and Department of Gynecology & Obstetrics, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China.
| | - Yanwen Xu
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Center for Reproductive Medicine and Department of Gynecology & Obstetrics, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China.
| | - Rui Zhang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China.
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217
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Gorbovytska V, Kim SK, Kuybu F, Götze M, Um D, Kang K, Pittroff A, Brennecke T, Schneider LM, Leitner A, Kim TK, Kuhn CD. Enhancer RNAs stimulate Pol II pause release by harnessing multivalent interactions to NELF. Nat Commun 2022; 13:2429. [PMID: 35508485 PMCID: PMC9068813 DOI: 10.1038/s41467-022-29934-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/24/2022] [Indexed: 12/12/2022] Open
Abstract
Enhancer RNAs (eRNAs) are long non-coding RNAs that originate from enhancers. Although eRNA transcription is a canonical feature of activated enhancers, the molecular features required for eRNA function and the mechanism of how eRNAs impinge on target gene transcription have not been established. Thus, using eRNA-dependent RNA polymerase II (Pol II) pause release as a model, we here investigate the requirement of sequence, structure and length of eRNAs for their ability to stimulate Pol II pause release by detaching NELF from paused Pol II. We find eRNAs not to exert their function through common structural or sequence motifs. Instead, eRNAs that exhibit a length >200 nucleotides and that contain unpaired guanosines make multiple, allosteric contacts with NELF subunits -A and -E to trigger efficient NELF release. By revealing the molecular determinants of eRNA function, our study establishes eRNAs as an important player in Pol II pause release, and it provides new insight into the regulation of metazoan transcription.
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Affiliation(s)
- Vladyslava Gorbovytska
- RNA Biochemistry, University of Bayreuth, Universitätsstrasse 30, 95447, Bayreuth, Germany
| | - Seung-Kyoon Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, 37673, Republic of Korea.,Department of Convergent Bioscience and Informatics, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Filiz Kuybu
- RNA Biochemistry, University of Bayreuth, Universitätsstrasse 30, 95447, Bayreuth, Germany
| | - Michael Götze
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093, Zurich, Switzerland
| | - Dahun Um
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Keunsoo Kang
- Department of Microbiology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Andreas Pittroff
- RNA Biochemistry, University of Bayreuth, Universitätsstrasse 30, 95447, Bayreuth, Germany
| | - Theresia Brennecke
- RNA Biochemistry, University of Bayreuth, Universitätsstrasse 30, 95447, Bayreuth, Germany
| | - Lisa-Marie Schneider
- RNA Biochemistry, University of Bayreuth, Universitätsstrasse 30, 95447, Bayreuth, Germany
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093, Zurich, Switzerland
| | - Tae-Kyung Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, 37673, Republic of Korea. .,Institute of Convergence Science, Yonsei University, Seoul, 03722, Republic of Korea.
| | - Claus-D Kuhn
- RNA Biochemistry, University of Bayreuth, Universitätsstrasse 30, 95447, Bayreuth, Germany.
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218
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Synthetic RNA-based post-transcriptional expression control methods and genetic circuits. Adv Drug Deliv Rev 2022; 184:114196. [PMID: 35288218 DOI: 10.1016/j.addr.2022.114196] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/27/2022] [Accepted: 03/08/2022] [Indexed: 12/19/2022]
Abstract
RNA-based synthetic genetic circuits provide an alternative for traditional transcription-based circuits in applications where genomic integration is to be avoided. Incorporating various post-transcriptional control methods into such circuits allows for controlling the behaviour of the circuit through the detection of certain biomolecular inputs or reconstituting defined circuit behaviours, thus manipulating cellular functions. In this review, recent developments of various types of post-transcriptional control methods in mammalian cells are discussed as well as auxiliary components that allow for the creation and development of mRNA-based switches. How such post-transcriptional switches are combined into synthetic circuits as well as their applications in biomedical and preclinical settings are also described. Finally, we examine the challenges that need to be surmounted before RNA-based synthetic circuits can be reliably deployed into clinical settings.
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219
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Bioinformatics Analysis of the Interaction of miRNAs and piRNAs with Human mRNA Genes Having di- and Trinucleotide Repeats. Genes (Basel) 2022; 13:genes13050800. [PMID: 35627185 PMCID: PMC9141802 DOI: 10.3390/genes13050800] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 02/04/2023] Open
Abstract
The variability of nucleotide repeats is considered one of the causes of diseases, but their biological function is not understood. In recent years, the interaction of miRNAs and piRNAs with the mRNAs of genes responsible for developing neurodegenerative and oncological diseases and diabetes have been actively studied. We explored candidate genes with nucleotide repeats to predict associations with miRNAs and piRNAs. The parameters of miRNAs and piRNA binding sites with mRNAs of human genes having nucleotide repeats were determined using the MirTarget program. This program defines the start of the initiation of miRNA and piRNA binding to mRNAs, the localization of miRNA and piRNA binding sites in the 5′-untranslated region (5′UTR), coding sequence (CDS) and 3′-untranslated region (3′UTR); the free energy of binding; and the schemes of nucleotide interactions of miRNAs and piRNAs with mRNAs. The characteristics of miRNAs and piRNA binding sites with mRNAs of 73 human genes were determined. The 5′UTR, 3′UTR and CDS of the mRNAs of genes are involved in the development of neurodegenerative, oncological and diabetes diseases with GU, AC dinucleotide and CCG, CAG, GCC, CGG, CGC trinucleotide repeats. The associations of miRNAs, piRNAs and candidate target genes could be recommended for developing methods for diagnosing diseases, including neurodegenerative diseases, oncological diseases and diabetes.
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220
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Chuang ST, Conklin B, Stein JB, Pan G, Lee KB. Nanotechnology-enabled immunoengineering approaches to advance therapeutic applications. NANO CONVERGENCE 2022; 9:19. [PMID: 35482149 PMCID: PMC9047473 DOI: 10.1186/s40580-022-00310-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/12/2022] [Indexed: 05/24/2023]
Abstract
Immunotherapy has reached clinical success in the last decade, with the emergence of new and effective treatments such as checkpoint blockade therapy and CAR T-cell therapy that have drastically improved patient outcomes. Still, these therapies can be improved to limit off-target effects, mitigate systemic toxicities, and increase overall efficacies. Nanoscale engineering offers strategies that enable researchers to attain these goals through the manipulation of immune cell functions, such as enhancing immunity against cancers and pathogens, controlling the site of immune response, and promoting tolerance via the delivery of small molecule drugs or biologics. By tuning the properties of the nanomaterials, such as size, shape, charge, and surface chemistry, different types of immune cells can be targeted and engineered, such as dendritic cells for immunization, or T cells for promoting adaptive immunity. Researchers have come to better understand the critical role the immune system plays in the progression of pathologies besides cancer, and developing nanoengineering approaches that seek to harness the potential of immune cell activities can lead to favorable outcomes for the treatment of injuries and diseases.
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Affiliation(s)
- Skylar T Chuang
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Brandon Conklin
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Joshua B Stein
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - George Pan
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Ki-Bum Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA.
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221
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Kovalski JR, Kuzuoglu‐Ozturk D, Ruggero D. Protein synthesis control in cancer: selectivity and therapeutic targeting. EMBO J 2022; 41:e109823. [PMID: 35315941 PMCID: PMC9016353 DOI: 10.15252/embj.2021109823] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 12/10/2021] [Accepted: 12/16/2021] [Indexed: 11/09/2022] Open
Abstract
Translational control of mRNAs is a point of convergence for many oncogenic signals through which cancer cells tune protein expression in tumorigenesis. Cancer cells rely on translational control to appropriately adapt to limited resources while maintaining cell growth and survival, which creates a selective therapeutic window compared to non-transformed cells. In this review, we first discuss how cancer cells modulate the translational machinery to rapidly and selectively synthesize proteins in response to internal oncogenic demands and external factors in the tumor microenvironment. We highlight the clinical potential of compounds that target different translation factors as anti-cancer therapies. Next, we detail how RNA sequence and structural elements interface with the translational machinery and RNA-binding proteins to coordinate the translation of specific pro-survival and pro-growth programs. Finally, we provide an overview of the current and emerging technologies that can be used to illuminate the mechanisms of selective translational control in cancer cells as well as within the microenvironment.
