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Guimaraes GJ, Kim J, Bartlett MG. Characterization of mRNA therapeutics. MASS SPECTROMETRY REVIEWS 2024; 43:1066-1090. [PMID: 37401740 DOI: 10.1002/mas.21856] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/25/2023] [Accepted: 05/17/2023] [Indexed: 07/05/2023]
Abstract
Therapeutic messenger RNAs (mRNAs) have emerged as powerful tools in the treatment of complex diseases, especially for conditions that lack efficacious treatment. The successful application of this modality can be attributed to its ability to encode entire proteins. While the large nature of these molecules has supported their success as therapeutics, its extended size creates several analytical challenges. To further support therapeutic mRNA development and its deployment in clinical trials, appropriate methods to support their characterization must be developed. In this review, we describe current analytical methods that have been used in the characterization of RNA quality, identity, and integrity. Advantages and limitations from several analytical techniques ranging from gel electrophoresis to liquid chromatography-mass spectrometry and from shotgun sequencing to intact mass measurements are discussed. We comprehensively describe the application of analytical methods in the measurements of capping efficiency, poly A tail analysis, as well as their applicability in stability studies.
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Affiliation(s)
- Guilherme J Guimaraes
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia, USA
| | - Jaeah Kim
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia, USA
| | - Michael G Bartlett
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia, USA
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2
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Chaudhuri A, Paul S, Banerjea M, Das B. Polyadenylated versions of small non-coding RNAs in Saccharomyces cerevisiae are degraded by Rrp6p/Rrp47p independent of the core nuclear exosome. MICROBIAL CELL (GRAZ, AUSTRIA) 2024; 11:155-186. [PMID: 38783922 PMCID: PMC11115967 DOI: 10.15698/mic2024.05.823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/03/2024] [Accepted: 03/05/2024] [Indexed: 05/25/2024]
Abstract
In Saccharomyces cerevisiae, polyadenylated forms of mature (and not precursor) small non-coding RNAs (sncRNAs) those fail to undergo proper 3'-end maturation are subject to an active degradation by Rrp6p and Rrp47p, which does not require the involvement of core exosome and TRAMP components. In agreement with this finding, Rrp6p/Rrp47p is demonstrated to exist as an exosome-independent complex, which preferentially associates with mature polyadenylated forms of these sncRNAs. Consistent with this observation, a C-terminally truncated version of Rrp6p (Rrp6p-ΔC2) lacking physical association with the core nuclear exosome supports their decay just like its full-length version. Polyadenylation is catalyzed by both the canonical and non-canonical poly(A) polymerases, Pap1p and Trf4p. Analysis of the polyadenylation profiles in WT and rrp6-Δ strains revealed that the majority of the polyadenylation sites correspond to either one to three nucleotides upstream or downstream of their mature ends and their poly(A) tails ranges from 10-15 adenylate residues. Most interestingly, the accumulated polyadenylated snRNAs are functional in the rrp6-Δ strain and are assembled into spliceosomes. Thus, Rrp6p-Rrp47p defines a core nuclear exosome-independent novel RNA turnover system in baker's yeast targeting imperfectly processed polyadenylated sncRNAs that accumulate in the absence of Rrp6p.
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Affiliation(s)
- Anusha Chaudhuri
- Present Position: Zentrum fǜr Molekulare, Medizin, Institut fǜr Kardiovaskuläre Regeneration, Haus 25B, Goethe-Universität, Theodor-Stern-Kai 7, Universitätsklinikum, 60590 Frankfurt am Main, Germany
| | - Soumita Paul
- Department of Life Science and Biotechnology, Jadavpur University, 188 Raja S.C. Mullick Road, Kolkata – 700 032, West Bengal, India
| | - Mayukh Banerjea
- Department of Life Science and Biotechnology, Jadavpur University, 188 Raja S.C. Mullick Road, Kolkata – 700 032, West Bengal, India
| | - Biswadip Das
- Department of Life Science and Biotechnology, Jadavpur University, 188 Raja S.C. Mullick Road, Kolkata – 700 032, West Bengal, India
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3
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Kaur P, Nagar S, Mehta R, Sahadeo K, Vancura A. Hydroxyurea and inactivation of checkpoint kinase MEC1 inhibit transcription termination and pre-mRNA cleavage at polyadenylation sites in budding yeast. Sci Rep 2023; 13:13106. [PMID: 37567961 PMCID: PMC10421882 DOI: 10.1038/s41598-023-40294-3] [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: 02/16/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023] Open
Abstract
The DNA damage response (DDR) is an evolutionarily conserved process essential for cell survival. The transcription changes triggered by DDR depend on the nature of DNA damage, activation of checkpoint kinases, and the stage of cell cycle. The transcription changes can be localized and affect only damaged DNA, but they can be also global and affect genes that are not damaged. While the purpose of localized transcription inhibition is to avoid transcription of damaged genes and make DNA accessible for repair, the purpose and mechanisms of global transcription inhibition of undamaged genes are less well understood. We show here that a brief cell treatment with hydroxyurea (HU) globally inhibits RNA synthesis and transcription by RNA polymerase I, II, and III (RNAPI, RNAPII, and RNAPIII). HU reduces efficiency of transcription termination and inhibits pre-mRNA cleavage at the polyadenylation (pA) sites, destabilizes mRNAs, and shortens poly(A) tails of mRNAs, indicating defects in pre-mRNA 3' end processing. Inactivation of the checkpoint kinase Mec1p downregulates the efficiency of transcription termination and reduces the efficiency of pre-mRNAs clevage at the pA sites, suggesting the involvement of DNA damage checkpoint in transcription termination and pre-mRNA 3' end processing.
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Affiliation(s)
- Pritpal Kaur
- Department of Biological Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY, 11439, USA
| | - Shreya Nagar
- Department of Biological Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY, 11439, USA
| | - Riddhi Mehta
- Department of Biological Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY, 11439, USA
| | - Kyle Sahadeo
- Department of Biological Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY, 11439, USA
| | - Ales Vancura
- Department of Biological Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY, 11439, USA.
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4
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Huang YS, Mendez R, Fernandez M, Richter JD. CPEB and translational control by cytoplasmic polyadenylation: impact on synaptic plasticity, learning, and memory. Mol Psychiatry 2023; 28:2728-2736. [PMID: 37131078 PMCID: PMC10620108 DOI: 10.1038/s41380-023-02088-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 05/04/2023]
Abstract
The late 1990s were banner years in molecular neuroscience; seminal studies demonstrated that local protein synthesis, at or near synapses, was necessary for synaptic plasticity, the underlying cellular basis of learning and memory [1, 2]. The newly made proteins were proposed to "tag" the stimulated synapse, distinguishing it from naive synapses, thereby forming a cellular memory [3]. Subsequent studies demonstrated that the transport of mRNAs from soma to dendrite was linked with translational unmasking at synapses upon synaptic stimulation. It soon became apparent that one prevalent mechanism governing these events is cytoplasmic polyadenylation, and that among the proteins that control this process, CPEB, plays a central role in synaptic plasticity, and learning and memory. In vertebrates, CPEB is a family of four proteins, all of which regulate translation in the brain, that have partially overlapping functions, but also have unique characteristics and RNA binding properties that make them control different aspects of higher cognitive function. Biochemical analysis of the vertebrate CPEBs demonstrate them to respond to different signaling pathways whose output leads to specific cellular responses. In addition, the different CPEBs, when their functions go awry, result in pathophysiological phenotypes resembling specific human neurological disorders. In this essay, we review key aspects of the vertebrate CPEB proteins and cytoplasmic polyadenylation within the context of brain function.
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Affiliation(s)
- Yi-Shuian Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
| | - Raul Mendez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Spain.
| | | | - Joel D Richter
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA.
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5
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Wang P, Zhou J, Sun W, Li H, Rehman S, Xu C, Li D, Zhuge Q. Poplar CCR4-associated factor PtCAF1I is necessary for poplar development and defense response. Int J Biol Macromol 2023:125090. [PMID: 37247707 DOI: 10.1016/j.ijbiomac.2023.125090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/17/2023] [Accepted: 05/22/2023] [Indexed: 05/31/2023]
Abstract
Poplar is one of the most widely used tree species in afforestation projects. CCR4 associated factor 1 (CAF1) is a major member of CCR4-NOT and plays an important role in eukaryotic mRNA deadenylation. However, its role in poplar remains unclear. In this study, the full-length cDNA of the PtCAF1I gene was cloned from the poplar by screening the highly expressed PtCAF1I gene in the identified PtCAF1 gene family by poplar sterilization. PtCAF1I was localized in the nucleus. Through sequence alignment, it was found that the PtCAF1I sequence contains three motifs and is highly similar to the CAF1 protein sequence of other species. In the quantitative expression analysis of tissues, the expression of PtCAF1I in different tissues of Populus trichocarpa, 'Nanlin895', and Shanxinyang was not much different. In addition, the analysis of the expression of the PtCAF1I gene under different stress treatments showed that PtCAF1I responded to abscisic acid (ABA), salicylic acid (SA), methyl jasmonate (MeJA), NaCl, PEG6000, hydrogen peroxide (H2O2) and cold stress to different degrees. To study the potential biological functions of PtCAF1I, 6 transgenic lines were obtained through transformation using an Agrobacterium tumefaciens infection system. The transcriptome sequencing results showed that DEGs were mainly concentrated in pathways of phenylpropanoid biosynthesis, biosynthesis of secondary metabolites, carbon metabolism, and carotenoid biosynthesis. Compared with WT poplar, the contents of cellulose, hemicellulose, lignin, total sugar, and flavonoids, and the cell wall thickness of PtCAF1I overexpression poplars were significantly higher. Under Septotinia populiperda treatment, transgenic poplars clearly exhibited certain disease resistance. Meanwhile, upregulation of the expression of JA and SA pathway-related genes also contributed to improving the disease tolerance of transgenic poplar. In conclusion, our results suggest that PtCAF1I plays an important role in the growth and development of poplars and their resistance to pathogens.
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Affiliation(s)
- Pu Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, State Key Laboratory of Tree Genetics and Breeding, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China.
| | - Jie Zhou
- Jiangsu Academy of Forestry, Nanjing 211153, China
| | - Weibo Sun
- Co-Innovation Center for Sustainable Forestry in Southern China, State Key Laboratory of Tree Genetics and Breeding, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China.
| | - Hongyan Li
- Co-Innovation Center for Sustainable Forestry in Southern China, State Key Laboratory of Tree Genetics and Breeding, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Shamsur Rehman
- Co-Innovation Center for Sustainable Forestry in Southern China, State Key Laboratory of Tree Genetics and Breeding, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Chen Xu
- Jiangsu Provincial Key Construction Laboratory of Special Biomass Resource Utilization, Nanjing Xiaozhuang University, Nanjing 211171, China
| | - Dawei Li
- Co-Innovation Center for Sustainable Forestry in Southern China, State Key Laboratory of Tree Genetics and Breeding, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China.
| | - Qiang Zhuge
- Co-Innovation Center for Sustainable Forestry in Southern China, State Key Laboratory of Tree Genetics and Breeding, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China.
