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Ousalem F, Ngo S, Oïffer T, Omairi-Nasser A, Hamon M, Monlezun L, Boël G. Global regulation via modulation of ribosome pausing by the ABC-F protein EttA. Nat Commun 2024; 15:6314. [PMID: 39060293 PMCID: PMC11282234 DOI: 10.1038/s41467-024-50627-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
Having multiple rounds of translation of the same mRNA creates dynamic complexities along with opportunities for regulation related to ribosome pausing and stalling at specific sequences. Yet, mechanisms controlling these critical processes and the principles guiding their evolution remain poorly understood. Through genetic, genomic, physiological, and biochemical approaches, we demonstrate that regulating ribosome pausing at specific amino acid sequences can produce ~2-fold changes in protein expression levels which strongly influence cell growth and therefore evolutionary fitness. We demonstrate, both in vivo and in vitro, that the ABC-F protein EttA directly controls the translation of mRNAs coding for a subset of enzymes in the tricarboxylic acid (TCA) cycle and its glyoxylate shunt, which modulates growth in some chemical environments. EttA also modulates expression of specific proteins involved in metabolically related physiological and stress-response pathways. These regulatory activities are mediated by EttA rescuing ribosomes paused at specific patterns of negatively charged residues within the first 30 amino acids of nascent proteins. We thus establish a unique global regulatory paradigm based on sequence-specific modulation of translational pausing.
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Affiliation(s)
- Farès Ousalem
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
- Biomarqueurs et nouvelles cibles thérapeutiques en oncologie, INSERM U981, Université Paris Saclay, Institut de Cancérologie Gustave Roussy, Villejuif Cedex, France
| | - Saravuth Ngo
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
| | - Thomas Oïffer
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
| | - Amin Omairi-Nasser
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
| | - Marion Hamon
- CNRS, Institut de Biologie Physico-Chimique, Plateforme de Protéomique, FR550, Paris, France
| | - Laura Monlezun
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
| | - Grégory Boël
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, Paris, France.
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2
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Courvan EMC, Parker RR. Hypoxia and inflammation induce synergistic transcriptome turnover in macrophages. Cell Rep 2024; 43:114452. [PMID: 38968068 DOI: 10.1016/j.celrep.2024.114452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 04/24/2024] [Accepted: 06/21/2024] [Indexed: 07/07/2024] Open
Abstract
Macrophages are effector immune cells that experience substantial changes to oxygenation when transiting through tissues, especially when entering tumors or infected wounds. How hypoxia alters gene expression and macrophage effector function at the post-transcriptional level remains poorly understood. Here, we use TimeLapse-seq to measure how inflammatory activation modifies the hypoxic response in primary macrophages. Nucleoside recoding sequencing allows the derivation of steady-state transcript levels, degradation rates, and transcriptional synthesis rates from the same dataset. We find that hypoxia produces distinct responses from resting and inflammatory macrophages. Hypoxia induces destabilization of mRNA transcripts, though inflammatory macrophages substantially increase mRNA degradation compared to resting macrophages. Increased RNA turnover results in the upregulation of ribosomal protein genes and downregulation of extracellular matrix components in inflammatory macrophages. Pathways regulated by mRNA decay in vitro are differentially regulated in tumor-associated macrophages implying that mixed stimuli could induce post-transcriptional regulation of macrophage function in solid tumors.
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Affiliation(s)
- Edward M C Courvan
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA; Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80303, USA.
| | - Roy R Parker
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA; Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80303, USA; BioFrontiers Institute, University of Colorado, Boulder, CO 80303, USA.
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3
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Castellano LA, McNamara RJ, Pallarés HM, Gamarnik AV, Alvarez DE, Bazzini AA. Dengue virus preferentially uses human and mosquito non-optimal codons. Mol Syst Biol 2024:10.1038/s44320-024-00052-7. [PMID: 39039212 DOI: 10.1038/s44320-024-00052-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 07/24/2024] Open
Abstract
Codon optimality refers to the effect that codon composition has on messenger RNA (mRNA) stability and translation level and implies that synonymous codons are not silent from a regulatory point of view. Here, we investigated the adaptation of virus genomes to the host optimality code using mosquito-borne dengue virus (DENV) as a model. We demonstrated that codon optimality exists in mosquito cells and showed that DENV preferentially uses nonoptimal (destabilizing) codons and avoids codons that are defined as optimal (stabilizing) in either human or mosquito cells. Human genes enriched in the codons preferentially and frequently used by DENV are upregulated during infection, and so is the tRNA decoding the nonoptimal and DENV preferentially used codon for arginine. We found that adaptation during single-host passaging in human or mosquito cells results in the selection of synonymous mutations towards DENV's preferred nonoptimal codons that increase virus fitness. Finally, our analyses revealed that hundreds of viruses preferentially use nonoptimal codons, with those infecting a single host displaying an even stronger bias, suggesting that host-pathogen interaction shapes virus-synonymous codon choice.
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Affiliation(s)
- Luciana A Castellano
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA
| | - Ryan J McNamara
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA
| | - Horacio M Pallarés
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires IIBBA-CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - Andrea V Gamarnik
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires IIBBA-CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - Diego E Alvarez
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín-CONICET, San Martín B1650, Argentina
| | - Ariel A Bazzini
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA.
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS, 66160, USA.
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4
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Ma N, Liu W, Xu N, Yin D, Zheng P, Wang G, Hui Y, Zhang J, Han G, Yang C, Lu Y, Cheng X. Relationship between circulating thrombospondin-1 messenger ribonucleic acid and microribonucleic acid-194 levels in Chinese patients with type 2 diabetic kidney disease: The outcomes of a case-control study. J Diabetes Investig 2024. [PMID: 38932465 DOI: 10.1111/jdi.14252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 05/16/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
AIMS/INTRODUCTION We investigated the relationship of circulating TSP-1 mRNA and miR-194 with diabetic kidney disease's degree. MATERIALS AND METHODS We enrolled 167 hospitalized type 2 diabetes patients in the endocrinology department. Patients were split into three groups according to urinary microalbumin: A, B and C. The control group comprised healthy outpatients (n = 163). The quantities of microribonucleic acid (miR)-194 and thrombospondin-1 (TSP-1) messenger ribonucleic acid (mRNA) in the participants' circulation were measured using a quantitative real-time polymerase chain reaction. RESULTS Circulating TSP-1 mRNA (P = 0.024) and miR-194 (P = 0.029) expressions significantly increased in type 2 diabetes patients. Circulating TSP-1 mRNA (P = 0.040) and miR-194 (P = 0.007) expression levels differed significantly among the three groups; circulating TSP-1 mRNA expression increased with urinary microalbumin. However, miR-194 declined in group B and increased in group C. Circulating TSP-1 mRNA was positively correlated with cystatin-c (r = 0.281; P = 0.021) and microalbumin/creatinine ratio (UmALB/Cr; r = 0.317; P = 0.009); miR-194 was positively correlated with UmALB/Cr (r = 0.405; P = 0.003). Stepwise multivariate linear regression analysis showed cystatin-c (β = 0.578; P = 0.021) and UmALB/Cr (β = 0.001; P = 0.009) as independent factors for TSP-1 mRNA; UmALB/Cr (β = 0.005; P = 0.028) as an independent factor for miR194. Areas under the curve for circulating TSP-1 mRNA and miR194 were 0.756 (95% confidence interval 0.620-0.893; sensitivity 0.69 and specificity 0.71, P < 0.01) and 0.584 (95% confidence interval 0.421-0.748; sensitivity 0.54 and specificity 0.52, P < 0.01), respectively. CONCLUSIONS Circulating TSP-1 mRNA and miR-194 expressions significantly increased in type 2 diabetes patients. The microalbumin group had lower levels of miR-194 (a risk factor that is valuable for type 2 diabetes kidney disease evaluation).
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Affiliation(s)
- Ning Ma
- Department of Endocrinology and Metabolism, Lianyungang No. 1 People's Hospital, Lianyungang, Jiangsu, China
- Department of Endocrinology and Metabolism, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Weiwei Liu
- Department of Endocrinology and Metabolism, Lianyungang No. 1 People's Hospital, Lianyungang, Jiangsu, China
| | - Ning Xu
- Department of Endocrinology and Metabolism, Lianyungang No. 1 People's Hospital, Lianyungang, Jiangsu, China
| | - Dong Yin
- Department of Endocrinology and Metabolism, Lianyungang No. 1 People's Hospital, Lianyungang, Jiangsu, China
| | - Ping Zheng
- Department of Endocrinology and Metabolism, Lianyungang No. 1 People's Hospital, Lianyungang, Jiangsu, China
| | - Guofeng Wang
- Department of Endocrinology and Metabolism, Lianyungang No. 1 People's Hospital, Lianyungang, Jiangsu, China
| | - Yuan Hui
- Department of Endocrinology and Metabolism, Lianyungang No. 1 People's Hospital, Lianyungang, Jiangsu, China
| | - Jiping Zhang
- Department of Endocrinology and Metabolism, Lianyungang No. 1 People's Hospital, Lianyungang, Jiangsu, China
| | - Guanjun Han
- Department of Endocrinology and Metabolism, Lianyungang No. 1 People's Hospital, Lianyungang, Jiangsu, China
| | - Chuanhui Yang
- Department of Endocrinology and Metabolism, Lianyungang No. 1 People's Hospital, Lianyungang, Jiangsu, China
| | - Yan Lu
- Department of Endocrinology and Metabolism, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Xingbo Cheng
- Department of Endocrinology and Metabolism, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
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Li Y, Yi Y, Gao X, Wang X, Zhao D, Wang R, Zhang LS, Gao B, Zhang Y, Zhang L, Cao Q, Chen K. 2'-O-methylation at internal sites on mRNA promotes mRNA stability. Mol Cell 2024; 84:2320-2336.e6. [PMID: 38906115 PMCID: PMC11196006 DOI: 10.1016/j.molcel.2024.04.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/13/2024] [Accepted: 04/17/2024] [Indexed: 06/23/2024]
Abstract
2'-O-methylation (Nm) is a prominent RNA modification well known in noncoding RNAs and more recently also found at many mRNA internal sites. However, their function and base-resolution stoichiometry remain underexplored. Here, we investigate the transcriptome-wide effect of internal site Nm on mRNA stability. Combining nanopore sequencing with our developed machine learning method, NanoNm, we identify thousands of Nm sites on mRNAs with a single-base resolution. We observe a positive effect of FBL-mediated Nm modification on mRNA stability and expression level. Elevated FBL expression in cancer cells is associated with increased expression levels for 2'-O-methylated mRNAs of cancer pathways, implying the role of FBL in post-transcriptional regulation. Lastly, we find that FBL-mediated 2'-O-methylation connects to widespread 3' UTR shortening, a mechanism that globally increases RNA stability. Collectively, we demonstrate that FBL-mediated Nm modifications at mRNA internal sites regulate gene expression by enhancing mRNA stability.
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Affiliation(s)
- Yanqiang Li
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Yang Yi
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Xinlei Gao
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Xin Wang
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Dongyu Zhao
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Rui Wang
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Li-Sheng Zhang
- Department of Chemistry, Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China; Department of Chemistry and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, Chicago, IL, USA
| | - Boyang Gao
- Department of Chemistry and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, Chicago, IL, USA
| | - Yadong Zhang
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Lili Zhang
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Qi Cao
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
| | - Kaifu Chen
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Boston, MA, USA; Prostate Cancer Program, Dana-Farber/Harvard Cancer Center, Boston, MA, USA.
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6
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Anzell AR, Kunz AB, Donovan JP, Tran TG, Lu X, Young S, Roman BL. Blood flow regulates acvrl1 transcription via ligand-dependent Alk1 activity. Angiogenesis 2024:10.1007/s10456-024-09924-w. [PMID: 38727966 DOI: 10.1007/s10456-024-09924-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/19/2024] [Indexed: 05/21/2024]
Abstract
Hereditary hemorrhagic telangiectasia (HHT) is an autosomal dominant disease characterized by the development of arteriovenous malformations (AVMs) that can result in significant morbidity and mortality. HHT is caused primarily by mutations in bone morphogenetic protein receptors ACVRL1/ALK1, a signaling receptor, or endoglin (ENG), an accessory receptor. Because overexpression of Acvrl1 prevents AVM development in both Acvrl1 and Eng null mice, enhancing ACVRL1 expression may be a promising approach to development of targeted therapies for HHT. Therefore, we sought to understand the molecular mechanism of ACVRL1 regulation. We previously demonstrated in zebrafish embryos that acvrl1 is predominantly expressed in arterial endothelial cells and that expression requires blood flow. Here, we document that flow dependence exhibits regional heterogeneity and that acvrl1 expression is rapidly restored after reinitiation of flow. Furthermore, we find that acvrl1 expression is significantly decreased in mutants that lack the circulating Alk1 ligand, Bmp10, and that, in the absence of flow, intravascular injection of BMP10 or the related ligand, BMP9, restores acvrl1 expression in an Alk1-dependent manner. Using a transgenic acvrl1:egfp reporter line, we find that flow and Bmp10 regulate acvrl1 at the level of transcription. Finally, we observe similar ALK1 ligand-dependent increases in ACVRL1 in human endothelial cells subjected to shear stress. These data suggest that ligand-dependent Alk1 activity acts downstream of blood flow to maintain or enhance acvrl1 expression via a positive feedback mechanism, and that ALK1 activating therapeutics may have dual functionality by increasing both ALK1 signaling flux and ACVRL1 expression.
