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Fang J, Qian Y, Chen J, Xu D, Cao N, Zhu G, Hu W, Hu H, Qian N, Yang S, Wang J, Liu X. Human antigen R regulates autophagic flux by stabilizing autophagy-associated mRNA in calcific aortic valve disease. Cardiovasc Res 2023; 119:2117-2129. [PMID: 37183487 DOI: 10.1093/cvr/cvad077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 03/23/2023] [Accepted: 04/10/2023] [Indexed: 05/16/2023] Open
Abstract
AIMS The incidence of calcific aortic valve disease (CAVD) has risen over the last decade and is expected to continue rising; however, pharmacological approaches have proven ineffective. In this study, we evaluated the role and underlying mechanisms of human antigen R (HuR)-mediated post-transcriptional regulation in CAVD. METHODS AND RESULTS We found that HuR was significantly upregulated in human calcified aortic valves and primary aortic valvular interstitial cells (VICs) following osteogenic stimulation. Subsequent functional studies revealed that HuR silencing ameliorated calcification both in vitro and in vivo. For the first time, we demonstrated that HuR directly interacted with the transcript of phosphatidylinositol-5-phosphate 4-kinase, type II, alpha (PIP4K2A), which mediates phosphatidylinositol signalling, facilitates autophagy, and acts as an mRNA stabilizer. HuR positively modulated PIP4K2A expression at the post-transcriptional level and consequently influenced the AKT/mTOR/ATG13 pathway to regulate autophagy and CAVD progression. CONCLUSION Our study provides new insights into the post-transcriptional regulatory role of HuR in modulating autophagy-positive factors to regulate the pathogenesis of CAVD. Our findings highlight the potential of HuR as an innovative therapeutic target in CAVD treatment.
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Affiliation(s)
- Juan Fang
- Department of Cardiology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Cardiovascular Disease of Zhejiang Province, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Yi Qian
- Department of Cardiology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Cardiovascular Disease of Zhejiang Province, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
- Department of Cardiology, The Fourth Affiliated Hospital, International Institutes of Medicine, Zhejiang University School of Medicine, Jinhua, Zhejiang Province, China
| | - Jinyong Chen
- Department of Cardiology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Cardiovascular Disease of Zhejiang Province, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Dilin Xu
- Department of Cardiology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Cardiovascular Disease of Zhejiang Province, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Naifang Cao
- Department of Cardiology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Cardiovascular Disease of Zhejiang Province, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Gangjie Zhu
- Department of Cardiology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Cardiovascular Disease of Zhejiang Province, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Wangxing Hu
- Department of Cardiology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Cardiovascular Disease of Zhejiang Province, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Haochang Hu
- Department of Cardiology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Cardiovascular Disease of Zhejiang Province, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Ningjing Qian
- Department of Cardiology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Cardiovascular Disease of Zhejiang Province, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Shuangshuang Yang
- Department of Cardiology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Cardiovascular Disease of Zhejiang Province, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Jian'an Wang
- Department of Cardiology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Cardiovascular Disease of Zhejiang Province, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Xianbao Liu
- Department of Cardiology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Cardiovascular Disease of Zhejiang Province, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
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Dai Q, Zhang LS, Sun HL, Pajdzik K, Yang L, Ye C, Ju CW, Liu S, Wang Y, Zheng Z, Zhang L, Harada BT, Dou X, Irkliyenko I, Feng X, Zhang W, Pan T, He C. Quantitative sequencing using BID-seq uncovers abundant pseudouridines in mammalian mRNA at base resolution. Nat Biotechnol 2023; 41:344-354. [PMID: 36302989 PMCID: PMC10017504 DOI: 10.1038/s41587-022-01505-w] [Citation(s) in RCA: 61] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 09/08/2022] [Indexed: 12/23/2022]
Abstract
Functional characterization of pseudouridine (Ψ) in mammalian mRNA has been hampered by the lack of a quantitative method that maps Ψ in the whole transcriptome. We report bisulfite-induced deletion sequencing (BID-seq), which uses a bisulfite-mediated reaction to convert pseudouridine stoichiometrically into deletion upon reverse transcription without cytosine deamination. BID-seq enables detection of abundant Ψ sites with stoichiometry information in several human cell lines and 12 different mouse tissues using 10-20 ng input RNA. We uncover consensus sequences for Ψ in mammalian mRNA and assign different 'writer' proteins to individual Ψ deposition. Our results reveal a transcript stabilization role of Ψ sites installed by TRUB1 in human cancer cells. We also detect the presence of Ψ within stop codons of mammalian mRNA and confirm the role of Ψ in promoting stop codon readthrough in vivo. BID-seq will enable future investigations of the roles of Ψ in diverse biological processes.
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Affiliation(s)
- Qing Dai
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
| | - Li-Sheng Zhang
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
| | - Hui-Lung Sun
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Kinga Pajdzik
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Lei Yang
- First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Chang Ye
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Cheng-Wei Ju
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA
| | - Shun Liu
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Yuru Wang
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Zhong Zheng
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Linda Zhang
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Bryan T Harada
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Xiaoyang Dou
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Iryna Irkliyenko
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Xinran Feng
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Wen Zhang
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
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3
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Cruz J, Lemos B. Post-transcriptional diversity in riboproteins and RNAs in aging and cancer. Semin Cancer Biol 2021; 76:292-300. [PMID: 34474152 PMCID: PMC8627441 DOI: 10.1016/j.semcancer.2021.08.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 08/28/2021] [Accepted: 08/29/2021] [Indexed: 12/19/2022]
Abstract
Post-transcriptional (PtscM) and post-translational (PtrnM) modifications of nucleotides and amino acids are covalent modifications able to change physio-chemical properties of RNAs and proteins. In the ribosome, the adequate assembly of rRNAs and ribosomal protein subunits in the nucleolus ensures suitable translational activity, with protein synthesis tuned according to intracellular demands of energy production, replication, proliferation, and growth. Disruption in the regulatory control of PtscM and PtrnM can impair ribosome biogenesis and ribosome function. Ribosomal impairment may, in turn, impact the synthesis of proteins engaged in functions as varied as telomere maintenance, apoptosis, and DNA repair, as well as intersect with mitochondria and telomerase activity. These cellular processes often malfunction in carcinogenesis and senescence. Here we discuss regulatory mechanisms of PtscMs and PtrnMs on ribosomal function. We also address chemical modification in rRNAs and their impacts on cellular metabolism, replication control, and senescence. Further, we highlight similarities and differences of PtscMs and PtrnMs in ribosomal intermediates during aging and carcinogenesis. Understanding these regulatory mechanisms may uncover critical steps for the development of more efficient oncologic and anti-aging therapies.
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Affiliation(s)
- Jurandir Cruz
- Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA; Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP 01246, Brazil
| | - Bernardo Lemos
- Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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4
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Bai CM, Rosani U, Zhang X, Xin LS, Bortoletto E, Wegner KM, Wang CM. Viral Decoys: The Only Two Herpesviruses Infecting Invertebrates Evolved Different Transcriptional Strategies to Deflect Post-Transcriptional Editing. Viruses 2021; 13:v13101971. [PMID: 34696401 PMCID: PMC8537636 DOI: 10.3390/v13101971] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 09/29/2021] [Indexed: 12/26/2022] Open
Abstract
The highly versatile group of Herpesviruses cause disease in a wide range of hosts. In invertebrates, only two herpesviruses are known: the malacoherpesviruses HaHV-1 and OsHV-1 infecting gastropods and bivalves, respectively. To understand viral transcript architecture and diversity we first reconstructed full-length viral genomes of HaHV-1 infecting Haliotis diversicolor supertexta and OsHV-1 infecting Scapharca broughtonii by DNA-seq. We then used RNA-seq over the time-course of experimental infections to establish viral transcriptional dynamics, followed by PacBio long-read sequencing of full-length transcripts to untangle viral transcript architectures at two selected time points. Despite similarities in genome structure, in the number of genes and in the diverse transcriptomic architectures, we measured a ten-fold higher transcript variability in HaHV-1, with more extended antisense gene transcription. Transcriptional dynamics also appeared different, both in timing and expression trends. Both viruses were heavily affected by post-transcriptional modifications performed by ADAR1 affecting sense-antisense gene pairs forming dsRNAs. However, OsHV-1 concentrated these modifications in a few genomic hotspots, whereas HaHV-1 diluted ADAR1 impact by elongated and polycistronic transcripts distributed over its whole genome. These transcriptional strategies might thus provide alternative potential roles for sense-antisense transcription in viral transcriptomes to evade the host's immune response in different virus-host combinations.
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Affiliation(s)
- Chang-Ming Bai
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266237, China; (C.-M.B.); (X.Z.); (L.-S.X.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Umberto Rosani
- Coastal Ecology Section, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Warden Sea Station, 25992 List auf Sylt, Germany; (U.R.); (K.M.W.)
- Department of Biology, University of Padova, 35121 Padova, Italy;
| | - Xiang Zhang
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266237, China; (C.-M.B.); (X.Z.); (L.-S.X.)
- College of Fisheries, Tianjin Agricultural University, Tianjin 300380, China
| | - Lu-Sheng Xin
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266237, China; (C.-M.B.); (X.Z.); (L.-S.X.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | | | - K. Mathias Wegner
- Coastal Ecology Section, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Warden Sea Station, 25992 List auf Sylt, Germany; (U.R.); (K.M.W.)
| | - Chong-Ming Wang
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266237, China; (C.-M.B.); (X.Z.); (L.-S.X.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Correspondence:
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5
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Li W, Jiang H. Nuclear Protein Condensates and Their Properties in Regulation of Gene Expression. J Mol Biol 2021; 434:167151. [PMID: 34271007 DOI: 10.1016/j.jmb.2021.167151] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/01/2021] [Accepted: 07/06/2021] [Indexed: 12/22/2022]
Abstract
Our understanding of the spatiotemporal regulation of eukaryotic gene expression has recently been greatly stimulated by the findings that many of the regulators of chromatin, transcription, and RNA processing form biomolecular condensates often assembled through liquid-liquid phase separation. Increasing number of reports suggest that these condensates functionally regulate gene expression, largely by concentrating the relevant biomolecules in the liquid-like micro-compartments. However, it remains poorly understood how the physicochemical properties, especially the material properties, of the condensates regulate gene expression activity. In this review, we discuss current data on various nuclear condensates and their biophysical properties with the underlying molecular interactions, and how they may functionally impact gene expression at the level of chromatin organization and activities, transcription, and RNA processing.
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Affiliation(s)
- Wei Li
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Hao Jiang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.
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6
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Tahir M. Coronavirus genomic nsp14-ExoN, structure, role, mechanism, and potential application as a drug target. J Med Virol 2021; 93:4258-4264. [PMID: 33837972 PMCID: PMC8250946 DOI: 10.1002/jmv.27009] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 12/20/2022]
Abstract
The recent coronavirus disease 2019 (COVID-19), causing a global pandemic with devastating effects on healthcare and social-economic systems, has no special antiviral therapies available for human coronaviruses (CoVs). The severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) possesses a nonstructural protein (nsp14), with amino-terminal domain coding for proofreading exoribonuclease (ExoN) that is required for high-fidelity replication. The ability of CoVs during genome replication and transcription to proofread and exclude mismatched nucleotides has long hindered the development of anti-CoV drugs. The resistance of SARS-CoV-2 to antivirals, especially nucleoside analogs (NAs), shows the need to identify new CoV inhibition targets. Therefore, this review highlights the importance of nsp14-ExoN as a target for inhibition. Also, nucleoside analogs could be used in combination with existing anti-CoV therapeutics to target the proofreading mechanism.
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Affiliation(s)
- Mohammed Tahir
- Department of BiologyUniversity of SulaimaniSulaimanyahKurdistanIraq
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7
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Schaefer MR. The Regulation of RNA Modification Systems: The Next Frontier in Epitranscriptomics? Genes (Basel) 2021; 12:genes12030345. [PMID: 33652758 PMCID: PMC7996938 DOI: 10.3390/genes12030345] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 12/12/2022] Open
Abstract
RNA modifications, long considered to be molecular curiosities embellishing just abundant and non-coding RNAs, have now moved into the focus of both academic and applied research. Dedicated research efforts (epitranscriptomics) aim at deciphering the underlying principles by determining RNA modification landscapes and investigating the molecular mechanisms that establish, interpret and modulate the information potential of RNA beyond the combination of four canonical nucleotides. This has resulted in mapping various epitranscriptomes at high resolution and in cataloguing the effects caused by aberrant RNA modification circuitry. While the scope of the obtained insights has been complex and exciting, most of current epitranscriptomics appears to be stuck in the process of producing data, with very few efforts to disentangle cause from consequence when studying a specific RNA modification system. This article discusses various knowledge gaps in this field with the aim to raise one specific question: how are the enzymes regulated that dynamically install and modify RNA modifications? Furthermore, various technologies will be highlighted whose development and use might allow identifying specific and context-dependent regulators of epitranscriptomic mechanisms. Given the complexity of individual epitranscriptomes, determining their regulatory principles will become crucially important, especially when aiming at modifying specific aspects of an epitranscriptome both for experimental and, potentially, therapeutic purposes.