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6
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Brouze A, Krawczyk PS, Dziembowski A, Mroczek S. Measuring the tail: Methods for poly(A) tail profiling. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1737. [PMID: 35617484 PMCID: PMC10078590 DOI: 10.1002/wrna.1737] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 01/31/2023]
Abstract
The 3'-end poly(A) tail is an important and potent feature of most mRNA molecules that affects mRNA fate and translation efficiency. Polyadenylation is a posttranscriptional process that occurs in the nucleus by canonical poly(A) polymerases (PAPs). In some specific instances, the poly(A) tail can also be extended in the cytoplasm by noncanonical poly(A) polymerases (ncPAPs). This epitranscriptomic regulation of mRNA recently became one of the most interesting aspects in the field. Advances in RNA sequencing technologies and software development have allowed the precise measurement of poly(A) tails, identification of new ncPAPs, expansion of the function of known enzymes, discovery and a better understanding of the physiological role of tail heterogeneity, and recognition of a correlation between tail length and RNA translatability. Here, we summarize the development of polyadenylation research methods, including classic low-throughput approaches, Illumina-based genome-wide analysis, and advanced state-of-art techniques that utilize long-read third-generation sequencing with Pacific Biosciences and Oxford Nanopore Technologies platforms. A boost in technical opportunities over recent decades has allowed a better understanding of the regulation of gene expression at the mRNA level. This article is categorized under: RNA Methods > RNA Analyses In Vitro and In Silico.
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Affiliation(s)
- Aleksandra Brouze
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Paweł Szczepan Krawczyk
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Andrzej Dziembowski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.,Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland.,Department of Embryology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Seweryn Mroczek
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.,Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
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7
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Implications of Poly(A) Tail Processing in Repeat Expansion Diseases. Cells 2022; 11:cells11040677. [PMID: 35203324 PMCID: PMC8870147 DOI: 10.3390/cells11040677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/11/2022] [Accepted: 02/13/2022] [Indexed: 11/21/2022] Open
Abstract
Repeat expansion diseases are a group of more than 40 disorders that affect mainly the nervous and/or muscular system and include myotonic dystrophies, Huntington’s disease, and fragile X syndrome. The mutation-driven expanded repeat tract occurs in specific genes and is composed of tri- to dodeca-nucleotide-long units. Mutant mRNA is a pathogenic factor or important contributor to the disease and has great potential as a therapeutic target. Although repeat expansion diseases are quite well known, there are limited studies concerning polyadenylation events for implicated transcripts that could have profound effects on transcript stability, localization, and translation efficiency. In this review, we briefly present polyadenylation and alternative polyadenylation (APA) mechanisms and discuss their role in the pathogenesis of selected diseases. We also discuss several methods for poly(A) tail measurement (both transcript-specific and transcriptome-wide analyses) and APA site identification—the further development and use of which may contribute to a better understanding of the correlation between APA events and repeat expansion diseases. Finally, we point out some future perspectives on the research into repeat expansion diseases, as well as APA studies.
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8
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Wang C, Yang Y, Wu X, Li J, Liu K, Fang D, Li B, Shan G, Mei X, Wang F, Mei Y. Reciprocal modulation of long noncoding RNA EMS and p53 regulates tumorigenesis. Proc Natl Acad Sci U S A 2022; 119:e2111409119. [PMID: 35022235 PMCID: PMC8784137 DOI: 10.1073/pnas.2111409119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 10/12/2021] [Indexed: 12/12/2022] Open
Abstract
p53 plays a central role in tumor suppression. Emerging evidence suggests long noncoding RNA (lncRNA) as an important class of regulatory molecules that control the p53 signaling. Here, we report that the oncogenic lncRNA E2F1 messenger RNA (mRNA) stabilizing factor (EMS) and p53 mutually repress each other's expression. EMS is negatively regulated by p53. As a direct transcriptional repression target of p53, EMS is surprisingly shown to inhibit p53 expression. EMS associates with cytoplasmic polyadenylation element-binding protein 2 (CPEB2) and thus, disrupts the CPEB2-p53 mRNA interaction. This disassociation attenuates CPEB2-mediated p53 mRNA polyadenylation and suppresses p53 translation. Functionally, EMS is able to exert its oncogenic activities, at least partially, via the CPEB2-p53 axis. Together, these findings reveal a double-negative feedback loop between p53 and EMS, through which p53 is finely controlled. Our study also demonstrates a critical role for EMS in promoting tumorigenesis via the negative regulation of p53.
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Affiliation(s)
- Chenfeng Wang
- The First Affiliated Hospital of University of Science and Technology of China (USTC), Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Yang Yang
- The First Affiliated Hospital of University of Science and Technology of China (USTC), Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Xianning Wu
- The First Affiliated Hospital of University of Science and Technology of China (USTC), Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Jingxin Li
- The First Affiliated Hospital of University of Science and Technology of China (USTC), Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Kaiyue Liu
- The First Affiliated Hospital of University of Science and Technology of China (USTC), Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Debao Fang
- The First Affiliated Hospital of University of Science and Technology of China (USTC), Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Bingyan Li
- The First Affiliated Hospital of University of Science and Technology of China (USTC), Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Ge Shan
- The First Affiliated Hospital of University of Science and Technology of China (USTC), Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Xinyu Mei
- The First Affiliated Hospital of University of Science and Technology of China (USTC), Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China;
| | - Fang Wang
- The First Affiliated Hospital of University of Science and Technology of China (USTC), Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China;
| | - Yide Mei
- The First Affiliated Hospital of University of Science and Technology of China (USTC), Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China;
- The Chinese Academy of Sciences (CAS) Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei 230027, China
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9
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Jolles B, Jean-Jean O. Poly(A) tail degradation in human cells: ATF4 mRNA as a model for biphasic deadenylation. Biochimie 2021; 185:128-134. [PMID: 33775689 DOI: 10.1016/j.biochi.2021.03.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 11/16/2022]
Abstract
Eukaryotic mRNA deadenylation is generally considered as a two-step process in which the PAN2-PAN3 complex initiates the poly(A) tail degradation while, in the second step, the CCR4-NOT complex completes deadenylation, leading to decapping and degradation of the mRNA body. However, the mechanism of the biphasic poly(A) tail deadenylation remains enigmatic in several points such as the timing of the switch between the two steps, the role of translation termination and the mRNAs population involved. Here, we have studied the deadenylation of endogenous mRNAs in human cells depleted in either PAN3 or translation termination factor eRF3. Among the mRNAs tested, we found that only the endogenous ATF4 mRNA meets the biphasic model for deadenylation and that eRF3 prevents the shortening of its poly(A) tail. For the other mRNAs, the poor effect of PAN3 depletion on their poly(A) tail shortening questions the mode of their deadenylation. It is possible that these mRNAs experience a single step deadenylation process. Alternatively, we propose that a very short initial deadenylation by PAN2-PAN3 is followed by a rapid transition to the second phase involving CCR4-NOT complex. These differences in the timing of the transition from one deadenylation step to the other could explain the difficulties encountered in the generalization of the biphasic deadenylation model.
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Affiliation(s)
- Béatrice Jolles
- Sorbonne Université, Institute of Biology Paris-Seine, IBPS, CNRS, Biological Adaptation and Ageing, B2A, F, 75005, Paris, France
| | - Olivier Jean-Jean
- Sorbonne Université, Institute of Biology Paris-Seine, IBPS, CNRS, Biological Adaptation and Ageing, B2A, F, 75005, Paris, France.
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10
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Kulsuptrakul J, Wang R, Meyers NL, Ott M, Puschnik AS. A genome-wide CRISPR screen identifies UFMylation and TRAMP-like complexes as host factors required for hepatitis A virus infection. Cell Rep 2021; 34:108859. [PMID: 33730579 PMCID: PMC8893346 DOI: 10.1016/j.celrep.2021.108859] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 12/21/2020] [Accepted: 02/19/2021] [Indexed: 12/17/2022] Open
Abstract
Hepatitis A virus (HAV) is a positive-sense RNA virus causing acute inflammation of the liver. Here, using a genome-scale CRISPR screen, we provide a comprehensive picture of the cellular factors that are exploited by HAV. We identify genes involved in sialic acid/ganglioside biosynthesis and members of the eukaryotic translation initiation factor complex, corroborating their putative roles for HAV. Additionally, we uncover all components of the cellular machinery for UFMylation, a ubiquitin-like protein modification. We show that HAV translation specifically depends on UFM1 conjugation of the ribosomal protein RPL26. Furthermore, we find that components related to the yeast Trf4/5-Air1/2-Mtr4 polyadenylation (TRAMP) complex are required for viral translation independent of controlling viral poly(A) tails or RNA stability. Finally, we demonstrate that pharmacological inhibition of the TRAMP-like complex decreases HAV replication in hepatocyte cells and human liver organoids, thus providing a strategy for host-directed therapy of HAV infection. To identify host factors required for the infection with hepatitis A virus, Kulsuptrakul et al. conducted a genome-wide CRISPR knockout screen in human hepatocytes. They reveal that UFMylation of the ribosomal protein RPL26 as well as the polyadenylation activity of a TRAMP-like complex enhance viral translation.
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Affiliation(s)
| | - Ruofan Wang
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | | | - Melanie Ott
- Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
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11
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Otsuka K, Mamiya A, Konishi M, Nozaki M, Kinoshita A, Tamaki H, Arita M, Saito M, Yamamoto K, Hachiya T, Noguchi K, Ueda T, Yagi Y, Kobayashi T, Nakamura T, Sato Y, Hirayama T, Sugiyama M. Temperature-dependent fasciation mutants provide a link between mitochondrial RNA processing and lateral root morphogenesis. eLife 2021; 10:61611. [PMID: 33443014 PMCID: PMC7846275 DOI: 10.7554/elife.61611] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 01/13/2021] [Indexed: 12/18/2022] Open
Abstract
Although mechanisms that activate organogenesis in plants are well established, much less is known about the subsequent fine-tuning of cell proliferation, which is crucial for creating properly structured and sized organs. Here we show, through analysis of temperature-dependent fasciation (TDF) mutants of Arabidopsis, root redifferentiation defective 1 (rrd1), rrd2, and root initiation defective 4 (rid4), that mitochondrial RNA processing is required for limiting cell division during early lateral root (LR) organogenesis. These mutants formed abnormally broadened (i.e. fasciated) LRs under high-temperature conditions due to extra cell division. All TDF proteins localized to mitochondria, where they were found to participate in RNA processing: RRD1 in mRNA deadenylation, and RRD2 and RID4 in mRNA editing. Further analysis suggested that LR fasciation in the TDF mutants is triggered by reactive oxygen species generation caused by defective mitochondrial respiration. Our findings provide novel clues for the physiological significance of mitochondrial activities in plant organogenesis.