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Affiliation(s)
- Anthony R Anzell
- Department of Human Genetics, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
- Pittsburgh Heart, Lung and Blood Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Amy B Kunz
- Department of Human Genetics, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
- Allegheny Health Network, Pittsburgh, PA, USA
| | - James P Donovan
- Department of Human Genetics, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Thanhlong G Tran
- Department of Human Genetics, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xinyan Lu
- Department of Human Genetics, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
| | - Sarah Young
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
- Carnegie Mellon University, University Libraries, Pittsburgh, PA, USA
| | - Beth L Roman
- Department of Human Genetics, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA.
- Pittsburgh Heart, Lung and Blood Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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Kagan F, Hejnol A. Comparative Analysis of Maternal Gene Expression Patterns Unravels Evolutionary Signatures Across Reproductive Modes. Mol Biol Evol 2024; 41:msae081. [PMID: 38679468 DOI: 10.1093/molbev/msae081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 03/09/2024] [Accepted: 04/23/2024] [Indexed: 05/01/2024] Open
Abstract
Maternal genes have a pivotal role in regulating metazoan early development. As such their functions have been extensively studied since the dawn of developmental biology. The temporal and spatial dynamics of their transcripts have been thoroughly described in model organisms and their functions have been undergoing heavy investigations. Yet, less is known about the evolutionary changes shaping their presence within diverse oocytes. Due to their unique maternal inheritance pattern, a high degree is predicted to be present when it comes to their expression. Insofar only limited and conflicting results have emerged around it. Here, we set out to elucidate which evolutionary changes could be detected in the maternal gene expression patterns using phylogenetic comparative methods on RNAseq data from 43 species. Using normalized gene expression values and fold change information throughout early development we set out to find the best-fitting evolutionary model. Through modeling, we find evidence supporting both the high degree of divergence and constraint on gene expression values, together with their temporal dynamics. Furthermore, we find that maternal gene expression alone can be used to explain the reproductive modes of different species. Together, these results suggest a highly dynamic evolutionary landscape of maternal gene expression. We also propose a possible functional dichotomy of maternal genes which is influenced by the reproductive strategy undertaken by examined species.
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Affiliation(s)
- Ferenc Kagan
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Andreas Hejnol
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- Faculty of Biological Sciences, Friedrich Schiller University, Institute for Zoology and Evolutionary Research, Jena, Germany
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8
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Zhang S, Lin R, Cui L, Jiang T, Shi J, Lu C, Li P, Zhou M. Alter codon bias of the P. pastoris genome to overcome a bottleneck in codon optimization strategy development and improve protein expression. Microbiol Res 2024; 282:127629. [PMID: 38330819 DOI: 10.1016/j.micres.2024.127629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/27/2023] [Accepted: 01/21/2024] [Indexed: 02/10/2024]
Abstract
Apart from its role in translation, codon bias is also an important mechanism to regulate mRNA levels. The traditional frequency-based codon optimization strategy is rather efficient in organisms such as N. crassa, but much less in yeast P. pastoris which is a popular host for heterologous protein expression. This is because that unlike N. crassa, the preferred codons of P. pastoris are actually AU-rich and hence codon optimization for extremely low GC content comes with issues of pre-mature transcriptional termination or low RNA stability in spite of translational advantages. To overcome this bottleneck, we focused on three reporter genes in P. pastoris first and confirmed the great advantage of GC-prone codon optimization on mRNA levels. Then we altered the codon bias profile of P. pastoris by introducing additional rare tRNA gene copies. Prior to that we constructed IPTG-regulated tRNA species to enable chassis cells to switch between different codon bias status. As demonstrated again with reporter genes, protein yield of luc and 0788 was successfully increased by 4-5 folds in chassis cells. In summary, here we provide an alternative codon optimization strategy for genes with unsatisfactory performance under traditional codon frequency-based optimization.
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Affiliation(s)
- Siyu Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Ru Lin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Luyao Cui
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Tianyi Jiang
- China Innovation Center of Roche, Shanghai 201203, China
| | - Jiacheng Shi
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Chaoyu Lu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Pengfei Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Mian Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.
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Musaev D, Abdelmessih M, Vejnar CE, Yartseva V, Weiss LA, Strayer EC, Takacs CM, Giraldez AJ. UPF1 regulates mRNA stability by sensing poorly translated coding sequences. Cell Rep 2024; 43:114074. [PMID: 38625794 PMCID: PMC11259039 DOI: 10.1016/j.celrep.2024.114074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 03/07/2024] [Accepted: 03/21/2024] [Indexed: 04/18/2024] Open
Abstract
Post-transcriptional mRNA regulation shapes gene expression, yet how cis-elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that the strength of translation initiation, upstream open reading frame (uORF) content, codon optimality, AU-rich elements, microRNA binding sites, and open reading frame (ORF) length function combinatorially to regulate mRNA stability. Machine-learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs, which are associated with a higher decay rate, including mRNAs with uORFs and those with exposed ORFs after stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated, such as mRNAs with long ORFs, ORF-like 3' UTRs, and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an exon-junction complex (EJC)-independent nonsense-mediated decay (NMD) pathway that we term ORF-mediated decay (OMD).
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Affiliation(s)
- Damir Musaev
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Mario Abdelmessih
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; AstraZeneca, Waltham, MA 02451, USA
| | - Charles E Vejnar
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Valeria Yartseva
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Kenai Therapeutics, San Diego, CA, USA
| | - Linnea A Weiss
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Ethan C Strayer
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Carter M Takacs
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; University of New Haven, West Haven, CT 06516, USA
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06510, USA.
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10
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Baia Amaral D, Egidy R, Perera A, Bazzini AA. miR-430 regulates zygotic mRNA during zebrafish embryogenesis. Genome Biol 2024; 25:74. [PMID: 38504288 PMCID: PMC10949700 DOI: 10.1186/s13059-024-03197-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 02/15/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND Early embryonic developmental programs are guided by the coordinated interplay between maternally inherited and zygotically manufactured RNAs and proteins. Although these processes happen concomitantly and affecting gene function during this period is bound to affect both pools of mRNAs, it has been challenging to study their expression dynamics separately. RESULTS By employing SLAM-seq, a nascent mRNA labeling transcriptomic approach, in a developmental time series we observe that over half of the early zebrafish embryo transcriptome consists of maternal-zygotic genes, emphasizing their pivotal role in early embryogenesis. We provide an hourly resolution of de novo transcriptional activation events and follow nascent mRNA trajectories, finding that most de novo transcriptional events are stable throughout this period. Additionally, by blocking microRNA-430 function, a key post transcriptional regulator during zebrafish embryogenesis, we directly show that it destabilizes hundreds of de novo transcribed mRNAs from pure zygotic as well as maternal-zygotic genes. This unveils a novel miR-430 function during embryogenesis, fine-tuning zygotic gene expression. CONCLUSION These insights into zebrafish early embryo transcriptome dynamics emphasize the significance of post-transcriptional regulators in zygotic genome activation. The findings pave the way for future investigations into the coordinated interplay between transcriptional and post-transcriptional landscapes required for the establishment of animal cell identities and functions.
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Affiliation(s)
- Danielson Baia Amaral
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA
| | - Rhonda Egidy
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA
| | - Anoja Perera
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA
| | - Ariel A Bazzini
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA.
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS, 66160, USA.
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11
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Ji W, Xu L, Sun X, Xu X, Zhang H, Luo H, Yao B, Zhang W, Su X, Huang H. Exploiting Systematic Engineering of the Expression Cassette as a Powerful Tool to Enhance Heterologous Gene Expression in Trichoderma reesei. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:5307-5317. [PMID: 38426871 DOI: 10.1021/acs.jafc.3c07988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Many endeavors in expressing a heterologous gene in microbial hosts rely on simply placing the gene of interest between a selected pair of promoters and terminator. However, although the expression efficiency could be improved by engineering the host cell, how modifying the expression cassette itself systematically would affect heterologous gene expression remains largely unknown. As the promoter and terminator bear plentiful cis-elements, herein using the Aspergillus niger mannanase with high application value in animal feeds and the eukaryotic filamentous fungus workhorse Trichoderma reesei as a model gene/host, systematic engineering of an expression cassette was investigated to decipher the effect of its mutagenesis on heterologous gene expression. Modifying the promoter, signal peptide, the eukaryotic-specific Kozak sequence, and the 3'-UTR could stepwise improve extracellular mannanase production from 17 U/mL to an ultimate 471 U/mL, representing a 27.7-fold increase in expression. The strategies can be generally applied in improving the production of heterologous proteins in eukaryotic microbial hosts.
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Affiliation(s)
- Wangli Ji
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Haidian District, Beijing 100081, China
| | - Li Xu
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing 100193, China
| | - Xianhua Sun
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing 100193, China
| | - Xinxin Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Haidian District, Beijing 100081, China
| | - Honglian Zhang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing 100193, China
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing 100193, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing 100193, China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Haidian District, Beijing 100081, China
| | - Xiaoyun Su
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing 100193, China
| | - Huoqing Huang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing 100193, China
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12
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Kim YA, Mousavi K, Yazdi A, Zwierzyna M, Cardinali M, Fox D, Peel T, Coller J, Aggarwal K, Maruggi G. Computational design of mRNA vaccines. Vaccine 2024; 42:1831-1840. [PMID: 37479613 DOI: 10.1016/j.vaccine.2023.07.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/23/2023] [Accepted: 07/10/2023] [Indexed: 07/23/2023]
Abstract
mRNA technology has emerged as a successful vaccine platform that offered a swift response to the COVID-19 pandemic. Accumulating evidence shows that vaccine efficacy, thermostability, and other important properties, are largely impacted by intrinsic properties of the mRNA molecule, such as RNA sequence and structure, both of which can be optimized. Designing mRNA sequence for vaccines presents a combinatorial problem due to an extremely large selection space. For instance, due to the degeneracy of the genetic code, there are over 10632 possible mRNA sequences that could encode the spike protein, the COVID-19 vaccines' target. Moreover, designing different elements of the mRNA sequence simultaneously against multiple objectives such as translational efficiency, reduced reactogenicity, and improved stability requires an efficient and sophisticated optimization strategy. Recently, there has been a growing interest in utilizing computational tools to redesign mRNA sequences to improve vaccine characteristics and expedite discovery timelines. In this review, we explore important biophysical features of mRNA to be considered for vaccine design and discuss how computational approaches can be applied to rapidly design mRNA sequences with desirable characteristics.
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Affiliation(s)
| | | | | | | | | | | | | | - Jeff Coller
- Johns Hopkins University, Baltimore, MD, USA
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13
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Hsaio S, Saglam N, Morrow D, Shain DH. Transcriptomic Profiling at the Maternal-to-Zygotic Transition in Leech, Helobdella austinensis. Genes (Basel) 2024; 15:283. [PMID: 38540342 PMCID: PMC10970458 DOI: 10.3390/genes15030283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 06/15/2024] Open
Abstract
The glossiphoniid leech, Helobdella austinensis, is an experimentally tractable member of the superphylum, Lophotrochozoa. Its large embryonic cells, stereotyped asymmetric cell divisions and ex vivo development capabilities makes it a favorable model for studying the molecular and cellular events of a representative spiralian. In this study, we focused on a narrow developmental time window of ~6-8 h, comprising stages just prior to and immediately following zygote deposition. Employing RNA-Seq methodology, we identified differentially expressed transcripts at this fundamental ontogenic boundary, known as the maternal-to-zygotic transition (MZT). Gene expression changes were characterized by the massive degradation of maternal RNAs (~45%) coupled with the rapid transcription of ~5000 zygotic genes (~20% of the genome) in the first mitotic cell cycle. The latter transcripts encoded a mixture of cell maintenance and regulatory proteins that predictably influence downstream developmental events.