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Affiliation(s)
- Matthias R Schaefer
- Centre for Anatomy & Cell Biology, Division of Cell-and Developmental Biology, Medical University of Vienna, Schwarzspanierstrasse 17, Haus C, 1st Floor, 1090 Vienna, Austria
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Heiss M, Hagelskamp F, Marchand V, Motorin Y, Kellner S. Cell culture NAIL-MS allows insight into human tRNA and rRNA modification dynamics in vivo. Nat Commun 2021; 12:389. [PMID: 33452242 PMCID: PMC7810713 DOI: 10.1038/s41467-020-20576-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 12/04/2020] [Indexed: 12/16/2022] Open
Abstract
Recently, studies about RNA modification dynamics in human RNAs are among the most controversially discussed. As a main reason, we identified the unavailability of a technique which allows the investigation of the temporal processing of RNA transcripts. Here, we present nucleic acid isotope labeling coupled mass spectrometry (NAIL-MS) for efficient, monoisotopic stable isotope labeling in both RNA and DNA in standard cell culture. We design pulse chase experiments and study the temporal placement of modified nucleosides in tRNAPhe and 18S rRNA. In existing RNAs, we observe a time-dependent constant loss of modified nucleosides which is masked by post-transcriptional methylation mechanisms and thus undetectable without NAIL-MS. During alkylation stress, NAIL-MS reveals an adaptation of tRNA modifications in new transcripts but not existing ones. Overall, we present a fast and reliable stable isotope labeling strategy which allows in-depth study of RNA modification dynamics in human cell culture.
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Affiliation(s)
- Matthias Heiss
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Felix Hagelskamp
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Virginie Marchand
- Université de Lorraine, CNRS, Inserm, UMS2008/US40 IBSLor and UMR7365 IMoPA, F-54000, Nancy, France
| | - Yuri Motorin
- Université de Lorraine, CNRS, Inserm, UMS2008/US40 IBSLor and UMR7365 IMoPA, F-54000, Nancy, France
| | - Stefanie Kellner
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany.
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str, 9, 60438, Frankfurt, Germany.
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Grosch M, Ittermann S, Shaposhnikov D, Drukker M. Chromatin-Associated Membraneless Organelles in Regulation of Cellular Differentiation. Stem Cell Reports 2020; 15:1220-1232. [PMID: 33217325 PMCID: PMC7724471 DOI: 10.1016/j.stemcr.2020.10.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 12/12/2022] Open
Abstract
Membrane-free intracellular biocondensates are enclosures of proteins and nucleic acids that form by phase separation. Extensive ensembles of nuclear "membraneless organelles" indicate their involvement in genome regulation. Indeed, nuclear bodies have been linked to regulation of gene expression by formation of condensates made of chromatin and RNA processing factors. Important questions pertain to the involvement of membraneless organelles in determining cell identity through their cell-type-specific composition and function. Paraspeckles provide a prism to these questions because they exhibit striking cell-type-specific patterns and since they are crucial in embryogenesis. Here, we outline known interactions between paraspeckles and chromatin, and postulate how such interactions may be important in regulation of cell fate transitions. Moreover, we propose long non-coding RNAs (lncRNAs) as candidates for similar regulation because many form foci that resemble biocondensates and exhibit dynamic patterns during differentiation. Finally, we outline approaches that could ascertain how chromatin-associated membraneless organelles regulate cellular differentiation.
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Affiliation(s)
- Markus Grosch
- Institute of Stem Cell Research, Helmholtz Center Munich, Neuherberg, Germany
| | - Sebastian Ittermann
- Institute of Stem Cell Research, Helmholtz Center Munich, Neuherberg, Germany
| | - Dmitry Shaposhnikov
- Institute of Stem Cell Research, Helmholtz Center Munich, Neuherberg, Germany
| | - Micha Drukker
- Institute of Stem Cell Research, Helmholtz Center Munich, Neuherberg, Germany; Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Gorlaeus Building, Einsteinweg 55, 2333 CC RA Leiden, The Netherlands.
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Iglesias-Pedraz JM, Fossatti-Jara DM, Valle-Riestra-Felice V, Cruz-Visalaya SR, Ayala Felix JA, Comai L. WRN modulates translation by influencing nuclear mRNA export in HeLa cancer cells. BMC Mol Cell Biol 2020; 21:71. [PMID: 33054770 PMCID: PMC7557079 DOI: 10.1186/s12860-020-00315-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/01/2020] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND The Werner syndrome protein (WRN) belongs to the RecQ family of helicases and its loss of function results in the premature aging disease Werner syndrome (WS). We previously demonstrated that an early cellular change induced by WRN depletion is a posttranscriptional decrease in the levels of enzymes involved in metabolic pathways that control macromolecular synthesis and protect from oxidative stress. This metabolic shift is tolerated by normal cells but causes mitochondria dysfunction and acute oxidative stress in rapidly growing cancer cells, thereby suppressing their proliferation. RESULTS To identify the mechanism underlying this metabolic shift, we examined global protein synthesis and mRNA nucleocytoplasmic distribution after WRN knockdown. We determined that WRN depletion in HeLa cells attenuates global protein synthesis without affecting the level of key components of the mRNA export machinery. We further observed that WRN depletion affects the nuclear export of mRNAs and demonstrated that WRN interacts with mRNA and the Nuclear RNA Export Factor 1 (NXF1). CONCLUSIONS Our findings suggest that WRN influences the export of mRNAs from the nucleus through its interaction with the NXF1 export receptor thereby affecting cellular proteostasis. In summary, we identified a new partner and a novel function of WRN, which is especially important for the proliferation of cancer cells.
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Affiliation(s)
- Juan Manuel Iglesias-Pedraz
- Departamento de Investigación, Desarrollo e Innovación, Laboratorio de Genética Molecular y Bioquímica, Universidad Científica del Sur, Villa El Salvador, 15842 Lima, Peru
| | - Diego Matia Fossatti-Jara
- Departamento de Investigación, Desarrollo e Innovación, Laboratorio de Genética Molecular y Bioquímica, Universidad Científica del Sur, Villa El Salvador, 15842 Lima, Peru
- Present address: National Centre for Biomolecular Research, Masaryk University, 62500 Brno, Czech Republic
| | - Valeria Valle-Riestra-Felice
- Departamento de Investigación, Desarrollo e Innovación, Laboratorio de Genética Molecular y Bioquímica, Universidad Científica del Sur, Villa El Salvador, 15842 Lima, Peru
| | - Sergio Rafael Cruz-Visalaya
- Departamento de Investigación, Desarrollo e Innovación, Laboratorio de Genética Molecular y Bioquímica, Universidad Científica del Sur, Villa El Salvador, 15842 Lima, Peru
| | - Jose Antonio Ayala Felix
- Departamento de Investigación, Desarrollo e Innovación, Laboratorio de Genética Molecular y Bioquímica, Universidad Científica del Sur, Villa El Salvador, 15842 Lima, Peru
| | - Lucio Comai
- Department of Molecular Microbiology and Immunology, Biochemistry and Molecular Medicine, Keck School of Medicine, Longevity Institute, Davis School of Gerontology, University of Southern California, Los Angeles, CA 90033 USA
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11
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Park HJ, You YN, Lee A, Jung H, Jo SH, Oh N, Kim HS, Lee HJ, Kim JK, Kim YS, Jung C, Cho HS. OsFKBP20-1b interacts with the splicing factor OsSR45 and participates in the environmental stress response at the post-transcriptional level in rice. Plant J 2020; 102:992-1007. [PMID: 31925835 DOI: 10.1111/tpj.14682] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 11/28/2019] [Accepted: 12/20/2019] [Indexed: 06/10/2023]
Abstract
Sessile plants have evolved distinct mechanisms to respond and adapt to adverse environmental conditions through diverse mechanisms including RNA processing. While the role of RNA processing in the stress response is well understood for Arabidopsis thaliana, limited information is available for rice (Oryza sativa). Here, we show that OsFKBP20-1b, belonging to the immunophilin family, interacts with the splicing factor OsSR45 in both nuclear speckles and cytoplasmic foci, and plays an essential role in post-transcriptional regulation of abiotic stress response. The expression of OsFKBP20-1b was highly upregulated under various abiotic stresses. Moreover genetic analysis revealed that OsFKBP20-1b positively affected transcription and pre-mRNA splicing of stress-responsive genes under abiotic stress conditions. In osfkbp20-1b loss-of-function mutants, the expression of stress-responsive genes was downregulated, while that of their splicing variants was increased. Conversely, in plants overexpressing OsFKBP20-1b, the expression of the same stress-responsive genes was strikingly upregulated under abiotic stress. In vivo experiments demonstrated that OsFKBP20-1b directly maintains protein stability of OsSR45 splicing factor. Furthermore, we found that the plant-specific OsFKBP20-1b gene has uniquely evolved as a paralogue only in some Poaceae species. Together, our findings suggest that OsFKBP20-1b-mediated RNA processing contributes to stress adaptation in rice.
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Affiliation(s)
- Hyun J Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Young N You
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Areum Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology, Daejeon, 34113, Korea
| | - Haemyeong Jung
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology, Daejeon, 34113, Korea
| | - Seung H Jo
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology, Daejeon, 34113, Korea
| | - Nuri Oh
- Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, Republic of Korea
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Hyo-Jun Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Ju-Kon Kim
- Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, Republic of Korea
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang, 25354, Republic of Korea
| | - Youn S Kim
- Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, Republic of Korea
| | - Choonkyun Jung
- Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, Republic of Korea
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang, 25354, Republic of Korea
| | - Hye S Cho
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology, Daejeon, 34113, Korea
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12
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Ma X, Si F, Liu X, Luan W. PRMdb: A Repository of Predicted RNA Modifications in Plants. Plant Cell Physiol 2020; 61:1213-1222. [PMID: 32542382 DOI: 10.1093/pcp/pcaa042] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 03/28/2020] [Indexed: 06/11/2023]
Abstract
Evidence is mounting that RNA modifications play essential roles in posttranscriptional regulation of gene expression. So far, over 150 RNA modifications catalyzed by distinct enzymes have been documented. In plants, genome-wide identification of RNA modifications is largely limited to the model species Arabidopsis thaliana, while lacking in diverse non-model plants. Here, we present PRMdb, a plant RNA modification database, based on the analysis of thousands of RNA-seq, degradome-seq and small RNA-seq data from a wide range of plant species using the well-documented tool HAMR (high-throughput analysis of modified ribonucleotide). PRMdb provides a user-friendly interface that enables easy browsing and searching of the tRNA and mRNA modification data. We show that PRMdb collects high-confidence RNA modifications including novel RNA modification sites that can be validated by genomic PCR and reverse transcription PCR. In summary, PRMdb provides a valuable web resource for deciphering the epitranscriptomes in diverse plant species and will facilitate functional studies of RNA modifications in plants. RPMdb is available via http://www.biosequencing.cn/PRMdb/.
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Affiliation(s)
- Xuan Ma
- College of Life Sciences, Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin 300387, China
| | - Fuyan Si
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaonan Liu
- College of Life Sciences, Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin 300387, China
| | - Weijiang Luan
- College of Life Sciences, Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin 300387, China
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13
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Abstract
Specific chemical modifications of biological molecules are an efficient way of regulating molecular function, and a plethora of downstream signalling pathways are influenced by the modification of DNA and proteins. Many of the enzymes responsible for regulating protein and DNA modifications are targets of current cancer therapies. RNA epitranscriptomics, the study of RNA modifications, is the new frontier of this arena. Despite being known since the 1970s, eukaryotic RNA modifications were mostly identified on transfer RNA and ribosomal RNA until the last decade, when they have been identified and characterized on mRNA and various non-coding RNAs. Increasing evidence suggests that RNA modification pathways are also misregulated in human cancers and may be ideal targets of cancer therapy. In this Review we highlight the RNA epitranscriptomic pathways implicated in cancer, describing their biological functions and their connections to the disease.
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Affiliation(s)
- Isaia Barbieri
- The Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
- Division of Cellular and Molecular Pathology, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Tony Kouzarides
- The Gurdon Institute, University of Cambridge, Cambridge, UK.