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Affiliation(s)
- Joanna R Kovalski
- Helen Diller Family Comprehensive Cancer CenterUniversity of California, San FranciscoSan FranciscoCAUSA
- Department of UrologyUniversity of California, San FranciscoSan FranciscoCAUSA
| | - Duygu Kuzuoglu‐Ozturk
- Helen Diller Family Comprehensive Cancer CenterUniversity of California, San FranciscoSan FranciscoCAUSA
- Department of UrologyUniversity of California, San FranciscoSan FranciscoCAUSA
| | - Davide Ruggero
- Helen Diller Family Comprehensive Cancer CenterUniversity of California, San FranciscoSan FranciscoCAUSA
- Department of UrologyUniversity of California, San FranciscoSan FranciscoCAUSA
- Department of Cellular and Molecular PharmacologyUniversity of California, San FranciscoSan FranciscoCAUSA
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222
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Li D, Yang J, Huang X, Zhou H, Wang J. eIF4A2 targets developmental potency and histone H3.3 transcripts for translational control of stem cell pluripotency. SCIENCE ADVANCES 2022; 8:eabm0478. [PMID: 35353581 PMCID: PMC8967233 DOI: 10.1126/sciadv.abm0478] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Translational control has emerged as a fundamental regulatory layer of proteome complexity that governs cellular identity and functions. As initiation is the rate-limiting step of translation, we carried out an RNA interference screen for key translation initiation factors required to maintain embryonic stem cell (ESC) identity. We identified eukaryotic translation initiation factor 4A2 (eIF4A2) and defined its mechanistic action through ribosomal protein S26-independent and -dependent ribosomes in translation initiation activation of messenger RNAs (mRNAs) encoding pluripotency factors and the histone variant H3.3 with demonstrated roles in maintaining stem cell pluripotency. eIF4A2 also mediates translation initiation activation of Ddx6, which acts together with eIF4A2 to restrict the totipotent two-cell transcription program in ESCs through Zscan4 mRNA degradation and translation repression. Accordingly, knockdown of eIF4A2 disrupts ESC proteome, causing the loss of ESC identity. Collectively, we establish a translational paradigm of the protein synthesis of pluripotency transcription factors and epigenetic regulators imposed on their established roles in controlling pluripotency.
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Affiliation(s)
- Dan Li
- Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jihong Yang
- Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Xin Huang
- Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Hongwei Zhou
- Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jianlong Wang
- Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
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223
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Garbuglia AR, Minosse C, Del Porto P. mRNA- and Adenovirus-Based Vaccines against SARS-CoV-2 in HIV-Positive People. Viruses 2022; 14:v14040748. [PMID: 35458478 PMCID: PMC9031858 DOI: 10.3390/v14040748] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 03/29/2022] [Accepted: 03/29/2022] [Indexed: 12/14/2022] Open
Abstract
About two years have passed since the identification of SARS-CoV-2 in China. The rapid spread of this virus all over the world and its high transmissibility and pathogenicity in humans have resulted in a global pandemic. The negative impact of COVID-19 on health, society and the economy at the global level has pushed researchers and pharmaceutical companies to develop effective vaccines to fight SARS-CoV-2. Thanks to this collaborative effort, the first COVID-19 vaccine was developed in less than a year. Since then, several COVID-19 vaccines have been validated for use by the World Health Organization. Among these, mRNA- (BNT162b2 and mRNA1273) and adenovirus-based (ChAdOx1) vaccines were developed through the use of novel technologies. While all three of these vaccines have shown effectiveness against the COVID-19 disease and their immunogenicity was characterized in clinical trials in the general population, data on their efficacy and immunogenicity in people living with HIV (PLWH) are limited. In this review, we provide a description of the characteristics of mRNA- and adenovirus-based vaccines and of the immune response elicited in the general population by vaccination. Then we describe the use of these vaccines and their efficacy and immunogenicity in people living with HIV and we conclude with a discussion regarding some open questions concerning the use of mRNA- and adenovirus-based COVID-19 vaccines in PLWH.
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Affiliation(s)
- Anna Rosa Garbuglia
- Laboratory of Virology, “Lazzaro Spallanzani” National Institute for Infectious Diseases, IRCCS, 00149 Rome, Italy;
- Correspondence:
| | - Claudia Minosse
- Laboratory of Virology, “Lazzaro Spallanzani” National Institute for Infectious Diseases, IRCCS, 00149 Rome, Italy;
| | - Paola Del Porto
- Department of Biology and Biotechnology ‘C. Darwin’, Sapienza University, 00100 Rome, Italy;
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224
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Wang R, Amoyel M. mRNA Translation Is Dynamically Regulated to Instruct Stem Cell Fate. Front Mol Biosci 2022; 9:863885. [PMID: 35433828 PMCID: PMC9008482 DOI: 10.3389/fmolb.2022.863885] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 02/25/2022] [Indexed: 12/12/2022] Open
Abstract
Stem cells preserve tissue homeostasis by replacing the cells lost through damage or natural turnover. Thus, stem cells and their daughters can adopt two identities, characterized by different programs of gene expression and metabolic activity. The composition and regulation of these programs have been extensively studied, particularly by identifying transcription factor networks that define cellular identity and the epigenetic changes that underlie the progressive restriction in gene expression potential. However, there is increasing evidence that post-transcriptional mechanisms influence gene expression in stem cells and their progeny, in particular through the control of mRNA translation. Here, we review the described roles of translational regulation in controlling all aspects of stem cell biology, from the decision to enter or exit quiescence to maintaining self-renewal and promoting differentiation. We focus on mechanisms controlling global translation rates in cells, mTOR signaling, eIF2ɑ phosphorylation, and ribosome biogenesis and how they allow stem cells to rapidly change their gene expression in response to tissue needs or environmental changes. These studies emphasize that translation acts as an additional layer of control in regulating gene expression in stem cells and that understanding this regulation is critical to gaining a full understanding of the mechanisms that underlie fate decisions in stem cells.
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Affiliation(s)
| | - Marc Amoyel
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
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225
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Epigenetic regulation of EIF4A1 through DNA methylation and an oncogenic role of eIF4A1 through BRD2 signaling in prostate cancer. Oncogene 2022; 41:2778-2785. [PMID: 35361883 PMCID: PMC9215223 DOI: 10.1038/s41388-022-02272-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 02/21/2022] [Accepted: 03/08/2022] [Indexed: 01/10/2023]
Abstract
In prostate cancers, elongation initiation factor 4A1 (eIF4A1) supports an oncogenic translation program and is highly expressed, but its role remains elusive. By use of human specimens and cell models, we addressed the role of eIF4A1 in prostate cancer in vitro and in vivo. EIF4A1 expression, as determined by mRNA and protein levels, was higher in primary prostate cancers relative to normal prostate tissue. Also, for primary prostate cancers, elevated mRNA levels of EIF4A1 correlated with DNA hypomethylation levels in the CpG-rich island of EIF4A1. Using a DNMT3a CRISPR-Cas9-based tool for specific targeting of DNA methylation, we characterized, in human prostate cancer cells, the epigenetic regulation of EIF4A1 transcripts through DNA methylation in the CpG-rich island of EIF4A1. Next, we investigated the oncogenic effect of EIF4A1 on cancer cell proliferation in vitro and tumor growth in vivo. For prostate cancer cells, EIF4A1 heterozygous knockout or knockdown inhibited protein translation and tumor growth. In addition, using RNA immunoprecipitation with RNA sequencing, we discovered the eIF4A1-mediated translational regulation of the oncogene BRD2, which contains the most enriched eIF4A1-binding motifs in its 5’ untranslated region, establishing an eIF4A1-BRD2 axis for oncogenic translation. Finally, we found a positive correlation between expression levels of eIF4A1 and BRD2 in primary prostate cancers. Our results demonstrate, for prostate cancer cells, epigenetic regulation of EIF4A1 transcripts through DNA methylation and an oncogenic roles of eIF4A1 through BRD2 signaling.
