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Fekry M, Stenberg G, Dobritzsch D, Danielson UH. Production of stable and pure ZC3H11A - An extensively disordered RNA binding protein. Protein Expr Purif 2024; 222:106542. [PMID: 38969281 DOI: 10.1016/j.pep.2024.106542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 07/02/2024] [Accepted: 07/03/2024] [Indexed: 07/07/2024]
Abstract
Human ZC3H11A is an RNA-binding zinc finger protein involved in mRNA export and required for the efficient growth of human nuclear replicating viruses. Its biochemical properties are largely unknown so our goal has been to produce the protein in a pure and stable form suitable for its characterization. This has been challenging since the protein is large (810 amino acids) and with only the N-terminal zinc finger domain (amino acids 1-86) being well structured, the remainder is intrinsically disordered. Our production strategies have encompassed recombinant expression of full-length, truncated and mutated ZC3H11A variants with varying purification tags and fusion proteins in several expression systems, with or without co-expression of chaperones and putative interaction partners. A range of purification schemes have been explored. Initially, only truncated ZC3H11A encompassing the zinc finger domain could successfully be produced in a stable form. It required recombinant expression in insect cells since expression in E. coli gave a protein that aggregated. To reduce problematic nucleic acid contaminations, Cys8, located in one of the zinc fingers, was substituted by Ala and Ser. Interestingly, this did not affect nucleic acid binding, but the full-length protein was stabilised while the truncated version was insoluble. Ultimately, we discovered that when using alkaline buffers (pH 9) for purification, full-length ZC3H11A expressed in Sf9 insect cells was obtained in a stable and >90 % pure form, and as a mixture of monomers, dimers, tetramers and hexamers. Many of the challenges experienced are consistent with its predicted structure and unusual charge distribution.
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Affiliation(s)
- Mostafa Fekry
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden; Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Gun Stenberg
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | | | - U Helena Danielson
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden; Science for Life Laboratory, Drug Discovery & Development Platform, Uppsala University, SE 751 23 Uppsala, Sweden.
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2
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Terasaki T, Semba Y, Sasaki K, Imanaga H, Setoguchi K, Yamauchi T, Hirabayashi S, Nakao F, Akahane K, Inukai T, Sanda T, Akashi K, Maeda T. The RNA helicases DDX19A/B modulate selinexor sensitivity by regulating MCL1 mRNA nuclear export in leukemia cells. Leukemia 2024; 38:1918-1928. [PMID: 38987275 DOI: 10.1038/s41375-024-02343-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 07/02/2024] [Accepted: 07/04/2024] [Indexed: 07/12/2024]
Abstract
Selinexor, a first-in-class exportin1 (XPO1) inhibitor, is an attractive anti-tumor agent because of its unique mechanisms of action; however, its dose-dependent toxicity and lack of biomarkers preclude its wide use in clinical applications. To identify key molecules/pathways regulating selinexor sensitivity, we performed genome-wide CRISPR/Cas9 dropout screens using two B-ALL lines. We identified, for the first time, that paralogous DDX19A and DDX19B RNA helicases modulate selinexor sensitivity by regulating MCL1 mRNA nuclear export. While single depletion of either DDX19A or DDX19B barely altered MCL1 protein levels, depletion of both significantly attenuated MCL1 mRNA nuclear export, reducing MCL1 protein levels. Importantly, combining selinexor treatment with depletion of either DDX19A or DDX19B markedly induced intrinsic apoptosis of leukemia cells, an effect rescued by MCL1 overexpression. Analysis of Depmap datasets indicated that a subset of T-ALL lines expresses minimal DDX19B mRNA levels. Moreover, we found that either selinexor treatment or DDX19A depletion effectively induced apoptosis of T-ALL lines expressing low DDX19B levels. We conclude that XPO1 and DDX19A/B coordinately regulate cellular MCL1 levels and propose that DDX19A/B could serve as biomarkers for selinexor treatment. Moreover, pharmacological targeting of DDX19 paralogs may represent a potential strategy to induce intrinsic apoptosis in leukemia cells.
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Affiliation(s)
- Tatsuya Terasaki
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Yuichiro Semba
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
- Division of Precision Medicine, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Kensuke Sasaki
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
- Center for Cellular and Molecular Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Hiroshi Imanaga
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
- Center for Cellular and Molecular Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Kiyoko Setoguchi
- Division of Precision Medicine, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Takuji Yamauchi
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Shigeki Hirabayashi
- Division of Precision Medicine, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Fumihiko Nakao
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Koshi Akahane
- Department of Pediatrics, School of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Takeshi Inukai
- Department of Pediatrics, School of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Takaomi Sanda
- Department of Hematology and Oncology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Koichi Akashi
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
- Center for Cellular and Molecular Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Takahiro Maeda
- Division of Precision Medicine, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan.
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3
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Glossop MS, Chelysheva I, Ketley RF, Alagia A, Gullerova M. TIRR regulates mRNA export and association with P-bodies in response to DNA damage. Nucleic Acids Res 2024:gkae688. [PMID: 39119906 DOI: 10.1093/nar/gkae688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 07/15/2024] [Accepted: 07/25/2024] [Indexed: 08/10/2024] Open
Abstract
To ensure the integrity of our genetic code, a coordinated network of signalling and repair proteins, known as the DNA damage response (DDR), detects and repairs DNA insults, the most toxic being double-strand breaks (DSBs). Tudor interacting repair regulator (TIRR) is a key factor in DSB repair, acting through its interaction with p53 binding protein 1 (53BP1). TIRR is also an RNA binding protein, yet its role in RNA regulation during the DDR remains elusive. Here, we show that TIRR selectively binds to a subset of messenger RNAs (mRNAs) in response to DNA damage. Upon DNA damage, TIRR interacts with the nuclear export protein Exportin-1 through a nuclear export signal. Furthermore, TIRR plays a crucial role in the modulation of RNA processing bodies (PBs). TIRR itself and TIRR-bound RNA co-localize with PBs, and TIRR depletion results in nuclear RNA retention and impaired PB formation. We also suggest a potential link between TIRR-regulated RNA export and efficient DDR. This work reveals intricate involvement of TIRR in orchestrating mRNA nuclear export and storage within PBs, emphasizing its significance in the regulation of RNA-mediated DDR.