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Affiliation(s)
- Kurataka Otsuka
- Botanical Gardens, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Akihito Mamiya
- Botanical Gardens, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Mineko Konishi
- Botanical Gardens, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Mamoru Nozaki
- Botanical Gardens, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Atsuko Kinoshita
- Botanical Gardens, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hiroaki Tamaki
- Botanical Gardens, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Masaki Arita
- Botanical Gardens, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Masato Saito
- Botanical Gardens, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Kayoko Yamamoto
- Botanical Gardens, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Takushi Hachiya
- Department of Molecular and Functional Genomics, Interdisciplinary Center for Science Research, Shimane University, Shimane, Japan
| | - Ko Noguchi
- Department of Applied Life Science, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Takashi Ueda
- Division of Cellular Dynamics, National Institute for Basic Biology, Aichi, Japan
| | - Yusuke Yagi
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Takehito Kobayashi
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Takahiro Nakamura
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Yasushi Sato
- Biology and Environmental Science, Graduate School of Science and Engineering, Ehime University, Ehime, Japan
| | - Takashi Hirayama
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
| | - Munetaka Sugiyama
- Botanical Gardens, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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12
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Yu F, Zhang Y, Cheng C, Wang W, Zhou Z, Rang W, Yu H, Wei Y, Wu Q, Zhang Y. Poly(A)-seq: A method for direct sequencing and analysis of the transcriptomic poly(A)-tails. PLoS One 2020; 15:e0234696. [PMID: 32544193 PMCID: PMC7297374 DOI: 10.1371/journal.pone.0234696] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 06/02/2020] [Indexed: 12/19/2022] Open
Abstract
Poly(A) tails at the 3' end of eukaryotic messenger RNAs control mRNA stability and translation efficiency. Facilitated by various NGS methods, alternative polyadenylation sites determining the 3'-UTR length of gene transcripts have been extensively studied. However, poly(A) lengths demonstrating dynamic and developmental regulation remain largely unexplored. The recently developed NGS-based methods for genome-wide poly(A) profiling have promoted the study of genom-wide poly(A) dynamics. Here we present a straight forward NGS-method for poly(A) profiling, which applies a direct 3'-end adaptor ligation and the template switching for 5'-end adaptor ligation for cDNA library construction. Poly(A) lengths are directly calculated from base call data using a self-developed pipeline pA-finder. The libraries were directly sequenced from the 3'-UTR regions into the followed poly(A) tails, firstly on NextSeq 500 to produce single-end 300-nt reads, demonstrating the method feasibility and that optimization of the fragmented RNA size for cDNA library construction could detecting longer poly (A) tails. We next applied Poly(A)-seq cDNA libraries containing 40-nt and 120-nt poly(A) tail spike-in RNAs on HiSeq X-ten and NovaSeq 6000 to obtain 150-nt and 250-nt pair-end reads. The sequencing profiles of the spike-in RNAs demonstrated both high accuracy and high quality score in reading poly(A) tails. The poly(A) signal bleeding into the 3' adaptor sequence and a sharp decreased quality score at the junction were observed, allowing the modification of pA-finder to remove homopolymeric signal bleeding. We hope that wide applications of Poly(A)-seq help facilitate the study of the development- and disease-related poly(A) dynamics and regulation, and of the recent emerging mixed tailing regulation.
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Affiliation(s)
- Fengyun Yu
- Laboratory for Genomics Regulation and Human Health, ABLife Inc., Wuhan, PR China
- ABLife BioBigData Instibute, Wuhan, PR China
| | - Yu Zhang
- Center for Genomics Analysis, ABLife Inc., Wuhan, PR China
| | - Chao Cheng
- ABLife BioBigData Instibute, Wuhan, PR China
- Center for Genomics Analysis, ABLife Inc., Wuhan, PR China
| | - Wenqing Wang
- Center for Genomics Analysis, ABLife Inc., Wuhan, PR China
| | - Zisong Zhou
- Center for Genomics Analysis, ABLife Inc., Wuhan, PR China
| | - Wenliang Rang
- Laboratory for Genomics Regulation and Human Health, ABLife Inc., Wuhan, PR China
| | - Han Yu
- Laboratory for Genomics Regulation and Human Health, ABLife Inc., Wuhan, PR China
| | - Yaxun Wei
- Center for Genomics Analysis, ABLife Inc., Wuhan, PR China
| | - Qijia Wu
- Laboratory for Genomics Regulation and Human Health, ABLife Inc., Wuhan, PR China
| | - Yi Zhang
- Laboratory for Genomics Regulation and Human Health, ABLife Inc., Wuhan, PR China
- ABLife BioBigData Instibute, Wuhan, PR China
- Center for Genomics Analysis, ABLife Inc., Wuhan, PR China
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13
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Translation Efficiency and Degradation of ER-Associated mRNAs Modulated by ER-Anchored poly(A)-Specific Ribonuclease (PARN). Cells 2020; 9:cells9010162. [PMID: 31936572 PMCID: PMC7017053 DOI: 10.3390/cells9010162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/05/2020] [Accepted: 01/07/2020] [Indexed: 12/21/2022] Open
Abstract
Translation is spatiotemporally regulated and endoplasmic reticulum (ER)-associated mRNAs are generally in efficient translation. It is unclear whether the ER-associated mRNAs are deadenylated or degraded on the ER surface in situ or in the cytosol. Here, we showed that ER possessed active deadenylases, particularly the poly(A)-specific ribonuclease (PARN), in common cell lines and mouse tissues. Consistently, purified recombinant PARN exhibited a strong ability to insert into the Langmuir monolayer and liposome. ER-anchored PARN was found to be able to reshape the poly(A) length profile of the ER-associated RNAs by suppressing long poly(A) tails without significantly influencing the cytosolic RNAs. The shortening of long poly(A) tails did not affect global translation efficiency, which suggests that the non-specific action of PARN towards long poly(A) tails was beyond the scope of translation regulation on the ER surface. Transcriptome sequencing analysis indicated that the ER-anchored PARN trigged the degradation of a small subset of ER-enriched transcripts. The ER-anchored PARN modulated the translation of its targets by redistributing ribosomes to heavy polysomes, which suggests that PARN might play a role in dynamic ribosome reallocation. During DNA damage response, MK2 phosphorylated PARN-Ser557 to modulate PARN translocation from the ER to cytosol. The ER-anchored PARN modulated DNA damage response and thereby cell viability by promoting the decay of ER-associated MDM2 transcripts with low ribosome occupancy. These findings revealed that highly regulated communication between mRNA degradation rate and translation efficiency is present on the ER surface in situ and PARN might contribute to this communication by modulating the dynamic ribosome reallocation between transcripts with low and high ribosome occupancies.
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Das S, Biswas S, Chaudhuri S, Bhattacharyya A, Das B. A Nuclear Zip Code in SKS1 mRNA Promotes Its Slow Export, Nuclear Retention, and Degradation by the Nuclear Exosome/DRN in Saccharomyces cerevisiae. J Mol Biol 2019; 431:3626-3646. [DOI: 10.1016/j.jmb.2019.07.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 06/26/2019] [Accepted: 07/01/2019] [Indexed: 01/12/2023]
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15
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Bargi-Souza P, Goulart-Silva F, Nunes MT. Posttranscriptional actions of triiodothyronine on Tshb expression in TαT1 cells: New insights into molecular mechanisms of negative feedback. Mol Cell Endocrinol 2018; 478:45-52. [PMID: 30031103 DOI: 10.1016/j.mce.2018.07.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 06/10/2018] [Accepted: 07/13/2018] [Indexed: 11/28/2022]
Abstract
Rapid actions of triiodothyronine (T3) on thyrotropin (TSH) synthesis and secretion have been described in hypothyroid male rats. However, the molecular mechanisms remain unknown. TαT1 cells, a thyrotroph cell line, was used herein to characterize the possible non-genomic actions of T3 on the expression of alpha (Cga) and Tshb genes, and the posttranscriptional processing and translation of both transcripts. The involvement of αVβ3 integrin was also assessed. T3 quickly reduced Tshb mRNA content, poly(A) tail length and its association with ribosomes. The effect of T3 on Tshb gene expression was detected even in the presence of a transcription inhibitor. The decrease in Tshb mRNA content and polyadenylation depend on T3 interaction with αVβ3 integrin, while T3 reduced Cga mRNA content by transcriptional action. The translational rate of both transcripts was reduced by a mechanism, which does not depend on T3-αVβ3 integrin interaction. Results indicate that, in parallel with the inhibitory transcriptional action in Cga and Tshb gene expression, T3 rapidly triggers additional posttranscriptional mechanisms, reducing the TSH synthesis. These non-genomic actions partially depend on T3-αVβ3 integrin interaction at the plasma membrane of thyrotrophs and add new insights to the molecular mechanisms involved in T3 negative feedback loop.
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Affiliation(s)
- Paula Bargi-Souza
- Department of Physiology and Biophysics of the Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, CEP 05508-000, Brazil
| | - Francemilson Goulart-Silva
- Department of Physiology and Biophysics of the Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, CEP 05508-000, Brazil
| | - Maria Tereza Nunes
- Department of Physiology and Biophysics of the Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, CEP 05508-000, Brazil.
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16
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de Castro Barbosa T, Salgueiro RB, Serrano-Nascimento C, Amaral FG, Cipolla-Neto J, Nunes MT. Molecular basis of growth hormone daily mRNA and protein synthesis in rats. Life Sci 2018; 207:36-41. [PMID: 29842863 DOI: 10.1016/j.lfs.2018.05.043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/09/2018] [Accepted: 05/25/2018] [Indexed: 10/16/2022]
Abstract
AIMS Daily and seasonal rhythms coordinate the endocrine and metabolic functions. The pituitary gland is the master regulator of several endocrine activities, and its function is classically regulated by endocrine signals from its target glands as well as from the hypothalamus. The growth hormone (GH) produced and secreted by the anterior pituitary presents a pulsatile secretion throughout the 24-hour cycle. However, the molecular mechanisms regulating the daily pattern of GH secretion are still unclear. Herein we investigated whether circadian GH mRNA and protein synthesis is modulated by acute adjustments in the stability and expression of GH mRNA. MAIN METHODS GH mRNA and protein content were evaluated by real-time PCR and Western blotting, respectively, in pituitary gland of rats euthanized every 3 h during a 24-h period at the Zeitgeber times (ZT3 to ZT24). The GH mRNA poly(A) tail length was determined by RACE-PAT assay. KEY FINDINGS We identified two main peaks of GH mRNA level in the pituitary gland of rats; one in the middle of the light-cycle and another in the middle of the dark-cycle. The latter was associated with an increase in pituitary GH protein content. Interestingly, an increment in the poly(A) tail length of the GH transcript was observed in association to reduced migration rate of the GH transcript and increased mRNA content in the dark-cycle period. SIGNIFICANCE Our findings provide evidence that changes in the GH mRNA poly(A) length may underlie the circadian pattern of GH mRNA and protein levels in the pituitary gland of rats.