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Affiliation(s)
- Samuel Hsaio
- Center for Computational and Integrative Biology, Rutgers The State University of New Jersey, Joint Health Sciences Center, 201 South Broadway, Camden, NJ 08103, USA
| | - Naim Saglam
- Department of Aquaculture and Fish Diseases, Fisheries Faculty, Firat University, 23200 Elazig, Türkiye
| | - David Morrow
- Biology Department, Rutgers The State University of New Jersey, Joint Health Sciences Center, 201 South Broadway, Camden, NJ 08103, USA
| | - Daniel H. Shain
- Center for Computational and Integrative Biology, Rutgers The State University of New Jersey, Joint Health Sciences Center, 201 South Broadway, Camden, NJ 08103, USA
- Biology Department, Rutgers The State University of New Jersey, Joint Health Sciences Center, 201 South Broadway, Camden, NJ 08103, USA
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14
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Wang J, Zhang G, Qian W, Li K. Decoding the Heterogeneity and Specialized Function of Translation Machinery Through Ribosome Profiling in Yeast Mutants of Initiation Factors. Adv Biol (Weinh) 2024; 8:e2300494. [PMID: 37997253 DOI: 10.1002/adbi.202300494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 09/24/2023] [Indexed: 11/25/2023]
Abstract
The nuanced heterogeneity and specialized functions of translation machinery are increasingly recognized as crucial for precise translational regulation. Here, high-throughput ribosomal profiling (ribo-seq) is used to analyze the specialized roles of eukaryotic initiation factors (eIFs) in the budding yeast. By examining changes in ribosomal distribution across the genome resulting from knockouts of eIF4A, eIF4B, eIF4G1, CAF20, or EAP1, or knockdowns of eIF1, eIF1A, eIF4E, or PAB1, two distinct initiation-factor groups, the "looping" and "scanning" groups are discerned, based on similarities in the ribosomal landscapes their perturbation induced. The study delves into the cis-regulatory sequence features of genes influenced predominantly by each group, revealing that genes more dependent on the looping-group factors generally have shorter transcripts and poly(A) tails. In contrast, genes more dependent on the scanning-group factors often possess upstream open reading frames and exhibit a higher GC content in their 5' untranslated regions. From the ribosomal RNA fragments identified in the ribo-seq data, ribosomal heterogeneity associated with perturbation of specific initiation factors is further identified, suggesting their potential roles in regulating ribosomal components. Collectively, the study illuminates the complexity of translational regulation driven by heterogeneity and specialized functions of translation machinery, presenting potential approaches for targeted gene translation manipulation.
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Affiliation(s)
- Jia Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Geyu Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenfeng Qian
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ke Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
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15
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Anzell AR, Kunz AB, Donovan JP, Tran TG, Lu X, Young S, Roman BL. Blood flow regulates acvrl1 transcription via ligand-dependent Alk1 activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.25.576046. [PMID: 38328175 PMCID: PMC10849739 DOI: 10.1101/2024.01.25.576046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Hereditary hemorrhagic telangiectasia (HHT) is an autosomal dominant disease characterized by the development of arteriovenous malformations (AVMs) that can result in significant morbidity and mortality. HHT is caused primarily by mutations in bone morphogenetic protein receptors ACVRL1/ALK1, a signaling receptor, or endoglin (ENG), an accessory receptor. Because overexpression of Acvrl1 prevents AVM development in both Acvrl1 and Eng null mice, enhancing ACVRL1 expression may be a promising approach to development of targeted therapies for HHT. Therefore, we sought to understand the molecular mechanism of ACVRL1 regulation. We previously demonstrated in zebrafish embryos that acvrl1 is predominantly expressed in arterial endothelial cells and that expression requires blood flow. Here, we document that flow dependence exhibits regional heterogeneity and that acvrl1 expression is rapidly restored after reinitiation of flow. Furthermore, we find that acvrl1 expression is significantly decreased in mutants that lack the circulating Alk1 ligand, Bmp10, and that BMP10 microinjection into the vasculature in the absence of flow enhances acvrl1 expression in an Alk1-dependent manner. Using a transgenic acvrl1:egfp reporter line, we find that flow and Bmp10 regulate acvrl1 at the level of transcription. Finally, we observe similar ALK1 ligand-dependent increases in ACVRL1 in human endothelial cells subjected to shear stress. These data suggest that Bmp10 acts downstream of blood flow to maintain or enhance acvrl1 expression via a positive feedback mechanism, and that ALK1 activating therapeutics may have dual functionality by increasing both ALK1 signaling flux and ACVRL1 expression.
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Affiliation(s)
- Anthony R. Anzell
- Department of Human Genetics, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
- Pittsburgh Heart, Lung and Blood Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Amy Biery Kunz
- Department of Human Genetics, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
- Current affiliation: Allegheny Health Network, Pittsburgh, PA, USA
| | - James P. Donovan
- Department of Human Genetics, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Thanhlong G. Tran
- Department of Human Genetics, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
- Current affiliation: National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xinyan Lu
- Department of Human Genetics, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
| | - Sarah Young
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
- Current affiliation: Carnegie Mellon University, University Libraries, Pittsburgh, PA, USA
| | - Beth L. Roman
- Department of Human Genetics, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
- Pittsburgh Heart, Lung and Blood Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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16
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Peng F, Nordgren CE, Murray JI. A spatiotemporally resolved atlas of mRNA decay in the C. elegans embryo reveals differential regulation of mRNA stability across stages and cell types. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.15.575757. [PMID: 38293118 PMCID: PMC10827189 DOI: 10.1101/2024.01.15.575757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
During embryonic development, cells undergo dynamic changes in gene expression that are required for appropriate cell fate specification. Although both transcription and mRNA degradation contribute to gene expression dynamics, patterns of mRNA decay are less well-understood. Here we directly measured spatiotemporally resolved mRNA decay rates transcriptome-wide throughout C. elegans embryogenesis by transcription inhibition followed by bulk and single-cell RNA-sequencing. This allowed us to calculate mRNA half-lives within specific cell types and developmental stages and identify differentially regulated mRNA decay throughout embryonic development. We identified transcript features that are correlated with mRNA stability and found that mRNA decay rates are associated with distinct peaks in gene expression over time. Moreover, we provide evidence that, on average, mRNA is more stable in the germline compared to in the soma and in later embryonic stages compared to in earlier stages. This work suggests that differential mRNA decay across cell states and time helps to shape developmental gene expression, and it provides a valuable resource for studies of mRNA turnover regulatory mechanisms.
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Affiliation(s)
- Felicia Peng
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - C Erik Nordgren
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - John Isaac Murray
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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17
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Schall PZ, Latham KE. Predictive modeling of oocyte maternal mRNA features for five mammalian species reveals potential shared and species-restricted regulators during maturation. Physiol Genomics 2024; 56:9-31. [PMID: 37842744 PMCID: PMC11281819 DOI: 10.1152/physiolgenomics.00048.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/26/2023] [Accepted: 10/09/2023] [Indexed: 10/17/2023] Open
Abstract
Oocyte maturation is accompanied by changes in abundances of thousands of mRNAs, many degraded and many preferentially stabilized. mRNA stability can be regulated by diverse features including GC content, codon bias, and motifs within the 3'-untranslated region (UTR) interacting with RNA binding proteins (RBPs) and miRNAs. Many studies have identified factors participating in mRNA splicing, bulk mRNA storage, and translational recruitment in mammalian oocytes, but the roles of potentially hundreds of expressed factors, how they regulate cohorts of thousands of mRNAs, and to what extent their functions are conserved across species has not been determined. We performed an extensive in silico cross-species analysis of features associated with mRNAs of different stability classes during oocyte maturation (stable, moderately degraded, and highly degraded) for five mammalian species. Using publicly available RNA sequencing data for germinal vesicle (GV) and MII oocyte transcriptomes, we determined that 3'-UTR length and synonymous codon usage are positively associated with stability, while greater GC content is negatively associated with stability. By applying machine learning and feature selection strategies, we identified RBPs and miRNAs that are predictive of mRNA stability, including some across multiple species and others more species-restricted. The results provide new insight into the mechanisms regulating maternal mRNA stabilization or degradation.NEW & NOTEWORTHY Conservation across species of mRNA features regulating maternal mRNA stability during mammalian oocyte maturation was analyzed. 3'-Untranslated region length and synonymous codon usage are positively associated with stability, while GC content is negatively associated. Just three RNA binding protein motifs were predicted to regulate mRNA stability across all five species examined, but associated pathways and functions are shared, indicating oocytes of different species arrive at comparable physiological destinations via different routes.
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Affiliation(s)
- Peter Z Schall
- Department of Animal Science, Michigan State University, East Lansing, Michigan, United States
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan, United States
- Comparative Medicine and Integrative Biology Program, Michigan State University, East Lansing, Michigan, United States
| | - Keith E Latham
- Department of Animal Science, Michigan State University, East Lansing, Michigan, United States
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan, United States
- Department of Obstetrics, Gynecology, and Reproductive Biology, Michigan State University, East Lansing, Michigan, United States
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18
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Barrington CL, Galindo G, Koch AL, Horton ER, Morrison EJ, Tisa S, Stasevich TJ, Rissland OS. Synonymous codon usage regulates translation initiation. Cell Rep 2023; 42:113413. [PMID: 38096059 PMCID: PMC10790568 DOI: 10.1016/j.celrep.2023.113413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 08/30/2023] [Accepted: 10/25/2023] [Indexed: 12/30/2023] Open
Abstract
Nonoptimal synonymous codons repress gene expression, but the underlying mechanisms are poorly understood. We and others have previously shown that nonoptimal codons slow translation elongation speeds and thereby trigger messenger RNA (mRNA) degradation. Nevertheless, transcript levels are often insufficient to explain protein levels, suggesting additional mechanisms by which codon usage regulates gene expression. Using reporters in human and Drosophila cells, we find that transcript levels account for less than half of the variation in protein abundance due to codon usage. This discrepancy is explained by translational differences whereby nonoptimal codons repress translation initiation. Nonoptimal transcripts are also less bound by the translation initiation factors eIF4E and eIF4G1, providing a mechanistic explanation for their reduced initiation rates. Importantly, translational repression can occur without mRNA decay and deadenylation, and it does not depend on the known nonoptimality sensor, CNOT3. Our results reveal a potent mechanism of regulation by codon usage where nonoptimal codons repress further rounds of translation.
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Affiliation(s)
- Chloe L Barrington
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA; RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Gabriel Galindo
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Amanda L Koch
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Emma R Horton
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA; RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Evan J Morrison
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA; RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Samantha Tisa
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA; RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Timothy J Stasevich
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Olivia S Rissland
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA; RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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19
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Zhao X, Ma D, Ishiguro K, Saito H, Akichika S, Matsuzawa I, Mito M, Irie T, Ishibashi K, Wakabayashi K, Sakaguchi Y, Yokoyama T, Mishima Y, Shirouzu M, Iwasaki S, Suzuki T, Suzuki T. Glycosylated queuosines in tRNAs optimize translational rate and post-embryonic growth. Cell 2023; 186:5517-5535.e24. [PMID: 37992713 DOI: 10.1016/j.cell.2023.10.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 08/14/2023] [Accepted: 10/26/2023] [Indexed: 11/24/2023]
Abstract
Transfer RNA (tRNA) modifications are critical for protein synthesis. Queuosine (Q), a 7-deaza-guanosine derivative, is present in tRNA anticodons. In vertebrate tRNAs for Tyr and Asp, Q is further glycosylated with galactose and mannose to generate galQ and manQ, respectively. However, biogenesis and physiological relevance of Q-glycosylation remain poorly understood. Here, we biochemically identified two RNA glycosylases, QTGAL and QTMAN, and successfully reconstituted Q-glycosylation of tRNAs using nucleotide diphosphate sugars. Ribosome profiling of knockout cells revealed that Q-glycosylation slowed down elongation at cognate codons, UAC and GAC (GAU), respectively. We also found that galactosylation of Q suppresses stop codon readthrough. Moreover, protein aggregates increased in cells lacking Q-glycosylation, indicating that Q-glycosylation contributes to proteostasis. Cryo-EM of human ribosome-tRNA complex revealed the molecular basis of codon recognition regulated by Q-glycosylations. Furthermore, zebrafish qtgal and qtman knockout lines displayed shortened body length, implying that Q-glycosylation is required for post-embryonic growth in vertebrates.