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Affiliation(s)
- Michelle S Glossop
- Sir William Dunn School of Pathology, Medical Sciences Division, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Irina Chelysheva
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford OX3 7LE, UK
| | - Ruth F Ketley
- Sir William Dunn School of Pathology, Medical Sciences Division, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Adele Alagia
- Sir William Dunn School of Pathology, Medical Sciences Division, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Monika Gullerova
- Sir William Dunn School of Pathology, Medical Sciences Division, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
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4
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Horvath A, Janapala Y, Woodward K, Mahmud S, Cleynen A, Gardiner E, Hannan R, Eyras E, Preiss T, Shirokikh N. Comprehensive translational profiling and STE AI uncover rapid control of protein biosynthesis during cell stress. Nucleic Acids Res 2024; 52:7925-7946. [PMID: 38721779 PMCID: PMC11260467 DOI: 10.1093/nar/gkae365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/21/2024] [Accepted: 04/25/2024] [Indexed: 07/23/2024] Open
Abstract
Translational control is important in all life, but it remains a challenge to accurately quantify. When ribosomes translate messenger (m)RNA into proteins, they attach to the mRNA in series, forming poly(ribo)somes, and can co-localize. Here, we computationally model new types of co-localized ribosomal complexes on mRNA and identify them using enhanced translation complex profile sequencing (eTCP-seq) based on rapid in vivo crosslinking. We detect long disome footprints outside regions of non-random elongation stalls and show these are linked to translation initiation and protein biosynthesis rates. We subject footprints of disomes and other translation complexes to artificial intelligence (AI) analysis and construct a new, accurate and self-normalized measure of translation, termed stochastic translation efficiency (STE). We then apply STE to investigate rapid changes to mRNA translation in yeast undergoing glucose depletion. Importantly, we show that, well beyond tagging elongation stalls, footprints of co-localized ribosomes provide rich insight into translational mechanisms, polysome dynamics and topology. STE AI ranks cellular mRNAs by absolute translation rates under given conditions, can assist in identifying its control elements and will facilitate the development of next-generation synthetic biology designs and mRNA-based therapeutics.
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Affiliation(s)
- Attila Horvath
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
| | - Yoshika Janapala
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
| | - Katrina Woodward
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
| | - Shafi Mahmud
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
| | - Alice Cleynen
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
- Institut Montpelliérain Alexander Grothendieck, Université de Montpellier, CNRS, Montpellier, France
| | - Elizabeth E Gardiner
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The National Platelet Research and Referral Centre, The Australian National University, Canberra, ACT 2601, Australia
| | - Ross D Hannan
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville 3010, Australia
- Peter MacCallum Cancer Centre, Melbourne 3000, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton 3800, Australia
- School of Biomedical Sciences, University of Queensland, St Lucia 4067, Australia
| | - Eduardo Eyras
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Centre for Computational Biomedical Sciences, The Australian National University, Canberra, ACT 2601, Australia
- EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, ACT 2601, Australia
| | - Thomas Preiss
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Nikolay E Shirokikh
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
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5
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Fonseca A, Riveras E, Moyano TC, Alvarez JM, Rosa S, Gutiérrez RA. Dynamic changes in mRNA nucleocytoplasmic localization in the nitrate response of Arabidopsis roots. PLANT, CELL & ENVIRONMENT 2024. [PMID: 38950037 DOI: 10.1111/pce.15018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 05/23/2024] [Accepted: 06/14/2024] [Indexed: 07/03/2024]
Abstract
Nitrate is a nutrient and signal that regulates gene expression. The nitrate response has been extensively characterized at the organism, organ, and cell-type-specific levels, but intracellular mRNA dynamics remain unexplored. To characterize nuclear and cytoplasmic transcriptome dynamics in response to nitrate, we performed a time-course expression analysis after nitrate treatment in isolated nuclei, cytoplasm, and whole roots. We identified 402 differentially localized transcripts (DLTs) in response to nitrate treatment. Induced DLT genes showed rapid and transient recruitment of the RNA polymerase II, together with an increase in the mRNA turnover rates. DLTs code for genes involved in metabolic processes, localization, and response to stimulus indicating DLTs include genes with relevant functions for the nitrate response that have not been previously identified. Using single-molecule RNA FISH, we observed early nuclear accumulation of the NITRATE REDUCTASE 1 (NIA1) transcripts in their transcription sites. We found that transcription of NIA1, a gene showing delayed cytoplasmic accumulation, is rapidly and transiently activated; however, its transcripts become unstable when they reach the cytoplasm. Our study reveals the dynamic localization of mRNAs between the nucleus and cytoplasm as an emerging feature in the temporal control of gene expression in response to nitrate treatment in Arabidopsis roots.