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Affiliation(s)
- T de Castro Barbosa
- Karolinska Institutet, Department of Medicine H7, Huddinge, Sweden; University of Sao Paulo, Department of Physiology and Biophysics, Sao Paulo, Brazil.
| | - R B Salgueiro
- University of Sao Paulo, Department of Physiology and Biophysics, Sao Paulo, Brazil
| | - C Serrano-Nascimento
- University of Sao Paulo, Department of Physiology and Biophysics, Sao Paulo, Brazil; Hospital Israelita Albert Einstein, Sao Paulo, Brazil
| | - F G Amaral
- University of Sao Paulo, Department of Physiology and Biophysics, Sao Paulo, Brazil; Federal University of Sao Paulo, Department of Physiology, Sao Paulo, Brazil
| | - J Cipolla-Neto
- University of Sao Paulo, Department of Physiology and Biophysics, Sao Paulo, Brazil
| | - M T Nunes
- University of Sao Paulo, Department of Physiology and Biophysics, Sao Paulo, Brazil
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17
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Translation termination-dependent deadenylation of MYC mRNA in human cells. Oncotarget 2018; 9:26171-26182. [PMID: 29899850 PMCID: PMC5995228 DOI: 10.18632/oncotarget.25459] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 05/08/2018] [Indexed: 11/25/2022] Open
Abstract
The earliest step in the mRNA degradation process is deadenylation, a progressive shortening of the mRNA poly(A) tail by deadenylases. The question of when deadenylation takes place remains open. MYC mRNA is one of the rare examples for which it was proposed a shortening of the poly(A) tail during ongoing translation. In this study, we analyzed the poly(A) tail length distribution of various mRNAs, including MYC mRNA. The mRNAs were isolated from the polysomal fractions of polysome profiling experiments and analyzed using ligase-mediated poly(A) test analysis. We show that, for all the mRNAs tested with the only exception of MYC, the poly(A) tail length distribution does not change in accordance with the number of ribosomes carried by the mRNA. Conversely, for MYC mRNA, we observed a poly(A) tail length decrease in the fractions containing the largest polysomes. Because the fractions with the highest number of ribosomes are also those for which translation termination is more frequent, we analyzed the poly(A) tail length distribution in polysomal fractions of cells depleted in translation termination factor eRF3. Our results show that the shortening of MYC mRNA poly(A) tail is alleviated by the silencing of translation termination factor eRF3. These findings suggest that MYC mRNA is co-translationally deadenylated and that the deadenylation process requires translation termination to proceed.
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18
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Yamaguchi T, Suzuki T, Sato T, Takahashi A, Watanabe H, Kadowaki A, Natsui M, Inagaki H, Arakawa S, Nakaoka S, Koizumi Y, Seki S, Adachi S, Fukao A, Fujiwara T, Natsume T, Kimura A, Komatsu M, Shimizu S, Ito H, Suzuki Y, Penninger JM, Yamamoto T, Imai Y, Kuba K. The CCR4-NOT deadenylase complex controls Atg7-dependent cell death and heart function. Sci Signal 2018; 11:11/516/eaan3638. [PMID: 29438013 DOI: 10.1126/scisignal.aan3638] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Shortening and removal of the polyadenylate [poly(A)] tail of mRNA, a process called deadenylation, is a key step in mRNA decay that is mediated through the CCR4-NOT (carbon catabolite repression 4-negative on TATA-less) complex. In our investigation of the regulation of mRNA deadenylation in the heart, we found that this complex was required to prevent cell death. Conditional deletion of the CCR4-NOT complex components Cnot1 or Cnot3 resulted in the formation of autophagic vacuoles and cardiomyocyte death, leading to lethal heart failure accompanied by long QT intervals. Cnot3 bound to and shortened the poly(A) tail of the mRNA encoding the key autophagy regulator Atg7. In Cnot3-depleted hearts, Atg7 expression was posttranscriptionally increased. Genetic ablation of Atg7, but not Atg5, increased survival and partially restored cardiac function of Cnot1 or Cnot3 knockout mice. We further showed that in Cnot3-depleted hearts, Atg7 interacted with p53 and modulated p53 activity to induce the expression of genes encoding cell death-promoting factors in cardiomyocytes, indicating that defects in deadenylation in the heart aberrantly activated Atg7 and p53 to promote cell death. Thus, mRNA deadenylation mediated by the CCR4-NOT complex is crucial to prevent Atg7-induced cell death and heart failure, suggesting a role for mRNA deadenylation in targeting autophagy genes to maintain normal cardiac homeostasis.
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Affiliation(s)
- Tomokazu Yamaguchi
- Department of Biochemistry and Metabolic Science, Akita University Graduate School of Medicine, 1-1-1 Hondo, Akita 010-8543, Japan
| | - Takashi Suzuki
- Department of Biochemistry and Metabolic Science, Akita University Graduate School of Medicine, 1-1-1 Hondo, Akita 010-8543, Japan
| | - Teruki Sato
- Department of Cardiovascular and Respiratory Medicine, Akita University Graduate School of Medicine, Akita 010-8543, Japan
| | - Akinori Takahashi
- Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Hiroyuki Watanabe
- Department of Cardiovascular and Respiratory Medicine, Akita University Graduate School of Medicine, Akita 010-8543, Japan
| | - Ayumi Kadowaki
- Department of Biochemistry and Metabolic Science, Akita University Graduate School of Medicine, 1-1-1 Hondo, Akita 010-8543, Japan
| | - Miyuki Natsui
- Department of Biochemistry and Metabolic Science, Akita University Graduate School of Medicine, 1-1-1 Hondo, Akita 010-8543, Japan
| | - Hideaki Inagaki
- Bioscience Education and Research Support Center, Akita University, Akita 010-8543, Japan
| | - Satoko Arakawa
- Department of Pathological Cell Biology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Shinji Nakaoka
- Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan.,Laboratory for Regulation of Intractable Infectious Diseases, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
| | - Yukio Koizumi
- Department of Biochemistry and Metabolic Science, Akita University Graduate School of Medicine, 1-1-1 Hondo, Akita 010-8543, Japan
| | - Shinsuke Seki
- Bioscience Education and Research Support Center, Akita University, Akita 010-8543, Japan
| | - Shungo Adachi
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan
| | - Akira Fukao
- Molecular Laboratory of Biochemistry, Department of Pharmacy, Kindai University, Higashi-Osaka 577-8502, Japan
| | - Toshinobu Fujiwara
- Molecular Laboratory of Biochemistry, Department of Pharmacy, Kindai University, Higashi-Osaka 577-8502, Japan
| | - Tohru Natsume
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan
| | - Akinori Kimura
- Department of Molecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Masaaki Komatsu
- Department of Biochemistry, School of Medicine, Niigata University, Niigata 951-8510, Japan
| | - Shigeomi Shimizu
- Department of Pathological Cell Biology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Hiroshi Ito
- Department of Cardiovascular and Respiratory Medicine, Akita University Graduate School of Medicine, Akita 010-8543, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Josef M Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Campus Vienna BioCenter, Vienna 1030, Austria
| | - Tadashi Yamamoto
- Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Yumiko Imai
- Laboratory for Regulation of Intractable Infectious Diseases, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
| | - Keiji Kuba
- Department of Biochemistry and Metabolic Science, Akita University Graduate School of Medicine, 1-1-1 Hondo, Akita 010-8543, Japan. .,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Tokyo 102-0076, Japan
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19
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Chartier A, Joly W, Simonelig M. Measurement of mRNA Poly(A) Tail Lengths in Drosophila Female Germ Cells and Germ-Line Stem Cells. Methods Mol Biol 2018; 1463:93-102. [PMID: 27734350 DOI: 10.1007/978-1-4939-4017-2_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
mRNA regulation by poly(A) tail length variations plays an important role in many developmental processes. Recent advances have shown that, in particular, deadenylation (the shortening of mRNA poly(A) tails) is essential for germ-line stem cell biology in the Drosophila ovary. Therefore, a rapid and accurate method to analyze poly(A) tail lengths of specific mRNAs in this tissue is valuable. Several methods of poly(A) test (PAT) assays have been reported to measure mRNA poly(A) tail lengths in vivo. Here, we describe two of these methods (PAT and ePAT) that we have adapted for Drosophila ovarian germ cells and germ-line stem cells.
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Affiliation(s)
- Aymeric Chartier
- mRNA Regulation and Development, Institut de Génétique Humaine, CNRS UPR1142 and University of Montpellier, 141 rue de la Cardonille, 34396, Montpellier Cedex 5, France
| | - Willy Joly
- mRNA Regulation and Development, Institut de Génétique Humaine, CNRS UPR1142 and University of Montpellier, 141 rue de la Cardonille, 34396, Montpellier Cedex 5, France
| | - Martine Simonelig
- mRNA Regulation and Development, Institut de Génétique Humaine, CNRS UPR1142 and University of Montpellier, 141 rue de la Cardonille, 34396, Montpellier Cedex 5, France
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20
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Short poly(A) tails are a conserved feature of highly expressed genes. Nat Struct Mol Biol 2017; 24:1057-1063. [PMID: 29106412 PMCID: PMC5877826 DOI: 10.1038/nsmb.3499] [Citation(s) in RCA: 166] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 10/10/2017] [Indexed: 12/19/2022]
Abstract
Poly(A) tails are important elements in mRNA translation and stability. However, recent genome-wide studies concluded that poly(A) tail length was generally not associated with translational efficiency in non-embryonic cells. To investigate if poly(A) tail size might be coupled to gene expression in an intact organism, we used an adapted TAIL-seq protocol to measure poly(A) tails in Caenorhabditis elegans. Surprisingly, we found that well-expressed transcripts contain relatively short, well-defined tails. This attribute appears dependent on translational efficiency, as transcripts enriched for optimal codons and ribosome association had the shortest tail sizes, while non-coding RNAs retained long tails. Across eukaryotes, short tails were a feature of abundant and well-translated mRNAs. Although this seems to contradict the dogma that deadenylation induces translational inhibition and mRNA decay, it instead suggests that well-expressed mRNAs accumulate with pruned tails that accommodate a minimal number of poly(A) binding proteins, which may be ideal for protective and translational functions.