- Department of Pathology, University of Cambridge, Cambridge, UK.
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14
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Zhang QJ, Luan JC, Song LB, Cong R, Ji CJ, Zhou X, Xia JD, Song NH. m6A RNA methylation regulators correlate with malignant progression and have potential predictive values in clear cell renal cell carcinoma. Exp Cell Res 2020; 392:112015. [PMID: 32333907 DOI: 10.1016/j.yexcr.2020.112015] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 04/14/2020] [Accepted: 04/16/2020] [Indexed: 02/06/2023]
Abstract
N6-methyladenosine (m6A) has been reported to be involved in several biological processes in tumors. In this study, we found that most of the m6A RNA methylation regulators were not only differentially expressed between clear cell renal cell carcinoma (ccRCC) and normal but also among ccRCC stratified by different clinicopathologic characters. Two ccRCC subgroups, cluster 1 and 2, were identified using consensus clustering based on the expression of m6A methylation regulators. Although no obvious differences were observed between two subgroups regarding clinicopathologic characters, except gender, patients in cluster 1 had a relatively more favorable survival rate than cluster 2. Moreover, we established a risk signature with two m6A methylation regulators, METTL3 and METTL14, which was not only of great value for prognosis prediction but also closely associated with clinicopathological features. In conclusion, m6A RNA methylation regulators play an important role in ccRCC progression and are potentially favorable for prognostic stratification.
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MESH Headings
- Adenosine/metabolism
- Adult
- Aged
- Aged, 80 and over
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carcinoma, Renal Cell/diagnosis
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/metabolism
- Carcinoma, Renal Cell/pathology
- Cohort Studies
- Disease Progression
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Kidney Neoplasms/diagnosis
- Kidney Neoplasms/genetics
- Kidney Neoplasms/metabolism
- Kidney Neoplasms/pathology
- Male
- Methylation/drug effects
- Methyltransferases/genetics
- Methyltransferases/metabolism
- Middle Aged
- Predictive Value of Tests
- Prognosis
- RNA Processing, Post-Transcriptional/drug effects
- RNA Processing, Post-Transcriptional/physiology
- Survival Analysis
- Transcriptome
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Affiliation(s)
- Qi-Jie Zhang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jiao-Chen Luan
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Le-Bin Song
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Rong Cong
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chen-Jian Ji
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiang Zhou
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jia-Dong Xia
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Ning-Hong Song
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
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15
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Good AL, Stoffers DA. Stress-Induced Translational Regulation Mediated by RNA Binding Proteins: Key Links to β-Cell Failure in Diabetes. Diabetes 2020; 69:499-507. [PMID: 32198193 PMCID: PMC7085242 DOI: 10.2337/dbi18-0068] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 01/16/2020] [Indexed: 12/21/2022]
Abstract
In type 2 diabetes, β-cells endure various forms of cellular stress, including oxidative stress and endoplasmic reticulum stress, secondary to increased demand for insulin production and extracellular perturbations, including hyperglycemia. Chronic exposure to stress causes impaired insulin secretion, apoptosis, and loss of cell identity, and a combination of these processes leads to β-cell failure and severe hyperglycemia. Therefore, a better understanding of the molecular mechanisms underlying stress responses in β-cells promises to reveal new therapeutic opportunities for type 2 diabetes. In this perspective, we discuss posttranscriptional control of gene expression as a critical, but underappreciated, layer of regulation with broad importance during stress responses. Specifically, regulation of mRNA translation occurs pervasively during stress to activate gene expression programs; however, the convenience of RNA sequencing has caused translational regulation to be overlooked compared with transcriptional controls. We highlight the role of RNA binding proteins in shaping selective translational regulation during stress and the mechanisms underlying this level of regulation. A growing body of evidence indicates that RNA binding proteins control an array of processes in β-cells, including the synthesis and secretion of insulin. Therefore, systematic evaluations of translational regulation and the upstream factors shaping this level of regulation are critical areas of investigation to expand our understanding of β-cell failure in type 2 diabetes.
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Affiliation(s)
- Austin L Good
- Institute for Diabetes, Obesity, and Metabolism and Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Doris A Stoffers
- Institute for Diabetes, Obesity, and Metabolism and Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
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16
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Wong RW, Balachandran A, Cheung PK, Cheng R, Pan Q, Stoilov P, Harrigan PR, Blencowe BJ, Branch DR, Cochrane A. An activator of G protein-coupled receptor and MEK1/2-ERK1/2 signaling inhibits HIV-1 replication by altering viral RNA processing. PLoS Pathog 2020; 16:e1008307. [PMID: 32069328 PMCID: PMC7048317 DOI: 10.1371/journal.ppat.1008307] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 02/28/2020] [Accepted: 01/06/2020] [Indexed: 12/17/2022] Open
Abstract
The ability of HIV-1 to evolve resistance to combined antiretroviral therapies (cARTs) has stimulated research into alternative means of controlling this infection. We assayed >60 modulators of RNA alternative splicing (AS) to identify new inhibitors of HIV-1 RNA processing-a segment of the viral lifecycle not targeted by current drugs-and discovered compound N-[4-chloro-3-(trifluoromethyl)phenyl]-7-nitro-2,1,3-benzoxadiazol-4-amine (5342191) as a potent inhibitor of both wild-type (Ba-L, NL4-3, LAI, IIIB, and N54) and drug-resistant strains of HIV-1 (IC50: ~700 nM) with no significant effect on cell viability at doses tested. 5342191 blocks expression of four essential HIV-1 structural and regulatory proteins (Gag, Env, Tat, and Rev) without affecting total protein synthesis of the cell. This response is associated with altered unspliced (US) and singly-spliced (SS) HIV-1 RNA accumulation (~60% reduction) and transport to the cytoplasm (loss of Rev) whereas parallel analysis of cellular RNAs revealed less than a 0.7% of host alternative splicing (AS) events (0.25-0.67% by ≥ 10-20%), gene expression (0.01-0.46% by ≥ 2-5 fold), and protein abundance (0.02-0.34% by ≥ 1.5-2 fold) being affected. Decreased expression of Tat, but not Gag/Env, upon 5342191 treatment was reversed by a proteasome inhibitor, suggesting that this compound alters the synthesis/degradation of this key viral factor. Consistent with an affect on HIV-1 RNA processing, 5342191 treatment of cells altered the abundance and phosphorylation of serine/arginine-rich splicing factor (SRSF) 1, 3, and 4. Despite the activation of several intracellular signaling pathways by 5342191 (Ras, MEK1/2-ERK1/2, and JNK1/2/3), inhibition of HIV-1 gene expression by this compound could be reversed by pre-treatment with either a G-protein α-subunit inhibitor or two different MEK1/2 inhibitors. These observations demonstrate enhanced sensitivity of HIV-1 gene expression to small changes in host RNA processing and highlights the potential of modulating host intracellular signaling as an alternative approach for controlling HIV-1 infection.
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Affiliation(s)
- Raymond W. Wong
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Ahalya Balachandran
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Peter K. Cheung
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Ran Cheng
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Qun Pan
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Peter Stoilov
- Department of Biochemistry, West Virginia University, Morgantown, West Virginia, United States of America
| | - P. Richard Harrigan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Department of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Benjamin J. Blencowe
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Donald R. Branch
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Division of Advanced Diagnostics, Infection and Immunity Group, Toronto General Hospital Research Institute, Toronto, Ontario, Canada
- Centre for Innovation, Canadian Blood Services, Toronto, Ontario, Canada
| | - Alan Cochrane
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
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17
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Chen L, Wang P, Bahal R, Manautou JE, Zhong XB. Ontogenic mRNA expression of RNA modification writers, erasers, and readers in mouse liver. PLoS One 2019; 14:e0227102. [PMID: 31891622 PMCID: PMC6938302 DOI: 10.1371/journal.pone.0227102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/12/2019] [Indexed: 01/09/2023] Open
Abstract
RNA modifications are recently emerged epigenetic modifications. These diverse RNA modifications have been shown to regulate multiple biological processes, including development. RNA modifications are dynamically controlled by the “writers, erasers, and readers”, where RNA modifying proteins are able to add, remove, and recognize specific chemical modification groups on RNAs. However, little is known about the ontogenic expression of these RNA modifying proteins in various organs, such as liver. In the present study, the hepatic mRNA expression of selected RNA modifying proteins involve in m6A, m1A, m5C, hm5C, m7G, and Ψ modifications was analyzed using the RNA-seq technique. Liver samples were collected from male C57BL/6 mice at several ages from prenatal through neonatal, infant, child to young adult. Results showed that most of the RNA modifying proteins were highly expressed in prenatal mouse liver with a dramatic drop at birth. After birth, most of the RNA modifying proteins showed a downregulation trend during liver maturation. Moreover, the RNA modifying proteins that belong to the same enzyme family were expressed at different abundances at the same ages in mouse liver. In conclusion, this study unveils that the mRNA expression of RNA modifying proteins follows specific ontogenic expression patterns in mice liver during maturation. These data indicated that the changes in expression of RNA modifying proteins might have a potential role to regulate gene expression in liver through alteration of RNA modification status.
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Affiliation(s)
- Liming Chen
- Department of Pharmaceutic Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut, United States of America
| | - Pei Wang
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Raman Bahal
- Department of Pharmaceutic Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut, United States of America
| | - José E. Manautou
- Department of Pharmaceutic Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut, United States of America
| | - Xiao-bo Zhong
- Department of Pharmaceutic Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut, United States of America
- * E-mail:
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18
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Wu CW, Wimberly K, Pietras A, Dodd W, Atlas MB, Choe KP. RNA processing errors triggered by cadmium and integrator complex disruption are signals for environmental stress. BMC Biol 2019; 17:56. [PMID: 31311534 PMCID: PMC6631800 DOI: 10.1186/s12915-019-0675-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 06/24/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Adaptive responses to stress are essential for cell and organismal survival. In metazoans, little is known about the impact of environmental stress on RNA homeostasis. RESULTS By studying the regulation of a cadmium-induced gene named numr-1 in Caenorhabditis elegans, we discovered that disruption of RNA processing acts as a signal for environmental stress. We find that NUMR-1 contains motifs common to RNA splicing factors and influences RNA splicing in vivo. A genome-wide screen reveals that numr-1 is strongly and specifically induced by silencing of genes that function in basal RNA metabolism including subunits of the metazoan integrator complex. Human integrator processes snRNAs for functioning with splicing factors, and we find that silencing of C. elegans integrator subunits disrupts snRNA processing, causes aberrant pre-mRNA splicing, and induces the heat shock response. Cadmium, which also strongly induces numr-1, has similar effects on RNA and the heat shock response. Lastly, we find that heat shock factor-1 is required for full numr-1 induction by cadmium. CONCLUSION Our results are consistent with a model in which disruption of integrator processing of RNA acts as a molecular damage signal initiating an adaptive stress response mediated by heat shock factor-1. When numr-1 is induced via this pathway in C. elegans, its function in RNA metabolism may allow it to mitigate further damage and thereby promote tolerance to cadmium.
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Affiliation(s)
- Cheng-Wei Wu
- Department of Veterinary Biomedical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK, S7N 5B4, Canada.
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL, 32611, USA.
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, S7N 5B3, Canada.
| | - Keon Wimberly
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Adele Pietras
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - William Dodd
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - M Blake Atlas
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Keith P Choe
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL, 32611, USA.
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19
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Mukherjee S, Sengupta S, Mukherjee A, Basak P, Majumder AL. Abiotic stress regulates expression of galactinol synthase genes post-transcriptionally through intron retention in rice. Planta 2019; 249:891-912. [PMID: 30465114 DOI: 10.1007/s00425-018-3046-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/13/2018] [Indexed: 06/09/2023]
Abstract
Expression of the Galactinol synthase genes in rice is regulated through post-transcriptional intron retention in response to abiotic stress and may be linked to Raffinose Family Oligosaccharide synthesis in osmotic perturbation. Galactinol synthase (GolS) is the first committed enzyme in raffinose family oligosaccharide (RFO) synthesis pathway and synthesizes galactinol from UDP-galactose and inositol. Expression of GolS genes has long been implicated in abiotic stress, especially drought and salinity. A non-canonical regulation mechanism controlling the splicing and maturation of rice GolS genes was identified in rice photosynthetic tissue. We found that the two isoforms of Oryza sativa GolS (OsGolS) gene, located in chromosomes 3(OsGolS1) and 7(OsGolS2) are interspersed by conserved introns harboring characteristic premature termination codons (PTC). During abiotic stress, the premature and mature transcripts of both isoforms were found to accumulate in a rhythmic manner for very small time-windows interrupted by phases of complete absence. Reporter gene assay using GolS promoters under abiotic stress does not reflect this accumulation profile, suggesting that this regulation occurs post-transcriptionally. We suggest that this may be due to a surveillance mechanism triggering the degradation of the premature transcript preventing its accumulation in the cell. The suggested mechanism fits the paradigm of PTC-induced Nonsense-Mediated Decay (NMD). In support of our hypothesis, when we pharmacologically blocked NMD, the full-length pre-mRNAs were increasingly accumulated in cell. To this end, our work suggests that a combined transcriptional and post transcriptional control exists in rice to regulate GolS expression under stress. Concurrent detection and processing of prematurely terminating transcripts coupled to repressed splicing can be described as a form of Regulated Unproductive Splicing and Translation (RUST) and may be linked to the stress adaptation of the plant, which is an interesting future research possibility.