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Affiliation(s)
- Xuewei Zhao
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Ding Ma
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Kensuke Ishiguro
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan; Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa 230-0045, Japan
| | - Hironori Saito
- RNA System Biochemistry Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8561, Japan
| | - Shinichiro Akichika
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Ikuya Matsuzawa
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Mari Mito
- RNA System Biochemistry Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Toru Irie
- Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Kota Ishibashi
- Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Kimi Wakabayashi
- Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Yuriko Sakaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Takeshi Yokoyama
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Yuichiro Mishima
- Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa 230-0045, Japan
| | - Shintaro Iwasaki
- RNA System Biochemistry Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8561, Japan
| | - Takeo Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan.
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan.
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20
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Ugajin N, Imami K, Takada H, Ishihama Y, Chiba S, Mishima Y. Znf598-mediated Rps10/eS10 ubiquitination contributes to the ribosome ubiquitination dynamics during zebrafish development. RNA (NEW YORK, N.Y.) 2023; 29:1910-1927. [PMID: 37751929 PMCID: PMC10653392 DOI: 10.1261/rna.079633.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 09/05/2023] [Indexed: 09/28/2023]
Abstract
The ribosome is a translational apparatus that comprises about 80 ribosomal proteins and four rRNAs. Recent studies reported that ribosome ubiquitination is crucial for translational regulation and ribosome-associated quality control (RQC). However, little is known about the dynamics of ribosome ubiquitination under complex biological processes of multicellular organisms. To explore ribosome ubiquitination during animal development, we generated a zebrafish strain that expresses a FLAG-tagged ribosomal protein Rpl36/eL36 from its endogenous locus. We examined ribosome ubiquitination during zebrafish development by combining affinity purification of ribosomes from rpl36-FLAG zebrafish embryos with immunoblotting analysis. Our findings showed that the ubiquitination of ribosomal proteins dynamically changed as development proceeded. We also showed that during zebrafish development, the ribosome was ubiquitinated by Znf598, an E3 ubiquitin ligase that activates RQC. Ribosomal protein Rps10/eS10 was found to be a key ubiquitinated protein during development. Furthermore, we showed that Rps10/eS10 ubiquitination-site mutations reduced the overall ubiquitination pattern of the ribosome. These results demonstrate the complexity and dynamics of ribosome ubiquitination during zebrafish development.
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Affiliation(s)
- Nozomi Ugajin
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Koshi Imami
- RIKEN Center for Integrative Medical Sciences, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiraku Takada
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shinobu Chiba
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Yuichiro Mishima
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
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21
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Nagorska A, Zaucker A, Lambert F, Inman A, Toral-Perez S, Gorodkin J, Wan Y, Smutny M, Sampath K. Translational control of furina by an RNA regulon is important for left-right patterning, heart morphogenesis and cardiac valve function. Development 2023; 150:dev201657. [PMID: 38032088 PMCID: PMC10730018 DOI: 10.1242/dev.201657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023]
Abstract
Heart development is a complex process that requires asymmetric positioning of the heart, cardiac growth and valve morphogenesis. The mechanisms controlling heart morphogenesis and valve formation are not fully understood. The pro-convertase FurinA functions in heart development across vertebrates. How FurinA activity is regulated during heart development is unknown. Through computational analysis of the zebrafish transcriptome, we identified an RNA motif in a variant FurinA transcript harbouring a long 3' untranslated region (3'UTR). The alternative 3'UTR furina isoform is expressed prior to organ positioning. Somatic deletions in the furina 3'UTR lead to embryonic left-right patterning defects. Reporter localisation and RNA-binding assays show that the furina 3'UTR forms complexes with the conserved RNA-binding translational repressor, Ybx1. Conditional ybx1 mutant embryos show premature and increased Furin reporter expression, abnormal cardiac morphogenesis and looping defects. Mutant ybx1 hearts have an expanded atrioventricular canal, abnormal sino-atrial valves and retrograde blood flow from the ventricle to the atrium. This is similar to observations in humans with heart valve regurgitation. Thus, the furina 3'UTR element/Ybx1 regulon is important for translational repression of FurinA and regulation of heart development.
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Affiliation(s)
- Agnieszka Nagorska
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Andreas Zaucker
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Finnlay Lambert
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A*STAR, Singapore 138672
| | - Angus Inman
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Sara Toral-Perez
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Jan Gorodkin
- Center for non-coding RNAs in Technology and Health, Department of Veterinary and Animal Sciences, Faculty for Health and Medical Sciences, University of Copenhagen, Grønnega °rdsvej 3, 1870 Frederiksberg C, Denmark
| | - Yue Wan
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A*STAR, Singapore 138672
| | - Michael Smutny
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
- Centre for Mechanochemical Cell Biology, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Karuna Sampath
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
- Centre for Mechanochemical Cell Biology, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
- Centre for Early Life, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
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22
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Takada Y, Fierro L, Sato K, Sanada T, Ishii A, Yamamoto T, Kotani T. Mature mRNA processing that deletes 3' end sequences directs translational activation and embryonic development. SCIENCE ADVANCES 2023; 9:eadg6532. [PMID: 38000026 PMCID: PMC10672166 DOI: 10.1126/sciadv.adg6532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 10/25/2023] [Indexed: 11/26/2023]
Abstract
Eggs accumulate thousands of translationally repressed mRNAs that are translated into proteins after fertilization to direct diverse developmental processes. However, molecular mechanisms underlying the translation of stored mRNAs after fertilization remain unclear. Here, we report a previously unknown RNA processing of 3' end sequences of mature mRNAs that activates the translation of stored mRNAs. Specifically, 9 to 72 nucleotides at the 3' ends of zebrafish pou5f3 and mouse Pou5f1 mRNAs were deleted in the early stages of development. Reporter assays illustrated the effective translation of the truncated forms of mRNAs. Moreover, promotion and inhibition of the shortening of 3' ends accelerated and attenuated Pou5f3 accumulation, respectively, resulting in defective development. Identification of proteins binding to unprocessed and/or processed mRNAs revealed that mRNA shortening acts as molecular switches. Comprehensive analysis revealed that >250 mRNAs underwent this processing. Therefore, our results provide a molecular principle that triggers the translational activation and directs development.
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Affiliation(s)
- Yuki Takada
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Ludivine Fierro
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Keisuke Sato
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Takahiro Sanada
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Anna Ishii
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Takehiro Yamamoto
- Department of Biochemistry, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Tomoya Kotani
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
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23
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He F, Jacobson A. Eukaryotic mRNA decapping factors: molecular mechanisms and activity. FEBS J 2023; 290:5057-5085. [PMID: 36098474 PMCID: PMC10008757 DOI: 10.1111/febs.16626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/11/2022] [Accepted: 09/12/2022] [Indexed: 11/30/2022]
Abstract
Decapping is the enzymatic removal of 5' cap structures from mRNAs in eukaryotic cells. Cap structures normally enhance mRNA translation and stability, and their excision commits an mRNA to complete 5'-3' exoribonucleolytic digestion and generally ends the physical and functional cellular presence of the mRNA. Decapping plays a pivotal role in eukaryotic cytoplasmic mRNA turnover and is a critical and highly regulated event in multiple 5'-3' mRNA decay pathways, including general 5'-3' decay, nonsense-mediated mRNA decay (NMD), AU-rich element-mediated mRNA decay, microRNA-mediated gene silencing, and targeted transcript-specific mRNA decay. In the yeast Saccharomyces cerevisiae, mRNA decapping is carried out by a single Dcp1-Dcp2 decapping enzyme in concert with the accessory activities of specific regulators commonly known as decapping activators or enhancers. These regulatory proteins include the general decapping activators Edc1, 2, and 3, Dhh1, Scd6, Pat1, and the Lsm1-7 complex, as well as the NMD-specific factors, Upf1, 2, and 3. Here, we focus on in vivo mRNA decapping regulation in yeast. We summarize recently uncovered molecular mechanisms that control selective targeting of the yeast decapping enzyme and discuss new roles for specific decapping activators in controlling decapping enzyme targeting, assembly of target-specific decapping complexes, and the monitoring of mRNA translation. Further, we discuss the kinetic contribution of mRNA decapping for overall decay of different substrate mRNAs and highlight experimental evidence pointing to the functional coordination and physical coupling between events in mRNA deadenylation, decapping, and 5'-3' exoribonucleolytic decay.
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Affiliation(s)
- Feng He
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, 368 Plantation Street, Worcester, MA 01655
| | - Allan Jacobson
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, 368 Plantation Street, Worcester, MA 01655
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24
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Sako H, Youssef M, Elisseeva O, Akimoto T, Suzuki K, Ushida T, Yamamoto T. microRNAs slow translating ribosomes to prevent protein misfolding in eukaryotes. EMBO J 2023; 42:e112469. [PMID: 37492926 PMCID: PMC10505912 DOI: 10.15252/embj.2022112469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 03/20/2023] [Accepted: 06/18/2023] [Indexed: 07/27/2023] Open
Abstract
Slower translation rates reduce protein misfolding. Such reductions in speed can be mediated by the presence of non-optimal codons, which allow time for proper folding to occur. Although this phenomenon is conserved from bacteria to humans, it is not known whether there are additional eukaryote-specific mechanisms which act in the same way. MicroRNAs (miRNAs), not present in prokaryotes, target both coding sequences (CDS) and 3' untranslated regions (UTR). Given their low suppressive efficiency, it has been unclear why miRNAs are equally likely to bind to a CDS. Here, we show that miRNAs transiently stall translating ribosomes, preventing protein misfolding with little negative effect on protein abundance. We first analyzed ribosome profiles and miRNA binding sites to examine whether miRNAs stall ribosomes. Furthermore, either global or specific miRNA deficiency accelerated ribosomes and induced aggregation of a misfolding-prone polypeptide reporter. These defects were rescued by slowing ribosomes using non-cleaving shRNAs as miRNA mimics. We finally show that proinsulin misfolding, associated with type II diabetes, was resolved by non-cleaving shRNAs. Our findings provide a eukaryote-specific mechanism of co-translational protein folding and a previously unknown mechanism of action to target protein misfolding diseases.
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Affiliation(s)
- Hiroaki Sako
- Cell Signal UnitOkinawa Institute of Science and Technology Graduate University (OIST)OkinawaJapan
| | - Mohieldin Youssef
- Cell Signal UnitOkinawa Institute of Science and Technology Graduate University (OIST)OkinawaJapan
| | - Olga Elisseeva
- Cell Signal UnitOkinawa Institute of Science and Technology Graduate University (OIST)OkinawaJapan
| | | | | | - Takashi Ushida
- Department of Mechanical EngineeringThe University of TokyoTokyoJapan
| | - Tadashi Yamamoto
- Cell Signal UnitOkinawa Institute of Science and Technology Graduate University (OIST)OkinawaJapan
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25
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Absmeier E, Chandrasekaran V, O'Reilly FJ, Stowell JAW, Rappsilber J, Passmore LA. Specific recognition and ubiquitination of translating ribosomes by mammalian CCR4-NOT. Nat Struct Mol Biol 2023; 30:1314-1322. [PMID: 37653243 PMCID: PMC7615087 DOI: 10.1038/s41594-023-01075-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 07/24/2023] [Indexed: 09/02/2023]
Abstract
Translation affects messenger RNA stability and, in yeast, this is mediated by the Ccr4-Not deadenylation complex. The details of this process in mammals remain unclear. Here, we use cryogenic electron microscopy (cryo-EM) and crosslinking mass spectrometry to show that mammalian CCR4-NOT specifically recognizes ribosomes that are stalled during translation elongation in an in vitro reconstituted system with rabbit and human components. Similar to yeast, mammalian CCR4-NOT inserts a helical bundle of its CNOT3 subunit into the empty E site of the ribosome. Our cryo-EM structure shows that CNOT3 also locks the L1 stalk in an open conformation to inhibit further translation. CCR4-NOT is required for stable association of the nonconstitutive subunit CNOT4, which ubiquitinates the ribosome, likely to signal stalled translation elongation. Overall, our work shows that human CCR4-NOT not only detects but also enforces ribosomal stalling to couple translation and mRNA decay.