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226
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Millette MM, Holland ED, Tenpas TJ, Dent EW. A Single Transcript Knockdown-Replacement Strategy Employing 5' UTR Secondary Structures to Precisely Titrate Rescue Protein Translation. Front Genome Ed 2022; 4:803375. [PMID: 35419562 PMCID: PMC8995503 DOI: 10.3389/fgeed.2022.803375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/31/2022] [Indexed: 11/16/2022] Open
Abstract
One overarching goal of gene therapy is the replacement of faulty genes with functional ones. A significant hurdle is presented by the fact that under- or over-expression of a protein may cause disease as readily as coding mutations. There is a clear and present need for pipelines to translate experimentally validated gene therapy strategies to clinical application. To address this we developed a modular, single-transgene expression system for replacing target genes with physiologically expressed variants. In order to accomplish this, we first designed a range of 5' UTR "attenuator" sequences which predictably diminish translation of the paired gene. These sequences provide wide general utility by allowing control over translation from high expression, ubiquitous promoters. Importantly, we demonstrate that this permits an entirely novel knockdown and rescue application by pairing microRNA-adapted shRNAs alongside their respective replacement gene on a single transcript. A noteworthy candidate for this corrective approach is the degenerative and uniformly fatal motor neuron disease ALS. A strong proportion of non-idiopathic ALS cases are caused by varied mutations to the SOD1 gene, and as clinical trials to treat ALS are being initiated, it is important to consider that loss-of-function mechanisms contribute to its pathology as strongly as any other factor. As a generalized approach to treat monogenic diseases caused by heterogeneous mutations, we demonstrate complete and predictable control over replacement of SOD1 in stable cell lines by varying the strength of attenuators.
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Affiliation(s)
- Matthew M. Millette
- Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin, Madison, WI, United States
- Neuroscience Training Program, University of Wisconsin, Madison, WI, United States
| | - Elizabeth D. Holland
- Neuroscience Training Program, University of Wisconsin, Madison, WI, United States
| | - Tanner J. Tenpas
- Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin, Madison, WI, United States
| | - Erik W. Dent
- Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin, Madison, WI, United States
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227
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Ross EM, Sanjana H, Nguyen LT, Cheng Y, Moore SS, Hayes BJ. Extensive Variation in Gene Expression is Revealed in 13 Fertility-Related Genes Using RNA-Seq, ISO-Seq, and CAGE-Seq From Brahman Cattle. Front Genet 2022; 13:784663. [PMID: 35401673 PMCID: PMC8990236 DOI: 10.3389/fgene.2022.784663] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
Fertility is a key driver of economic profitability in cattle production. A number of studies have identified genes associated with fertility using genome wide association studies and differential gene expression analysis; however, the genes themselves are poorly characterized in cattle. Here, we selected 13 genes from the literature which have previously been shown to have strong evidence for an association with fertility in Brahman cattle (Bos taurus indicus) or closely related breeds. We examine the expression variation of the 13 genes that are associated with cattle fertility using RNA-seq, CAGE-seq, and ISO-seq data from 11 different tissue samples from an adult Brahman cow and a Brahman fetus. Tissues examined include blood, liver, lung, kidney, muscle, spleen, ovary, and uterus from the cow and liver and lung from the fetus. The analysis revealed several novel isoforms, including seven from SERPINA7. The use of three expression characterization methodologies (5′ cap selected ISO-seq, CAGE-seq, and RNA-seq) allowed the identification of isoforms that varied in their length of 5′ and 3′ untranslated regions, variation otherwise undetectable (collapsed as degraded RNA) in generic isoform identification pipelines. The combinations of different sequencing technologies allowed us to overcome the limitations of relatively low sequence depth in the ISO-seq data. The lower sequence depth of the ISO-seq data was also reflected in the lack of observed expression of some genes that were observed in the CAGE-seq and RNA-seq data from the same tissue. We identified allele specific expression that was tissue-specific in AR, IGF1, SOX9, STAT3, and TAF9B. Finally, we characterized an exon of TAF9B as partially nested within the neighboring gene phosphoglycerate kinase 1. As this study only examined two animals, even more transcriptional variation may be present in a genetically diverse population. This analysis reveals the large amount of transcriptional variation within mammalian fertility genes and illuminates the fact that the transcriptional landscape cannot be fully characterized using a single technology alone.
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Affiliation(s)
- Elizabeth M. Ross
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
- *Correspondence: Elizabeth M. Ross,
| | - Hari Sanjana
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Loan T. Nguyen
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - YuanYuan Cheng
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Stephen S. Moore
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Ben J. Hayes
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
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228
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Fang E, Liu X, Li M, Zhang Z, Song L, Zhu B, Wu X, Liu J, Zhao D, Li Y. Advances in COVID-19 mRNA vaccine development. Signal Transduct Target Ther 2022; 7:94. [PMID: 35322018 PMCID: PMC8940982 DOI: 10.1038/s41392-022-00950-y] [Citation(s) in RCA: 186] [Impact Index Per Article: 93.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/10/2022] [Accepted: 03/03/2022] [Indexed: 12/15/2022] Open
Abstract
To date, the coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has determined 399,600,607 cases and 5,757,562 deaths worldwide. COVID-19 is a serious threat to human health globally. The World Health Organization (WHO) has declared COVID-19 pandemic a major public health emergency. Vaccination is the most effective and economical intervention for controlling the spread of epidemics, and consequently saving lives and protecting the health of the population. Various techniques have been employed in the development of COVID-19 vaccines. Among these, the COVID-19 messenger RNA (mRNA) vaccine has been drawing increasing attention owing to its great application prospects and advantages, which include short development cycle, easy industrialization, simple production process, flexibility to respond to new variants, and the capacity to induce better immune response. This review summarizes current knowledge on the structural characteristics, antigen design strategies, delivery systems, industrialization potential, quality control, latest clinical trials and real-world data of COVID-19 mRNA vaccines as well as mRNA technology. Current challenges and future directions in the development of preventive mRNA vaccines for major infectious diseases are also discussed.
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Affiliation(s)
- Enyue Fang
- National Institute for Food and Drug Control, Beijing, 102629, China
- Wuhan Institute of Biological Products, Co., Ltd., Wuhan, 430207, China
| | - Xiaohui Liu
- National Institute for Food and Drug Control, Beijing, 102629, China
| | - Miao Li
- National Institute for Food and Drug Control, Beijing, 102629, China
| | - Zelun Zhang
- National Institute for Food and Drug Control, Beijing, 102629, China
| | - Lifang Song
- National Institute for Food and Drug Control, Beijing, 102629, China
| | - Baiyu Zhu
- Texas A&M University, College Station, TX, 77843, USA
| | - Xiaohong Wu
- National Institute for Food and Drug Control, Beijing, 102629, China
| | - Jingjing Liu
- National Institute for Food and Drug Control, Beijing, 102629, China
| | - Danhua Zhao
- National Institute for Food and Drug Control, Beijing, 102629, China
| | - Yuhua Li
- National Institute for Food and Drug Control, Beijing, 102629, China.
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229
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Leppek K, Byeon GW, Kladwang W, Wayment-Steele HK, Kerr CH, Xu AF, Kim DS, Topkar VV, Choe C, Rothschild D, Tiu GC, Wellington-Oguri R, Fujii K, Sharma E, Watkins AM, Nicol JJ, Romano J, Tunguz B, Diaz F, Cai H, Guo P, Wu J, Meng F, Shi S, Participants E, Dormitzer PR, Solórzano A, Barna M, Das R. Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics. Nat Commun 2022; 13:1536. [PMID: 35318324 PMCID: PMC8940940 DOI: 10.1038/s41467-022-28776-w] [Citation(s) in RCA: 99] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 02/07/2022] [Indexed: 02/07/2023] Open
Abstract
Therapeutic mRNAs and vaccines are being developed for a broad range of human diseases, including COVID-19. However, their optimization is hindered by mRNA instability and inefficient protein expression. Here, we describe design principles that overcome these barriers. We develop an RNA sequencing-based platform called PERSIST-seq to systematically delineate in-cell mRNA stability, ribosome load, as well as in-solution stability of a library of diverse mRNAs. We find that, surprisingly, in-cell stability is a greater driver of protein output than high ribosome load. We further introduce a method called In-line-seq, applied to thousands of diverse RNAs, that reveals sequence and structure-based rules for mitigating hydrolytic degradation. Our findings show that highly structured "superfolder" mRNAs can be designed to improve both stability and expression with further enhancement through pseudouridine nucleoside modification. Together, our study demonstrates simultaneous improvement of mRNA stability and protein expression and provides a computational-experimental platform for the enhancement of mRNA medicines.