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Affiliation(s)
- Sritama Mukherjee
- Division of Plant Biology, Bose Institute (Centenary Campus), Kolkata, West Bengal, 700054, India
- Botany Department, Bethune College, Kolkata, West Bengal, 700006, India
| | - Sonali Sengupta
- Division of Plant Biology, Bose Institute (Centenary Campus), Kolkata, West Bengal, 700054, India.
- School of Plant Environment and Soil Sciences, LSUAg Center, Baton Rouge, LA, 70803, USA.
| | - Abhishek Mukherjee
- Division of Plant Biology, Bose Institute (Centenary Campus), Kolkata, West Bengal, 700054, India
| | - Papri Basak
- Division of Plant Biology, Bose Institute (Centenary Campus), Kolkata, West Bengal, 700054, India
| | - Arun Lahiri Majumder
- Division of Plant Biology, Bose Institute (Centenary Campus), Kolkata, West Bengal, 700054, India.
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20
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Pai AA, Luca F. Environmental influences on RNA processing: Biochemical, molecular and genetic regulators of cellular response. Wiley Interdiscip Rev RNA 2019; 10:e1503. [PMID: 30216698 PMCID: PMC6294667 DOI: 10.1002/wrna.1503] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/19/2018] [Accepted: 08/01/2018] [Indexed: 12/16/2022]
Abstract
RNA processing has emerged as a key mechanistic step in the regulation of the cellular response to environmental perturbation. Recent work has uncovered extensive remodeling of transcriptome composition upon environmental perturbation and linked the impacts of this molecular plasticity to health and disease outcomes. These isoform changes and their underlying mechanisms are varied-involving alternative sites of transcription initiation, alternative splicing, and alternative cleavage at the 3' end of the mRNA. The mechanisms and consequences of differential RNA processing have been characterized across a range of common environmental insults, including chemical stimuli, immune stimuli, heat stress, and cancer pathogenesis. In each case, there are perturbation-specific contributions of local (cis) regulatory elements or global (trans) factors and downstream consequences. Overall, it is clear that choices in isoform usage involve a balance between the usage of specific genetic elements (i.e., splice sites, polyadenylation sites) and the timing at which certain decisions are made (i.e., transcription elongation rate). Fine-tuned cellular responses to environmental perturbation are often dependent on the genetic makeup of the cell. Genetic analyses of interindividual variation in splicing have identified genetic effects on splicing that contribute to variation in complex traits. Finally, the increase in the number of tissue types and environmental conditions analyzed for RNA processing is paralleled by the need to develop appropriate analytical tools. The combination of large datasets, novel methods and conditions explored promises to provide a much greater understanding of the role of RNA processing response in human phenotypic variation. This article is categorized under: RNA Processing > RNA Editing and Modification RNA Evolution and Genomics > Computational Analyses of RNA RNA Processing > Splicing Mechanisms RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Athma A Pai
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, and Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan
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21
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Ouwenga R, Lake AM, Aryal S, Lagunas T, Dougherty JD. The Differences in Local Translatome across Distinct Neuron Types Is Mediated by Both Baseline Cellular Differences and Post-transcriptional Mechanisms. eNeuro 2018; 5:ENEURO.0320-18.2018. [PMID: 30723792 PMCID: PMC6361723 DOI: 10.1523/eneuro.0320-18.2018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 12/05/2018] [Accepted: 12/12/2018] [Indexed: 12/13/2022] Open
Abstract
Local translation in neurites is a phenomenon that enhances the spatial segregation of proteins and their functions away from the cell body, yet it is unclear how local translation varies across neuronal cell types. Further, it is unclear whether differences in local translation across cell types simply reflect differences in transcription or whether there is also a cell type-specific post-transcriptional regulation of the location and translation of specific mRNAs. Most of the mRNAs discovered as being locally translated have been identified from hippocampal neurons because their laminar organization facilitates neurite-specific dissection and microscopy methods. Given the diversity of neurons across the brain, studies have not yet analyzed how locally translated mRNAs differ across cell types. Here, we used the SynapTRAP method to harvest two broad cell types in the mouse forebrain: GABAergic neurons and layer 5 projection neurons. While some transcripts overlap, the majority of the local translatome is not shared across these cell types. In addition to differences driven by baseline expression levels, some transcripts also exhibit cell type-specific post-transcriptional regulation. Finally, we provide evidence that GABAergic neurons specifically localize mRNAs for peptide neurotransmitters, including somatostatin and cortistatin, suggesting localized production of these key signaling molecules in the neurites of GABAergic neurons. Overall, this work suggests that differences in local translation in neurites across neuronal cell types are poised to contribute substantially to the heterogeneity in neuronal phenotypes.
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Affiliation(s)
- Rebecca Ouwenga
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, Missouri 63110
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Allison M. Lake
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Shivani Aryal
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Tomas Lagunas
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, Missouri 63110
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Joseph D. Dougherty
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri 63110
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, Missouri 63110
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22
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Wei J, Liu F, Lu Z, Fei Q, Ai Y, He PC, Shi H, Cui X, Su R, Klungland A, Jia G, Chen J, He C. Differential m 6A, m 6A m, and m 1A Demethylation Mediated by FTO in the Cell Nucleus and Cytoplasm. Mol Cell 2018; 71:973-985.e5. [PMID: 30197295 PMCID: PMC6151148 DOI: 10.1016/j.molcel.2018.08.011] [Citation(s) in RCA: 452] [Impact Index Per Article: 75.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 06/03/2018] [Accepted: 08/02/2018] [Indexed: 10/28/2022]
Abstract
FTO, the first RNA demethylase discovered, mediates the demethylation of internal N6-methyladenosine (m6A) and N6, 2-O-dimethyladenosine (m6Am) at the +1 position from the 5' cap in mRNA. Here we demonstrate that the cellular distribution of FTO is distinct among different cell lines, affecting the access of FTO to different RNA substrates. We find that FTO binds multiple RNA species, including mRNA, snRNA, and tRNA, and can demethylate internal m6A and cap m6Am in mRNA, internal m6A in U6 RNA, internal and cap m6Am in snRNAs, and N1-methyladenosine (m1A) in tRNA. FTO-mediated demethylation has a greater effect on the transcript levels of mRNAs possessing internal m6A than the ones with cap m6Am in the tested cells. We also show that FTO can directly repress translation by catalyzing m1A tRNA demethylation. Collectively, FTO-mediated RNA demethylation occurs to m6A and m6Am in mRNA and snRNA as well as m1A in tRNA.
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Affiliation(s)
- Jiangbo Wei
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA
| | - Fange Liu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA
| | - Zhike Lu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA; Institute of Natural Sciences, Westlake Institute for Advanced Study, Westlake University, 18 Shilongshan Road, Hangzhou 310064, China
| | - Qili Fei
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA
| | - Yuxi Ai
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA
| | - P Cody He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA
| | - Hailing Shi
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA
| | - Xiaolong Cui
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA
| | - Rui Su
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Arne Klungland
- Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, Norway Institute of Basic Medical Sciences, University of Oslo, PO Box 1018 Blindern, 0315 Oslo, Norway
| | - Guifang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA.
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23
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Peters G, Maertens J, Lammertyn J, De Mey M. Exploring of the feature space of de novo developed post-transcriptional riboregulators. PLoS Comput Biol 2018; 14:e1006170. [PMID: 30118473 PMCID: PMC6114898 DOI: 10.1371/journal.pcbi.1006170] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 08/29/2018] [Accepted: 04/30/2018] [Indexed: 11/23/2022] Open
Abstract
Metabolic engineering increasingly depends upon RNA technology to customly rewire the metabolism to maximize production. To this end, pure riboregulators allow dynamic gene repression without the need of a potentially burdensome coexpressed protein like typical Hfq binding small RNAs and clustered regularly interspaced short palindromic repeats technology. Despite this clear advantage, no clear general design principles are available to de novo develop repressing riboregulators, limiting the availability and the reliable development of these type of riboregulators. Here, to overcome this lack of knowledge on the functionality of repressing riboregulators, translation inhibiting RNAs are developed from scratch. These de novo developed riboregulators explore features related to thermodynamical and structural factors previously attributed to translation initiation modulation. In total, 12 structural and thermodynamic features were defined of which six features were retained after removing correlations from an in silico generated riboregulator library. From this translation inhibiting RNA library, 18 riboregulators were selected using a experimental design and subsequently constructed and co-expressed with two target untranslated regions to link the translation inhibiting RNA features to functionality. The pure riboregulators in the design of experiments showed repression down to 6% of the original protein expression levels, which could only be partially explained by a ordinary least squares regression model. To allow reliable forward engineering, a partial least squares regression model was constructed and validated to link the properties of translation inhibiting RNA riboregulators to gene repression. In this model both structural and thermodynamic features were important for efficient gene repression by pure riboregulators. This approach enables a more reliable de novo forward engineering of effective pure riboregulators, which further expands the RNA toolbox for gene expression modulation. To allow reliable forward engineering of microbial cell factories, various metabolic engineering efforts rely on RNA-based technology. As such, programmable riboregulators allow dynamic control over gene expression. However, no clear design principles exist for de novo developed repressing riboregulators, which limits their applicability. Here, various engineering principles are identified and computationally explored. Subsequently, various design criteria are used in an experimental design, which were explored in an in vivo study. This resulted in a regression model that enables a more reliable computational design of repression small RNAs.
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Affiliation(s)
- Gert Peters
- Centre for Synthetic Biology, Ghent University, Ghent, Belgium
| | - Jo Maertens
- Centre for Synthetic Biology, Ghent University, Ghent, Belgium
| | | | - Marjan De Mey
- Centre for Synthetic Biology, Ghent University, Ghent, Belgium
- * E-mail:
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24
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Achkar NP, Cho SK, Poulsen C, Arce AL, Re DA, Giudicatti AJ, Karayekov E, Ryu MY, Choi SW, Harholt J, Casal JJ, Yang SW, Manavella PA. A Quick HYL1-Dependent Reactivation of MicroRNA Production Is Required for a Proper Developmental Response after Extended Periods of Light Deprivation. Dev Cell 2018; 46:236-247.e6. [PMID: 30016624 DOI: 10.1016/j.devcel.2018.06.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 03/14/2018] [Accepted: 06/19/2018] [Indexed: 12/31/2022]
Abstract
Light is the most influential environmental stimulus for plant growth. In response to deficient light, plants reprogram their development to adjust their growth in search for a light source. A fine reprogramming of gene expression orchestrates this adaptive trait. Here we show that plants alter microRNA (miRNA) biogenesis in response to light transition. When plants suffer an unusual extended period of light deprivation, the miRNA biogenesis factor HYPONASTIC LEAVES 1 (HYL1) is degraded but an inactive pool of phosphorylated protein remains stable inside the nucleus. Degradation of HYL1 leads to the release of gene silencing, triggering a proper response to dark and shade. Upon light restoration, a quick dephosphorylation of HYL1 leads to the reactivation of miRNA biogenesis and a switch toward a developmental program that maximizes the light uptake. Our findings define a unique and fast regulatory mechanism controlling the plant silencing machinery during plant light response.
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Affiliation(s)
- Natalia P Achkar
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL-FBCB), Santa Fe 3000, Argentina
| | - Seok Keun Cho
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
| | | | - Agustin L Arce
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL-FBCB), Santa Fe 3000, Argentina
| | - Delfina A Re
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL-FBCB), Santa Fe 3000, Argentina
| | - Axel J Giudicatti
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL-FBCB), Santa Fe 3000, Argentina
| | - Elizabeth Karayekov
- IFEVA, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires 1417, Argentina
| | - Moon Young Ryu
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
| | - Suk Won Choi
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
| | - Jesper Harholt
- Carlsberg Research Laboratory, Copenhagen V 1799, Denmark
| | - Jorge J Casal
- IFEVA, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires 1417, Argentina; Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICET, Buenos Aires 1405, Argentina
| | - Seong Wook Yang
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea; Department of Plant and Environmental Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark.
| | - Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL-FBCB), Santa Fe 3000, Argentina.