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Affiliation(s)
- Alejandro Fonseca
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Center for Genome Regulation, Millennium Institute Center for Genome Regulation (CRG), Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Plant Biology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Eleodoro Riveras
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Center for Genome Regulation, Millennium Institute Center for Genome Regulation (CRG), Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Tomás C Moyano
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Center for Genome Regulation, Millennium Institute Center for Genome Regulation (CRG), Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - José M Alvarez
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Stefanie Rosa
- Department of Plant Biology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Rodrigo A Gutiérrez
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Center for Genome Regulation, Millennium Institute Center for Genome Regulation (CRG), Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
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6
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Rödel A, Weig I, Tiedemann S, Schwartz U, Längst G, Moehle C, Grasser M, Grasser KD. Arabidopsis mRNA export factor MOS11: molecular interactions and role in abiotic stress responses. THE NEW PHYTOLOGIST 2024; 243:180-194. [PMID: 38650347 DOI: 10.1111/nph.19773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 04/01/2024] [Indexed: 04/25/2024]
Abstract
Transcription and export (TREX) is a multi-subunit complex that links synthesis, processing and export of mRNAs. It interacts with the RNA helicase UAP56 and export factors such as MOS11 and ALYs to facilitate nucleocytosolic transport of mRNAs. Plant MOS11 is a conserved, but sparsely researched RNA-binding export factor, related to yeast Tho1 and mammalian CIP29/SARNP. Using biochemical approaches, the domains of Arabidopsis thaliana MOS11 required for interaction with UAP56 and RNA-binding were identified. Further analyses revealed marked genetic interactions between MOS11 and ALY genes. Cell fractionation in combination with transcript profiling demonstrated that MOS11 is required for export of a subset of mRNAs that are shorter and more GC-rich than MOS11-independent transcripts. The central α-helical domain of MOS11 proved essential for physical interaction with UAP56 and for RNA-binding. MOS11 is involved in the nucleocytosolic transport of mRNAs that are upregulated under stress conditions and accordingly mos11 mutant plants turned out to be sensitive to elevated NaCl concentrations and heat stress. Collectively, our analyses identify functional interaction domains of MOS11. In addition, the results establish that mRNA export is critically involved in the plant response to stress conditions and that MOS11 plays a prominent role at this.
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Affiliation(s)
- Amelie Rödel
- Cell Biology & Plant Biochemistry, Biochemistry Center, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Ina Weig
- Cell Biology & Plant Biochemistry, Biochemistry Center, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Sophie Tiedemann
- Cell Biology & Plant Biochemistry, Biochemistry Center, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Uwe Schwartz
- NGS Analysis Center, Biology and Pre-Clinical Medicine, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Gernot Längst
- Institute for Biochemistry III, Biochemistry Center, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Christoph Moehle
- Center of Excellence for Fluorescent Bioanalytics (KFB), University of Regensburg, Am Biopark 9, D-93053, Regensburg, Germany
| | - Marion Grasser
- Cell Biology & Plant Biochemistry, Biochemistry Center, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Klaus D Grasser
- Cell Biology & Plant Biochemistry, Biochemistry Center, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
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7
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Cao SM, Wu H, Yuan GH, Pan YH, Zhang J, Liu YX, Li S, Xu YF, Wei MY, Yang L, Chen LL. Altered nucleocytoplasmic export of adenosine-rich circRNAs by PABPC1 contributes to neuronal function. Mol Cell 2024; 84:2304-2319.e8. [PMID: 38838666 DOI: 10.1016/j.molcel.2024.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 04/02/2024] [Accepted: 05/10/2024] [Indexed: 06/07/2024]
Abstract
Circular RNAs (circRNAs) are upregulated during neurogenesis. Where and how circRNAs are localized and what roles they play during this process have remained elusive. Comparing the nuclear and cytoplasmic circRNAs between H9 cells and H9-derived forebrain (FB) neurons, we identify that a subset of adenosine (A)-rich circRNAs are restricted in H9 nuclei but exported to cytosols upon differentiation. Such a subcellular relocation of circRNAs is modulated by the poly(A)-binding protein PABPC1. In the H9 nucleus, newly produced (A)-rich circRNAs are bound by PABPC1 and trapped by the nuclear basket protein TPR to prevent their export. Modulating (A)-rich motifs in circRNAs alters their subcellular localization, and introducing (A)-rich circRNAs in H9 cytosols results in mRNA translation suppression. Moreover, decreased nuclear PABPC1 upon neuronal differentiation enables the export of (A)-rich circRNAs, including circRTN4(2,3), which is required for neurite outgrowth. These findings uncover subcellular localization features of circRNAs, linking their processing and function during neurogenesis.
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Affiliation(s)
- Shi-Meng Cao
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hao Wu
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Guo-Hua Yuan
- Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Yu-Hang Pan
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jun Zhang
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yu-Xin Liu
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Siqi Li
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yi-Feng Xu
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Meng-Yuan Wei
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Li Yang
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Ling-Ling Chen
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; New Cornerstone Science Laboratory, Shenzhen 518054, China.
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8
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Khan D, Ramachandiran I, Vasu K, China A, Khan K, Cumbo F, Halawani D, Terenzi F, Zin I, Long B, Costain G, Blaser S, Carnevale A, Gogonea V, Dutta R, Blankenberg D, Yoon G, Fox PL. Homozygous EPRS1 missense variant causing hypomyelinating leukodystrophy-15 alters variant-distal mRNA m 6A site accessibility. Nat Commun 2024; 15:4284. [PMID: 38769304 PMCID: PMC11106242 DOI: 10.1038/s41467-024-48549-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 05/03/2024] [Indexed: 05/22/2024] Open
Abstract
Hypomyelinating leukodystrophy (HLD) is an autosomal recessive disorder characterized by defective central nervous system myelination. Exome sequencing of two siblings with severe cognitive and motor impairment and progressive hypomyelination characteristic of HLD revealed homozygosity for a missense single-nucleotide variant (SNV) in EPRS1 (c.4444 C > A; p.Pro1482Thr), encoding glutamyl-prolyl-tRNA synthetase, consistent with HLD15. Patient lymphoblastoid cell lines express markedly reduced EPRS1 protein due to dual defects in nuclear export and cytoplasmic translation of variant EPRS1 mRNA. Variant mRNA exhibits reduced METTL3 methyltransferase-mediated writing of N6-methyladenosine (m6A) and reduced reading by YTHDC1 and YTHDF1/3 required for efficient mRNA nuclear export and translation, respectively. In contrast to current models, the variant does not alter the sequence of m6A target sites, but instead reduces their accessibility for modification. The defect was rescued by antisense morpholinos predicted to expose m6A sites on target EPRS1 mRNA, or by m6A modification of the mRNA by METTL3-dCas13b, a targeted RNA methylation editor. Our bioinformatic analysis predicts widespread occurrence of SNVs associated with human health and disease that similarly alter accessibility of distal mRNA m6A sites. These results reveal a new RNA-dependent etiologic mechanism by which SNVs can influence gene expression and disease, consequently generating opportunities for personalized, RNA-based therapeutics targeting these disorders.