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Affiliation(s)
- Kathrin Leppek
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Gun Woo Byeon
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Wipapat Kladwang
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA
| | | | - Craig H Kerr
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Adele F Xu
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Do Soon Kim
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA
| | - Ved V Topkar
- Program in Biophysics, Stanford University, Stanford, CA, 94305, USA
| | - Christian Choe
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Daphna Rothschild
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Gerald C Tiu
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | | | - Kotaro Fujii
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Eesha Sharma
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA
| | - Andrew M Watkins
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA
| | - John J Nicol
- Eterna Massive Open Laboratory, Stanford University, Stanford, CA, 94305, USA
| | - Jonathan Romano
- Eterna Massive Open Laboratory, Stanford University, Stanford, CA, 94305, USA
- Department of Computer Science and Engineering, State University of New York at Buffalo, Buffalo, New York, 14260, USA
| | - Bojan Tunguz
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA
- NVIDIA Corporation, 2788 San Tomas Expy, Santa Clara, CA, 95051, USA
| | - Fernando Diaz
- Pfizer Vaccine Research and Development, Pearl River, NY, USA
| | - Hui Cai
- Pfizer Vaccine Research and Development, Pearl River, NY, USA
| | - Pengbo Guo
- Pfizer Vaccine Research and Development, Pearl River, NY, USA
| | - Jiewei Wu
- Pfizer Vaccine Research and Development, Pearl River, NY, USA
| | - Fanyu Meng
- Pfizer Vaccine Research and Development, Pearl River, NY, USA
| | - Shuai Shi
- Pfizer Vaccine Research and Development, Pearl River, NY, USA
| | - Eterna Participants
- Eterna Massive Open Laboratory, Stanford University, Stanford, CA, 94305, USA
| | - Philip R Dormitzer
- Pfizer Vaccine Research and Development, Pearl River, NY, USA
- GlaxoSmithKline, 1000 Winter St., Waltham, MA, 02453, USA
| | | | - Maria Barna
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA.
| | - Rhiju Das
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA.
- Program in Biophysics, Stanford University, Stanford, CA, 94305, USA.
- Eterna Massive Open Laboratory, Stanford University, Stanford, CA, 94305, USA.
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230
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Vaasjo LO. LncRNAs and Chromatin Modifications Pattern m6A Methylation at the Untranslated Regions of mRNAs. Front Genet 2022; 13:866772. [PMID: 35368653 PMCID: PMC8968631 DOI: 10.3389/fgene.2022.866772] [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: 01/31/2022] [Accepted: 02/28/2022] [Indexed: 12/16/2022] Open
Abstract
New roles for RNA in mediating gene expression are being discovered at an alarming rate. A broad array of pathways control patterning of N6-methyladenosine (m6A) methylation on RNA transcripts. This review comprehensively discusses long non-coding RNAs (lncRNAs) as an additional dynamic regulator of m6A methylation, with a focus on the untranslated regions (UTRs) of mRNAs. Although there is extensive literature describing m6A modification of lncRNA, the function of lncRNA in guiding m6A writers has not been thoroughly explored. The independent control of lncRNA expression, its heterogeneous roles in RNA metabolism, and its interactions with epigenetic machinery, alludes to their potential in dynamic patterning of m6A methylation. While epigenetic regulation by histone modification of H3K36me3 has been demonstrated to pattern RNA m6A methylation, these modifications were specific to the coding and 3′UTR regions. However, there are observations that 5′UTR m6A is distinct from that of the coding and 3′UTR regions, and substantial evidence supports the active regulation of 5′UTR m6A methylation. Consequently, two potential mechanisms in patterning the UTRs m6A methylation are discussed; (1) Anti-sense lncRNA (AS-lncRNA) can either bind directly to the UTR, or (2) act indirectly via recruitment of chromatin-modifying complexes to pattern m6A. Both pathways can guide the m6A writer complex, facilitate m6A methylation and modulate protein translation. Findings in the lncRNA-histone-m6A axis could potentially contribute to the discovery of new functions of lncRNAs and clarify lncRNA-m6A findings in translational medicine.
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Affiliation(s)
- Lee O. Vaasjo
- Cellular and Molecular Biology, Tulane University, New Orleans, LA, United States
- Neuroscience Program, Brain Institute, Tulane University, New Orleans, LA, United States
- *Correspondence: Lee O. Vaasjo,
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231
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Huff AL, Jaffee EM, Zaidi N. Messenger RNA vaccines for cancer immunotherapy: progress promotes promise. J Clin Invest 2022; 132:e156211. [PMID: 35289317 PMCID: PMC8920340 DOI: 10.1172/jci156211] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The COVID-19 pandemic has elevated mRNA vaccines to global recognition due to their unprecedented success rate in protecting against a deadly virus. This international success is underscored by the remarkable versatility, favorable immunogenicity, and overall safety of the mRNA platform in diverse populations. Although mRNA vaccines have been studied in preclinical models and patients with cancer for almost three decades, development has been slow. The recent technological advances responsible for the COVID-19 vaccines have potential implications for successfully adapting this vaccine platform for cancer therapeutics. Here we discuss the lessons learned along with the chemical, biologic, and immunologic adaptations needed to optimize mRNA technology to successfully treat cancers.
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Affiliation(s)
- Amanda L. Huff
- Department of Oncology
- The Sidney Kimmel Comprehensive Cancer Center
- The Skip Viragh Center for Pancreatic Cancer Research and Clinical Care
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, and
- The Cancer Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Elizabeth M. Jaffee
- Department of Oncology
- The Sidney Kimmel Comprehensive Cancer Center
- The Skip Viragh Center for Pancreatic Cancer Research and Clinical Care
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, and
- The Cancer Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Neeha Zaidi
- Department of Oncology
- The Sidney Kimmel Comprehensive Cancer Center
- The Skip Viragh Center for Pancreatic Cancer Research and Clinical Care
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, and
- The Cancer Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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232
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Zogg H, Singh R, Ro S. Current Advances in RNA Therapeutics for Human Diseases. Int J Mol Sci 2022; 23:ijms23052736. [PMID: 35269876 PMCID: PMC8911101 DOI: 10.3390/ijms23052736] [Citation(s) in RCA: 83] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 02/25/2022] [Accepted: 02/25/2022] [Indexed: 12/11/2022] Open
Abstract
Following the discovery of nucleic acids by Friedrich Miescher in 1868, DNA and RNA were recognized as the genetic code containing the necessary information for proper cell functioning. In the years following these discoveries, vast knowledge of the seemingly endless roles of RNA have become better understood. Additionally, many new types of RNAs were discovered that seemed to have no coding properties (non-coding RNAs), such as microRNAs (miRNAs). The discovery of these new RNAs created a new avenue for treating various human diseases. However, RNA is relatively unstable and is degraded fairly rapidly once administered; this has led to the development of novel delivery mechanisms, such as nanoparticles to increase stability as well as to prevent off-target effects of these molecules. Current advances in RNA-based therapies have substantial promise in treating and preventing many human diseases and disorders through fixing the pathology instead of merely treating the symptomology similarly to traditional therapeutics. Although many RNA therapeutics have made it to clinical trials, only a few have been FDA approved thus far. Additionally, the results of clinical trials for RNA therapeutics have been ambivalent to date, with some studies demonstrating potent efficacy, whereas others have limited effectiveness and/or toxicity. Momentum is building in the clinic for RNA therapeutics; future clinical care of human diseases will likely comprise promising RNA therapeutics. This review focuses on the current advances of RNA therapeutics and addresses current challenges with their development.
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233
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Wang Y, Zhang R, Tang L, Yang L. Nonviral Delivery Systems of mRNA Vaccines for Cancer Gene Therapy. Pharmaceutics 2022; 14:512. [PMID: 35335891 PMCID: PMC8949480 DOI: 10.3390/pharmaceutics14030512] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/12/2022] [Accepted: 02/23/2022] [Indexed: 01/14/2023] Open
Abstract
In recent years, the use of messenger RNA (mRNA) in the fields of gene therapy, immunotherapy, and stem cell biomedicine has received extensive attention. With the development of scientific technology, mRNA applications for tumor treatment have matured. Since the SARS-CoV-2 infection outbreak in 2019, the development of engineered mRNA and mRNA vaccines has accelerated rapidly. mRNA is easy to produce, scalable, modifiable, and not integrated into the host genome, showing tremendous potential for cancer gene therapy and immunotherapy when used in combination with traditional strategies. The core mechanism of mRNA therapy is vehicle-based delivery of in vitro transcribed mRNA (IVT mRNA), which is large, negatively charged, and easily degradable, into the cytoplasm and subsequent expression of the corresponding proteins. However, effectively delivering mRNA into cells and successfully activating the immune response are the keys to the clinical transformation of mRNA therapy. In this review, we focus on nonviral nanodelivery systems of mRNA vaccines used for cancer gene therapy and immunotherapy.