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Affiliation(s)
- Eva Absmeier
- MRC Laboratory of Molecular Biology (LMB), Cambridge, UK
- Freie University of Berlin, Berlin, Germany
| | | | | | | | - Juri Rappsilber
- Technical University of Berlin, Chair of Bioanalytics, Berlin, Germany
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
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26
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Ayers TN, Nicotra ML, Lee MT. Parallels and contrasts between the cnidarian and bilaterian maternal-to-zygotic transition are revealed in Hydractinia embryos. PLoS Genet 2023; 19:e1010845. [PMID: 37440598 PMCID: PMC10368294 DOI: 10.1371/journal.pgen.1010845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/25/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
Embryogenesis requires coordinated gene regulatory activities early on that establish the trajectory of subsequent development, during a period called the maternal-to-zygotic transition (MZT). The MZT comprises transcriptional activation of the embryonic genome and post-transcriptional regulation of egg-inherited maternal mRNA. Investigation into the MZT in animals has focused almost exclusively on bilaterians, which include all classical models such as flies, worms, sea urchin, and vertebrates, thus limiting our capacity to understand the gene regulatory paradigms uniting the MZT across all animals. Here, we elucidate the MZT of a non-bilaterian, the cnidarian Hydractinia symbiolongicarpus. Using parallel poly(A)-selected and non poly(A)-dependent RNA-seq approaches, we find that the Hydractinia MZT is composed of regulatory activities similar to many bilaterians, including cytoplasmic readenylation of maternally contributed mRNA, delayed genome activation, and separate phases of maternal mRNA deadenylation and degradation that likely depend on both maternally and zygotically encoded clearance factors, including microRNAs. But we also observe massive upregulation of histone genes and an expanded repertoire of predicted H4K20 methyltransferases, aspects thus far particular to the Hydractinia MZT and potentially underlying a novel mode of early embryonic chromatin regulation. Thus, similar regulatory strategies with taxon-specific elaboration underlie the MZT in both bilaterian and non-bilaterian embryos, providing insight into how an essential developmental transition may have arisen in ancestral animals.
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Affiliation(s)
- Taylor N. Ayers
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh Pennsylvania, United States of America
| | - Matthew L. Nicotra
- Thomas E. Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Miler T. Lee
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh Pennsylvania, United States of America
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27
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Abstract
Messenger RNA (mRNA) stability and translational efficiency are two crucial aspects of the post-transcriptional process that profoundly impact protein production in a cell. While it is widely known that ribosomes produce proteins, studies during the past decade have surprisingly revealed that ribosomes also control mRNA stability in a codon-dependent manner, a process referred to as codon optimality. Therefore, codons, the three-nucleotide words read by the ribosome, have a potent effect on mRNA stability and provide cis-regulatory information that extends beyond the amino acids they encode. While the codon optimality molecular mechanism is still unclear, the translation elongation rate appears to trigger mRNA decay. Thus, transfer RNAs emerge as potential master gene regulators affecting mRNA stability. Furthermore, while few factors related to codon optimality have been identified in yeast, the orthologous genes in vertebrates do not necessary share the same functions. Here, we discuss codon optimality findings and gene regulation layers related to codon composition in different eukaryotic species.
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Affiliation(s)
- Qiushuang Wu
- Stowers Institute for Medical Research, Kansas City, Missouri, USA;
| | - Ariel A Bazzini
- Stowers Institute for Medical Research, Kansas City, Missouri, USA;
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, Kansas, USA
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28
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Nagao A, Nakanishi Y, Yamaguchi Y, Mishina Y, Karoji M, Toya T, Fujita T, Iwasaki S, Miyauchi K, Sakaguchi Y, Suzuki T. Quality control of protein synthesis in the early elongation stage. Nat Commun 2023; 14:2704. [PMID: 37198183 PMCID: PMC10192219 DOI: 10.1038/s41467-023-38077-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 04/14/2023] [Indexed: 05/19/2023] Open
Abstract
In the early stage of bacterial translation, peptidyl-tRNAs frequently dissociate from the ribosome (pep-tRNA drop-off) and are recycled by peptidyl-tRNA hydrolase. Here, we establish a highly sensitive method for profiling of pep-tRNAs using mass spectrometry, and successfully detect a large number of nascent peptides from pep-tRNAs accumulated in Escherichia coli pthts strain. Based on molecular mass analysis, we found about 20% of the peptides bear single amino-acid substitutions of the N-terminal sequences of E. coli ORFs. Detailed analysis of individual pep-tRNAs and reporter assay revealed that most of the substitutions take place at the C-terminal drop-off site and that the miscoded pep-tRNAs rarely participate in the next round of elongation but dissociate from the ribosome. These findings suggest that pep-tRNA drop-off is an active mechanism by which the ribosome rejects miscoded pep-tRNAs in the early elongation, thereby contributing to quality control of protein synthesis after peptide bond formation.
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Affiliation(s)
- Asuteka Nagao
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan.
| | - Yui Nakanishi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Yutaro Yamaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Yoshifumi Mishina
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Minami Karoji
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Takafumi Toya
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Tomoya Fujita
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
| | - Kenjyo Miyauchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Yuriko Sakaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan.
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29
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Ayers TN, Nicotra ML, Lee MT. Parallels and contrasts between the cnidarian and bilaterian maternal-to-zygotic transition are revealed in Hydractinia embryos. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.540083. [PMID: 37214839 PMCID: PMC10197650 DOI: 10.1101/2023.05.09.540083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Embryogenesis requires coordinated gene regulatory activities early on that establish the trajectory of subsequent development, during a period called the maternal-to-zygotic transition (MZT). The MZT comprises transcriptional activation of the embryonic genome and post-transcriptional regulation of egg-inherited maternal mRNA. Investigation into the MZT in animals has focused almost exclusively on bilaterians, which include all classical models such as flies, worms, sea urchin, and vertebrates, thus limiting our capacity to understand the gene regulatory paradigms uniting the MZT across all animals. Here, we elucidate the MZT of a non-bilaterian, the cnidarian Hydractinia symbiolongicarpus . Using parallel poly(A)-selected and non poly(A)-dependent RNA-seq approaches, we find that the Hydractinia MZT is composed of regulatory activities analogous to many bilaterians, including cytoplasmic readenylation of maternally contributed mRNA, delayed genome activation, and separate phases of maternal mRNA deadenylation and degradation that likely depend on both maternally and zygotically encoded clearance factors, including microRNAs. But we also observe massive upregulation of histone genes and an expanded repertoire of predicted H4K20 methyltransferases, aspects thus far unique to the Hydractinia MZT and potentially underlying a novel mode of early embryonic chromatin regulation. Thus, similar regulatory strategies with taxon-specific elaboration underlie the MZT in both bilaterian and non-bilaterian embryos, providing insight into how an essential developmental transition may have arisen in ancestral animals.
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Affiliation(s)
- Taylor N. Ayers
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15213 U.S.A
| | - Matthew L. Nicotra
- Thomas E. Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, PA 15261 U.S.A
| | - Miler T. Lee
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15213 U.S.A
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30
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Jung J, Ohk J, Kim H, Holt CE, Park HJ, Jung H. mRNA transport, translation, and decay in adult mammalian central nervous system axons. Neuron 2023; 111:650-668.e4. [PMID: 36584679 DOI: 10.1016/j.neuron.2022.12.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/31/2022] [Accepted: 12/08/2022] [Indexed: 12/30/2022]
Abstract
Localized mRNA translation regulates synapse function and axon maintenance, but how compartment-specific mRNA repertoires are regulated is largely unknown. We developed an axonal transcriptome capture method that allows deep sequencing of metabolically labeled mRNAs from retinal ganglion cell axon terminals in mouse. Comparing axonal-to-somal transcriptomes and axonal translatome-to-transcriptome enables genome-wide visualization of mRNA transport and translation and unveils potential regulators tuned to each process. FMRP and TDP-43 stand out as key regulators of transport, and experiments in Fmr1 knockout mice validate FMRP's role in the axonal transportation of synapse-related mRNAs. Pulse-and-chase experiments enable genome-wide assessment of mRNA stability in axons and reveal a strong coupling between mRNA translation and decay. Measuring the absolute mRNA abundance per axon terminal shows that the adult axonal transcriptome is stably maintained by persistent transport. Our datasets provide a rich resource for unique insights into RNA-based mechanisms in maintaining presynaptic structure and function in vivo.
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Affiliation(s)
- Jane Jung
- Department of Anatomy, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Jiyeon Ohk
- Department of Anatomy, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Hyeyoung Kim
- Department of Anatomy, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Christine E Holt
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Hyun Jung Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea.
| | - Hosung Jung
- Department of Anatomy, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea.
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31
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Picard MAL, Leblay F, Cassan C, Willemsen A, Daron J, Bauffe F, Decourcelle M, Demange A, Bravo IG. Transcriptomic, proteomic, and functional consequences of codon usage bias in human cells during heterologous gene expression. Protein Sci 2023; 32:e4576. [PMID: 36692287 PMCID: PMC9926478 DOI: 10.1002/pro.4576] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/12/2023] [Accepted: 01/14/2023] [Indexed: 01/25/2023]
Abstract
Differences in codon frequency between genomes, genes, or positions along a gene, modulate transcription and translation efficiency, leading to phenotypic and functional differences. Here, we present a multiscale analysis of the effects of synonymous codon recoding during heterologous gene expression in human cells, quantifying the phenotypic consequences of codon usage bias at different molecular and cellular levels, with an emphasis on translation elongation. Six synonymous versions of an antibiotic resistance gene were generated, fused to a fluorescent reporter, and independently expressed in HEK293 cells. Multiscale phenotype was analyzed by means of quantitative transcriptome and proteome assessment, as proxies for gene expression; cellular fluorescence, as a proxy for single-cell level expression; and real-time cell proliferation in absence or presence of antibiotic, as a proxy for the cell fitness. We show that differences in codon usage bias strongly impact the molecular and cellular phenotype: (i) they result in large differences in mRNA levels and protein levels, leading to differences of over 15 times in translation efficiency; (ii) they introduce unpredicted splicing events; (iii) they lead to reproducible phenotypic heterogeneity; and (iv) they lead to a trade-off between the benefit of antibiotic resistance and the burden of heterologous expression. In human cells in culture, codon usage bias modulates gene expression by modifying mRNA availability and suitability for translation, leading to differences in protein levels and eventually eliciting functional phenotypic changes.
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Affiliation(s)
- Marion A. L. Picard
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Fiona Leblay
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Cécile Cassan
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Anouk Willemsen
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Josquin Daron
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Frédérique Bauffe
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Mathilde Decourcelle
- BioCampus Montpellier (University of Montpellier, CNRS, INSERM)MontpellierFrance
| | - Antonin Demange
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Ignacio G. Bravo
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
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32
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Bhat P, Cabrera-Quio LE, Herzog VA, Fasching N, Pauli A, Ameres SL. SLAMseq resolves the kinetics of maternal and zygotic gene expression during early zebrafish embryogenesis. Cell Rep 2023; 42:112070. [PMID: 36757845 DOI: 10.1016/j.celrep.2023.112070] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 11/27/2022] [Accepted: 01/20/2023] [Indexed: 02/10/2023] Open
Abstract
The maternal-to-zygotic transition (MZT) is a key developmental process in metazoan embryos that involves the activation of zygotic transcription (ZGA) and degradation of maternal transcripts. We employed metabolic mRNA sequencing (SLAMseq) to deconvolute the compound embryonic transcriptome in zebrafish. While mitochondrial zygotic transcripts prevail prior to MZT, we uncover the spurious transcription of hundreds of short and intron-poor genes as early as the 2-cell stage. Upon ZGA, most zygotic transcripts originate from thousands of maternal-zygotic (MZ) genes that are transcribed at rates comparable to those of hundreds of purely zygotic genes and replenish maternal mRNAs at distinct timescales. Rapid replacement of MZ transcripts involves transcript decay features unrelated to major maternal degradation pathways and promotes de novo synthesis of the core gene expression machinery by increasing poly(A)-tail length and translation efficiency. SLAMseq hence provides insights into the timescales, molecular features, and regulation of MZT during zebrafish embryogenesis.
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Affiliation(s)
- Pooja Bhat
- Institute of Molecular Biotechnology (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Luis E Cabrera-Quio
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria; Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Veronika A Herzog
- Institute of Molecular Biotechnology (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Nina Fasching
- Institute of Molecular Biotechnology (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Andrea Pauli
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria.
| | - Stefan L Ameres
- Institute of Molecular Biotechnology (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria; Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC), 1030 Vienna, Austria.