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Affiliation(s)
- Debjit Khan
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Iyappan Ramachandiran
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Kommireddy Vasu
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Arnab China
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Krishnendu Khan
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Fabio Cumbo
- Genomic Medicine Institute, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Dalia Halawani
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Fulvia Terenzi
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Isaac Zin
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
- Department of Chemistry, Cleveland State University, Cleveland, OH, USA
| | - Briana Long
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Gregory Costain
- Department of Paediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Susan Blaser
- Department of Diagnostic Imaging, Division of Neuroradiology, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Amanda Carnevale
- Department of Paediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Valentin Gogonea
- Department of Chemistry, Cleveland State University, Cleveland, OH, USA
| | - Ranjan Dutta
- Department of Neuroscience, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Daniel Blankenberg
- Genomic Medicine Institute, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Grace Yoon
- Department of Paediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada.
- Department of Paediatrics, Division of Neurology, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada.
| | - Paul L Fox
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA.
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9
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González-Iglesias A, Arcas A, Domingo-Muelas A, Mancini E, Galcerán J, Valcárcel J, Fariñas I, Nieto MA. Intron detention tightly regulates the stemness/differentiation switch in the adult neurogenic niche. Nat Commun 2024; 15:2837. [PMID: 38565566 PMCID: PMC10987655 DOI: 10.1038/s41467-024-47092-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/13/2024] [Indexed: 04/04/2024] Open
Abstract
The adult mammalian brain retains some capacity to replenish neurons and glia, holding promise for brain regeneration. Thus, understanding the mechanisms controlling adult neural stem cell (NSC) differentiation is crucial. Paradoxically, adult NSCs in the subependymal zone transcribe genes associated with both multipotency maintenance and neural differentiation, but the mechanism that prevents conflicts in fate decisions due to these opposing transcriptional programmes is unknown. Here we describe intron detention as such control mechanism. In NSCs, while multiple mRNAs from stemness genes are spliced and exported to the cytoplasm, transcripts from differentiation genes remain unspliced and detained in the nucleus, and the opposite is true under neural differentiation conditions. We also show that m6A methylation is the mechanism that releases intron detention and triggers nuclear export, enabling rapid and synchronized responses. m6A RNA methylation operates as an on/off switch for transcripts with antagonistic functions, tightly controlling the timing of NSCs commitment to differentiation.
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Affiliation(s)
| | - Aida Arcas
- Instituto de Neurociencias (CSIC-UMH), Sant Joan d'Alacant, 03550, Spain
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, 31008, Spain
| | - Ana Domingo-Muelas
- Departamento de Biología Celular, Biología Funcional y Antropología Física and Instituto de Biotecnología y Biomedicina, Universidad de Valencia, Burjassot, 46100, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28029, Madrid, Spain
- Carlos Simon Foundation, 46980, Paterna, Valencia, Spain
- Department of Cell and Developmental Biology, Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Igenomix Foundation, 46980, Paterna, Valencia, Spain
| | - Estefania Mancini
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, 08003, Spain
| | - Joan Galcerán
- Instituto de Neurociencias (CSIC-UMH), Sant Joan d'Alacant, 03550, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Raras (CIBERER), 28029, Madrid, Spain
| | - Juan Valcárcel
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, 08003, Spain
- Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Spain
| | - Isabel Fariñas
- Departamento de Biología Celular, Biología Funcional y Antropología Física and Instituto de Biotecnología y Biomedicina, Universidad de Valencia, Burjassot, 46100, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28029, Madrid, Spain
| | - M Angela Nieto
- Instituto de Neurociencias (CSIC-UMH), Sant Joan d'Alacant, 03550, Spain.
- Centro de Investigación Biomédica en Red sobre Enfermedades Raras (CIBERER), 28029, Madrid, Spain.
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10
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Ngo LH, Bert AG, Dredge BK, Williams T, Murphy V, Li W, Hamilton WB, Carey KT, Toubia J, Pillman KA, Liu D, Desogus J, Chao JA, Deans AJ, Goodall GJ, Wickramasinghe VO. Nuclear export of circular RNA. Nature 2024; 627:212-220. [PMID: 38355801 DOI: 10.1038/s41586-024-07060-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 01/12/2024] [Indexed: 02/16/2024]
Abstract
Circular RNAs (circRNAs), which are increasingly being implicated in a variety of functions in normal and cancerous cells1-5, are formed by back-splicing of precursor mRNAs in the nucleus6-10. circRNAs are predominantly localized in the cytoplasm, indicating that they must be exported from the nucleus. Here we identify a pathway that is specific for the nuclear export of circular RNA. This pathway requires Ran-GTP, exportin-2 and IGF2BP1. Enhancing the nuclear Ran-GTP gradient by depletion or chemical inhibition of the major protein exporter CRM1 selectively increases the nuclear export of circRNAs, while reducing the nuclear Ran-GTP gradient selectively blocks circRNA export. Depletion or knockout of exportin-2 specifically inhibits nuclear export of circRNA. Analysis of nuclear circRNA-binding proteins reveals that interaction between IGF2BP1 and circRNA is enhanced by Ran-GTP. The formation of circRNA export complexes in the nucleus is promoted by Ran-GTP through its interactions with exportin-2, circRNA and IGF2BP1. Our findings demonstrate that adaptors such as IGF2BP1 that bind directly to circular RNAs recruit Ran-GTP and exportin-2 to export circRNAs in a mechanism that is analogous to protein export, rather than mRNA export.