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21
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Meers MP, Henriques T, Lavender CA, McKay DJ, Strahl BD, Duronio RJ, Adelman K, Matera AG. Histone gene replacement reveals a post-transcriptional role for H3K36 in maintaining metazoan transcriptome fidelity. eLife 2017; 6. [PMID: 28346137 PMCID: PMC5404926 DOI: 10.7554/elife.23249] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 03/23/2017] [Indexed: 12/17/2022] Open
Abstract
Histone H3 lysine 36 methylation (H3K36me) is thought to participate in a host of co-transcriptional regulatory events. To study the function of this residue independent from the enzymes that modify it, we used a ‘histone replacement’ system in Drosophila to generate a non-modifiable H3K36 lysine-to-arginine (H3K36R) mutant. We observed global dysregulation of mRNA levels in H3K36R animals that correlates with the incidence of H3K36me3. Similar to previous studies, we found that mutation of H3K36 also resulted in H4 hyperacetylation. However, neither cryptic transcription initiation, nor alternative pre-mRNA splicing, contributed to the observed changes in expression, in contrast with previously reported roles for H3K36me. Interestingly, knockdown of the RNA surveillance nuclease, Xrn1, and members of the CCR4-Not deadenylase complex, restored mRNA levels for a class of downregulated, H3K36me3-rich genes. We propose a post-transcriptional role for modification of replication-dependent H3K36 in the control of metazoan gene expression. DOI:http://dx.doi.org/10.7554/eLife.23249.001 In a single human cell there is enough DNA to stretch over a meter if laid end to end. To fit this DNA inside the cell – which is less than 20 micrometers in diameter – the DNA is tightly wrapped around millions of proteins known as histones, which look like “beads” along a “string” of DNA. These histones can prevent other proteins from binding to DNA and activating specific genes. Therefore, cells use enzymes to chemically modify histones to allow particular stretches of DNA to be unwrapped at specific times. Proteins are made up of building blocks called amino acids. A specific amino acid on histones known as H3K36 is modified in certain sections of DNA that suggest it affects the activities of many genes. However, the precise role of this amino acid remains unclear. Previous studies have tried to investigate this by removing the enzymes that modify it, but these enzymes can also modify many other proteins, making it difficult to know what exactly causes the changes in gene activity. Fruit flies are often used in experiments as models of how genetic processes work in humans and other animals. Like us, fruit flies also package their DNA using histones. To investigate the role of H3K36, Meers et al. generated a mutant fruit fly that has a version of the amino acid that cannot be chemically modified by the normal enzymes. Unexpectedly, the experiments suggest that some changes in gene activity that have been previously reported to be caused by modifying H3K36 might actually be due to other factors. Meers et al. found that H3K36 modifications may instead “mark” certain genes to be more active than they otherwise would be. These findings provide a starting point for understanding exactly how H3K36 regulates gene activity. The next challenge is to refine our understanding of how H3K36 modification affects genes in cancer and other diseases, which may aid the development of new therapies to treat these conditions. DOI:http://dx.doi.org/10.7554/eLife.23249.002
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Affiliation(s)
- Michael P Meers
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, United States.,Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Telmo Henriques
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Science, Durham, United States
| | - Christopher A Lavender
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Science, Durham, United States
| | - Daniel J McKay
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, United States.,Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, United States.,Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, United States.,Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Brian D Strahl
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, United States.,Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Robert J Duronio
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, United States.,Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, United States.,Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, United States.,Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, United States.,Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Karen Adelman
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Science, Durham, United States
| | - A Gregory Matera
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, United States.,Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, United States.,Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, United States.,Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, United States.,Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, United States
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22
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SOUZA JANAINASDE, BRUNETTO ERIKAL, NUNES MARIATEREZA. Iron restriction increases myoglobin gene and protein expression in Soleus muscle of rats. AN ACAD BRAS CIENC 2016; 88:2277-2290. [DOI: 10.1590/0001-3765201620160173] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 07/12/2016] [Indexed: 12/21/2022] Open
Affiliation(s)
- JANAINA S. DE SOUZA
- Universidade de São Paulo, Brazil; Universidade Federal de São Paulo, Brazil
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23
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Bangru S, Kalsotra A. Advances in analyzing RNA diversity in eukaryotic transcriptomes: peering through the Omics lens. F1000Res 2016; 5:2668. [PMID: 27909578 PMCID: PMC5112568 DOI: 10.12688/f1000research.9511.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/08/2016] [Indexed: 12/12/2022] Open
Abstract
Alternative splicing, polyadenylation, and chemical modifications of RNA generate astonishing complexity within eukaryotic transcriptomes. The last decade has brought numerous advances in sequencing technologies that allow biologists to investigate these phenomena with greater depth and accuracy while reducing time and cost. A commensurate development in biochemical techniques for the enrichment and analysis of different RNA variants has accompanied the advancement of global sequencing analysis platforms. Here, we present a detailed overview of the latest biochemical methods, along with bioinformatics pipelines that have aided in identifying different RNA variants. We also highlight the ongoing developments and challenges associated with RNA variant detection and quantification, including sample heterogeneity and isolation, as well as 'Omics' big data handling.
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Affiliation(s)
- Sushant Bangru
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Illinois, USA
| | - Auinash Kalsotra
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Illinois, USA; Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Illinois, USA; College of Medicine, University of Illinois at Urbana-Champaign, Illinois, USA
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Characterization of the Role of Hexamer AGUAAA and Poly(A) Tail in Coronavirus Polyadenylation. PLoS One 2016; 11:e0165077. [PMID: 27760233 PMCID: PMC5070815 DOI: 10.1371/journal.pone.0165077] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 10/05/2016] [Indexed: 01/21/2023] Open
Abstract
Similar to eukaryotic mRNA, the positive-strand coronavirus genome of ~30 kilobases is 5’-capped and 3’-polyadenylated. It has been demonstrated that the length of the coronaviral poly(A) tail is not static but regulated during infection; however, little is known regarding the factors involved in coronaviral polyadenylation and its regulation. Here, we show that during infection, the level of coronavirus poly(A) tail lengthening depends on the initial length upon infection and that the minimum length to initiate lengthening may lie between 5 and 9 nucleotides. By mutagenesis analysis, it was found that (i) the hexamer AGUAAA and poly(A) tail are two important elements responsible for synthesis of the coronavirus poly(A) tail and may function in concert to accomplish polyadenylation and (ii) the function of the hexamer AGUAAA in coronaviral polyadenylation is position dependent. Based on these findings, we propose a process for how the coronaviral poly(A) tail is synthesized and undergoes variation. Our results provide the first genetic evidence to gain insight into coronaviral polyadenylation.
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Lim J, Lee M, Son A, Chang H, Kim VN. mTAIL-seq reveals dynamic poly(A) tail regulation in oocyte-to-embryo development. Genes Dev 2016; 30:1671-82. [PMID: 27445395 PMCID: PMC4973296 DOI: 10.1101/gad.284802.116] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 06/28/2016] [Indexed: 12/04/2022]
Abstract
Here, Lim et al. report a new version of TAIL-seq (mRNA TAIL-seq [mTAIL-seq]) with enhanced sequencing depth for mRNAs (by ∼1000-fold compared with the previous version). Using their new methodology, the authors investigated mRNA tailing in Drosophila oocytes and embryos and demonstrated a relationship between poly(A) tail length and translational efficiency during egg activation. Eukaryotic mRNAs are subject to multiple types of tailing that critically influence mRNA stability and translatability. To investigate RNA tails at the genomic scale, we previously developed TAIL-seq, but its low sensitivity precluded its application to biological materials of minute quantity. In this study, we report a new version of TAIL-seq (mRNA TAIL-seq [mTAIL-seq]) with enhanced sequencing depth for mRNAs (by ∼1000-fold compared with the previous version). The improved method allows us to investigate the regulation of poly(A) tails in Drosophila oocytes and embryos. We found that maternal mRNAs are polyadenylated mainly during late oogenesis, prior to fertilization, and that further modulation occurs upon egg activation. Wispy, a noncanonical poly(A) polymerase, adenylates the vast majority of maternal mRNAs, with a few intriguing exceptions such as ribosomal protein transcripts. By comparing mTAIL-seq data with ribosome profiling data, we found a strong coupling between poly(A) tail length and translational efficiency during egg activation. Our data suggest that regulation of poly(A) tails in oocytes shapes the translatomic landscape of embryos, thereby directing the onset of animal development. By virtue of the high sensitivity, low cost, technical robustness, and broad accessibility, mTAIL-seq will be a potent tool to improve our understanding of mRNA tailing in diverse biological systems.
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Affiliation(s)
- Jaechul Lim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Mihye Lee
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Ahyeon Son
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Hyeshik Chang
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea
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Inoue T, Morita M, Hijikata A, Fukuda-Yuzawa Y, Adachi S, Isono K, Ikawa T, Kawamoto H, Koseki H, Natsume T, Fukao T, Ohara O, Yamamoto T, Kurosaki T. CNOT3 contributes to early B cell development by controlling Igh rearrangement and p53 mRNA stability. ACTA ACUST UNITED AC 2015; 212:1465-79. [PMID: 26238124 PMCID: PMC4548056 DOI: 10.1084/jem.20150384] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 07/16/2015] [Indexed: 11/07/2022]
Abstract
Inoue et al. report that CNOT3, a subunit of the CCR4–NOT deadenylase complex regulating mRNA decay and translational repression, controls Igh gene rearrangement and destabilizes the mRNA of the tumor suppressor p53. Loss of CNOT3 results in a block of pro- to pre–B cell transition. The CCR4–NOT deadenylase complex plays crucial roles in mRNA decay and translational repression induced by poly(A) tail shortening. Although the in vitro activities of each component of this complex have been well characterized, its in vivo role in immune cells remains unclear. Here we show that mice lacking the CNOT3 subunit of this complex, specifically in B cells, have a developmental block at the pro- to pre–B cell transition. CNOT3 regulated generation of germline transcripts in the VH region of the immunoglobulin heavy chain (Igh) locus, compaction of the locus, and subsequent Igh gene rearrangement and destabilized tumor suppressor p53 mRNA. The developmental defect in the absence of CNOT3 could be partially rescued by ablation of p53 or introduction of a pre-rearranged Igh transgene. Thus, our data suggest that the CCR4–NOT complex regulates B cell differentiation by controlling Igh rearrangement and destabilizing p53 mRNA.
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Affiliation(s)
- Takeshi Inoue
- Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
| | - Masahiro Morita
- Department of Biochemistry and Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, Quebec H3A 1A3, Canada Department of Biochemistry and Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Atsushi Hijikata
- Laboratory for Integrative Genomics, Laboratory for Developmental Genetics, Laboratory for Immune Regeneration, and Laboratory for Lymphocyte Differentiation, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa 230-0045, Japan
| | - Yoko Fukuda-Yuzawa
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Shungo Adachi
- Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo 135-0064, Japan
| | - Kyoichi Isono
- Laboratory for Integrative Genomics, Laboratory for Developmental Genetics, Laboratory for Immune Regeneration, and Laboratory for Lymphocyte Differentiation, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa 230-0045, Japan
| | - Tomokatsu Ikawa
- Laboratory for Integrative Genomics, Laboratory for Developmental Genetics, Laboratory for Immune Regeneration, and Laboratory for Lymphocyte Differentiation, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa 230-0045, Japan Laboratory for Lymphocyte Development, RIKEN Research Center for Allergy and Immunology, Yokohama, Kanagawa 230-0045, Japan
| | - Hiroshi Kawamoto
- Laboratory for Lymphocyte Development, RIKEN Research Center for Allergy and Immunology, Yokohama, Kanagawa 230-0045, Japan Department of Immunology, Institute for Frontier Medical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Haruhiko Koseki
- Laboratory for Integrative Genomics, Laboratory for Developmental Genetics, Laboratory for Immune Regeneration, and Laboratory for Lymphocyte Differentiation, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa 230-0045, Japan
| | - Tohru Natsume
- Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo 135-0064, Japan
| | - Taro Fukao
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Osamu Ohara
- Laboratory for Integrative Genomics, Laboratory for Developmental Genetics, Laboratory for Immune Regeneration, and Laboratory for Lymphocyte Differentiation, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa 230-0045, Japan
| | - Tadashi Yamamoto
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Tomohiro Kurosaki
- Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan Laboratory for Integrative Genomics, Laboratory for Developmental Genetics, Laboratory for Immune Regeneration, and Laboratory for Lymphocyte Differentiation, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa 230-0045, Japan
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Bargi-Souza P, Romano RM, Goulart-Silva F, Brunetto EL, Nunes MT. T(3) rapidly regulates several steps of alpha subunit glycoprotein (CGA) synthesis and secretion in the pituitary of male rats: Potential repercussions on TSH, FSH and LH secretion. Mol Cell Endocrinol 2015; 409:73-81. [PMID: 25869399 DOI: 10.1016/j.mce.2015.04.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 03/30/2015] [Accepted: 04/06/2015] [Indexed: 11/22/2022]
Abstract
TSH, FSH and LH share the same glycoprotein alpha chain (CGA) as part of their protein structure. Therefore, it is possible that thyroid and gonadal dysfunction may affect the CGA expression. This study evaluated several steps of CGA synthesis and secretion in thyrotrophs and gonadotrophs of control and hypothyroid rats, acutely or chronically-treated with T3. Hypothyroidism increased the Cga mRNA expression and its association to ribosome, but decreased intracellular CGA content. These parameters were reversed after acute or chronic T3 treatment. We conclude that T3 not only down-regulates Cga mRNA expression, as expected, but also inhibits the association of Cga mRNA to ribosome, as well as the CGA secretion. These findings add novel insights into our understanding of the role of T3 on the regulation of the Cga gene expression and CGA secretion, which might have a potential repercussion in all pituitary glycoprotein hormone synthesis and secretion.