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33
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Xiao Y, Chen J, Yang S, Sun H, Xie L, Li J, Jing N, Zhu X. Maternal mRNA deadenylation and allocation via Rbm14 condensates facilitate vertebrate blastula development. EMBO J 2023; 42:e111364. [PMID: 36477743 PMCID: PMC9890236 DOI: 10.15252/embj.2022111364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 11/12/2022] [Accepted: 11/17/2022] [Indexed: 12/12/2022] Open
Abstract
Early embryonic development depends on proper utilization and clearance of maternal transcriptomes. How these processes are spatiotemporally regulated remains unclear. Here we show that nuclear RNA-binding protein Rbm14 and maternal mRNAs co-phase separate into cytoplasmic condensates to facilitate vertebrate blastula-to-gastrula development. In zebrafish, Rbm14 condensates were highly abundant in blastomeres and markedly reduced after prominent activation of zygotic transcription. They concentrated at spindle poles by associating with centrosomal γ-tubulin puncta and displayed mainly asymmetric divisions with a global symmetry across embryonic midline in 8- and 16-cell embryos. Their formation was dose-dependently stimulated by m6 A, but repressed by m5 C modification of the maternal mRNA. Furthermore, deadenylase Parn co-phase separated with these condensates, and this was required for deadenylation of the mRNAs in early blastomeres. Depletion of Rbm14 impaired embryonic cell differentiations and full activations of the zygotic genome in both zebrafish and mouse and resulted in developmental arrest at the blastula stage. Our results suggest that cytoplasmic Rbm14 condensate formation regulates early embryogenesis by facilitating deadenylation, protection, and mitotic allocation of m6 A-modified maternal mRNAs, and by releasing the poly(A)-less transcripts upon regulated disassembly to allow their re-polyadenylation and translation or clearance.
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Affiliation(s)
- Yue Xiao
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhouChina
| | - Jiehui Chen
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghaiChina
| | - Suming Yang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghaiChina
| | - Honghua Sun
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghaiChina
| | - Lele Xie
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghaiChina
| | - Jinsong Li
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghaiChina
| | - Naihe Jing
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghaiChina
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouChina
| | - Xueliang Zhu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhouChina
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghaiChina
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Leca I, Phillips AW, Ushakova L, Cushion TD, Keays DA. Codon modification of Tuba1a alters mRNA levels and causes a severe neurodevelopmental phenotype in mice. Sci Rep 2023; 13:1215. [PMID: 36681692 PMCID: PMC9867703 DOI: 10.1038/s41598-023-27782-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 01/09/2023] [Indexed: 01/22/2023] Open
Abstract
The tubulinopathies are an umbrella of rare diseases that result from mutations in tubulin genes and are frequently characterised by severe brain malformations. The characteristics of a given disease reflect the expression pattern of the transcript, the function of a given tubulin gene, and the role microtubules play in a particular cell type. Mouse models have proved to be valuable tools that have provided insight into the molecular and cellular mechanisms that underlie the disease state. In this manuscript we compare two Tuba1a mouse models, both of which express wild-type TUBA1A protein but employ different codon usage. We show that modification of the Tuba1a mRNA sequence results in homozygous lethality and a severe neurodevelopmental phenotype. This is associated with a decrease in the number of post-mitotic neurons, PAX6 positive progenitors, and an increase in the number of apoptotic cells. We attribute this to a decrease in the stability of the modified Tuba1a transcript, and the absence of compensation by the other neurogenic tubulins. Our findings highlight the importance of maintaining the wild-type coding sequence when engineering mouse lines and the impact of synonymous genetic variation.
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Affiliation(s)
- Ines Leca
- Vienna Biocenter (VBC), Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria
| | - Alexander William Phillips
- Vienna Biocenter (VBC), Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria
- Department of Biology, Ludwig-Maximilians-University Munich, 82152, Planegg-Martinsried, Germany
| | - Lyubov Ushakova
- Vienna Biocenter (VBC), Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria
| | - Thomas David Cushion
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3EG, UK
| | - David Anthony Keays
- Vienna Biocenter (VBC), Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria.
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3EG, UK.
- Department of Biology, Ludwig-Maximilians-University Munich, 82152, Planegg-Martinsried, Germany.
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35
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The role of post-transcriptional modifications during development. Biol Futur 2022:10.1007/s42977-022-00142-3. [PMID: 36481986 DOI: 10.1007/s42977-022-00142-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022]
Abstract
AbstractWhile the existence of post-transcriptional modifications of RNA nucleotides has been known for decades, in most RNA species the exact positions of these modifications and their physiological function have been elusive until recently. Technological advances, such as high-throughput next-generation sequencing (NGS) methods and nanopore-based mapping technologies, have made it possible to map the position of these modifications with single nucleotide accuracy, and genetic screens have uncovered the “writer”, “reader” and “eraser” proteins that help to install, interpret and remove such modifications, respectively. These discoveries led to intensive research programmes with the aim of uncovering the roles of these modifications during diverse biological processes. In this review, we assess novel discoveries related to the role of post-transcriptional modifications during animal development, highlighting how these discoveries can affect multiple aspects of development from fertilization to differentiation in many species.
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36
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Burke PC, Park H, Subramaniam AR. A nascent peptide code for translational control of mRNA stability in human cells. Nat Commun 2022; 13:6829. [PMID: 36369503 PMCID: PMC9652226 DOI: 10.1038/s41467-022-34664-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 11/02/2022] [Indexed: 11/13/2022] Open
Abstract
Stability of eukaryotic mRNAs is associated with their codon, amino acid, and GC content. Yet, coding sequence motifs that predictably alter mRNA stability in human cells remain poorly defined. Here, we develop a massively parallel assay to measure mRNA effects of thousands of synthetic and endogenous coding sequence motifs in human cells. We identify several families of simple dipeptide repeats whose translation triggers mRNA destabilization. Rather than individual amino acids, specific combinations of bulky and positively charged amino acids are critical for the destabilizing effects of dipeptide repeats. Remarkably, dipeptide sequences that form extended β strands in silico and in vitro slowdown ribosomes and reduce mRNA levels in vivo. The resulting nascent peptide code underlies the mRNA effects of hundreds of endogenous peptide sequences in the human proteome. Our work suggests an intrinsic role for the ribosome as a selectivity filter against the synthesis of bulky and aggregation-prone peptides.
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Affiliation(s)
- Phillip C. Burke
- grid.270240.30000 0001 2180 1622Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109 USA ,grid.34477.330000000122986657Department of Microbiology, University of Washington, Seattle, WA 98195 USA
| | - Heungwon Park
- grid.270240.30000 0001 2180 1622Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109 USA
| | - Arvind Rasi Subramaniam
- grid.270240.30000 0001 2180 1622Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109 USA ,grid.34477.330000000122986657Department of Microbiology, University of Washington, Seattle, WA 98195 USA
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37
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Rashad S, Byrne SR, Saigusa D, Xiang J, Zhou Y, Zhang L, Begley TJ, Tominaga T, Niizuma K. Codon Usage and mRNA Stability are Translational Determinants of Cellular Response to Canonical Ferroptosis Inducers. Neuroscience 2022; 501:103-130. [PMID: 35987429 PMCID: PMC10023133 DOI: 10.1016/j.neuroscience.2022.08.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 08/02/2022] [Accepted: 08/08/2022] [Indexed: 11/29/2022]
Abstract
Ferroptosis is a non-apoptotic cell death mechanism characterized by the generation of lipid peroxides. While many effectors in the ferroptosis pathway have been mapped, its epitranscriptional regulation is not yet fully understood. Ferroptosis can be induced via system xCT inhibition (Class I) or GPX4 inhibition (Class II). Previous works have revealed important differences in cellular response to different ferroptosis inducers. Importantly, blocking mRNA transcription or translation appears to protect cells against Class I ferroptosis inducing agents but not Class II. In this work, we examined the impact of blocking transcription (via Actinomycin D) or translation (via Cycloheximide) on Erastin (Class I) or RSL3 (Class II) induced ferroptosis. Blocking transcription or translation protected cells against Erastin but was detrimental against RSL3. Cycloheximide led to increased levels of GSH alone or when co-treated with Erastin via the activation of the reverse transsulfuration pathway. RNA sequencing analysis revealed early activation of a strong alternative splice program before observed changes in transcription. mRNA stability analysis revealed divergent mRNA stability changes in cellular response to Erastin or RSL3. Importantly, codon optimality biases were drastically different in either condition. Our data also implicated translation repression and rate as an important determinant of the cellular response to ferroptosis inducers. Given that mRNA stability and codon usage can be influenced via the tRNA epitranscriptome, we evaluated the role of a tRNA modifying enzyme in ferroptosis stress response. Alkbh1, a tRNA demethylase, led to translation repression and increased the resistance to Erastin but made cells more sensitive to RSL3.
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Affiliation(s)
- Sherif Rashad
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan; Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan; Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan.
| | - Shane R Byrne
- Department of Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Daisuke Saigusa
- Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University, Tokyo, Japan; Department of Integrative Genomics, Tohoku University Medical Megabank Organization, Sendai, Japan
| | - Jingdong Xiang
- Department of Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yuan Zhou
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Liyin Zhang
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Thomas J Begley
- The RNA Institute, University at Albany, Albany, NY, USA; Department of Biological Sciences, University at Albany, Albany, NY, USA; RNA Epitranscriptomics and Proteomics Resource, University at Albany, Albany, NY, USA
| | - Teiji Tominaga
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kuniyasu Niizuma
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan; Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan; Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan
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38
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Zou Z, Zhang C, Wang Q, Hou Z, Xiong Z, Kong F, Wang Q, Song J, Liu B, Liu B, Wang L, Lai F, Fan Q, Tao W, Zhao S, Ma X, Li M, Wu K, Zhao H, Chen ZJ, Xie W. Translatome and transcriptome co-profiling reveals a role of TPRXs in human zygotic genome activation. Science 2022; 378:abo7923. [PMID: 36074823 DOI: 10.1126/science.abo7923] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Translational regulation plays a critical role during the oocyte-to-embryo transition (OET) and zygotic genome activation (ZGA). Here, we integrated ultra-low-input Ribo-seq with mRNA-seq to co-profile the translatome and transcriptome in human oocytes and early embryos. Comparison with mouse counterparts identified widespread differentially translated genes functioning in epigenetic reprogramming, transposon defense, and small RNA biogenesis, in part driven by species-specific regulatory elements in 3' untranslated regions. Moreover, PRD-like homeobox transcription factors, including TPRXL, TPRX1, and TPRX2, are highly translated around ZGA. TPRX1/2/L knockdown leads to defective ZGA and preimplantation development. Ectopically expressed TPRXs bind and activate key ZGA genes in human embryonic stem cells. These data reveal the conservation and divergence of translation landscapes during OET and identify critical regulators of human ZGA.
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Affiliation(s)
- Zhuoning Zou
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Chuanxin Zhang
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China
| | - Qiuyan Wang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhenzhen Hou
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China
| | - Zhuqing Xiong
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Feng Kong
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qiujun Wang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jinzhu Song
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China
| | - Boyang Liu
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China
| | - Bofeng Liu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lijuan Wang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Fangnong Lai
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qiang Fan
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wenrong Tao
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China
| | - Shuai Zhao
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China
| | - Xiaonan Ma
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China
| | - Miao Li
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China
| | - Keliang Wu
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China
| | - Han Zhao
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China.,Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, China
| | - Zi-Jiang Chen
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China.,Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, China.,Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai 200135, China.,Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200135, China
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
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39
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Durmaz YT, Shatadal A, Friend K. Geneticin reduces mRNA stability. PLoS One 2022; 17:e0272058. [PMID: 35901009 PMCID: PMC9333311 DOI: 10.1371/journal.pone.0272058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 07/12/2022] [Indexed: 11/30/2022] Open
Abstract
Messenger RNA (mRNA) translation can lead to higher rates of mRNA decay, suggesting the ribosome plays a role in mRNA destruction. Furthermore, mRNA features, such as codon identities, which are directly probed by the ribosome, correlate with mRNA decay rates. Many amino acids are encoded by synonymous codons, some of which are decoded by more abundant tRNAs leading to more optimal translation and increased mRNA stability. Variable translation rates for synonymous codons can lead to ribosomal collisions as ribosomes transit regions with suboptimal codons, and ribosomal collisions can promote mRNA decay. In addition to different translation rates, the presence of certain codons can also lead to higher or lower rates of amino acid misincorporation which could potentially lead to protein misfolding if a substituted amino acid fails to make critical contacts in a structure. Here, we test whether Geneticin—G418, an aminoglycoside antibiotic known to promote amino acid misincorporation—affects mRNA stability. We observe that G418 decreases firefly luciferase mRNA stability in an in vitro translation system and also reduces mRNA stability in mouse embryonic stem cells (mESCs). G418-sensitive mRNAs are enriched for certain optimal codons that contain G or C in the wobble position, arguing that G418 blunts the stabilizing effects of codon optimality.