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25
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Singh RK, Feller A, Roovers M, Van Elder D, Wauters L, Droogmans L, Versées W. Structural and biochemical analysis of the dual-specificity Trm10 enzyme from Thermococcus kodakaraensis prompts reconsideration of its catalytic mechanism. RNA 2018; 24:1080-1092. [PMID: 29848639 PMCID: PMC6049504 DOI: 10.1261/rna.064345.117] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 05/21/2018] [Indexed: 06/08/2023]
Abstract
tRNA molecules get heavily modified post-transcriptionally. The N-1 methylation of purines at position 9 of eukaryal and archaeal tRNA is catalyzed by the SPOUT methyltranferase Trm10. Remarkably, while certain Trm10 orthologs are specific for either guanosine or adenosine, others show a dual specificity. Structural and functional studies have been performed on guanosine- and adenosine-specific enzymes. Here we report the structure and biochemical analysis of the dual-specificity enzyme from Thermococcus kodakaraensis (TkTrm10). We report the first crystal structure of a construct of this enzyme, consisting of the N-terminal domain and the catalytic SPOUT domain. Moreover, crystal structures of the SPOUT domain, either in the apo form or bound to S-adenosyl-l-methionine or S-adenosyl-l-homocysteine reveal the conformational plasticity of two active site loops upon substrate binding. Kinetic analysis shows that TkTrm10 has a high affinity for its tRNA substrates, while the enzyme on its own has a very low methyltransferase activity. Mutation of either of two active site aspartate residues (Asp206 and Asp245) to Asn or Ala results in only modest effects on the N-1 methylation reaction, with a small shift toward a preference for m1G formation over m1A formation. Only a double D206A/D245A mutation severely impairs activity. These results are in line with the recent finding that the single active-site aspartate was dispensable for activity in the guanosine-specific Trm10 from yeast, and suggest that also dual-specificity Trm10 orthologs use a noncanonical tRNA methyltransferase mechanism without residues acting as general base catalysts.
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Affiliation(s)
- Ranjan Kumar Singh
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
- VIB-VUB Center For Structural Biology, 1050 Brussels, Belgium
| | - André Feller
- Laboratoire de Microbiologie, Université libre de Bruxelles (ULB), 6041 Gosselies, Belgium
| | - Martine Roovers
- Institut de Recherches Microbiologiques Jean-Marie Wiame - Labiris, 1070 Brussels, Belgium
| | - Dany Van Elder
- Laboratoire de Microbiologie, Université libre de Bruxelles (ULB), 6041 Gosselies, Belgium
| | - Lina Wauters
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
- VIB-VUB Center For Structural Biology, 1050 Brussels, Belgium
- Department of Cell Biochemistry, University of Groningen, Groningen 9747 AG, Netherlands
| | - Louis Droogmans
- Laboratoire de Microbiologie, Université libre de Bruxelles (ULB), 6041 Gosselies, Belgium
| | - Wim Versées
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
- VIB-VUB Center For Structural Biology, 1050 Brussels, Belgium
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26
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Chrislip KM, Hengst-Zhang JA, Jacob ST. Polyadenylation of SV40 late pre-mRNA is dependent on phosphorylation of an essential component associated with the 3' end processing machinery. Gene Expr 2018; 1:197-206. [PMID: 1668146 PMCID: PMC5952190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We investigated whether phosphorylation of the essential components involved in the 3' end processing of mRNAs was required for mRNA polyadenylation. The proteins in HeLa nuclear extract were dephosphorylated with alkaline phosphatase, which is known to remove the phosphate moieties from serine and tyrosine. The dephosphorylated extract was used for analyzing cleavage-dependent polyadenylation of SV40 late pre-mRNA. The phosphatase treatment of the extract completely blocked the polyadenylation reaction, whereas dephosphorylation of the extract did not inhibit the cleavage reaction. Since the cleavage depends upon functional integrity of the specificity factor, it is unlikely that the phosphorylated state of the latter factor is required for the 3' end processing. Sodium vanadate, a potent inhibitor of alkaline phosphatase, markedly reduced the inhibitory effect of the phosphatase on the polyadenylation reaction. Dephosphorylation of the extract also prevented formation of the polyadenylation-specific complex with pre-mRNA, whereas the cleavage-specific complexes were formed under this condition. The Mn-dependent polyadenylation, which is largely poly(A) extension reaction, was relatively resistant to the phosphatase treatment. These data indicate that phosphorylation of a key factor is essential for the 3' end processing of pre-mRNA, and suggest that the factor may be poly(A) polymerase.
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Affiliation(s)
- K M Chrislip
- Department of Pharmacology and Molecular Biology, Chicago Medical School, North Chicago, Illinois 60064
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27
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Pilch DR, Marzluff WF. Expression of histone-U1 snRNA chimeric genes: U1 promoters are compatible with histone 3' end formation. Gene Expr 2018; 1:41-53. [PMID: 1820206 PMCID: PMC5952198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Chimeric genes which fuse the mouse histone H2a gene and the mouse U1b gene were constructed and introduced into CHO cells by cotransfection. In the UH genes, the U1b gene promoter and the start of the U1b gene were fused to the H2a gene in the 5' untranslated region. In the HU genes, the U1b 3' end was inserted into the 3' untranslated region of the H2a gene replacing the normal histone 3' end. Transcripts from the UH genes initiated at the start of the U1 gene and ended at the normal histone 3' end. Transcripts from the HU chimeric genes did not end at the U1 3' end but extended at least 80 nucleotides further and had heterogeneous 3' ends. Placing both a U1 snRNA promoter and a U1 snRNA 3' end around a histone coding region resulted in transcripts which initiate and terminate at the appropriate U1 ends. These results are consistent with previous reports that formation of the U1 3' ends require U1 promoters, but indicate that the histone 3' end can be formed on transcripts initiating at U1 promoters. The transcripts initiated at the U1 start site and ending at the histone 3' end are present on polyribosomes and show proper posttranscriptional regulation.
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Affiliation(s)
- D R Pilch
- Department of Chemistry, Florida State University, Tallahassee 32306
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28
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Mohanty BK, Kushner SR. Enzymes Involved in Posttranscriptional RNA Metabolism in Gram-Negative Bacteria. Microbiol Spectr 2018; 6:10.1128/microbiolspec.RWR-0011-2017. [PMID: 29676246 PMCID: PMC5912700 DOI: 10.1128/microbiolspec.rwr-0011-2017] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Indexed: 02/08/2023] Open
Abstract
Gene expression in Gram-negative bacteria is regulated at many levels, including transcription initiation, RNA processing, RNA/RNA interactions, mRNA decay, and translational controls involving enzymes that alter translational efficiency. In this review, we discuss the various enzymes that control transcription, translation, and RNA stability through RNA processing and degradation. RNA processing is essential to generate functional RNAs, while degradation helps control the steady-state level of each individual transcript. For example, all the pre-tRNAs are transcribed with extra nucleotides at both their 5' and 3' termini, which are subsequently processed to produce mature tRNAs that can be aminoacylated. Similarly, rRNAs that are transcribed as part of a 30S polycistronic transcript are matured to individual 16S, 23S, and 5S rRNAs. Decay of mRNAs plays a key role in gene regulation through controlling the steady-state level of each transcript, which is essential for maintaining appropriate protein levels. In addition, degradation of both translated and nontranslated RNAs recycles nucleotides to facilitate new RNA synthesis. To carry out all these reactions, Gram-negative bacteria employ a large number of endonucleases, exonucleases, RNA helicases, and poly(A) polymerase, as well as proteins that regulate the catalytic activity of particular RNases. Under certain stress conditions, an additional group of specialized endonucleases facilitate the cell's ability to adapt and survive. Many of the enzymes, such as RNase E, RNase III, polynucleotide phosphorylase, RNase R, and poly(A) polymerase I, participate in multiple RNA processing and decay pathways.
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Affiliation(s)
| | - Sidney R Kushner
- Department of Genetics
- Department of Microbiology, University of Georgia, Athens, GA 30602
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29
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Blewett NH, Maraia RJ. La involvement in tRNA and other RNA processing events including differences among yeast and other eukaryotes. Biochim Biophys Acta Gene Regul Mech 2018; 1861:361-372. [PMID: 29397330 DOI: 10.1016/j.bbagrm.2018.01.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 12/29/2017] [Accepted: 01/17/2018] [Indexed: 10/25/2022]
Abstract
The conserved nuclear RNA-binding factor known as La protein arose in an ancient eukaryote, phylogenetically associated with another eukaryotic hallmark, synthesis of tRNA by RNA polymerase III (RNAP III). Because 3'-oligo(U) is the sequence-specific signal for transcription termination by RNAP III as well as the high affinity binding site for La, the latter is linked to the intranuclear posttranscriptional processing of eukaryotic precursor-tRNAs. The pre-tRNA processing pathway must accommodate a variety of substrates that are destined for both common steps as well as tRNA-specific events. The order of intranuclear pre-tRNA processing steps is mediated in part by three activities derived from interaction with La protein: 3'-end protection from untimely decay by 3' exonucleases, nuclear retention and chaperone activity that helps prevent pre-tRNA misfolding and mischanneling into offline pathways. A focus of this perspective will be on differences between yeast and mammals in the subcellular partitioning of pre-tRNA intermediates and differential interactions with La. We review how this is most relevant to pre-tRNA splicing which occurs in the cytoplasm of yeasts but in nuclei of higher eukaryotes. Also divergent is La architecture, comprised of three RNA-binding domains in organisms in all examined branches of the eukaryal tree except yeast, which have lost the C-terminal RNA recognition motif-2α (RRM2α) domain. We also review emerging data that suggest mammalian La interacts with nuclear pre-tRNA splicing intermediates and may impact this branch of the tRNA maturation pathway. Finally, because La is involved in intranuclear tRNA biogenesis we review relevant aspects of tRNA-associated neurodegenerative diseases. This article is part of a Special Issue entitled: SI: Regulation of tRNA synthesis and modification in physiological conditions and disease edited by Dr. Boguta Magdalena.
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Affiliation(s)
- Nathan H Blewett
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Richard J Maraia
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA; Commissioned Corps, U.S. Public Health Service, Rockville, MD, USA.
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30
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Abstract
Much progress in our understanding of RNA metabolism has been made since the first RNA nucleoside modification was identified in 1957. Many of these modifications are found in noncoding RNAs but recent interest has focused on coding RNAs. Here, we summarize current knowledge of cellular consequences of RNA modifications, with a special emphasis on neuropsychiatric disorders. We present evidence for the existence of an "RNA code," similar to the histone code, that fine-tunes gene expression in the nervous system by using combinations of different RNA modifications. Unlike the relatively stable genetic code, this combinatorial RNA epigenetic code, or epitranscriptome, may be dynamically reprogrammed as a cause or consequence of psychiatric disorders. We discuss potential mechanisms linking disregulation of the epitranscriptome with brain disorders and identify potential new avenues of research.
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Affiliation(s)
- Y. Jung
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
| | - D. Goldman
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
- Office of the Clinical Director, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
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31
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Tsai K, Courtney DG, Cullen BR. Addition of m6A to SV40 late mRNAs enhances viral structural gene expression and replication. PLoS Pathog 2018; 14:e1006919. [PMID: 29447282 PMCID: PMC5831754 DOI: 10.1371/journal.ppat.1006919] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 02/28/2018] [Accepted: 02/02/2018] [Indexed: 11/18/2022] Open
Abstract
Polyomaviruses are a family of small DNA tumor viruses that includes several pathogenic human members, including Merkel cell polyomavirus, BK virus and JC virus. As is characteristic of DNA tumor viruses, gene expression in polyomaviruses is temporally regulated into an early phase, consisting of the viral regulatory proteins, and a late phase, consisting of the viral structural proteins. Previously, the late transcripts expressed by the prototypic polyomavirus simian virus 40 (SV40) were reported to contain several adenosines bearing methyl groups at the N6 position (m6A), although the precise location of these m6A residues, and their phenotypic effects, have not been investigated. Here, we first demonstrate that overexpression of the key m6A reader protein YTHDF2 induces more rapid viral replication, and larger viral plaques, in SV40 infected BSC40 cells, while mutational inactivation of the endogenous YTHDF2 gene, or the m6A methyltransferase METTL3, has the opposite effect, thus suggesting a positive role for m6A in the regulation of SV40 gene expression. To directly test this hypothesis, we mapped sites of m6A addition on SV40 transcripts and identified two m6A sites on the viral early transcripts and eleven m6A sites on the late mRNAs. Using synonymous mutations, we inactivated the majority of the m6A sites on the SV40 late mRNAs and observed that the resultant viral mutant replicated more slowly than wild type SV40. Alternative splicing of SV40 late mRNAs was unaffected by the reduction in m6A residues and our data instead suggest that m6A enhances the translation of viral late transcripts. Together, these data argue that the addition of m6A residues to the late transcripts encoded by SV40 plays an important role in enhancing viral gene expression and, hence, replication.