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Affiliation(s)
- Paula Bargi-Souza
- Department of Physiology and Biophysics of the Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Renata Marino Romano
- Department of Physiology and Biophysics of the Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Francemilson Goulart-Silva
- Department of Physiology and Biophysics of the Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Erika Lia Brunetto
- Department of Physiology and Biophysics of the Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Maria Tereza Nunes
- Department of Physiology and Biophysics of the Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil.
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28
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Shi M, Zhang H, Wang L, Zhu C, Sheng K, Du Y, Wang K, Dias A, Chen S, Whitman M, Wang E, Reed R, Cheng H. Premature Termination Codons Are Recognized in the Nucleus in A Reading-Frame Dependent Manner. Cell Discov 2015; 1. [PMID: 26491543 PMCID: PMC4610414 DOI: 10.1038/celldisc.2015.1] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
mRNAs containing premature termination codons (PTCs) are known to be degraded via nonsense-mediated mRNA decay (NMD). Unexpectedly, we found that mRNAs containing any type of PTC (UAA, UAG, UGA) are detained in the nucleus whereas their wild-type counterparts are rapidly exported. This retention is strictly reading-frame dependent. Strikingly, our data indicate that translating ribosomes in the nucleus proofread the frame and detect the PTCs in the nucleus. Moreover, the shuttling NMD protein Upf1 specifically associates with PTC+ mRNA in the nucleus and is required for nuclear retention of PTC+ mRNA. Together, our data lead to a working model that PTCs are recognized in the nucleus by translating ribosomes, resulting in recruitment of Upf1, which in turn functions in nuclear retention of PTC+ mRNA. Nuclear PTC recognition adds a new layer of proofreading for mRNA and may be vital for ensuring the extraordinary fidelity required for protein production.
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Affiliation(s)
- Min Shi
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Heng Zhang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lantian Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Changlan Zhu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ke Sheng
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yanhua Du
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ke Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Anusha Dias
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - She Chen
- National Institute of Biological Sciences, Beijing 102206
| | - Malcolm Whitman
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Enduo Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Robin Reed
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Hong Cheng
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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29
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Wolniak SM, Boothby TC, van der Weele CM. Posttranscriptional control over rapid development and ciliogenesis in Marsilea. Methods Cell Biol 2015; 127:403-44. [PMID: 25837402 DOI: 10.1016/bs.mcb.2015.01.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Marsilea vestita is a semiaquatic fern that produces its spores (meiotic products) as it undergoes a process of natural desiccation. During the period of desiccation, the spores mature, and produce large quantities of pre-mRNA, which is partially processed and stored in nuclear speckles and can remain stable during a period of extended quiescence in the dry spore. Rehydration of the spores initiates a highly coordinated developmental program, featuring nine successive mitotic division cycles that occur at precise times and in precise planes within the spore wall to produce 39 cells, 32 of which are spermatids. The spermatids then undergo de novo basal body formation, the assembly of a massive cytoskeleton, nuclear and cell elongation, and finally ciliogenesis, before being released from the spore wall. The entire developmental program requires only 11 h to reach completion, and is synchronous in a population of spores rehydrated at the same time. Rapid development in this endosporic gametophyte is controlled posttranscriptionally, where stored pre-mRNAs, many of which are intron-retaining transcripts, are unmasked, processed, and translated under tight spatial and temporal control. Here, we describe posttranscriptional mechanisms that exert temporal and spatial control over this developmental program, which culminates in the production of ∼140 ciliary axonemes in each spermatozoid.
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Affiliation(s)
- Stephen M Wolniak
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park MD 20742, USA
| | - Thomas C Boothby
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park MD 20742, USA
| | - Corine M van der Weele
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park MD 20742, USA
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30
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Tsuchiya Y, Murai S, Yamashita S. Dual inhibition of Cdc2 protein kinase activation during apoptosis inXenopusegg extracts. FEBS J 2015; 282:1256-70. [DOI: 10.1111/febs.13217] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 01/12/2015] [Accepted: 01/26/2015] [Indexed: 11/27/2022]
Affiliation(s)
- Yuichi Tsuchiya
- Department of Biochemistry; Toho University School of Medicine; Ota-ku Tokyo Japan
| | - Shin Murai
- Department of Biochemistry; Toho University School of Medicine; Ota-ku Tokyo Japan
| | - Shigeru Yamashita
- Department of Biochemistry; Toho University School of Medicine; Ota-ku Tokyo Japan
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31
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Lee MC, Jänicke A, Beilharz TH. Using Klenow-mediated extension to measure poly(A)-tail length and position in the transcriptome. Methods Mol Biol 2014; 1125:25-42. [PMID: 24590777 DOI: 10.1007/978-1-62703-971-0_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The poly(A)-tail that terminates most mRNA and many noncoding RNA is a convenient "hook" to isolate mRNA. However the length of this tail and its position within the primary RNA transcript can also hold diagnostic value for RNA metabolism. In general, mRNA with a long poly(A)-tail is well translated, whereas a short poly(A)-tail can indicate translational silencing. A short poly(A)-tail is also appended to RNA-decay intermediates via the TRAMP complex. A number of approaches have been developed to measure the length and position of the poly(A)-tail. Here, we describe a simple method to "tag" adenylated RNA using the native function of DNA polymerase I to extend an RNA primer on a DNA template in second-strand DNA synthesis. This function can be harnessed as a means to purify, visualize, and quantitate poly(A)-dynamics of individual RNA and the transcriptome en masse.
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Affiliation(s)
- Man Chun Lee
- Department of Biochemistry and Molecular Biology, Monash University Australia, Melbourne, VIC, Australia
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32
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Jalkanen AL, Coleman SJ, Wilusz J. Determinants and implications of mRNA poly(A) tail size--does this protein make my tail look big? Semin Cell Dev Biol 2014; 34:24-32. [PMID: 24910447 DOI: 10.1016/j.semcdb.2014.05.018] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 05/31/2014] [Indexed: 12/22/2022]
Abstract
While the phenomenon of polyadenylation has been well-studied, the dynamics of poly(A) tail size and its impact on transcript function and cell biology are less well-appreciated. The goal of this review is to encourage readers to view the poly(A) tail as a dynamic, changeable aspect of a transcript rather than a simple static entity that marks the 3' end of an mRNA. This could open up new angles of regulation in the post-transcriptional control of gene expression throughout development, differentiation and cancer.
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Affiliation(s)
- Aimee L Jalkanen
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Stephen J Coleman
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA.
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33
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Carrascoso I, Sánchez-Jiménez C, Izquierdo JM. Long-term reduction of T-cell intracellular antigens leads to increased beta-actin expression. Mol Cancer 2014; 13:90. [PMID: 24766723 PMCID: PMC4113145 DOI: 10.1186/1476-4598-13-90] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 04/17/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The permanent down-regulated expression of T-cell intracellular antigen (TIA) proteins in HeLa cells improves cytoskeleton-mediated functions such as cell proliferation and tumor growth. METHODS Making use of human and mouse cells with knocked down/out expression of T-cell intracellular antigen 1 (TIA1) and/or TIA1 related/like (TIAR/TIAL1) proteins and classical RNA (e.g. reverse transcription-quantitative polymerase chain reaction, polysomal profiling analysis using sucrose gradients, immunoblotting, immunoprecipitation, electrophoretic mobility shift assays, ultraviolet light crosslinking and poly (A+) test analysis) and cellular (e.g. immunofluorescence microscopy and quimeric mRNA transfections) biology methods, we have analyzed the regulatory role of TIA proteins in the post-transcriptional modulation of beta-actin (ACTB) mRNA. RESULTS Our observations show that the acquisition of above cellular capacities is concomitant with increased expression levels of the actin beta subunit (ACTB) protein. Regulating TIA abundance does not modify ACTB mRNA levels, however, an increase of ACTB mRNA translation is observed. This regulatory capacity of TIA proteins is linked to the ACTB mRNA 3'-untranslated region (3'-UTR), where these proteins could function as RNA binding proteins. The expression of GFP from a chimeric reporter containing human ΑCΤΒ 3'-UTR recapitulates the translational control found by the endogenous ACTB mRNA in the absence of TIA proteins. Additionally, murine embryonic fibroblasts (MEF) knocked out for TIA1 rise mouse ACTB protein expression compared to the controls. Once again steady-state levels of mouse ACTB mRNA remained unchanged. CONCLUSIONS Collectively, these results suggest that TIA proteins can function as long-term regulators of the ACTB mRNA metabolism in mouse and human cells.
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Affiliation(s)
| | | | - José M Izquierdo
- Centro de Biología Molecular 'Severo Ochoa', Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC/UAM), C/Nicolás Cabrera 1, Cantoblanco, DP 28049 Madrid, Spain.
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34
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A poly(A)-specific ribonuclease directly regulates the poly(A) status of mitochondrial mRNA in Arabidopsis. Nat Commun 2014; 4:2247. [PMID: 23912222 DOI: 10.1038/ncomms3247] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 07/05/2013] [Indexed: 01/17/2023] Open
Abstract
Coordination of gene expression in the organelles and the nucleus is important for eukaryotic cell function. Transcriptional and post-transcriptional gene regulation in mitochondria remains incompletely understood in most eukaryotes, including plants. Here we show that poly(A)-specific ribonuclease, which influences the poly(A) status of cytoplasmic mRNA in many eukaryotes, directly regulates the poly(A) tract of mitochondrial mRNA in conjunction with a bacterial-type poly(A) polymerase, AGS1, in Arabidopsis. An Arabidopsis poly(A)-specific ribonuclease-deficient mutant, ahg2-1, accumulates polyadenylated mitochondrial mRNA and shows defects in mitochondrial protein complex levels. Mutations of AGS1 suppress the ahg2-1 phenotype. Mitochondrial localizations of AHG2 and AGS1 are required for their functions in the regulation of the poly(A) tract of mitochondrial mRNA. Our findings suggest that AHG2 and AGS1 constitute a regulatory system that controls mitochondrial mRNA poly(A) status in Arabidopsis.