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Affiliation(s)
- Yavuz T. Durmaz
- Department of Chemistry and Biochemistry, Washington and Lee University, Lexington, Virginia, United States of America
| | - Alankrit Shatadal
- Department of Chemistry and Biochemistry, Washington and Lee University, Lexington, Virginia, United States of America
| | - Kyle Friend
- Department of Chemistry and Biochemistry, Washington and Lee University, Lexington, Virginia, United States of America
- * E-mail:
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40
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Veltri AJ, D'Orazio KN, Lessen LN, Loll-Krippleber R, Brown GW, Green R. Distinct elongation stalls during translation are linked with distinct pathways for mRNA degradation. eLife 2022; 11:e76038. [PMID: 35894211 PMCID: PMC9352352 DOI: 10.7554/elife.76038] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Key protein adapters couple translation to mRNA decay on specific classes of problematic mRNAs in eukaryotes. Slow decoding on non-optimal codons leads to codon-optimality-mediated decay (COMD) and prolonged arrest at stall sites leads to no-go decay (NGD). The identities of the decay factors underlying these processes and the mechanisms by which they respond to translational distress remain open areas of investigation. We use carefully designed reporter mRNAs to perform genetic screens and functional assays in Saccharomyces cerevisiae. We characterize the roles of Hel2, Syh1, and Smy2 in coordinating translational repression and mRNA decay on NGD reporter mRNAs, finding that Syh1 and, to a lesser extent its paralog Smy2, act in a distinct pathway from Hel2. This Syh1/Smy2-mediated pathway acts as a redundant, compensatory pathway to elicit NGD when Hel2-dependent NGD is impaired. Importantly, we observe that these NGD factors are not involved in the degradation of mRNAs enriched in non-optimal codons. Further, we establish that a key factor previously implicated in COMD, Not5, contributes modestly to the degradation of an NGD-targeted mRNA. Finally, we use ribosome profiling to reveal distinct ribosomal states associated with each reporter mRNA that readily rationalize the contributions of NGD and COMD factors to degradation of these reporters. Taken together, these results provide new insight into the role of Syh1 and Smy2 in NGD and into the ribosomal states that correlate with the activation of distinct pathways targeting mRNAs for degradation in yeast.
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Affiliation(s)
- Anthony J Veltri
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Karole N D'Orazio
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Laura N Lessen
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimoreUnited States
| | | | - Grant W Brown
- Department of Biochemistry and Donnelly Centre, University of TorontoTorontoCanada
| | - Rachel Green
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimoreUnited States
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41
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Diez M, Medina-Muñoz SG, Castellano LA, da Silva Pescador G, Wu Q, Bazzini AA. iCodon customizes gene expression based on the codon composition. Sci Rep 2022; 12:12126. [PMID: 35840631 PMCID: PMC9287306 DOI: 10.1038/s41598-022-15526-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 06/24/2022] [Indexed: 11/09/2022] Open
Abstract
Messenger RNA (mRNA) stability substantially impacts steady-state gene expression levels in a cell. mRNA stability is strongly affected by codon composition in a translation-dependent manner across species, through a mechanism termed codon optimality. We have developed iCodon (www.iCodon.org), an algorithm for customizing mRNA expression through the introduction of synonymous codon substitutions into the coding sequence. iCodon is optimized for four vertebrate transcriptomes: mouse, human, frog, and fish. Users can predict the mRNA stability of any coding sequence based on its codon composition and subsequently generate more stable (optimized) or unstable (deoptimized) variants encoding for the same protein. Further, we show that codon optimality predictions correlate with both mRNA stability using a massive reporter library and expression levels using fluorescent reporters and analysis of endogenous gene expression in zebrafish embryos and/or human cells. Therefore, iCodon will benefit basic biological research, as well as a wide range of applications for biotechnology and biomedicine.
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Affiliation(s)
- Michay Diez
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO, 64110, USA
| | - Santiago Gerardo Medina-Muñoz
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO, 64110, USA.,National Laboratory of Genomics for Biodiversity (LANGEBIO), Unit of Advanced Genomics, 36824, Irapuato, Mexico
| | | | | | - Qiushuang Wu
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO, 64110, USA
| | - Ariel Alejandro Bazzini
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO, 64110, USA. .,Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS, 66160, USA.
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Huang N, Gao Y, Zhang M, Guo L, Qin L, Liao S, Wang H. METTL3-Mediated m6A RNA Methylation of ZBTB4 Interferes With Trophoblast Invasion and Maybe Involved in RSA. Front Cell Dev Biol 2022; 10:894810. [PMID: 35774226 PMCID: PMC9237410 DOI: 10.3389/fcell.2022.894810] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 05/03/2022] [Indexed: 11/14/2022] Open
Abstract
N6-methyladenosine (m6A) was the most abundant modification of mRNA and lncRNA in mammalian cells and played an important role in many biological processes. However, whether m6A modification was associated with recurrent spontaneous abortion (RSA) and its roles were still unclear. Methods: Methylated RNA immunoprecipitation sequencing (MeRIP-Seq) was used to study the global m6A modification pattern in RSAs and controls. RNA sequencing (RNA-Seq) was used to study the level of global mRNA in two groups. Real-time quantitative PCR (RT-qPCR) was used to verify the level of mRNA of METTL3 and ZBTB4. MeRIP–qPCR was conducted to test the level of ZBTB4 m6A modification in two groups. In order to further explore whether ZBTB4 was the substrate of METTL3, the HTR-8/SVneo (HTR-8) cell line was selected for the knockdown and overexpression of METTL3. To study whether METTL3 regulated the ZBTB4 expression by recognizing ZBTB4 mRNA m6A motifs in coding sequences (CDS), dual-luciferase reporter assay was conducted. RNA stability assays using actinomycin D were conducted to study the RNA stability of the HTR-8 cell line with METTL3 overexpression and knockdown. To illustrate the role of METTL3 in the invasion of trophoblast, matrigel invasion assays and transwell migration assays were conducted using the HTR-8 cell line with METTL3 overexpression and knockdown. Results: A total of 65 genes were found with significant differences both in m6A modification and mRNA expression. We found m6A methyltransferase METTL3 was significantly down-regulated in the RSA group. Through gene function analysis, RT-qPCR, MeRIP–qPCR validation experiment, knockdown, and overexpression of METTL3 in the HTR-8 cell line, ZBTB4 was selected as one target of METTL3. Furthermore, we clarified that METTL3 regulated the expression of ZBTB4 by recognizing ZBTB4 mRNA m6A motifs in the CDS using the dual-luciferase reporter assay and METTL3 regulated the invasion of trophoblast by altering the stability and expression of ZBTB4 by RNA stability, matrigel invasion, and transwell migration assays. Conclusion: Our study revealed the mechanism by which METTL3 regulated the stability and expression of ZBTB4 and the trophoblast migration ability of RSA. A new perspective was provided for exploring the mechanism of embryonic development in RSA patients.
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Affiliation(s)
- Nana Huang
- Henan Provincial People’s Hospital, Medical Genetics Institute of Henan Province, Zhengzhou University People’s Hospital, Zhengzhou, China
| | - Yue Gao
- Henan Provincial People’s Hospital, Medical Genetics Institute of Henan Province, Zhengzhou University People’s Hospital, Zhengzhou, China
| | - Mengting Zhang
- Henan Provincial People’s Hospital, Medical Genetics Institute of Henan Province, Zhengzhou University People’s Hospital, Zhengzhou, China
| | - Liangjie Guo
- Henan Provincial People’s Hospital, Medical Genetics Institute of Henan Province, Zhengzhou University People’s Hospital, Zhengzhou, China
| | - Litao Qin
- Henan Provincial People’s Hospital, Medical Genetics Institute of Henan Province, Zhengzhou University People’s Hospital, Zhengzhou, China
| | - Shixiu Liao
- Henan Provincial People’s Hospital, Medical Genetics Institute of Henan Province, Zhengzhou University People’s Hospital, Zhengzhou, China
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Henan Institute of Reproduction Health Science and Technology, Zhengzhou, China
- *Correspondence: Shixiu Liao, ; Hongdan Wang,
| | - Hongdan Wang
- Henan Provincial People’s Hospital, Medical Genetics Institute of Henan Province, Zhengzhou University People’s Hospital, Zhengzhou, China
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Henan Institute of Reproduction Health Science and Technology, Zhengzhou, China
- *Correspondence: Shixiu Liao, ; Hongdan Wang,
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Phase separation of Ddx3xb helicase regulates maternal-to-zygotic transition in zebrafish. Cell Res 2022; 32:715-728. [PMID: 35661831 PMCID: PMC9343644 DOI: 10.1038/s41422-022-00655-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 03/10/2022] [Indexed: 12/14/2022] Open
Abstract
Vertebrate embryogenesis involves a conserved and fundamental process, called the maternal-to-zygotic transition (MZT), which marks the switch from a maternal factors-dominated state to a zygotic factors-driven state. Yet the precise mechanism underlying MZT remains largely unknown. Here we report that the RNA helicase Ddx3xb in zebrafish undergoes liquid-liquid phase separation (LLPS) via its N-terminal intrinsically disordered region (IDR), and an increase in ATP content promotes the condensation of Ddx3xb during MZT. Mutant form of Ddx3xb losing LLPS ability fails to rescue the developmental defect of Ddx3xb-deficient embryos. Interestingly, the IDR of either FUS or hnRNPA1 can functionally replace the N-terminal IDR in Ddx3xb. Phase separation of Ddx3xb facilitates the unwinding of 5' UTR structures of maternal mRNAs to enhance their translation. Our study reveals an unprecedent mechanism whereby the Ddx3xb phase separation regulates MZT by promoting maternal mRNA translation.
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Codon optimality-mediated mRNA degradation: Linking translational elongation to mRNA stability. Mol Cell 2022; 82:1467-1476. [PMID: 35452615 PMCID: PMC10111967 DOI: 10.1016/j.molcel.2022.03.032] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/11/2022] [Accepted: 03/25/2022] [Indexed: 01/21/2023]
Abstract
Messenger RNA (mRNA) translation by the ribosome represents the final step of a complicated molecular dance from DNA to protein. Although classically considered a decipherer that translates a 64-word genetic code into a proteome of astonishing complexity, the ribosome can also shape the transcriptome by controlling mRNA stability. Recent work has discovered that the ribosome is an arbiter of the general mRNA degradation pathway, wherein the ribosome transit rate serves as a major determinant of transcript half-lives. Specifically, members of the degradation complex sense ribosome translocation rates as a function of ribosome elongation rates. Central to this notion is the concept of codon optimality: although all codons impact translation rates, some are deciphered quickly, whereas others cause ribosome hesitation as a consequence of relative cognate tRNA concentration. These transient pauses induce a unique ribosome conformational state that is probed by the deadenylase complex, thereby inducing an orchestrated set of events that enhance both poly(A) shortening and cap removal. Together, these data imply that the coding region of an mRNA not only encodes for protein content but also impacts protein levels through determining the transcript's fate.
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O'Grady T, Njock MS, Lion M, Bruyr J, Mariavelle E, Galvan B, Boeckx A, Struman I, Dequiedt F. Sorting and packaging of RNA into extracellular vesicles shape intracellular transcript levels. BMC Biol 2022; 20:72. [PMID: 35331218 PMCID: PMC8944098 DOI: 10.1186/s12915-022-01277-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/11/2022] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Extracellular vesicles (EVs) are released by nearly every cell type and have attracted much attention for their ability to transfer protein and diverse RNA species from donor to recipient cells. Much attention has been given so far to the features of EV short RNAs such as miRNAs. However, while the presence of mRNA and long noncoding RNA (lncRNA) transcripts in EVs has also been reported by multiple different groups, the properties and function of these longer transcripts have been less thoroughly explored than EV miRNA. Additionally, the impact of EV export on the transcriptome of exporting cells has remained almost completely unexamined. Here, we globally investigate mRNA and lncRNA transcripts in endothelial EVs in multiple different conditions. RESULTS In basal conditions, long RNA transcripts enriched in EVs have longer than average half-lives and distinctive stability-related sequence and structure characteristics including shorter transcript length, higher exon density, and fewer 3' UTR A/U-rich elements. EV-enriched long RNA transcripts are also enriched in HNRNPA2B1 binding motifs and are impacted by HNRNPA2B1 depletion, implicating this RNA-binding protein in the sorting of long RNA to EVs. After signaling-dependent modification of the cellular transcriptome, we observed that, unexpectedly, the rate of EV enrichment relative to cells was altered for many mRNA and lncRNA transcripts. This change in EV enrichment was negatively correlated with intracellular abundance, with transcripts whose export to EVs increased showing decreased abundance in cells and vice versa. Correspondingly, after treatment with inhibitors of EV secretion, levels of mRNA and lncRNA transcripts that are normally highly exported to EVs increased in cells, indicating a measurable impact of EV export on the long RNA transcriptome of the exporting cells. Compounds with different mechanisms of inhibition of EV secretion affected the cellular transcriptome differently, suggesting the existence of multiple EV subtypes with different long RNA profiles. CONCLUSIONS We present evidence for an impact of EV physiology on the characteristics of EV-producing cell transcriptomes. Our work suggests a new paradigm in which the sorting and packaging of transcripts into EVs participate, together with transcription and RNA decay, in controlling RNA homeostasis and shape the cellular long RNA abundance profile.