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Affiliation(s)
- Kevin Tsai
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - David G. Courtney
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Bryan R. Cullen
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
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32
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Abstract
Recent years have witnessed a remarkable interest in exploring the significance of pervasive noncoding transcripts in diverse eukaryotes. Classical cytogenetic studies using the Drosophila model system unraveled the perplexing attributes and "functions" of the "gene"-poor heterochromatin. Recent molecular studies in the fly model are likewise revealing the very diverse and significant roles played by long noncoding RNAs (lncRNAs) in development, gene regulation, chromatin organization, cell and nuclear architecture, etc. There has been a rapid increase in the number of identified lncRNAs, although a much larger number still remains unknown. The diversity of modes of actions and functions of the limited number of Drosophila lncRNAs, which have been examined, already reflects the profound roles of such RNAs in generating and sustaining the biological complexities of eukaryotes. Several of the known Drosophila lncRNAs originate as independent sense or antisense transcripts from promoter or intergenic, intronic, or 5'/3'-UTR regions, while many of them are independent genes that produce only lncRNAs or coding as well as noncoding RNAs. The different lncRNAs affect chromatin organization (local or large-scale pan-chromosomal), transcription, RNA processing/stability, or translation either directly through interaction with their target DNA sequences or indirectly by acting as intermediary molecules for specific regulatory proteins or may act as decoys/sinks, or storage sites for specific proteins or groups of proteins, or may provide a structural framework for the assembly of substructures in nucleus/cytoplasm. It is interesting that many of the "functions" alluded to heterochromatin in earlier cytogenetic studies appear to find correlates with the known subtle as well as far-reaching actions of the different small and long noncoding RNAs. Further studies exploiting the very rich and powerful genetic and molecular resources available for the Drosophila model are expected to unravel the mystery underlying the long reach of ncRNAs.
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Affiliation(s)
- Subhash C Lakhotia
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005, India.
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Ohbayashi I, Lin CY, Shinohara N, Matsumura Y, Machida Y, Horiguchi G, Tsukaya H, Sugiyama M. Evidence for a Role of ANAC082 as a Ribosomal Stress Response Mediator Leading to Growth Defects and Developmental Alterations in Arabidopsis. Plant Cell 2017; 29:2644-2660. [PMID: 28899981 PMCID: PMC5774571 DOI: 10.1105/tpc.17.00255] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 08/24/2017] [Accepted: 09/11/2017] [Indexed: 05/20/2023]
Abstract
Ribosome-related mutants in Arabidopsis thaliana share several notable characteristics regarding growth and development, which implies the existence of a common pathway that responds to disorders in ribosome biogenesis. As a first step to explore this pathway genetically, we screened a mutagenized population of root initiation defective2 (rid2), a temperature-sensitive mutant that is impaired in pre-rRNA processing, and isolated suppressor of root initiation defective two1 (sriw1), a suppressor mutant in which the defects of cell proliferation observed in rid2 at the restrictive temperature was markedly rescued. sriw1 was identified as a missense mutation of the NAC transcription factor gene ANAC082 The sriw1 mutation greatly alleviated the developmental abnormalities of rid2 and four other tested ribosome-related mutants, including rid3 However, the impaired pre-rRNA processing in rid2 and rid3 was not relieved by sriw1 Expression of ANAC082 was localized to regions where phenotypic effects of ribosome-related mutations are readily evident and was elevated in rid2 and rid3 compared with the wild type. These findings suggest that ANAC082 acts downstream of perturbation of biogenesis of the ribosome and may mediate a set of stress responses leading to developmental alterations and cell proliferation defects.
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Affiliation(s)
- Iwai Ohbayashi
- Botanical Gardens, Graduate School of Science, The University of Tokyo, Tokyo 112-0001, Japan
| | - Chung-Yi Lin
- Botanical Gardens, Graduate School of Science, The University of Tokyo, Tokyo 112-0001, Japan
| | - Naoki Shinohara
- Botanical Gardens, Graduate School of Science, The University of Tokyo, Tokyo 112-0001, Japan
| | - Yoko Matsumura
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Yasunori Machida
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Gorou Horiguchi
- Department of Life Science, College of Science, Rikkyo University, Tokyo 171-8501, Japan
| | - Hirokazu Tsukaya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
- Okazaki Institute for Integrative Bioscience, Okazaki 444-8787, Japan
| | - Munetaka Sugiyama
- Botanical Gardens, Graduate School of Science, The University of Tokyo, Tokyo 112-0001, Japan
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34
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Abstract
The RNA interference (RNAi) pathway was recently expanded by the discovery of multiple alternative pathways for processing of natural microRNA (miRNA) and man-made short hairpin RNA (shRNA) molecules. One non-canonical pathway bypasses Dicer cleavage and requires instead processing by Argonaute2 (Ago2), which also executes the subsequent silencing step. We named these molecules AgoshRNA, which generate only a single active RNA strand and thus avoid off-target effects that can be induced by the passenger strand of a regular shRNA. Previously, we characterized AgoshRNA processing by deep sequencing and demonstrated that—after Ago2 cleavage—AgoshRNAs acquire a short 3’ tail of 1–3 A-nucleotides and are subsequently trimmed, likely by the poly(A)-specific ribonuclease (PARN). As a result, the mature single-stranded AgoshRNA may dock more stably into Ago2. Here we set out to analyze the activity of different synthetic AgoshRNA processing intermediates. Ago2 was found to bind preferentially to partially single-stranded AgoshRNA in vitro. In contrast, only the double-stranded AgoshRNA precursor associated with Ago2 in cells, correlating with efficient intracellular processing and reporter knockdown activity. These results suggest the presence of a cellular co-factor involved in AgoshRNA loading into Ago2 in vivo. We also demonstrate specific AgoshRNA loading in Ago2, but not Ago1/3/4, thus further reducing unwanted side effects.
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Affiliation(s)
- Alex Harwig
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Zita Kruize
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Zhenhuang Yang
- Institute of Molecular Medicine, Universitätsklinikum Schleswig-Holstein, University of Lübeck, Lübeck, Germany
| | - Tobias Restle
- Institute of Molecular Medicine, Universitätsklinikum Schleswig-Holstein, University of Lübeck, Lübeck, Germany
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- * E-mail:
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Liang B, Wang X, Song X, Bai R, Yang H, Yang Z, Xiao C, Bian Y. MicroRNA-20a/b regulates cholesterol efflux through post-transcriptional repression of ATP-binding cassette transporter A1. Biochim Biophys Acta Mol Cell Biol Lipids 2017; 1862:929-938. [PMID: 28602962 DOI: 10.1016/j.bbalip.2017.06.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 05/27/2017] [Accepted: 06/07/2017] [Indexed: 12/16/2022]
Abstract
ATP-binding cassette transporter A1 (ABCA1) plays a crucial role in reverse cholesterol transport and exhibits anti-atherosclerosis effects. Some microRNAs (miRs) regulate ABCA1 expression, and recent studies have shown that miR-20a/b might play a critical role in atherosclerotic diseases. Here, we attempted to clarify the potential contribution of miR-20a/b in post-transcriptional regulation of ABCA1, cholesterol efflux, and atherosclerosis. We performed bioinformatics analysis and found that miR-20a/b was highly conserved and directly bound to ABCA1 mRNA with low binding free energy. Luciferase-reporter assay also confirmed that miR-20a/b significantly reduced luciferase activity associated with the ABCA1 3' untranslated region reporter construct. Additionally, miR-20a/b decreased ABCA1 expression, which, in turn, decreased cholesterol efflux and increased cholesterol content in THP-1 and RAW 264.7 macrophage-derived foam cells. In contrast, miR-20a/b inhibitors increased ABCA1 expression and cholesterol efflux, decreased cholesterol content, and inhibited foam-cell formation. Consistent with our in vitro results, miR-20a/b-treated ApoE-/- mice showed decreased ABCA1expression in the liver and reductions of reverse cholesterol transport in vivo. Furthermore, miR-20a/b regulated the formation of nascent high-density lipoprotein and promoted atherosclerotic development, whereas miR-20a/b knockdown attenuated atherosclerotic formation. miR-20 is a new miRNA capable of targeting ABCA1 and regulating ABCA1 expression. Therefore, miR-20 inhibition constitutes a new strategy for ABCA1-based treatment of atherosclerosis.
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Affiliation(s)
- Bin Liang
- Department of Cardiology, The Second Hospital of Shanxi Medical University, 382 Wuyi Road, Taiyuan, China; Key Laboratory of Cardiovascular Medicine and Clinical Pharmacology of Shanxi Province, 382 Wuyi Road, Taiyuan, China
| | - Xin Wang
- Department of Rheumatology, The Second Hospital of Shanxi Medical University, 382 Wuyi Road, Taiyuan, China
| | - Xiaosu Song
- Department of Cardiology, The Second Hospital of Shanxi Medical University, 382 Wuyi Road, Taiyuan, China; Key Laboratory of Cardiovascular Medicine and Clinical Pharmacology of Shanxi Province, 382 Wuyi Road, Taiyuan, China
| | - Rui Bai
- Department of Cardiology, The Second Hospital of Shanxi Medical University, 382 Wuyi Road, Taiyuan, China; Key Laboratory of Cardiovascular Medicine and Clinical Pharmacology of Shanxi Province, 382 Wuyi Road, Taiyuan, China
| | - Huiyu Yang
- Department of Cardiology, The Second Hospital of Shanxi Medical University, 382 Wuyi Road, Taiyuan, China; Key Laboratory of Cardiovascular Medicine and Clinical Pharmacology of Shanxi Province, 382 Wuyi Road, Taiyuan, China
| | - Zhiming Yang
- Department of Cardiology, The Second Hospital of Shanxi Medical University, 382 Wuyi Road, Taiyuan, China; Key Laboratory of Cardiovascular Medicine and Clinical Pharmacology of Shanxi Province, 382 Wuyi Road, Taiyuan, China
| | - Chuanshi Xiao
- Key Laboratory of Cardiovascular Medicine and Clinical Pharmacology of Shanxi Province, 382 Wuyi Road, Taiyuan, China; Department of Cardiology, The First Hospital of Shanxi Medical University, 85 Jiefang South Road, Taiyuan, China
| | - Yunfei Bian
- Department of Cardiology, The Second Hospital of Shanxi Medical University, 382 Wuyi Road, Taiyuan, China; Key Laboratory of Cardiovascular Medicine and Clinical Pharmacology of Shanxi Province, 382 Wuyi Road, Taiyuan, China.
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von Arnim AG, Hellmann HA. Meeting report: processing, translation, decay - three ways to keep RNA sizzling. Plant Cell Environ 2016; 39:2624-2628. [PMID: 27859406 DOI: 10.1111/pce.12819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 08/17/2016] [Accepted: 08/21/2016] [Indexed: 06/06/2023]
Abstract
This meeting report highlights key trends that emerged from a conference entitled Post-Transcriptional Gene Regulation in Plants, which was held 14-15 July 2016, as a satellite meeting of the annual meeting of the American Society of Plant Biologists in Austin, Texas. The molecular biology of RNA is emerging as an integral part of the framework for plants' responses to environmental challenges such as drought and heat, hypoxia, nutrient deprivation, light and pathogens. Moreover, the conference illustrated how a multitude of customized and pioneering omics-related technologies are being applied, more and more often in combination, to describe and dissect the complexities of gene expression at the post-transcriptional level.