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35
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Chang H, Lim J, Ha M, Kim VN. TAIL-seq: genome-wide determination of poly(A) tail length and 3' end modifications. Mol Cell 2014; 53:1044-52. [PMID: 24582499 DOI: 10.1016/j.molcel.2014.02.007] [Citation(s) in RCA: 318] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 12/23/2013] [Accepted: 02/03/2014] [Indexed: 01/05/2023]
Abstract
Global investigation of the 3' extremity of mRNA (3'-terminome), despite its importance in gene regulation, has not been feasible due to technical challenges associated with homopolymeric sequences and relative paucity of mRNA. We here develop a method, TAIL-seq, to sequence the very end of mRNA molecules. TAIL-seq allows us to measure poly(A) tail length at the genomic scale. Median poly(A) length is 50-100 nt in HeLa and NIH 3T3 cells. Poly(A) length correlates with mRNA half-life, but not with translational efficiency. Surprisingly, we discover widespread uridylation and guanylation at the downstream of poly(A) tail. The U tails are generally attached to short poly(A) tails (<25 nt), while the G tails are found mainly on longer poly(A) tails (>40 nt), implicating their generic roles in mRNA stability control. TAIL-seq is a potent tool to dissect dynamic control of mRNA turnover and translational control, and to discover unforeseen features of RNA cleavage and tailing.
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Affiliation(s)
- Hyeshik Chang
- Center for RNA Research, Institute for Basic Science, Seoul 151-742, Korea; School of Biological Sciences, Seoul National University, Seoul 151-742, Korea
| | - Jaechul Lim
- Center for RNA Research, Institute for Basic Science, Seoul 151-742, Korea; School of Biological Sciences, Seoul National University, Seoul 151-742, Korea
| | - Minju Ha
- Center for RNA Research, Institute for Basic Science, Seoul 151-742, Korea; School of Biological Sciences, Seoul National University, Seoul 151-742, Korea
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 151-742, Korea; School of Biological Sciences, Seoul National University, Seoul 151-742, Korea.
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36
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Minasaki R, Rudel D, Eckmann CR. Increased sensitivity and accuracy of a single-stranded DNA splint-mediated ligation assay (sPAT) reveals poly(A) tail length dynamics of developmentally regulated mRNAs. RNA Biol 2014; 11:111-23. [PMID: 24526206 DOI: 10.4161/rna.27992] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Poly(A) tail length is a readout of an mRNA's translatability and stability, especially in developmental systems. PolyAdenylation Test (PAT) assays attempt to quickly measure the average poly(A) tail length of RNAs of experimental interest. Here we present sPAT, splint-mediated PAT, a procedure that uses a DNA splint to aid in the ligation of an RNA-tag to the poly(A) tail of an mRNA. In comparison to other PAT methodologies, including ePAT, sPAT is highly sensitive to low-abundance mRNAs, gives a more accurate profile of the poly(A) tail distribution, and requires little starting material. To demonstrate its strength, we calibrated sPAT on defined poly(A) tails of synthetic mRNAs, reassessed developmentally regulated poly(A) tail-length changes of known mRNAs from established model organisms, and extended it to the emerging evolutionary developmental nematode model Pristionchus pacificus. Lastly, we used sPAT to analyze the contribution of the two cytoplasmic poly(A) polymerases GLD-2 and GLD-4, and the deadenylase CCR-4, onto Caenorhabditis elegans gld-1 mRNA that encodes a translationally controlled tumor suppressor whose poly(A) tail length measurement proved elusive.
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Affiliation(s)
- Ryuji Minasaki
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG); Pfotenhauerstrasse 108; 01307 Dresden, Germany
| | - David Rudel
- Department of Biology; East Carolina University; Greenville, NC USA
| | - Christian R Eckmann
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG); Pfotenhauerstrasse 108; 01307 Dresden, Germany
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Poly(A)-tail profiling reveals an embryonic switch in translational control. Nature 2014; 508:66-71. [PMID: 24476825 PMCID: PMC4086860 DOI: 10.1038/nature13007] [Citation(s) in RCA: 446] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 12/23/2013] [Indexed: 12/16/2022]
Abstract
Poly(A) tails enhance the stability and translation of most eukaryotic
mRNAs, but difficulties in globally measuring poly(A)-tail lengths have impeded
greater understanding of poly(A)-tail function. Here, we describe poly(A)-tail
length profiling by sequencing (PAL-seq) and apply it to measure tail lengths of
millions of individual RNAs isolated from yeasts, cell lines,
Arabidopsis leaves, mouse liver, and zebrafish and frog
embryos. Poly(A)-tail lengths were conserved between orthologous mRNAs, with
mRNAs encoding ribosomal proteins and other “housekeeping”
proteins tending to have shorter tails. As expected, tail lengths were coupled
to translational efficiency in early zebrafish and frog embryos. However, this
strong coupling diminished at gastrulation and was absent in non-embryonic
samples, indicating a rapid developmental switch in the nature of translational
control. This switch complements an earlier switch to zygotic transcriptional
control and explains why the predominant effect of microRNA-mediated
deadenylation concurrently shifts from translational repression to mRNA
destabilization.
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38
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Gohin M, Fournier E, Dufort I, Sirard MA. Discovery, identification and sequence analysis of RNAs selected for very short or long poly A tail in immature bovine oocytes. Mol Hum Reprod 2013; 20:127-38. [PMID: 24233545 DOI: 10.1093/molehr/gat080] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
A major challenge in applying genomics to oocyte physiology is that many RNAs are present but will not be translated into proteins, making it difficult to draw conclusions from RNAseq and array data. Oocyte maturation and early embryo development rely on maternal storage of specific RNAs with a short poly(A) tail, which must be elongated for translation. To resolve the role of key genes during that period, we aimed to characterize both extremes of mRNA: deadenylated RNA and long polyA tails mRNA population in immature bovine oocytes. Using magnetic beads coupled to oligodT, we isolated deadenylated (A-, 20-50 adenosines) from polyadenylated (A+, up to 200 adenosines) RNAs. After transcriptomic analysis, we observed that A+ candidates are associated with short-term processes required for immediate cell survival (translation or protein transport) or meiotic resumption, while several A- candidates are involved in processes (chromatin modification, gene transcription and post-transcriptional modifications) that will be extremely important in the development of the early embryo. In addition to a list of candidates probably translated early or late, sequence analysis revealed that cytoplasmic polyadenylation element (CPE) and U(3)GU(3) were enriched in A- sequences. Moreover, a motif associated with polyadenylation signals (MAPS, U(5)CU(2)) appeared to be enriched in 3'untranslated regions (UTR) with CPE or U(3)GU(3) sequences in bovine but also in zebrafish and Xenopus tropicalis. To further validate our methodology, we measured specific tail length of known candidates (AURKA, PTTG1, H2A1) but also determined the poly(A) tail length of other candidate RNAs (H3F3A, H1FOO, DAZAP2, ATF1, ATF2, KAT5, DAZL, ELAVL2). In conclusion, we have reported a methodology to isolate deadenylated from polyadenylated RNAs in samples with small total RNA quantities such as mammals. Moreover, we identified deadenylated RNAs in bovine oocytes that may be stored for the long-term process of early embryo development and described a conserved motif enriched in the 3'UTR of deadenylated RNAs.
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Affiliation(s)
- Maella Gohin
- Centre de Recherche en Biologie de la Reproduction, Faculté des Sciences de L'Agriculture et de L'Alimentation, Département des Sciences Animales, 2440 Bl. Hochelaga, Pavillon INAF, Université Laval, Québec, QC, Canada G1V 0A6
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39
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Estradiol induces transcriptional and posttranscriptional modifications in versican expression in the mouse uterus. J Mol Histol 2012; 44:221-9. [PMID: 23271141 PMCID: PMC3617353 DOI: 10.1007/s10735-012-9476-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2012] [Accepted: 12/14/2012] [Indexed: 12/30/2022]
Abstract
We have previously shown the differential expression of versican in the mouse uterus under ovarian hormone influence. We also demonstrated there is not a direct correlation between mRNA levels and protein expression, suggesting posttranscriptional events, such as alteration in mRNA stability. This posttranscriptional effect may result in the elongation and stabilization of transcripts poly(A) tail. Thus, the aim of this study was to analyze whether estradiol (E2) regulates versican mRNA stability and expression in a dose-related and time-dependent manner. For this purpose female mice were ovariectomized and treated with a single injection of 0.1 or 10 μg E2. To block transcription a group of females received a single injection of alpha-amanitin before hormone administration. Uterine tissues were collected 30 min, 1, 3, 6, 12 and 24 h after treatments and processed for quantitative real time PCR (qPCR), RACE-PAT Assay and immunohistochemistry. qPCR showed that versican mRNA levels are higher than control from 3 to 24 h after E2 administration, whereas after transcription inhibition versican mRNA unexpectedly increases within 3 h, which can be explained when transcriptional blockers alter the degradation rate of the transcript, resulting in the superinduction of this mRNA. Accordingly, analysis of versican transcript poly(A) tail evidenced a longer product 3 h after treatment, but not after 12 h. Versican immunoreaction becomes conspicuous in the superficial stroma only 3 h after E2 injection, whereas the whole stroma is immunoreactive from 6 h onward. These results demonstrate that E2 modulates versican at the transcriptional and posttranscriptional levels in a time-dependent manner.
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40
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Diniz GP, Takano APC, Bruneto E, Silva FGD, Nunes MT, Barreto-Chaves MLM. New insight into the mechanisms associated with the rapid effect of T₃ on AT1R expression. J Mol Endocrinol 2012; 49:11-20. [PMID: 22525353 DOI: 10.1530/jme-11-0141] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The angiotensin II type 1 receptor (AT1R) is involved in the development of cardiac hypertrophy promoted by thyroid hormone. Recently, we demonstrated that triiodothyronine (T₃) rapidly increases AT1R mRNA and protein levels in cardiomyocyte cultures. However, the molecular mechanisms responsible for these rapid events are not yet known. In this study, we investigated the T₃ effect on AT1R mRNA polyadenylation in cultured cardiomyocytes as well as on the expression of microRNA-350 (miR-350), which targets AT1R mRNA. The transcriptional and translational actions mediated by T₃ on AT1R levels were also assessed. The total content of ubiquitinated proteins in cardiomyocytes treated with T₃ was investigated. Our data confirmed that T₃ rapidly raised AT1R mRNA and protein levels, as assessed by real-time PCR and western blotting respectively. The use of inhibitors of mRNA and protein synthesis prevented the rapid increase in AT1R protein levels mediated by T₃. In addition, T₃ rapidly increased the poly-A tail length of the AT1R mRNA, as determined by rapid amplification of cDNA ends poly-A test, and decreased the content of ubiquitinated proteins in cardiomyocytes. On the other hand, T₃ treatment increased miR-350 expression. In parallel with its transcriptional and translational effects on the AT1R, T₃ exerted a rapid posttranscriptional action on AT1R mRNA polyadenylation, which might be contributing to increase transcript stability, as well as on translational efficiency, resulting to the rapid increase in AT1R mRNA expression and protein levels. Finally, these results show, for the first time, that T₃ rapidly triggers distinct mechanisms, which might contribute to the regulation of AT1R levels in cardiomyocytes.
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Affiliation(s)
- Gabriela Placoná Diniz
- Department of Anatomy and Department of Physiology, Institute of Biomedical Sciences, University of São Paulo, Avenida Prof. Lineu Prestes 2415, Cidade Universitária, São Paulo SP 05508-900, Brazil
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41
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Grammel M, Hang H, Conrad NK. Chemical reporters for monitoring RNA synthesis and poly(A) tail dynamics. Chembiochem 2012; 13:1112-5. [PMID: 22513998 DOI: 10.1002/cbic.201200091] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2012] [Indexed: 11/11/2022]
Abstract
A versatile "clickable" nucleoside: Metabolic labeling of cells is useful in studying the dynamics of biological molecules. N(6) pA can be utilized by all three mammalian RNA polymerases, as well as poly(A) polymerase. Because of its alkyne modification, RNA labeled with N(6) pA can be visualized and purified by using click chemistry.