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Affiliation(s)
| | | | | | - Li Yang
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; (Y.W.); (R.Z.); (L.T.)
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234
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Ba F, Liu Y, Liu WQ, Tian X, Li J. SYMBIOSIS: synthetic manipulable biobricks via orthogonal serine integrase systems. Nucleic Acids Res 2022; 50:2973-2985. [PMID: 35191490 PMCID: PMC8934643 DOI: 10.1093/nar/gkac124] [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: 11/04/2021] [Revised: 02/04/2022] [Accepted: 02/09/2022] [Indexed: 11/14/2022] Open
Abstract
Serine integrases are emerging as one of the most powerful biological tools for synthetic biology. They have been widely used across genome engineering and genetic circuit design. However, developing serine integrase-based tools for directly/precisely manipulating synthetic biobricks is still missing. Here, we report SYMBIOSIS, a versatile method that can robustly manipulate DNA parts in vivo and in vitro. First, we propose a 'keys match locks' model to demonstrate that three orthogonal serine integrases are able to irreversibly and stably switch on seven synthetic biobricks with high accuracy in vivo. Then, we demonstrate that purified integrases can facilitate the assembly of 'donor' and 'acceptor' plasmids in vitro to construct composite plasmids. Finally, we use SYMBIOSIS to assemble different chromoprotein genes and create novel colored Escherichia coli. We anticipate that our SYMBIOSIS strategy will accelerate synthetic biobrick manipulation, genetic circuit design and multiple plasmid assembly for synthetic biology with broad potential applications.
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Affiliation(s)
- Fang Ba
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yushi Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Wan-Qiu Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xintong Tian
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jian Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
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235
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Hoque ME, Mahendran T, Basu S. Reversal of G-Quadruplexes' Role in Translation Control When Present in the Context of an IRES. Biomolecules 2022; 12:314. [PMID: 35204814 PMCID: PMC8869680 DOI: 10.3390/biom12020314] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/08/2022] [Accepted: 02/14/2022] [Indexed: 02/01/2023] Open
Abstract
G-quadruplexes (GQs) are secondary nucleic acid structures that play regulatory roles in various cellular processes. G-quadruplex-forming sequences present within the 5' UTR of mRNAs can function not only as repressors of translation but also as elements required for optimum function. Based upon previous reports, the majority of the 5' UTR GQ structures inhibit translation, presumably by blocking the ribosome scanning process that is essential for detection of the initiation codon. However, there are certain mRNAs containing GQs that have been identified as positive regulators of translation, as they are needed for translation initiation. While most cellular mRNAs utilize the 5' cap structure to undergo cap-dependent translation initiation, many rely on cap-independent translation under certain conditions in which the cap-dependent initiation mechanism is not viable or slowed down, for example, during development, under stress and in many diseases. Cap-independent translation mainly occurs via Internal Ribosomal Entry Sites (IRESs) that are located in the 5' UTR of mRNAs and are equipped with structural features that can recruit the ribosome or other factors to initiate translation without the need for a 5' cap. In this review, we will focus only on the role of RNA GQs present in the 5' UTR of mRNAs, where they play a critical role in translation initiation, and discuss the potential mechanism of this phenomenon, which is yet to be fully delineated.
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Affiliation(s)
| | | | - Soumitra Basu
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA; (M.E.H.); (T.M.)
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236
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New Genomic Signals Underlying the Emergence of Human Proto-Genes. Genes (Basel) 2022; 13:genes13020284. [PMID: 35205330 PMCID: PMC8871994 DOI: 10.3390/genes13020284] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 12/04/2022] Open
Abstract
De novo genes are novel genes which emerge from non-coding DNA. Until now, little is known about de novo genes’ properties, correlated to their age and mechanisms of emergence. In this study, we investigate four related properties: introns, upstream regulatory motifs, 5′ Untranslated regions (UTRs) and protein domains, in 23,135 human proto-genes. We found that proto-genes contain introns, whose number and position correlates with the genomic position of proto-gene emergence. The origin of these introns is debated, as our results suggest that 41% of proto-genes might have captured existing introns, and 13.7% of them do not splice the ORF. We show that proto-genes which emerged via overprinting tend to be more enriched in core promotor motifs, while intergenic and intronic genes are more enriched in enhancers, even if the TATA motif is most commonly found upstream in these genes. Intergenic and intronic 5′ UTRs of proto-genes have a lower potential to stabilise mRNA structures than exonic proto-genes and established human genes. Finally, we confirm that proteins expressed by proto-genes gain new putative domains with age. Overall, we find that regulatory motifs inducing transcription and translation of previously non-coding sequences may facilitate proto-gene emergence. Our study demonstrates that introns, 5′ UTRs, and domains have specific properties in proto-genes. We also emphasize that the genomic positions of de novo genes strongly impacts these properties.
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237
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Neumann T, Tuller T. Modeling the ribosomal small subunit dynamic in Saccharomyces cerevisiae based on TCP-seq data. Nucleic Acids Res 2022; 50:1297-1316. [PMID: 35100399 PMCID: PMC8860609 DOI: 10.1093/nar/gkac021] [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: 03/25/2021] [Revised: 12/31/2021] [Accepted: 01/07/2022] [Indexed: 11/13/2022] Open
Abstract
Translation Complex Profile Sequencing (TCP-seq), a protocol that was developed and implemented on Saccharomyces cerevisiae, provides the footprints of the small subunit (SSU) of the ribosome (with additional factors) across the entire transcriptome of the analyzed organism. In this study, based on the TCP-seq data, we developed for the first-time a predictive model of the SSU density and analyzed the effect of transcript features on the dynamics of the SSU scan in the 5′UTR. Among others, our model is based on novel tools for detecting complex statistical relations tailored to TCP-seq. We quantitatively estimated the effect of several important features, including the context of the upstream AUG, the upstream ORF length and the mRNA folding strength. Specifically, we suggest that around 50% of the variance related to the read counts (RC) distribution near a start codon can be attributed to the AUG context score. We provide the first large scale direct quantitative evidence that shows that indeed AUG context affects the small sub-unit movement. In addition, we suggest that strong folding may cause the detachment of the SSU from the mRNA. We also identified a number of novel sequence motifs that can affect the SSU scan; some of these motifs affect transcription factors and RNA binding proteins. The results presented in this study provide a better understanding of the biophysical aspects related to the SSU scan along the 5′UTR and of translation initiation in S. cerevisiae, a fundamental step toward a comprehensive modeling of initiation.
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Affiliation(s)
- Tamar Neumann
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
- The Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv 6997801, Israel
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238
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Bailly A, Milhavet O, Lemaitre JM. RNA-Based Strategies for Cell Reprogramming toward Pluripotency. Pharmaceutics 2022; 14:317. [PMID: 35214051 PMCID: PMC8876983 DOI: 10.3390/pharmaceutics14020317] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/16/2022] [Accepted: 01/25/2022] [Indexed: 02/04/2023] Open
Abstract
Cell therapy approaches to treat a wide range of pathologies have greatly benefited from cell reprogramming techniques that allow the conversion of a somatic cell into a pluripotent cell. Many technological developments have been made since the initial major discovery of this biological process. Recently reprogramming methods based on the use of RNA have emerged and seem very promising. Thus, in this review we will focus on presenting the interest of such methods for cell reprogramming but also how these RNA-based strategies can be extended to eventually lead to medical applications to improve healthspan and longevity.