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Affiliation(s)
- Albrecht G von Arnim
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN, 37996-0840, USA
| | - Hanjo A Hellmann
- School of Biological Sciences, Washington State University, PO Box 644236, Pullman, WA, 99164-4236, USA
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37
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Lin GW, Lu P, Zeng T, Tang HL, Chen YH, Liu SJ, Gao MM, Zhao QH, Yi YH, Long YS. GAPDH-mediated posttranscriptional regulations of sodium channel Scn1a and Scn3a genes under seizure and ketogenic diet conditions. Neuropharmacology 2016; 113:480-489. [PMID: 27816501 DOI: 10.1016/j.neuropharm.2016.11.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Revised: 10/28/2016] [Accepted: 11/01/2016] [Indexed: 01/12/2023]
Abstract
Abnormal expressions of sodium channel SCN1A and SCN3A genes alter neural excitability that are believed to contribute to the pathogenesis of epilepsy, a long-term risk of recurrent seizures. Ketogenic diet (KD), a high-fat and low-carbohydrate treatment for difficult-to-control (refractory) epilepsy in children, has been suggested to reverse gene expression patterns. Here, we reveal a novel role of GAPDH on the posttranscriptional regulation of mouse Scn1a and Scn3a expressions under seizure and KD conditions. We show that GAPDH binds to a conserved region in the 3' UTRs of human and mouse SCN1A and SCN3A genes, which decreases and increases genes' expressions by affecting mRNA stability through SCN1A 3' UTR and SCN3A 3' UTR, respectively. In seizure mice, the upregulation and phosphorylation of GAPDH enhance its binding to the 3' UTR, which lead to downregulation of Scn1a and upregulation of Scn3a. Furthermore, administration of KD generates β-hydroxybutyric acid which rescues the abnormal expressions of Scn1a and Scn3a by weakening the GAPDH's binding to the element. Taken together, these data suggest that GAPDH-mediated expression regulation of sodium channel genes may be associated with epilepsy and the anticonvulsant action of KD.
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Affiliation(s)
- Guo-Wang Lin
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 501260, China
| | - Ping Lu
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 501260, China
| | - Tao Zeng
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 501260, China
| | - Hui-Ling Tang
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 501260, China
| | - Yong-Hong Chen
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 501260, China
| | - Shu-Jing Liu
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 501260, China
| | - Mei-Mei Gao
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 501260, China
| | - Qi-Hua Zhao
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 501260, China
| | - Yong-Hong Yi
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 501260, China
| | - Yue-Sheng Long
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 501260, China.
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38
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Abstract
Cells adapt to their environment by linking external stimuli to an intricate network of transcriptional, post-transcriptional and translational processes. Among these, mechanisms that couple environmental cues to the regulation of protein translation are not well understood. Chemical modifications of RNA allow rapid cellular responses to external stimuli by modulating a wide range of fundamental biochemical properties and processes, including the stability, splicing and translation of messenger RNA. In this Review, we focus on the occurrence of N6-methyladenosine (m6A), 5-methylcytosine (m5C) and pseudouridine (Ψ) in RNA, and describe how these RNA modifications are implicated in regulating pluripotency, stem cell self-renewal and fate specification. Both post-transcriptional modifications and the enzymes that catalyse them modulate stem cell differentiation pathways and are essential for normal development.
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Affiliation(s)
- Michaela Frye
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Sandra Blanco
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
- CIC bioGUNE, Bizkaia Technology Park, Building 801A, Derio, Bizkaia 48160, Spain
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39
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Dang F, Sun X, Ma X, Wu R, Zhang D, Chen Y, Xu Q, Wu Y, Liu Y. Insulin post-transcriptionally modulates Bmal1 protein to affect the hepatic circadian clock. Nat Commun 2016; 7:12696. [PMID: 27576939 PMCID: PMC5013695 DOI: 10.1038/ncomms12696] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 07/25/2016] [Indexed: 12/15/2022] Open
Abstract
Although food availability is a potent synchronizer of the peripheral circadian clock in mammals, the underlying mechanisms are unclear. Here, we show that hepatic Bmal1, a core transcription activator of the molecular clock, is post-transcriptionally regulated by signals from insulin, an important hormone that is temporally controlled by feeding. Insulin promotes postprandial Akt-mediated Ser42-phosphorylation of Bmal1 to induce its dissociation from DNA, interaction with 14-3-3 protein and subsequently nuclear exclusion, which results in the suppression of Bmal1 transcriptional activity. Inverted feeding cycles not only shift the phase of daily insulin oscillation, but also elevate the amplitude due to food overconsumption. This enhanced and reversed insulin signalling initiates the reset of clock gene rhythms by altering Bmal1 nuclear accumulation in mouse liver. These results reveal the molecular mechanism of insulin signalling in regulating peripheral circadian rhythms.
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Affiliation(s)
- Fabin Dang
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
- Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiujie Sun
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
- Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiang Ma
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
- Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Rong Wu
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
- Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Deyi Zhang
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
- Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Yaqiong Chen
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Qian Xu
- Department of Endocrinology, The First Affiliated Hospital of Harbin Medical University, No. 23 Youzheng Street, NanGang District, Harbin 150001, China
| | - Yuting Wu
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Yi Liu
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
- Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
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40
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Zhang W, Wang P, Chen S, Zhang Z, Liang T, Liu C. Rhythmic expression of miR-27b-3p targets the clock gene Bmal1 at the posttranscriptional level in the mouse liver. FASEB J 2016; 30:2151-60. [PMID: 26919869 DOI: 10.1096/fj.201500120] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 02/04/2016] [Indexed: 12/16/2023]
Abstract
Circadian clocks orchestrate daily oscillations in mammalian behaviors, physiology, and gene expression. MicroRNAs (miRNAs) play a crucial role in fine-tuning of the circadian system. However, little is known about the direct regulation of the clock genes by specific miRNAs. In this study, we found that miR-27b-3p exhibits rhythmic expression in the metabolic tissues of the mice subjected to constant darkness. MiR-27b-3p's expression is induced in livers of unfed and ob/ob mice. In addition, the oscillation phases of miR-27b-3p can be reversed by restricted feeding, suggesting a role of peripheral clock in regulating its rhythmicity. Bioinformatics analysis indicated that aryl hydrocarbon receptor nuclear translocator-like (also known as Bmal1) may be a direct target of miR-27b-3p. Luciferase reporter assay showed that miR-27b-3p suppressed Bmal1 3' UTR activity in a dose-dependent manner, and mutagenesis of their binding site abolished this suppression. Furthermore, overexpression of miR-27b-3p dose-dependently reduced the protein expression levels of BMAL1 and impaired the endogenous BMAL1 and gluconeogenic protein rhythmicity. Collectively, our results suggest that miR-27b-3p plays an important role in the posttranscriptional regulation of BMAL1 protein in the liver. MiR-27b-3p may serve as a novel node to integrate the circadian clock and energy metabolism.-Zhang, W., Wang, P., Chen, S., Zhang, Z., Liang, T., Liu, C. Rhythmic expression of miR-27b-3p targets the clock gene Bmal1 at the posttranscriptional level in the mouse liver.
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Affiliation(s)
- Wenxiang Zhang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Peng Wang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Siyu Chen
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhao Zhang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Tingming Liang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Chang Liu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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41
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Khleborodova A, Pan X, Nagre NN, Ryan K. An investigation into the role of ATP in the mammalian pre-mRNA 3' cleavage reaction. Biochimie 2016; 125:213-22. [PMID: 27060432 DOI: 10.1016/j.biochi.2016.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 04/04/2016] [Indexed: 01/05/2023]
Abstract
RNA Polymerase II transcribes beyond what later becomes the 3' end of a mature messenger RNA (mRNA). The formation of most mRNA 3' ends results from pre-mRNA cleavage followed by polyadenylation. In vitro studies have shown that low concentrations of ATP stimulate the 3' cleavage reaction while high concentrations inhibit it, but the origin of these ATP effects is unknown. ATP might enable a cleavage factor kinase or activate a cleavage factor directly. To distinguish between these possibilities, we tested several ATP structural analogs in a pre-mRNA 3' cleavage reaction reconstituted from DEAE-fractionated cleavage factors. We found that adenosine 5'-(β,γ-methylene)triphosphate (AMP-PCP) is an effective in vitro 3' cleavage inhibitor with an IC50 of ∼300 μM, but that most other ATP analogs, including adenosine 5'-(β,γ-imido)triphosphate, which cannot serve as a protein kinase substrate, promoted 3' cleavage but less efficiently than ATP. In combination with previous literature data, our results do not support ATP stimulation of 3' cleavage through cleavage factor phosphorylation in vitro. Instead, the more likely mechanism is that ATP stimulates cleavage factor activity through direct cleavage factor binding. The mammalian 3' cleavage factors known to bind ATP include the cleavage factor II (CF IIm) Clp1 subunit, the CF Im25 subunit and poly(A) polymerase alpha (PAP). The yeast homolog of the CF IIm complex also binds ATP through yClp1. To investigate the mammalian complex, we used a cell-line expressing FLAG-tagged Clp1 to co-immunoprecipitate Pcf11 as a function of ATP concentration. FLAG-Clp1 co-precipitated Pcf11 with or without ATP and the complex was not affected by AMP-PCP. Diadenosine tetraphosphate (Ap4A), an ATP analog that binds the Nudix domain of the CF Im25 subunit with higher affinity than ATP, neither stimulated 3' cleavage in place of ATP nor antagonized ATP-stimulated 3' cleavage. The ATP-binding site of PAP was disrupted by site directed mutagenesis but a reconstituted 3' cleavage reaction containing a mutant PAP unable to bind ATP nevertheless underwent ATP-stimulated 3' cleavage. Fluctuating ATP levels might contribute to the regulation of pre-mRNA 3' cleavage, but the three subunits investigated here do not appear to be responsible for the ATP-stimulation of pre-mRNA cleavage.
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Affiliation(s)
- Asya Khleborodova
- Department of Chemistry and Biochemistry, The City College of New York, The City University, New York, NY 10031, USA; Biochemistry Ph.D. Program, The City University of New York Graduate Center, New York, NY 10016, USA
| | - Xiaozhou Pan
- Department of Chemistry and Biochemistry, The City College of New York, The City University, New York, NY 10031, USA
| | - Nagaraja N Nagre
- Department of Chemistry and Biochemistry, The City College of New York, The City University, New York, NY 10031, USA
| | - Kevin Ryan
- Department of Chemistry and Biochemistry, The City College of New York, The City University, New York, NY 10031, USA; Biochemistry Ph.D. Program, The City University of New York Graduate Center, New York, NY 10016, USA; Chemistry Ph.D. Program, The City University of New York Graduate Center, New York, NY 10016, USA.
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42
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Abstract
PURPOSE OF REVIEW Significant advances have been made in understanding the functional roles of evolutionarily conserved chemical modifications in RNA. By focusing on cytosine-5 methylation, we will highlight the latest insight into the mechanisms how posttranscriptional methylation contributes to cell fate decisions, with implications for cancer development. RECENT FINDINGS Several mutations in RNA-modifying enzymes have been identified to cause complex human diseases, and linked posttranscriptional modifications to fundamental cellular processes. Distinct posttranscriptional modifications are implicated in the regulation of stem cell maintenance and cellular differentiation. The dynamic deposition of a methyl mark into noncoding RNAs modulates the adaptive cellular responses to stress and alterations of methylation levels may lead to cancer. SUMMARY Posttranscriptional modifications such as cytosine-5 methylation are dynamically regulated and may influence tumour development, maintenance, and progression.
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Affiliation(s)
- Martyna C. Popis
- Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, United Kingdom
| | - Sandra Blanco
- Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, United Kingdom
| | - Michaela Frye
- Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, United Kingdom
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43
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Brzuzan P, Kramer C, Łakomiak A, Jakimiuk E, Florczyk M, Woźny M. c-myc in whitefish (Coregonus lavaretus): structure, expression, and insights into possible posttranscriptional regulatory mechanism. Fish Physiol Biochem 2015; 41:1155-1171. [PMID: 25995172 DOI: 10.1007/s10695-015-0077-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 05/15/2015] [Indexed: 06/04/2023]
Abstract
c-myc has a crucial function in growth control, differentiation, and apoptosis of vertebrate cells. Despite the important role of c-myc in mediating the biological effects, studies of c-myc gene expression and factors that control it in organisms other than mammals, such as fish, have been rare. In the current study, we asked whether c-myc mRNA of whitefish, a feasible organism for pollution monitoring in aquatic systems and a model in toxicological research, contains activity sites for regulatory motifs in its 5'- and 3'-UTRs, similar to those found in mammals. We were particularly interested in whether miRNA-34, a known negative regulator of c-myc's in mammals, is able to regulate c-myc in fish. To answer these questions, we determined the mRNA sequence of whitefish c-myc and inferred the structure of the protein that it codes for. We found that the active sites of mRNA and structures of the inferred c-myc protein are similar to those found in mammals and other fish. Remarkably, levels of c-myc mRNA expression were very high in ovaries compared to other tissues of whitefish, thus corroborating previous data in fish. Using bioinformatic searches on c-myc 3'-UTR, we confirmed the presence of two miRNA-34a (miR-34a) response elements. Luciferase reporter assay showed that activity of reporters containing either the miR response elements or entire c-myc 3'-UTR was significantly reduced (p < 0.001) by ectopic expression of miR-34a. Therefore, we further investigated possible involvement of miR-34a in c-myc gene silencing by profiling the expression of both genes in livers of whitefish treated for 8, 24, 48 h with MC-LR, a potent c-myc inducer in mammals. Although the difference was only significant at p = 0.08, the expression of c-myc mRNA in challenged whitefish after 24 h of the treatment was notably higher than that in livers of control fish. Concurrently, we noticed slight but significant up-regulation of miR-34a after 24 and 48 h of the challenge (p < 0.05); however, we found no significant correlation of the c-myc mRNA levels and miR-34a expression. Together, these results suggest that miR-34a might regulate c-myc gene expression in whitefish liver; however, their involvement in MC-LR hepatotoxicity should be clarified in future studies.