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Affiliation(s)
- Markus Grammel
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, 1230 York Avenue Box 250, New York, NY 10065, USA
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42
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MicroRNAs and their targets: recognition, regulation and an emerging reciprocal relationship. Nat Rev Genet 2012; 13:271-82. [PMID: 22411466 DOI: 10.1038/nrg3162] [Citation(s) in RCA: 1212] [Impact Index Per Article: 101.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
MicroRNAs (miRNAs) have emerged as key gene regulators in diverse biological pathways. These small non-coding RNAs bind to target sequences in mRNAs, typically resulting in repressed gene expression. Several methods are now available for identifying miRNA target sites, but the mere presence of an miRNA-binding site is insufficient for predicting target regulation. Regulation of targets by miRNAs is subject to various levels of control, and recent developments have presented a new twist; targets can reciprocally control the level and function of miRNAs. This mutual regulation of miRNAs and target genes is challenging our understanding of the gene-regulatory role of miRNAs in vivo and has important implications for the use of these RNAs in therapeutic settings.
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43
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Serrano-Nascimento C, Calil-Silveira J, Goulart-Silva F, Nunes MT. New insights about the posttranscriptional mechanisms triggered by iodide excess on sodium/iodide symporter (NIS) expression in PCCl3 cells. Mol Cell Endocrinol 2012; 349:154-61. [PMID: 22001309 DOI: 10.1016/j.mce.2011.09.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 09/06/2011] [Accepted: 09/24/2011] [Indexed: 10/17/2022]
Abstract
Iodide excess acutely downregulates NIS mRNA expression, as already demonstrated. PCCl3 cells treated or not with NaI, NaI+NaClO(4) or NaI+Methimazole, for 30 min to 24 h, were used to further explore how iodide reduces NIS gene expression. NIS mRNA expression was evaluated by Real-Time PCR; its poly(A) tail length, by RACE-PAT; its translation rate, by polysome profile; total NIS content, by Western blotting. NIS mRNA decay rate was evaluated in actinomycin-D-treated cells, incubated with or without NaI for 0-6 h. Iodide treatment caused a reduction in NIS mRNA expression, half-life, poly(A) tail length, recruitment to ribosomes, as well as NIS protein expression. Perchlorate, but not methimazole, prevented these effects. Therefore, reduced poly(A) tail length of NIS mRNA seems to be related to its decreased half-life, in addition to its translation impairment. These data provide new insights about the molecular mechanisms involved in the rapid and posttranscriptional inhibitory effect of iodide on NIS expression.
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Affiliation(s)
- Caroline Serrano-Nascimento
- Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of São Paulo, 05508-000 São Paulo, SP, Brazil
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44
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CPEB2-eEF2 interaction impedes HIF-1α RNA translation. EMBO J 2011; 31:959-71. [PMID: 22157746 DOI: 10.1038/emboj.2011.448] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2011] [Accepted: 11/15/2011] [Indexed: 12/21/2022] Open
Abstract
Translation of mRNA into protein proceeds in three phases: initiation, elongation, and termination. Regulated translation allows the prompt production of selective proteins in response to physiological needs and is often controlled by sequence-specific RNA-binding proteins that function at initiation. Whether the elongation phase of translation can be modulated individually by trans-acting factors to synthesize polypeptides at variable rates remains to be determined. Here, we demonstrate that the RNA-binding protein, cytoplasmic polyadenylation element binding protein (CPEB)2, interacts with the elongation factor, eEF2, to reduce eEF2/ribosome-triggered GTP hydrolysis in vitro and slow down peptide elongation of CPEB2-bound RNA in vivo. The interaction of CPEB2 with eEF2 downregulates HIF-1α RNA translation under normoxic conditions; however, when cells encounter oxidative stress, CPEB2 dissociates from HIF-1α RNA, leading to rapid synthesis of HIF-1α for hypoxic adaptation. This study delineates the molecular mechanism of CPEB2-repressed translation and presents a unique model for controlling transcript-selective translation at elongation.
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45
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Cup blocks the precocious activation of the orb autoregulatory loop. PLoS One 2011; 6:e28261. [PMID: 22164257 PMCID: PMC3229553 DOI: 10.1371/journal.pone.0028261] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Accepted: 11/04/2011] [Indexed: 12/04/2022] Open
Abstract
Translational regulation of localized mRNAs is essential for patterning and axes determination in many organisms. In the Drosophila ovary, the germline-specific Orb protein mediates the translational activation of a variety of mRNAs localized in the oocyte. One of the Orb target mRNAs is orb itself, and this autoregulatory activity ensures that Orb proteins specifically accumulate in the developing oocyte. Orb is an RNA-binding protein and is a member of the cytoplasmic polyadenylation element binding (CPEB) protein family. We report here that Cup forms a complex in vivo with Orb. We also show that cup negatively regulates orb and is required to block the precocious activation of the orb positive autoregulatory loop. In cup mutant ovaries, high levels of Orb accumulate in the nurse cells, leading to what appears to be a failure in oocyte specification as a number of oocyte markers inappropriately accumulate in nurse cells. In addition, while orb mRNA is mislocalized and destabilized, a longer poly(A) tail is maintained than in wild type ovaries. Analysis of Orb phosphoisoforms reveals that loss of cup leads to the accumulation of hyperphosphorylated Orb, suggesting that an important function of cup in orb-dependent mRNA localization pathways is to impede Orb activation.
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Zaratiegui M, Castel SE, Irvine DV, Kloc A, Ren J, Li F, de Castro E, Marín L, Chang AY, Goto D, Cande WZ, Antequera F, Arcangioli B, Martienssen RA. RNAi promotes heterochromatic silencing through replication-coupled release of RNA Pol II. Nature 2011; 479:135-8. [PMID: 22002604 PMCID: PMC3391703 DOI: 10.1038/nature10501] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Accepted: 08/25/2011] [Indexed: 11/25/2022]
Abstract
Heterochromatin comprises tightly compacted repetitive regions of eukaryotic chromosomes. The inheritance of heterochromatin through mitosis requires RNA interference (RNAi), which guides histone modification 1 during the DNA replication phase of the cell cycle2. Here, we show that the alternating arrangement of origins of replication and non-coding RNA in pericentromeric heterochromatin results in competition between transcription and replication. Co-transcriptional RNAi releases RNA polymerase II (PolII), allowing completion of DNA replication by the leading strand DNA polymerase, and associated histone modifying enzymes3 which spread heterochromatin with the replication fork. In the absence of RNAi, stalled forks are repaired by homologous recombination without histone modification.
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Affiliation(s)
- Mikel Zaratiegui
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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Goulart-Silva F, Serrano-Nascimento C, Nunes M. Hypothyroidism decreases proinsulin gene expression and the attachment of its mRNA and eEF1A protein to the actin cytoskeleton of INS-1E cells. Braz J Med Biol Res 2011; 44:1060-7. [DOI: 10.1590/s0100-879x2011007500121] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Accepted: 08/31/2011] [Indexed: 11/22/2022] Open
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48
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Misfolded human tRNA isodecoder binds and neutralizes a 3' UTR-embedded Alu element. Proc Natl Acad Sci U S A 2011; 108:E794-802. [PMID: 21896722 DOI: 10.1073/pnas.1103698108] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Several classes of small noncoding RNAs are key players in cellular metabolism including mRNA decoding, RNA processing, and mRNA stability. Here we show that a tRNA(Asp) isodecoder, corresponding to a human tRNA-derived sequence, binds to an embedded Alu RNA element contained in the 3' UTR of the human aspartyl-tRNA synthetase mRNA. This interaction between two well-known classes of RNA molecules, tRNA and Alu RNA, is driven by an unexpected structural motif and induces a global rearrangement of the 3' UTR. Besides, this 3' UTR contains two functional polyadenylation signals. We propose a model where the tRNA/Alu interaction would modulate the accessibility of the two alternative polyadenylation sites and regulate the stability of the mRNA. This unique regulation mechanism would link gene expression to RNA polymerase III transcription and may have implications in a primate-specific signal pathway.
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Abstract
Cytoplasmic polyadenylation is a post-transcriptional mechanism regulating mRNA stability and translation. The human p53 3'-untranslated region (3'-UTR) contains two regions similar to cytoplasmic polyadenylation elements (CPEs) just upstream of the poly(A) hexanucleotide. Evaluation of the p53 CPE-like elements was performed by luciferase reporter assays, qPCR, and poly(A) assays. Herein, we report the down regulation of a luciferase reporter fused to the p53 3'-UTR, when human CPE-binding protein 1 (hCPEB1) is overexpressed. This inhibition is partially rescued when hCPEB1fused to hGLD-2 [a human cytoplasmic poly(A) polymerase] is overexpressed instead. The stability of a luciferase mRNA containing the p53 3'-UTR downstream, is decreased when hCPEB1 is overexpressed as seen by qPCR. Expression of hGLD-2 restores the mRNA stability. This is due to elongation of the poly(A) tail as seen by a PCR-based poly(A) test and in vitro poly(A) assay. Taken together, our results suggest that hCPEB1 and hGLD-2 are antagonizing factors regulating p53 mRNA stability.
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Affiliation(s)
- Jacob A Glahder
- Department of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, Denmark
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50
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de Lima-Salgado TM, Alba-Loureiro TC, do Nascimento CS, Nunes MT, Curi R. Molecular mechanisms by which saturated fatty acids modulate TNF-α expression in mouse macrophage lineage. Cell Biochem Biophys 2011; 59:89-97. [PMID: 20809180 DOI: 10.1007/s12013-010-9117-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Many macrophage functions are modulated by fatty acids (FAs), including cytokine release, such as tumor necrosis factor-α (TNF-α). TNF-α is of great interest due to its role in the inflammation process observed in several diseases such as rheumatoid arthritis, atherosclerosis, and obesity. However, the mechanisms by which FA effects occur have not been completely elucidated yet. In this study, we used a mouse monocyte lineage (J774 cells) to evaluate the effect of 50 and 100 μM of saturated (palmitic and stearic acids), monounsaturated (oleic acid) and polyunsaturated (linoleic acid) FAs on TNF-α production. Alterations in gene expression, poly(A) tail length and activation of transcription factors were evaluated. Oleic and linoleic acids, usually known as neutral or pro-inflammatory FA, inhibited LPS-induced TNF-α secretion by the cells. Saturated FAs were potent inducers of TNF-α expression and secretion under basal and inflammatory conditions (in the presence of LPS). Although the effect of the saturated FA was similar, the mechanism involved in each case seem to be distinct, as palmitic acid increased EGR-1 and CREB binding activity and stearic acid increased mRNA poly(A) tail. These results may contribute to the understanding of the molecular mechanisms by which saturated FAs modulate the inflammatory response and may lead to design of associations of dietary and pharmacological strategies to counteract the pathological effects of TNF-α.
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Affiliation(s)
- Thais Martins de Lima-Salgado
- Laboratory of Clinical Emergency, Emergency Medicine Department, Medical School, University of São Paulo, SP, Brazil.
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