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Affiliation(s)
- Anaëlle Bailly
- IRMB, University Montpellier, INSERM, 34295 Montpellier, France
- INGRAALYS, SA, IRMB, Incubator Cyborg, 34295 Montpellier, France
| | - Ollivier Milhavet
- IRMB, University Montpellier, INSERM, CNRS, 34295 Montpellier, France
- SAFE-iPSC Facility, CHU Montpellier, 34295 Montpellier, France
| | - Jean-Marc Lemaitre
- IRMB, University Montpellier, INSERM, 34295 Montpellier, France
- SAFE-iPSC Facility, CHU Montpellier, 34295 Montpellier, France
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239
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Uppala JK, Sathe L, Chakraborty A, Bhattacharjee S, Pulvino AT, Dey M. The cap-proximal RNA secondary structure inhibits preinitiation complex formation on HAC1 mRNA. J Biol Chem 2022; 298:101648. [PMID: 35101452 PMCID: PMC8881652 DOI: 10.1016/j.jbc.2022.101648] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 11/17/2022] Open
Abstract
Translation of HAC1 mRNA in the budding yeast Saccharomyces cerevisiae is derepressed when RNase Ire1 removes its intron via nonconventional cytosolic splicing in response to accumulation of unfolded proteins inside the endoplasmic reticulum. The spliced HAC1 mRNA is translated into a transcription factor that changes the cellular gene expression patterns to increase the protein folding capacity of cells. Previously, we showed that a segment of the intronic sequence interacts with the 5′-UTR of the unspliced mRNA, resulting in repression of HAC1 translation at the initiation stage. However, the exact mechanism of translational derepression is not clear. Here, we show that at least 11-base-pairing interactions between the 5′-UTR and intron (UI) are sufficient to repress HAC1 translation. We also show that overexpression of the helicase eukaryotic initiation factor 4A derepressed translation of an unspliced HAC1 mRNA containing only 11-bp interactions between the 5′-UTR and intronic sequences. In addition, our genetic screen identifies that single mutations in the UI interaction site could derepress translation of the unspliced HAC1 mRNA. Furthermore, we show that the addition of 24 RNA bases between the mRNA 5′-cap and the UI interaction site derepressed translation of the unspliced HAC1 mRNA. Together, our data provide a mechanistic explanation for why the cap-proximal UI–RNA duplex inhibits the recruitment of translating ribosomes to HAC1 mRNA, thus keeping mRNA translationally repressed.
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Affiliation(s)
- Jagadeesh Kumar Uppala
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Leena Sathe
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Abhijit Chakraborty
- Center for Autoimmunity and Inflammation, Center for Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Sankhajit Bhattacharjee
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Anthony Thomas Pulvino
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Madhusudan Dey
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA.
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240
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Translational control of E2f1 regulates the Drosophila cell cycle. Proc Natl Acad Sci U S A 2022; 119:2113704119. [PMID: 35074910 PMCID: PMC8795540 DOI: 10.1073/pnas.2113704119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/10/2021] [Indexed: 12/21/2022] Open
Abstract
E2F transcription factors are master regulators of the eukaryotic cell cycle. In Drosophila, the sole activating E2F, E2F1, is both required for and sufficient to promote G1→S progression. E2F1 activity is regulated both by binding to RB Family repressors and by posttranscriptional control of E2F1 protein levels by the EGFR and TOR signaling pathways. Here, we investigate cis-regulatory elements in the E2f1 messenger RNA (mRNA) that enable E2f1 translation to respond to these signals and promote mitotic proliferation of wing imaginal disc and intestinal stem cells. We show that small upstream open reading frames (uORFs) in the 5' untranslated region (UTR) of the E2f1 mRNA limit its translation, impacting rates of cell proliferation. E2f1 transgenes lacking these 5'UTR uORFs caused TOR-independent expression and excess cell proliferation, suggesting that TOR activity can bypass uORF-mediated translational repression. EGFR signaling also enhanced translation but through a mechanism less dependent on 5'UTR uORFs. Further, we mapped a region in the E2f1 mRNA that contains a translational enhancer, which may also be targeted by TOR signaling. This study reveals translational control mechanisms through which growth signaling regulates cell cycle progression.
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241
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Chen C, Zhang X, Wang Y, Chen X, Chen W, Dan S, She S, Hu W, Dai J, Hu J, Cao Q, Liu Q, Huang Y, Qin B, Kang B, Wang YJ. Translational and post-translational control of human naïve versus primed pluripotency. iScience 2022; 25:103645. [PMID: 35005567 PMCID: PMC8718978 DOI: 10.1016/j.isci.2021.103645] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 10/22/2021] [Accepted: 12/10/2021] [Indexed: 01/05/2023] Open
Abstract
Deciphering the regulatory network for human naive and primed pluripotency is of fundamental theoretical and applicable significance. Here, by combining quantitative proteomics, phosphoproteomics, and acetylproteomics analyses, we revealed RNA processing and translation as the most differentially regulated processes between naive and primed human embryonic stem cells (hESCs). Although glycolytic primed hESCs rely predominantly on the eukaryotic initiation factor 4E (eIF4E)-mediated cap-dependent pathway for protein translation, naive hESCs with reduced mammalian target of rapamycin complex (mTORC1) activity are more tolerant to eIF4E inhibition, and their bivalent metabolism allows for translating selective mRNAs via both eIF4E-dependent and eIF4E-independent/eIF4A2-dependent pathways to form a more compact naive proteome. Globally up-regulated proteostasis and down-regulated post-translational modifications help to further refine the naive proteome that is compatible with the more rapid cycling of naive hESCs, where CDK1 plays an indispensable coordinative role. These findings may assist in better understanding the unrestricted lineage potential of naive hESCs and in further optimizing conditions for future clinical applications RNA processing and translation are most different between naive and primed hESCs Glycolytic primed hESCs mainly rely on eIF4E-dependent translation Bivalent metabolism in naive hESCs promotes eIF4E-independent translation CDK1 is required for naive pluripotency partially by activating E-cadherin signaling
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Affiliation(s)
- Cheng Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China.,Shaoxing People's Hospital, Shaoxing Hospital, Zhejiang University School of Medicine, Shaoxing, Zhejiang 312000, China
| | - Xiaobing Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Yisha Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Xinyu Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Wenjie Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Songsong Dan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Shiqi She
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China.,Zhejiang Museum of Natural History, Hangzhou, Zhejiang 310014, China
| | - Weiwei Hu
- Shanghai Bioprofile Technology Co., Ltd., Shanghai 200241, China
| | - Jie Dai
- Shanghai Bioprofile Technology Co., Ltd., Shanghai 200241, China
| | - Jianwen Hu
- Shanghai Bioprofile Technology Co., Ltd., Shanghai 200241, China
| | - Qingyi Cao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Qianyu Liu
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yinghua Huang
- Laboratory of Metabolism and Cell Fate, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Baoming Qin
- Laboratory of Metabolism and Cell Fate, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Bo Kang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Ying-Jie Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
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242
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Yap YT, Li W, Zhou Q, Haj-Diab S, Chowdhury DD, Vaishnav A, Harding P, Williams DC, Edwards BF, Strauss JF, Zhang Z. The Ancient and Evolved Mouse Sperm-Associated Antigen 6 Genes Have Different Biologic Functions In Vivo. Cells 2022; 11:336. [PMID: 35159146 PMCID: PMC8834003 DOI: 10.3390/cells11030336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 01/09/2023] Open
Abstract
Sperm-associated antigen 6 (SPAG6) is the mammalian orthologue of Chlamydomonas PF16, an axonemal central pair protein involved in flagellar motility. In mice, two Spag6 genes have been identified. The ancestral gene, on mouse chromosome 2, is named Spag6. A related gene originally called Spag6, localized on mouse chromosome 16, evolved from the ancient Spag6 gene. It has been renamed Spag6-like (Spag6l). Spag6 encodes a 1.6 kb transcript consisting of 11 exons, while Spag6l encodes a 2.4 kb transcript which contains an additional non-coding exon in the 3'-end as well as the 11 exons found in Spag6. The two Spag6 genes share high similarities in their nucleotide and amino acid sequences. Unlike Spag6l mRNA, which is widely expressed, Spag6 mRNA expression is limited to a smaller number of tissues, including the testis and brain. In transfected mammalian cells, SPAG6/GFP is localized on microtubules, a similar localization as SPAG6L. A global Spag6l knockout mouse model was generated previously. In addition to a role in modulating the ciliary beat, SPAG6L has many unexpected functions, including roles in the regulation of ciliogenesis/spermatogenesis, hearing, and the immunological synapse, among others. To investigate the role of the ancient Spag6 gene, we phenotyped global Spag6 knockout mice. All homozygous mutant mice were grossly normal, and fertility was not affected in both males and females. The homozygous males had normal sperm parameters, including sperm number, motility, and morphology. Examination of testis histology revealed normal spermatogenesis. Testicular protein expression levels of selected SPAG6L binding partners, including SPAG16L, were not changed in the Spag6 knockout mice, even though the SPAG16L level was significantly reduced in the Spag6l knockout mice. Structural analysis of the two SPAG6 proteins shows that both adopt very similar folds, with differences in a few amino acids, many of which are solvent-exposed. These differences endow the two proteins with different functional characteristics, even though both have eight armadillo repeats that mediate protein-protein interaction. Our studies suggest that SPAG6 and SPAG6L have different functions in vivo, with the evolved SPAG6L protein being more important. Since the two proteins have some overlapping binding partners, SPAG6 could have functions that are yet to be identified.