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Affiliation(s)
- Linh H Ngo
- RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Andrew G Bert
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia, Australia
| | - B Kate Dredge
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia, Australia
- Adelaide Centre for Epigenetics, School of Biomedicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia, Australia
- South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Tobias Williams
- RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Vincent Murphy
- Genome Stability Unit, St Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Wanqiu Li
- RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Department of Pharmacology, Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine and Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, China
| | - William B Hamilton
- RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Kirstyn T Carey
- RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - John Toubia
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia, Australia
| | - Katherine A Pillman
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia, Australia
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Dawei Liu
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia, Australia
| | - Jessica Desogus
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Jeffrey A Chao
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Andrew J Deans
- Genome Stability Unit, St Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Gregory J Goodall
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia, Australia.
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia, Australia.
- Department of Medicine, University of Adelaide, Adelaide, South Australia, Australia.
| | - Vihandha O Wickramasinghe
- RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia.
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11
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Werren EA, LaForce GR, Srivastava A, Perillo DR, Li S, Johnson K, Baris S, Berger B, Regan SL, Pfennig CD, de Munnik S, Pfundt R, Hebbar M, Jimenez-Heredia R, Karakoc-Aydiner E, Ozen A, Dmytrus J, Krolo A, Corning K, Prijoles EJ, Louie RJ, Lebel RR, Le TL, Amiel J, Gordon CT, Boztug K, Girisha KM, Shukla A, Bielas SL, Schaffer AE. TREX tetramer disruption alters RNA processing necessary for corticogenesis in THOC6 Intellectual Disability Syndrome. Nat Commun 2024; 15:1640. [PMID: 38388531 PMCID: PMC10884030 DOI: 10.1038/s41467-024-45948-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 02/07/2024] [Indexed: 02/24/2024] Open
Abstract
THOC6 variants are the genetic basis of autosomal recessive THOC6 Intellectual Disability Syndrome (TIDS). THOC6 is critical for mammalian Transcription Export complex (TREX) tetramer formation, which is composed of four six-subunit THO monomers. The TREX tetramer facilitates mammalian RNA processing, in addition to the nuclear mRNA export functions of the TREX dimer conserved through yeast. Human and mouse TIDS model systems revealed novel THOC6-dependent, species-specific TREX tetramer functions. Germline biallelic Thoc6 loss-of-function (LOF) variants result in mouse embryonic lethality. Biallelic THOC6 LOF variants reduce the binding affinity of ALYREF to THOC5 without affecting the protein expression of TREX members, implicating impaired TREX tetramer formation. Defects in RNA nuclear export functions were not detected in biallelic THOC6 LOF human neural cells. Instead, mis-splicing was detected in human and mouse neural tissue, revealing novel THOC6-mediated TREX coordination of mRNA processing. We demonstrate that THOC6 is required for key signaling pathways known to regulate the transition from proliferative to neurogenic divisions during human corticogenesis. Together, these findings implicate altered RNA processing in the developmental biology of TIDS neuropathology.
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Affiliation(s)
- Elizabeth A Werren
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Advanced Precision Medicine Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Geneva R LaForce
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Anshika Srivastava
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, 226014, India
| | - Delia R Perillo
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Shaokun Li
- Advanced Precision Medicine Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Katherine Johnson
- Advanced Precision Medicine Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Safa Baris
- Division of Pediatric Allergy and Immunology, School of Medicine, Marmara University, Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, The Isil Berat Barlan Center for Translational Medicine, Istanbul, 34722, Turkey
| | - Brandon Berger
- Advanced Precision Medicine Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Samantha L Regan
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Christian D Pfennig
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Sonja de Munnik
- Department of Human Genetics, Radboud University Medical Centre Nijmegen, Nijmegen, 6524, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Centre Nijmegen, Nijmegen, 6524, the Netherlands
| | - Malavika Hebbar
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, 98195, Seattle, WA, USA
| | - Raúl Jimenez-Heredia
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, 1090, Austria
| | - Elif Karakoc-Aydiner
- Division of Pediatric Allergy and Immunology, School of Medicine, Marmara University, Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, The Isil Berat Barlan Center for Translational Medicine, Istanbul, 34722, Turkey
| | - Ahmet Ozen
- Division of Pediatric Allergy and Immunology, School of Medicine, Marmara University, Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, The Isil Berat Barlan Center for Translational Medicine, Istanbul, 34722, Turkey
| | - Jasmin Dmytrus
- Research Centre for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
| | - Ana Krolo
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, 1090, Austria
| | - Ken Corning
- Greenwood Genetic Center, Greenwood, SC, 29646, USA
| | - E J Prijoles
- Greenwood Genetic Center, Greenwood, SC, 29646, USA
| | | | - Robert Roger Lebel
- Section of Medical Genetics, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Thuy-Linh Le
- Imagine Institute, INSERM U1163, Paris Cité University, Paris, 75015, France