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Affiliation(s)
- Tina O'Grady
- Laboratory of Gene Expression and Cancer, GIGA-MBD, University of Liège, B34, Avenue de l'Hôpital 11, 4000, Liège, Belgium
| | - Makon-Sébastien Njock
- Laboratory of Molecular Angiogenesis, GIGA-Cancer, University of Liège, B34, Avenue de l'Hôpital 11, 4000, Liège, Belgium
| | - Michelle Lion
- Laboratory of Gene Expression and Cancer, GIGA-MBD, University of Liège, B34, Avenue de l'Hôpital 11, 4000, Liège, Belgium
| | - Jonathan Bruyr
- Laboratory of Gene Expression and Cancer, GIGA-MBD, University of Liège, B34, Avenue de l'Hôpital 11, 4000, Liège, Belgium
| | - Emeline Mariavelle
- Laboratory of Gene Expression and Cancer, GIGA-MBD, University of Liège, B34, Avenue de l'Hôpital 11, 4000, Liège, Belgium
| | - Bartimée Galvan
- Laboratory of Gene Expression and Cancer, GIGA-MBD, University of Liège, B34, Avenue de l'Hôpital 11, 4000, Liège, Belgium
| | - Amandine Boeckx
- Laboratory of Molecular Angiogenesis, GIGA-Cancer, University of Liège, B34, Avenue de l'Hôpital 11, 4000, Liège, Belgium
| | - Ingrid Struman
- Laboratory of Molecular Angiogenesis, GIGA-Cancer, University of Liège, B34, Avenue de l'Hôpital 11, 4000, Liège, Belgium
| | - Franck Dequiedt
- Laboratory of Gene Expression and Cancer, GIGA-MBD, University of Liège, B34, Avenue de l'Hôpital 11, 4000, Liège, Belgium.
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Li JR, Tang M, Li Y, Amos CI, Cheng C. Genetic variants associated mRNA stability in lung. BMC Genomics 2022; 23:196. [PMID: 35272635 PMCID: PMC8915503 DOI: 10.1186/s12864-022-08405-y] [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: 07/31/2021] [Accepted: 02/21/2022] [Indexed: 12/04/2022] Open
Abstract
Background Expression quantitative trait loci (eQTLs) analyses have been widely used to identify genetic variants associated with gene expression levels to understand what molecular mechanisms underlie genetic traits. The resultant eQTLs might affect the expression of associated genes through transcriptional or post-transcriptional regulation. In this study, we attempt to distinguish these two types of regulation by identifying genetic variants associated with mRNA stability of genes (stQTLs). Results Here, we presented a computational framework that takes advantage of recently developed methods to infer the mRNA stability of genes based on RNA-seq data and performed association analysis to identify stQTLs. Using the Genotype-Tissue Expression (GTEx) lung RNA-Seq data, we identified a total of 142,801 stQTLs for 3942 genes and 186,132 eQTLs for 4751 genes from 15,122,700 genetic variants for 13,476 genes on the autosomes, respectively. Interestingly, our results indicated that stQTLs were enriched in the CDS and 3’UTR regions, while eQTLs are enriched in the CDS, 3’UTR, 5’UTR, and upstream regions. We also found that stQTLs are more likely than eQTLs to overlap with RNA binding protein (RBP) and microRNA (miRNA) binding sites. Our analyses demonstrate that simultaneous identification of stQTLs and eQTLs can provide more mechanistic insight on the association between genetic variants and gene expression levels. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08405-y.
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Affiliation(s)
- Jian-Rong Li
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA.,Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Mabel Tang
- Department of BioSciences, Biochemistry and Cell Biology, Rice University, Houston, TX, USA
| | - Yafang Li
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA.,Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA.,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Christopher I Amos
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA.,Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA.,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Chao Cheng
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA. .,Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA. .,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
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Mishima Y, Han P, Ishibashi K, Kimura S, Iwasaki S. Ribosome slowdown triggers codon-mediated mRNA decay independently of ribosome quality control. EMBO J 2022; 41:e109256. [PMID: 35040509 PMCID: PMC8886528 DOI: 10.15252/embj.2021109256] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 12/06/2021] [Accepted: 12/09/2021] [Indexed: 12/11/2022] Open
Abstract
The control of mRNA stability plays a central role in regulating gene expression patterns. Recent studies have revealed that codon composition in the open reading frame determines mRNA stability in multiple organisms. Based on genome-wide correlation approaches, this previously unrecognized role for the genetic code is attributable to the kinetics of the codon-decoding process by the ribosome. However, complementary experimental analyses are required to clarify the codon effects on mRNA stability and the related cotranslational mRNA decay pathways, for example, those triggered by aberrant ribosome stalling. In the current study, we performed a set of reporter-based analyses to define codon-mediated mRNA decay and ribosome stall-dependent mRNA decay in zebrafish embryos. Our analysis showed that the effect of codons on mRNA stability stems from the decoding process, independent of the ribosome quality control factor Znf598 and stalling-dependent mRNA decay. We propose that codon-mediated mRNA decay is rather triggered by transiently slowed ribosomes engaging in a productive translation cycle in zebrafish embryos.
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Affiliation(s)
- Yuichiro Mishima
- Department of Frontier Life SciencesFaculty of Life SciencesKyoto Sangyo UniversityKyotoJapan,RNA Systems Biochemistry LaboratoryRIKEN Cluster for Pioneering ResearchSaitamaJapan
| | - Peixun Han
- RNA Systems Biochemistry LaboratoryRIKEN Cluster for Pioneering ResearchSaitamaJapan,Department of Computational Biology and Medical SciencesGraduate School of Frontier SciencesThe University of TokyoChibaJapan
| | - Kota Ishibashi
- Department of Frontier Life SciencesFaculty of Life SciencesKyoto Sangyo UniversityKyotoJapan
| | - Seisuke Kimura
- Department of Industrial Life SciencesFaculty of Life SciencesKyoto Sangyo UniversityKyotoJapan,Center for Plant SciencesKyoto Sangyo UniversityKyotoJapan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry LaboratoryRIKEN Cluster for Pioneering ResearchSaitamaJapan,Department of Computational Biology and Medical SciencesGraduate School of Frontier SciencesThe University of TokyoChibaJapan
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Yue J, Wei Y, Zhao M. The Reversible Methylation of m6A Is Involved in Plant Virus Infection. BIOLOGY 2022; 11:biology11020271. [PMID: 35205137 PMCID: PMC8869485 DOI: 10.3390/biology11020271] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/20/2022] [Accepted: 02/06/2022] [Indexed: 02/01/2023]
Abstract
Simple Summary N6-methyladenosine (m6A) is the most prevalent modification in the mRNAs of many eukaryotic species. The abundance and effects of m6A are determined by dynamic interactions between its methyltransferases (“writers”), demethylases (“erasers”), and binding proteins (“readers”). It has been indicated that there is a strong correlation between m6A and virus infection in mammals. In the case of plant virus infection, it appears that m6A plays a dual role. On the one hand, m6A acts as a plant immune response induced by virus infection, inhibiting viral replication or translation through methylation of viral genome RNAs. On the other hand, m6A acts as part of an infection strategy employed by plant viruses to overcome the host immune system by interacting with m6A-related proteins. We proposed that antagonists of m6A-related proteins might be used to design new strategies for plant virus control in the future. Abstract In recent years, m6A RNA methylation has attracted broad interest and is becoming a hot research topic. It has been demonstrated that there is a strong association between m6A and viral infection in the human system. The life cycles of plant RNA viruses are often coordinated with the mechanisms of their RNA modification. Here, we reviewed recent advances in m6A methylation in plant viruses. It appears that m6A methylation plays a dual role during viral infection in plants. On the one hand, m6A methylation acts as an antiviral immune response induced by virus infection, which inhibits viral replication or translation through the methylation of viral genome RNAs. On the other hand, plant viruses could disrupt the m6A methylation through interacting with the key proteins of the m6A pathway to avoid modification. Those plant viruses containing ALKB domain are discussed as well. Based on this mechanism, we propose that new strategies for plant virus control could be designed with competitive antagonists of m6A-associated proteins.
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Roles of mRNA poly(A) tails in regulation of eukaryotic gene expression. Nat Rev Mol Cell Biol 2022; 23:93-106. [PMID: 34594027 PMCID: PMC7614307 DOI: 10.1038/s41580-021-00417-y] [Citation(s) in RCA: 186] [Impact Index Per Article: 93.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2021] [Indexed: 02/06/2023]
Abstract
In eukaryotes, poly(A) tails are present on almost every mRNA. Early experiments led to the hypothesis that poly(A) tails and the cytoplasmic polyadenylate-binding protein (PABPC) promote translation and prevent mRNA degradation, but the details remained unclear. More recent data suggest that the role of poly(A) tails is much more complex: poly(A)-binding protein can stimulate poly(A) tail removal (deadenylation) and the poly(A) tails of stable, highly translated mRNAs at steady state are much shorter than expected. Furthermore, the rate of translation elongation affects deadenylation. Consequently, the interplay between poly(A) tails, PABPC, translation and mRNA decay has a major role in gene regulation. In this Review, we discuss recent work that is revolutionizing our understanding of the roles of poly(A) tails in the cytoplasm. Specifically, we discuss the roles of poly(A) tails in translation and control of mRNA stability and how poly(A) tails are removed by exonucleases (deadenylases), including CCR4-NOT and PAN2-PAN3. We also discuss how deadenylation rate is determined, the integration of deadenylation with other cellular processes and the function of PABPC. We conclude with an outlook for the future of research in this field.
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50
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Yaish O, Orenstein Y. Computational modeling of mRNA degradation dynamics using deep neural networks. Bioinformatics 2022; 38:1087-1101. [PMID: 34849591 DOI: 10.1093/bioinformatics/btab800] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 11/12/2021] [Accepted: 11/22/2021] [Indexed: 02/04/2023] Open
Abstract
MOTIVATION messenger RNA (mRNA) degradation plays critical roles in post-transcriptional gene regulation. A major component of mRNA degradation is determined by 3'-UTR elements. Hence, researchers are interested in studying mRNA dynamics as a function of 3'-UTR elements. A recent study measured the mRNA degradation dynamics of tens of thousands of 3'-UTR sequences using a massively parallel reporter assay. However, the computational approach used to model mRNA degradation was based on a simplifying assumption of a linear degradation rate. Consequently, the underlying mechanism of 3'-UTR elements is still not fully understood. RESULTS Here, we developed deep neural networks to predict mRNA degradation dynamics and interpreted the networks to identify regulatory elements in the 3'-UTR and their positional effect. Given an input of a 110 nt-long 3'-UTR sequence and an initial mRNA level, the model predicts mRNA levels of eight consecutive time points. Our deep neural networks significantly improved prediction performance of mRNA degradation dynamics compared with extant methods for the task. Moreover, we demonstrated that models predicting the dynamics of two identical 3'-UTR sequences, differing by their poly(A) tail, performed better than single-task models. On the interpretability front, by using Integrated Gradients, our convolutional neural networks (CNNs) models identified known and novel cis-regulatory sequence elements of mRNA degradation. By applying a novel systematic evaluation of model interpretability, we demonstrated that the recurrent neural network models are inferior to the CNN models in terms of interpretability and that random initialization ensemble improves both prediction and interoperability performance. Moreover, using a mutagenesis analysis, we newly discovered the positional effect of various 3'-UTR elements. AVAILABILITY AND IMPLEMENTATION All the code developed through this study is available at github.com/OrensteinLab/DeepUTR/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ofir Yaish
- School of Electrical and Computer Engineering, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Yaron Orenstein
- School of Electrical and Computer Engineering, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
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