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Affiliation(s)
- P Brzuzan
- Department of Environmental Biotechnology, Faculty of Environmental Sciences, University of Warmia and Mazury in Olsztyn, ul. Słoneczna 45G, 10-709, Olsztyn, Poland.
| | - C Kramer
- Department of Environmental Biotechnology, Faculty of Environmental Sciences, University of Warmia and Mazury in Olsztyn, ul. Słoneczna 45G, 10-709, Olsztyn, Poland
| | - A Łakomiak
- Department of Environmental Biotechnology, Faculty of Environmental Sciences, University of Warmia and Mazury in Olsztyn, ul. Słoneczna 45G, 10-709, Olsztyn, Poland
| | - E Jakimiuk
- Department of Veterinary Prevention and Feed Hygiene, Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, ul. Oczapowskiego 13, 10-950, Olsztyn, Poland
| | - M Florczyk
- Department of Environmental Biotechnology, Faculty of Environmental Sciences, University of Warmia and Mazury in Olsztyn, ul. Słoneczna 45G, 10-709, Olsztyn, Poland
| | - M Woźny
- Department of Environmental Biotechnology, Faculty of Environmental Sciences, University of Warmia and Mazury in Olsztyn, ul. Słoneczna 45G, 10-709, Olsztyn, Poland
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Affiliation(s)
- Yunfeng Zhou
- Shenzhen University Diabetes Center, AstraZeneca-Shenzhen University Joint Institute of Nephrology, Shenzhen University Health Science Center, Shenzhen, China
| | - Xiaoyan Zhang
- Shenzhen University Diabetes Center, AstraZeneca-Shenzhen University Joint Institute of Nephrology, Shenzhen University Health Science Center, Shenzhen, China
| | - Youfei Guan
- Shenzhen University Diabetes Center, AstraZeneca-Shenzhen University Joint Institute of Nephrology, Shenzhen University Health Science Center, Shenzhen, China.
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Yu C, Xin W, Zhen J, Liu Y, Javed A, Wang R, Wan Q. Human antigen R mediated post-transcriptional regulation of epithelial-mesenchymal transition related genes in diabetic nephropathy. J Diabetes 2015; 7:562-72. [PMID: 25265983 DOI: 10.1111/1753-0407.12220] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 06/04/2014] [Accepted: 09/08/2014] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Human antigen R (HuR) is a ubiquitously expressed RNA-binding protein that modulates gene expression at the post-transcriptional level. While cytoplasmic HuR expression was identified as a marker in epithelial-mesenchymal transition (EMT) process of several types of cancer, its role in diabetic nephropathy (DN) remains unclear. METHODS Renal biopsies from Type 2 diabetic patients and STZ-induced DN rats were stained for HuR and EMT markers. Redistribution of HuR was detected by immunostaining and western blot in high glucose stimulated cells. RNAi was used to supress HuR expression. The binding affinity for EMT-related genes was evaluated by immunoprecipitation. RESULTS Cytoplasmic HuR expression was elevated in human and rat DN specimens along with EMT changes compared to normal controls. HuR shuttling between nucleus and cytoplasm facilitated epithelial to mesenchymal transition in renal epithelial cells. The suppression of HuR partially inhibited EMT of high glucose stimulated HK-2 cells. Furthermore, HuR bound to 3'-UTRs of critical cytokines or transcription factors mRNA involved in EMT process. CONCLUSION Acquired phenotypic traits of EMT were partially through the enhanced HuR-binding proteins and its post-transcriptional regulation role in DN.
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Affiliation(s)
- Che Yu
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
| | - Wei Xin
- Department of Central Laboratory, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
| | - Junhui Zhen
- Department of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
| | - Yi Liu
- Department of Respiratory Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
| | - Akhtar Javed
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
| | - Rong Wang
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
| | - Qiang Wan
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
- Institute of Endocrinology, Shandong Academy of Clinical Medicine, Jinan, China
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Losh JS, King AK, Bakelar J, Taylor L, Loomis J, Rosenzweig JA, Johnson SJ, van Hoof A. Interaction between the RNA-dependent ATPase and poly(A) polymerase subunits of the TRAMP complex is mediated by short peptides and important for snoRNA processing. Nucleic Acids Res 2015; 43:1848-58. [PMID: 25589546 PMCID: PMC4330371 DOI: 10.1093/nar/gkv005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The RNA exosome is one of the main 3′ to 5′ exoribonucleases in eukaryotic cells. Although it is responsible for degradation or processing of a wide variety of substrate RNAs, it is very specific and distinguishes between substrate and non-substrate RNAs as well as between substrates that need to be 3′ processed and those that need to be completely degraded. This specificity does not appear to be determined by the exosome itself but rather by about a dozen other proteins. Four of these exosome cofactors have enzymatic activity, namely, the nuclear RNA-dependent ATPase Mtr4, its cytoplasmic paralog Ski2 and the nuclear non-canonical poly(A) polymerases, Trf4 and Trf5. Mtr4 and either Trf4 or Trf5 assemble into a TRAMP complex. However, how these enzymes assemble into a TRAMP complex and the functional consequences of TRAMP complex assembly remain unknown. Here, we identify an important interaction site between Mtr4 and Trf5, and show that disrupting the Mtr4/Trf interaction disrupts specific TRAMP and exosome functions, including snoRNA processing.
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Affiliation(s)
- Jillian S. Losh
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center-Houston, Houston, TX 77030, USA
- The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX, USA
| | - Alejandra Klauer King
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center-Houston, Houston, TX 77030, USA
- The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX, USA
| | - Jeremy Bakelar
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322–0300, USA
| | - Lacy Taylor
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322–0300, USA
| | - John Loomis
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center-Houston, Houston, TX 77030, USA
| | - Jason A. Rosenzweig
- Department of Biology and Department of Environmental and Interdisciplinary Sciences, Texas Southern University, Houston, TX 77004, USA
| | - Sean J. Johnson
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322–0300, USA
| | - Ambro van Hoof
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center-Houston, Houston, TX 77030, USA
- The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX, USA
- To whom correspondence should be addressed. Tel: +1 713 500 5234;
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Abstract
Pentatricopeptide repeat (PPR) proteins are a large family of modular RNA-binding proteins which mediate several aspects of gene expression primarily in organelles but also in the nucleus. These proteins facilitate processing, splicing, editing, stability and translation of RNAs. While major advances in PPR research have been achieved with plant PPR proteins, the significance of non-plant PPR proteins is becoming of increasing importance. PPR proteins are classified into different subclasses based on their domain architecture, which is often a reflection of their function. This review provides an overview of the significant findings regarding the functions, evolution and applications of PPR proteins. Horizontal gene transfer appears to have played a major role in the sporadic phylogenetic distribution of different PPR subclasses in both eukaryotes and prokaryotes. Additionally, the use of synthetic biology and protein engineering to create designer PPR proteins to control gene expression in vivo is discussed. This review also highlights some of the aspects of PPR research that require more attention particularly in non-plant organisms. This includes the lack of research into the recently discovered PPR-TGM subclass, which is not only the first PPR subclass absent from plants but present in economically and clinically-relevant pathogens. Investigation into the structure and function of PPR-TGM proteins in these pathogens presents a novel opportunity for the exploitation of PPR proteins as drug targets to prevent disease.
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Affiliation(s)
- Sam Manna
- Department of Microbiology, La Trobe University, Melbourne, Victoria, Australia.
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48
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Abstract
Pentatricopeptide repeat (PPR) proteins are a large family of modular RNA-binding proteins which mediate several aspects of gene expression primarily in organelles but also in the nucleus. These proteins facilitate processing, splicing, editing, stability and translation of RNAs. While major advances in PPR research have been achieved with plant PPR proteins, the significance of non-plant PPR proteins is becoming of increasing importance. PPR proteins are classified into different subclasses based on their domain architecture, which is often a reflection of their function. This review provides an overview of the significant findings regarding the functions, evolution and applications of PPR proteins. Horizontal gene transfer appears to have played a major role in the sporadic phylogenetic distribution of different PPR subclasses in both eukaryotes and prokaryotes. Additionally, the use of synthetic biology and protein engineering to create designer PPR proteins to control gene expression in vivo is discussed. This review also highlights some of the aspects of PPR research that require more attention particularly in non-plant organisms. This includes the lack of research into the recently discovered PPR-TGM subclass, which is not only the first PPR subclass absent from plants but present in economically and clinically-relevant pathogens. Investigation into the structure and function of PPR-TGM proteins in these pathogens presents a novel opportunity for the exploitation of PPR proteins as drug targets to prevent disease.
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Affiliation(s)
- Sam Manna
- Department of Microbiology, La Trobe University, Melbourne, Victoria, Australia.
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Klassen R, Grunewald P, Thüring KL, Eichler C, Helm M, Schaffrath R. Loss of anticodon wobble uridine modifications affects tRNA(Lys) function and protein levels in Saccharomyces cerevisiae. PLoS One 2015; 10:e0119261. [PMID: 25747122 PMCID: PMC4352028 DOI: 10.1371/journal.pone.0119261] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 01/22/2015] [Indexed: 11/22/2022] Open
Abstract
In eukaryotes, wobble uridines in the anticodons of tRNALysUUU, tRNAGluUUC and tRNAGlnUUG are modified to 5-methoxy-carbonyl-methyl-2-thio-uridine (mcm5s2U). While mutations in subunits of the Elongator complex (Elp1-Elp6), which disable mcm5 side chain formation, or removal of components of the thiolation pathway (Ncs2/Ncs6, Urm1, Uba4) are individually tolerated, the combination of both modification defects has been reported to have lethal effects on Saccharomyces cerevisiae. Contrary to such absolute requirement of mcm5s2U for viability, we demonstrate here that in the S. cerevisiae S288C-derived background, both pathways can be simultaneously inactivated, resulting in combined loss of tRNA anticodon modifications (mcm5U and s2U) without a lethal effect. However, an elp3 disruption strain displays synthetic sick interaction and synergistic temperature sensitivity when combined with either uba4 or urm1 mutations, suggesting major translational defects in the absence of mcm5s2U modifications. Consistent with this notion, we find cellular protein levels drastically decreased in an elp3uba4 double mutant and show that this effect as well as growth phenotypes can be partially rescued by excess of tRNALysUUU. These results may indicate a global translational or protein homeostasis defect in cells simultaneously lacking mcm5 and s2 wobble uridine modification that could account for growth impairment and mainly originates from tRNALysUUU hypomodification and malfunction.
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Affiliation(s)
- Roland Klassen
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany
- * E-mail: (RK); (RS)
| | - Pia Grunewald
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany
| | - Kathrin L. Thüring
- Institut für Pharmazie und Biochemie, Johannes Gutenberg Universität Mainz, Mainz, Germany
| | - Christian Eichler
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany
| | - Mark Helm
- Institut für Pharmazie und Biochemie, Johannes Gutenberg Universität Mainz, Mainz, Germany
| | - Raffael Schaffrath
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany
- * E-mail: (RK); (RS)
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Koza P. [RNA processing TDP-43 protein has a main pathological role in FTLD and ALS]. Postepy Biochem 2015; 61:159-167. [PMID: 26689008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
TDP-43 is mainly a nuclear protein belonging to the heterogeneous ribonucleoproteins family. It plays a crucial role in the regulation of gene transcription and RNA processing. In 2006, TDP-43 was characterized as the main component of ubiquitin-positive inclusions observed in Frontotemporal Lobar Degeneration (FTLD) and Amyotrophic Lateral Sclerosis (ALS) cases. Since then, its central role in a number of neurodegenerative diseases was confirmed, originating the TDP-43 proteinopathies term. Pathological TDP-43 redistributes and accumulates in the cytoplasm forming toxic aggregates. Plethora of animal models recapitulating features typical for human TDP-43 proteinopathies has been generated. However, the mechanism involving TDP-43 and causing functional disturbances, like dementia and motoneurons degeneration, remains unknown. Loss and gain of function hypotheses are proposed, but they still need to be verified.
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