| | - Jeanne Amiel
- Imagine Institute, INSERM U1163, Paris Cité University, Paris, 75015, France
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, AP-HP, Paris, 75015, France
| | | | - Kaan Boztug
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, 1090, Austria
- Research Centre for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, 1090, Austria
- St. Anna Children's Hospital and Children's Cancer Research Institute, Department of Pediatrics, Medical University of Vienna, Vienna, 1090, Austria
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Stephanie L Bielas
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
| | - Ashleigh E Schaffer
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
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12
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Zheng Y, Wang M, Yin J, Duan Y, Wu C, Xu Z, Bu Y, Wang J, Chen Q, Zhu G, Zhao K, Zhang L, Hua R, Xu Y, Hu X, Cheng X, Xia Y. Hepatitis B virus RNAs co-opt ELAVL1 for stabilization and CRM1-dependent nuclear export. PLoS Pathog 2024; 20:e1011999. [PMID: 38306394 PMCID: PMC10866535 DOI: 10.1371/journal.ppat.1011999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 02/14/2024] [Accepted: 01/25/2024] [Indexed: 02/04/2024] Open
Abstract
Hepatitis B virus (HBV) chronically infects 296 million people worldwide, posing a major global health threat. Export of HBV RNAs from the nucleus to the cytoplasm is indispensable for viral protein translation and genome replication, however the mechanisms regulating this critical process remain largely elusive. Here, we identify a key host factor embryonic lethal, abnormal vision, Drosophila-like 1 (ELAVL1) that binds HBV RNAs and controls their nuclear export. Using an unbiased quantitative proteomics screen, we demonstrate direct binding of ELAVL1 to the HBV pregenomic RNA (pgRNA). ELAVL1 knockdown inhibits HBV RNAs posttranscriptional regulation and suppresses viral replication. Further mechanistic studies reveal ELAVL1 recruits the nuclear export receptor CRM1 through ANP32A and ANP32B to transport HBV RNAs to the cytoplasm via specific AU-rich elements, which can be targeted by a compound CMLD-2. Moreover, ELAVL1 protects HBV RNAs from DIS3+RRP6+ RNA exosome mediated nuclear RNA degradation. Notably, we find HBV core protein is dispensable for HBV RNA-CRM1 interaction and nuclear export. Our results unveil ELAVL1 as a crucial host factor that regulates HBV RNAs stability and trafficking. By orchestrating viral RNA nuclear export, ELAVL1 is indispensable for the HBV life cycle. Our study highlights a virus-host interaction that may be exploited as a new therapeutic target against chronic hepatitis B.
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Affiliation(s)
- Yingcheng Zheng
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
- School of Life Sciences, Hubei University, Wuhan, China
| | - Mengfei Wang
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Jiatong Yin
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Yurong Duan
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Chuanjian Wu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Zaichao Xu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Yanan Bu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Jingjing Wang
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Quan Chen
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Guoguo Zhu
- Department of Emergency, General Hospital of Central Theater Command of People’s Liberation Army of China, Wuhan, China
| | - Kaitao Zhao
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Lu Zhang
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Rong Hua
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Yanping Xu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Xiyu Hu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Xiaoming Cheng
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, China
- Hubei Jiangxia Laboratory, Wuhan, China
| | - Yuchen Xia
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
- Hubei Jiangxia Laboratory, Wuhan, China
- Pingyuan Laboratory, Henan, China
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13
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Smith AB, Ganguly DR, Moore M, Bowerman AF, Janapala Y, Shirokikh NE, Pogson BJ, Crisp PA. Dynamics of mRNA fate during light stress and recovery: from transcription to stability and translation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:818-839. [PMID: 37947266 PMCID: PMC10952913 DOI: 10.1111/tpj.16531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 09/20/2023] [Accepted: 10/23/2023] [Indexed: 11/12/2023]
Abstract
Transcript stability is an important determinant of its abundance and, consequently, translational output. Transcript destabilisation can be rapid and is well suited for modulating the cellular response. However, it is unclear the extent to which RNA stability is altered under changing environmental conditions in plants. We previously hypothesised that recovery-induced transcript destabilisation facilitated a phenomenon of rapid recovery gene downregulation (RRGD) in Arabidopsis thaliana (Arabidopsis) following light stress, based on mathematical calculations to account for ongoing transcription. Here, we test this hypothesis and investigate processes regulating transcript abundance and fate by quantifying changes in transcription, stability and translation before, during and after light stress. We adapt syringe infiltration to apply a transcriptional inhibitor to soil-grown plants in combination with stress treatments. Compared with measurements in juvenile plants and cell culture, we find reduced stability across a range of transcripts encoding proteins involved in RNA binding and processing. We also observe light-induced destabilisation of transcripts, followed by their stabilisation during recovery. We propose that this destabilisation facilitates RRGD, possibly in combination with transcriptional shut-off that was confirmed for HSP101, ROF1 and GOLS1. We also show that translation remains highly dynamic over the course of light stress and recovery, with a bias towards transcript-specific increases in ribosome association, independent of changes in total transcript abundance, after 30 min of light stress. Taken together, we provide evidence for the combinatorial regulation of transcription and stability that occurs to coordinate translation during light stress and recovery in Arabidopsis.