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Affiliation(s)
- Yi Tian Yap
- Department of Physiology, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (Y.T.Y.); (W.L.); (Q.Z.); (S.H.-D.)
| | - Wei Li
- Department of Physiology, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (Y.T.Y.); (W.L.); (Q.Z.); (S.H.-D.)
| | - Qi Zhou
- Department of Physiology, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (Y.T.Y.); (W.L.); (Q.Z.); (S.H.-D.)
- Department of Occupational and Environmental Medicine, School of Public Health, Wuhan University of Science and Technology, Wuhan 430060, China
| | - Sarah Haj-Diab
- Department of Physiology, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (Y.T.Y.); (W.L.); (Q.Z.); (S.H.-D.)
| | - Dipanwita Dutta Chowdhury
- Department of Biochemistry, Microbiology & Immunology, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (D.D.C.); (A.V.); (B.F.E.)
| | - Asmita Vaishnav
- Department of Biochemistry, Microbiology & Immunology, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (D.D.C.); (A.V.); (B.F.E.)
| | - Pamela Harding
- Hypertension & Vascular Research Division, Henry Ford Health System, Detroit, MI 48201, USA;
| | - David C. Williams
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
| | - Brian F. Edwards
- Department of Biochemistry, Microbiology & Immunology, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (D.D.C.); (A.V.); (B.F.E.)
| | - Jerome F. Strauss
- Center for Research on Reproduction and Women’s Health, Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Zhibing Zhang
- Department of Physiology, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (Y.T.Y.); (W.L.); (Q.Z.); (S.H.-D.)
- The C.S. Mott Center for Human Growth and Development, Department of Obstetrics & Gynecology, Wayne State University, Detroit, MI 48201, USA
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243
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RNA-Binding Proteins as Regulators of Internal Initiation of Viral mRNA Translation. Viruses 2022; 14:v14020188. [PMID: 35215780 PMCID: PMC8879377 DOI: 10.3390/v14020188] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/03/2022] [Accepted: 01/14/2022] [Indexed: 12/17/2022] Open
Abstract
Viruses are obligate intracellular parasites that depend on the host’s protein synthesis machinery for translating their mRNAs. The viral mRNA (vRNA) competes with the host mRNA to recruit the translational machinery, including ribosomes, tRNAs, and the limited eukaryotic translation initiation factor (eIFs) pool. Many viruses utilize non-canonical strategies such as targeting host eIFs and RNA elements known as internal ribosome entry sites (IRESs) to reprogram cellular gene expression, ensuring preferential translation of vRNAs. In this review, we discuss vRNA IRES-mediated translation initiation, highlighting the role of RNA-binding proteins (RBPs), other than the canonical translation initiation factors, in regulating their activity.
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244
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Li J, Xie G, Tian Y, Li W, Wu Y, Chen F, Lin Y, Lin X, Wing-Ngor Au S, Cao J, He W, Wang H. RNA m 6A methylation regulates the dissemination of cancer cells via modulating expression and membrane localization of β-catenin. Mol Ther 2022; 30:1578-1596. [PMID: 35033632 PMCID: PMC9077323 DOI: 10.1016/j.ymthe.2022.01.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 08/23/2021] [Accepted: 01/12/2022] [Indexed: 12/01/2022] Open
Abstract
N6-methyladenosine (m6A) methylation, which is modified by METTL3/METTL14 complex, is a dominant internal modification in mammalian RNA and tightly links to cancer progression. Here, we reveal that METTL3-promoted cell migration, invasion and epithelial to mesenchymal transition (EMT) are associated with the expression and membrane localization of β-catenin (encoded by CTNNB1), as opposed to Wnt signaling activation in various types of cancer cells, including cervical, lung, and liver cancers. Specifically, METTL3 regulates the transcription, mRNA decay, translation and sub-cellular localization of β-catenin. For CTNNB1 expression, METTL3 indirectly suppresses CTNNB1 transcription via stabilizing its transcription suppressor E2F1 mRNA; deposition of 5'UTR m6A in CTNNB1 promotes its decay in a content-dependent manner via YTHDF2 recognition; 5'UTR m6A in CTNNB1 suppresses its translation efficiency, while global METTL3 level controls the canonical and non-canonical translation of CTNNB1, which is probably associated with the interaction between YTHDF1 and eIF4E1/eIF4E3. For β-catenin translocation, METTL3 represses membrane localization of β-catenin and its interaction with E-Cadherin by downregulating c-Met kinase, leading to the inhibition of cell motility. In vitro, in vivo and clinical analysis confirm the essential roles of β-catenin and its expression regulators in cancer cell dissemination. The findings not only expand our understanding of m6A modification and its roles in gene expression and subcellular localization of targets, but also suggest that METTL3/β-catenin axis might be a potential target to inhibit cancer metastasis.
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Affiliation(s)
- Jiexin Li
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Guoyou Xie
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Yifan Tian
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Wanglin Li
- Department of General Surgery, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, The Second Affiliated Hospital of South China University of Technology, Guangzhou 510180, China
| | - Yingmin Wu
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Feng Chen
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Yu Lin
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China; Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xinyao Lin
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Shannon Wing-Ngor Au
- Centra for Protein Science and Crystallography, School of Life Science, The Chinese University of Hong Kong, Hong Kong, China
| | - Jie Cao
- Department of General Surgery, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, The Second Affiliated Hospital of South China University of Technology, Guangzhou 510180, China.
| | - Weiling He
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.
| | - Hongsheng Wang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China.
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245
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Niu K, Zhang X, Song Q, Feng Q. G-Quadruplex Regulation of VEGFA mRNA Translation by RBM4. Int J Mol Sci 2022; 23:ijms23020743. [PMID: 35054929 PMCID: PMC8776124 DOI: 10.3390/ijms23020743] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 02/01/2023] Open
Abstract
In eukaryotes, mRNAs translation is mainly mediated in a cap-dependent or cap-independent manner. The latter is primarily initiated at the internal ribosome entry site (IRES) in the 5'-UTR of mRNAs. It has been reported that the G-quadruplex structure (G4) in the IRES elements could regulate the IRES activity. We previously confirmed RBM4 (also known as LARK) as a G4-binding protein in human. In this study, to investigate whether RBM4 is involved in the regulation of the IRES activity by binding with the G4 structure within the IRES element, the IRES-A element in the 5'-UTR of vascular endothelial growth factor A (VEGFA) was constructed into a dicistronic reporter vector, psiCHECK2, and the effect of RBM4 on the IRES activity was tested in 293T cells. The results showed that the IRES insertion significantly increased the FLuc expression activity, indicating that this G4-containing IRES was active in 293T cells. When the G4 structure in the IRES was disrupted by base mutation, the IRES activity was significantly decreased. The IRES activity was notably increased when the cells were treated with G4 stabilizer PDS. EMSA results showed that RBM4 specifically bound the G4 structure in the IRES element. The knockdown of RBM4 substantially reduced the IRES activity, whereas over-expressing RBM4 increased the IRES activity. Taking all results together, we demonstrated that RBM4 promoted the mRNA translation of VEGFA gene by binding to the G4 structure in the IRES.
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Affiliation(s)
- Kangkang Niu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China; (K.N.); (X.Z.)
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Xiaojuan Zhang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China; (K.N.); (X.Z.)
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Qisheng Song
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA;
| | - Qili Feng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China; (K.N.); (X.Z.)