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Affiliation(s)
- Aaron B. Smith
- Research School of BiologyThe Australian National UniversityCanberraAustralian Capital Territory2601Australia
| | - Diep R. Ganguly
- CSIRO Synthetic Biology Future Science PlatformCanberraAustralian Capital Territory2601Australia
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Marten Moore
- Research School of BiologyThe Australian National UniversityCanberraAustralian Capital Territory2601Australia
| | - Andrew F. Bowerman
- Research School of BiologyThe Australian National UniversityCanberraAustralian Capital Territory2601Australia
| | - Yoshika Janapala
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery InstituteMonash UniversityClaytonVictoria3800Australia
| | - Nikolay E. Shirokikh
- The John Curtin School of Medical Research, The Shine‐Dalgarno Centre for RNA InnovationThe Australian National UniversityCanberraAustralian Capital Territory2601Australia
| | - Barry J. Pogson
- Research School of BiologyThe Australian National UniversityCanberraAustralian Capital Territory2601Australia
| | - Peter A. Crisp
- School of Agriculture and Food SciencesThe University of QueenslandBrisbaneQueensland4072Australia
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14
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Niikura M, Fukutomi T, Mitobe J, Kobayashi F. Characterization of a nuclear transport factor 2-like domain-containing protein in Plasmodium berghei. Malar J 2024; 23:13. [PMID: 38195464 PMCID: PMC10777651 DOI: 10.1186/s12936-024-04839-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 01/03/2024] [Indexed: 01/11/2024] Open
Abstract
BACKGROUND Plasmodium lacks an mRNA export receptor ortholog, such as yeast Mex67. Yeast Mex67 contains a nuclear transport factor 2 (NTF2)-like domain, suggesting that NTF2-like domain-containing proteins might be associated with mRNA export in Plasmodium. In this study, the relationship between mRNA export and an NTF2-like domain-containing protein, PBANKA_1019700, was investigated using the ANKA strain of rodent malaria parasite Plasmodium berghei. METHODS The deletion mutant Δ1019700 was generated by introducing gene-targeting vectors into the P. berghei ANKA genome, and parasite growth and virulence were examined. To investigate whether PBANKA_1019700 is involved in mRNA export, live-cell fluorescence imaging and immunoprecipitation coupled to mass spectrometry (IP-MS) were performed using transgenic parasites expressing fusion proteins (1019700::mCherry). RESULTS Deletion of PBANKA_1019700 affected the sexual phase but not the asexual phase of malaria parasites. Live-cell fluorescence imaging showed that PBANKA_1019700 localizes to the cytoplasm. Moreover, IP-MS analysis of 1019700::mCherry indicated that PBANKA_1019700 interacts with ubiquitin-related proteins but not nuclear proteins. CONCLUSIONS PBANKA_1019700 is a noncanonical NTF2-like superfamily protein.
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Affiliation(s)
- Mamoru Niikura
- Department of Infectious Diseases, Kyorin University School of Medicine, Tokyo, Japan.
| | - Toshiyuki Fukutomi
- Department of Pharmacology and Toxicology, Kyorin University School of Medicine, Tokyo, Japan
| | - Jiro Mitobe
- Department of Infectious Diseases, Kyorin University School of Medicine, Tokyo, Japan
| | - Fumie Kobayashi
- Department of Environmental Science, School of Life and Environmental Science, Azabu University, Kanagawa, 252-5201, Japan
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15
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Zhang Y, Chen XN, Zhang H, Wen JK, Gao HT, Shi B, Wang DD, Han ZW, Gu JF, Zhao CM, Xue WY, Zhang YP, Qu CB, Yang Z. CDK13 promotes lipid deposition and prostate cancer progression by stimulating NSUN5-mediated m5C modification of ACC1 mRNA. Cell Death Differ 2023; 30:2462-2476. [PMID: 37845385 PMCID: PMC10733287 DOI: 10.1038/s41418-023-01223-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 09/05/2023] [Indexed: 10/18/2023] Open
Abstract
Cyclin-dependent kinases (CDKs) regulate cell cycle progression and the transcription of a number of genes, including lipid metabolism-related genes, and aberrant lipid metabolism is involved in prostate carcinogenesis. Previous studies have shown that CDK13 expression is upregulated and fatty acid synthesis is increased in prostate cancer (PCa). However, the molecular mechanisms linking CDK13 upregulation and aberrant lipid metabolism in PCa cells remain largely unknown. Here, we showed that upregulation of CDK13 in PCa cells increases the fatty acyl chains and lipid classes, leading to lipid deposition in the cells, which is positively correlated with the expression of acetyl-CoA carboxylase (ACC1), the first rate-limiting enzyme in fatty acid synthesis. Gain- and loss-of-function studies showed that ACC1 mediates CDK13-induced lipid accumulation and PCa progression by enhancing lipid synthesis. Mechanistically, CDK13 interacts with RNA-methyltransferase NSUN5 to promote its phosphorylation at Ser327. In turn, phosphorylated NSUN5 catalyzes the m5C modification of ACC1 mRNA, and then the m5C-modified ACC1 mRNA binds to ALYREF to enhance its stability and nuclear export, thereby contributing to an increase in ACC1 expression and lipid deposition in PCa cells. Overall, our results disclose a novel function of CDK13 in regulating the ACC1 expression and identify a previously unrecognized CDK13/NSUN5/ACC1 pathway that mediates fatty acid synthesis and lipid accumulation in PCa cells, and targeting this newly identified pathway may be a novel therapeutic option for the treatment of PCa.
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Affiliation(s)
- Yong Zhang
- Department of Urology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
| | - Xiao-Nan Chen
- Department of Urology, Shengjing Hospital of China Medical University, 36 Sanhao Street, Shenyang, 110004, P R China
| | - Hong Zhang
- Department of Biochemistry and Molecular Biology, Ministry of Education of China, Hebei Medical University, No. 361 Zhongshan E Rd, Shijiazhuang, 050017, China
| | - Jin-Kun Wen
- Department of Biochemistry and Molecular Biology, Ministry of Education of China, Hebei Medical University, No. 361 Zhongshan E Rd, Shijiazhuang, 050017, China
| | - Hai-Tao Gao
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Bei Shi
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Dan-Dan Wang
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Zhen-Wei Han
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Jun-Fei Gu
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Chen-Ming Zhao
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Wen-Yong Xue
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Yan-Ping Zhang
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Chang-Bao Qu
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China.
| | - Zhan Yang
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China.