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
- Correspondence:
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246
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Fülöp Á, Torma G, Moldován N, Szenthe K, Bánáti F, Almsarrhad IAA, Csabai Z, Tombácz D, Minárovits J, Boldogkői Z. Integrative profiling of Epstein-Barr virus transcriptome using a multiplatform approach. Virol J 2022; 19:7. [PMID: 34991630 PMCID: PMC8740505 DOI: 10.1186/s12985-021-01734-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/20/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Epstein-Barr virus (EBV) is an important human pathogenic gammaherpesvirus with carcinogenic potential. The EBV transcriptome has previously been analyzed using both Illumina-based short read-sequencing and Pacific Biosciences RS II-based long-read sequencing technologies. Since the various sequencing methods have distinct strengths and limitations, the use of multiplatform approaches have proven to be valuable. The aim of this study is to provide a more complete picture on the transcriptomic architecture of EBV. METHODS In this work, we apply the Oxford Nanopore Technologies MinION (long-read sequencing) platform for the generation of novel transcriptomic data, and integrate these with other's data generated by another LRS approach, Pacific BioSciences RSII sequencing and Illumina CAGE-Seq and Poly(A)-Seq approaches. Both amplified and non-amplified cDNA sequencings were applied for the generation of sequencing reads, including both oligo-d(T) and random oligonucleotide-primed reverse transcription. EBV transcripts are identified and annotated using the LoRTIA software suite developed in our laboratory. RESULTS This study detected novel genes embedded into longer host genes containing 5'-truncated in-frame open reading frames, which potentially encode N-terminally truncated proteins. We also detected a number of novel non-coding RNAs and transcript length isoforms encoded by the same genes but differing in their start and/or end sites. This study also reports the discovery of novel splice isoforms, many of which may represent altered coding potential, and of novel replication-origin-associated transcripts. Additionally, novel mono- and multigenic transcripts were identified. An intricate meshwork of transcriptional overlaps was revealed. CONCLUSIONS An integrative approach applying multi-technique sequencing technologies is suitable for reliable identification of complex transcriptomes because each techniques has different advantages and limitations, and the they can be used for the validation of the results obtained by a particular approach.
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Affiliation(s)
- Ádám Fülöp
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi B. u. 4., Szeged, 6720 Hungary
| | - Gábor Torma
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi B. u. 4., Szeged, 6720 Hungary
| | - Norbert Moldován
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi B. u. 4., Szeged, 6720 Hungary
| | - Kálmán Szenthe
- Carlsbad Research Organization Ltd., Szabadság u. 2., Újrónafő, 9244 Hungary
| | - Ferenc Bánáti
- RT-Europe Research Center, Vár tér 2., Mosonmagyaróvár, 9200 Hungary
| | - Islam A. A. Almsarrhad
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi B. u. 4., Szeged, 6720 Hungary
| | - Zsolt Csabai
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi B. u. 4., Szeged, 6720 Hungary
| | - Dóra Tombácz
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi B. u. 4., Szeged, 6720 Hungary
| | - János Minárovits
- Department of Oral Biology and Experimental Dental Research, University of Szeged, Tisza Lajos krt. 64, Szeged, 6720 Hungary
| | - Zsolt Boldogkői
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi B. u. 4., Szeged, 6720 Hungary
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247
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Castillo-Hair SM, Seelig G. Machine Learning for Designing Next-Generation mRNA Therapeutics. Acc Chem Res 2022; 55:24-34. [PMID: 34905691 DOI: 10.1021/acs.accounts.1c00621] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Over just the last 2 years, mRNA therapeutics and vaccines have undergone a rapid transition from an intriguing concept to real-world impact. However, whereas some aspects of mRNA therapeutics, such as the use of chemical modifications to increase stability and reduce immunogenicity, have been extensively optimized for over two decades, other aspects, particularly the selection and design of the noncoding leader and trailer sequences which control translation efficiency and stability, have received comparably less attention. In practice, such 5' and 3' untranslated regions (UTRs) are often borrowed from highly expressed human genes with few or no modifications, as in the case for the Pfizer/BioNTech Covid vaccine. Focusing on the 5'UTR, we here argue that model-driven design is a promising alternative that provides unprecedented control over 5'UTR function. We review recent work that combines synthetic biology with machine learning to build quantitative models that relate ribosome loading, and thus translation efficiency, to the 5'UTR sequence. We first introduce an experimental approach that uses polysome profiling and high-throughput sequencing to quantify ribosome loading for hundreds of thousands of 5'UTRs in parallel. We apply this approach to measure ribosome loading in synthetic RNA libraries with a random sequence inserted into the 5'UTR. We then review Optimus 5-Prime, a convolutional neural network model trained on the experimental data. We highlight that very accurate models of biological regulation can be learned from synthetic data sets with degenerate 5'UTRs. We validate model predictions not only on held-out data sets from our random library but also on a large library of over 30 000 human 5'UTR fragments and using translation reporter data collected independently by other groups. Both the experiment and model are compatible with commonly used chemically modified nucleosides, in particular, pseudouridine (Ψ) and 1-methyl-pseudouridine (m1Ψ). We find that, in general, 5'UTRs have very similar impacts when combined with different protein-coding sequences and even in the context of different chemical modifications. We demonstrate that Optimus 5-Prime can be combined with design algorithms to generate de novo sequences with precisely defined translation efficiencies. We emphasize recent developments in design algorithms that rely on activation maximization and generative modeling to improve both the fitness and diversity of designed sequences. Compared with prior approaches such as genetic algorithms, we show that these approaches are not only faster but also less likely to get stuck in local sequence optima. Finally, we discuss how the approach reviewed here can be generalized to other gene regions and applications.
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Affiliation(s)
- Sebastian M. Castillo-Hair
- Department of Electrical & Computer Engineering, University of Washington, Seattle, Washington 98195, United States
- eScience Institute, University of Washington, Seattle, Washington 98195, United States
| | - Georg Seelig
- Department of Electrical & Computer Engineering, University of Washington, Seattle, Washington 98195, United States
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, Washington 98195, United States
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248
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Abstract
In the past 20 years, the mRNA vaccine technology has evolved from the first proof of concept to the first licensed vaccine against emerging pandemics such as SARS-CoV-2. Two mRNA vaccines targeting SARS-CoV-2 have received emergency use authorization by US FDA, conditional marketing authorization by EMA, as well as multiple additional national regulatory authorities. The simple composition of an mRNA encoding the antigen formulated in a lipid nanoparticle enables a fast adaptation to new emerging pathogens. This can speed up vaccine development in pandemics from antigen and sequence selection to clinical trial to only a few months. mRNA vaccines are well tolerated and efficacious in animal models for multiple pathogens and will further contribute to the development of vaccines for other unaddressed diseases. Here, we give an overview of the mRNA vaccine design and factors for further optimization of this new promising technology and discuss current knowledge on the mode of action of mRNA vaccines interacting with the innate and adaptive immune system.
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249
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Oertlin C, Watt K, Ristau J, Larsson O. Anota2seq Analysis for Transcriptome-Wide Studies of mRNA Translation. Methods Mol Biol 2022; 2418:243-268. [PMID: 35119670 DOI: 10.1007/978-1-0716-1920-9_15] [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
mRNA translation plays a critical role in determining proteome composition. In health, regulation of mRNA translation facilitates rapid gene expression responses to intra- and extracellular signals. Moreover, dysregulated mRNA translation is a common feature in disease states, including neurological disorders and cancer. Yet, most studies of gene expression focus on analysis of mRNA levels, leaving variations in translational efficiencies largely uncharacterized. Here, we outline procedures to identify mRNA-selective alterations in translational efficiencies on a transcriptome-wide scale using the anota2seq package. Anota2seq compares expression data originating from translated mRNA to data from matched total mRNA to identify changes in translated mRNA not paralleled by corresponding changes in total mRNA (interpreted as changes in translational efficiencies impacting protein levels), congruent changes in total and translated mRNA (interpreted as changes in transcription and/or mRNA stability), and changes in total mRNA not paralleled by corresponding alterations in translated mRNA (interpreted as translational buffering). To illustrate the functionality of the anota2seq analysis package, we demonstrate a detailed analysis using a polysome-profiling data set quantified by RNA sequencing, revealing that estrogen receptor α modulates gene expression via a type of translational buffering termed offsetting. Notably, this anota2seq analysis procedure is also applicable to ribosome-profiling (RiboSeq) data sets and can be adapted to a variety of other data types and experimental contexts. Finally, we provide guidance for extending anota2seq analysis to examine associations between untranslated regions and altered translational efficiencies as well as targeted cellular functions to gain insights into mechanisms and phenotypic consequences of altered mRNA translation. Thus, this step-by-step manual allows users to interrogate selective changes in mRNA translation on a transcriptome-wide scale using the Bioconductor package anota2seq.
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Affiliation(s)
- Christian Oertlin
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Kathleen Watt
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Johannes Ristau
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Ola Larsson
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden.
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250
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Wilkins KC, Venkataramanan S, Floor SN. Lysate and cell-based assays to probe the translational role of RNA helicases. Methods Enzymol 2022; 673:141-168. [DOI: 10.1016/bs.mie.2022.03.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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