- Center of Tumor Immunology and Cytotherapy, Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China.
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16
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Liang J, Cai H, Hou C, Song F, Jiang Y, Wang Z, Qiu D, Zhu Y, Wang F, Yu D, Hou J. METTL14 inhibits malignant progression of oral squamous cell carcinoma by targeting the autophagy-related gene RB1CC1 in an m6A-IGF2BP2-dependent manner. Clin Sci (Lond) 2023; 137:1373-1389. [PMID: 37615536 PMCID: PMC10500204 DOI: 10.1042/cs20230219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 08/10/2023] [Accepted: 08/24/2023] [Indexed: 08/25/2023]
Abstract
N6-methyladenosine (m6A) plays crucial roles in tumorigenesis and autophagy. However, the underlying mechanisms mediated by m6A and autophagy in the malignant progression of oral squamous cell carcinoma (OSCC) remain unclear. In the present study, we revealed that down-regulated expression of METTL14 was correlated with advanced clinicopathological characteristics and poor prognosis in OSCC. METTL14 knockdown significantly inhibited autophagy and facilitated malignant progression in vitro, and promoted tumor growth and metastasis in vivo. A cell model of rapamycin-induced autophagy was established to identify RB1CC1 as a potential target gene involved in m6A-regulated autophagy in OSCC, through RNA sequencing and methylated RNA immunoprecipitation sequencing (meRIP-seq) analysis. Mechanistically, we confirmed that METTL14 posttranscriptionally enhanced RB1CC1 expression in an m6A-IGF2BP2-dependent manner, thereby affecting autophagy and progression in OSCC, through methylated RNA immunoprecipitation qRT-PCR (meRIP-qPCR), RNA stability assays, mutagenesis assays and dual-luciferase reporter. Collectively, our findings demonstrated that METTL14 serves as an OSCC suppressor by regulating the autophagy-related gene RB1CC1 through m6A modification, which may provide a new insight for the diagnosis and therapy of OSCC.
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Affiliation(s)
- Jianfeng Liang
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Hongshi Cai
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Chen Hou
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Fan Song
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Yaoqi Jiang
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Ziyi Wang
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Danqi Qiu
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Yue Zhu
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Fang Wang
- Department of Oral Surgery, Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200000, China
| | - Dongsheng Yu
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Jinsong Hou
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
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17
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Bachhav B, de Rossi J, Llanos CD, Segatori L. Cell factory engineering: Challenges and opportunities for synthetic biology applications. Biotechnol Bioeng 2023; 120:2441-2459. [PMID: 36859509 PMCID: PMC10440303 DOI: 10.1002/bit.28365] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/14/2023] [Accepted: 02/27/2023] [Indexed: 03/03/2023]
Abstract
The production of high-quality recombinant proteins is critical to maintaining a continuous supply of biopharmaceuticals, such as therapeutic antibodies. Engineering mammalian cell factories presents a number of limitations typically associated with the proteotoxic stress induced upon aberrant accumulation of off-pathway protein folding intermediates, which eventually culminate in the induction of apoptosis. In this review, we will discuss advances in cell engineering and their applications at different hierarchical levels of control of the expression of recombinant proteins, from transcription and translational to posttranslational modifications and subcellular trafficking. We also highlight challenges and unique opportunities to apply modern synthetic biology tools to the design of programmable cell factories for improved biomanufacturing of therapeutic proteins.
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Affiliation(s)
- Bhagyashree Bachhav
- Department of Chemical and Biochemical Engineering, Rice University, Houston, United States
| | - Jacopo de Rossi
- Systems, Synthetic, and Physical Biology, Rice University, Houston, United States
| | - Carlos D. Llanos
- Systems, Synthetic, and Physical Biology, Rice University, Houston, United States
| | - Laura Segatori
- Department of Chemical and Biochemical Engineering, Rice University, Houston, United States
- Systems, Synthetic, and Physical Biology, Rice University, Houston, United States
- Department of Bioengineering, Rice University, Houston, United States
- Department of Biosciences, Rice University, Houston, United States
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18
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Wang S, Sun S. Translation dysregulation in neurodegenerative diseases: a focus on ALS. Mol Neurodegener 2023; 18:58. [PMID: 37626421 PMCID: PMC10464328 DOI: 10.1186/s13024-023-00642-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 07/21/2023] [Indexed: 08/27/2023] Open
Abstract
RNA translation is tightly controlled in eukaryotic cells to regulate gene expression and maintain proteome homeostasis. RNA binding proteins, translation factors, and cell signaling pathways all modulate the translation process. Defective translation is involved in multiple neurological diseases including amyotrophic lateral sclerosis (ALS). ALS is a progressive neurodegenerative disorder and poses a major public health challenge worldwide. Over the past few years, tremendous advances have been made in the understanding of the genetics and pathogenesis of ALS. Dysfunction of RNA metabolisms, including RNA translation, has been closely associated with ALS. Here, we first introduce the general mechanisms of translational regulation under physiological and stress conditions and review well-known examples of translation defects in neurodegenerative diseases. We then focus on ALS-linked genes and discuss the recent progress on how translation is affected by various mutant genes and the repeat expansion-mediated non-canonical translation in ALS.
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Affiliation(s)
- Shaopeng Wang
- Department of Physiology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Shuying Sun
- Department of Physiology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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19
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Wang Y, Zhou X. N 6-methyladenosine and Its Implications in Viruses. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:695-706. [PMID: 35835441 PMCID: PMC10787122 DOI: 10.1016/j.gpb.2022.04.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 01/21/2022] [Accepted: 04/19/2022] [Indexed: 12/27/2022]
Abstract
N6-methyladenine (m6A) is the most abundant RNA modification in mammalian messenger RNAs (mRNAs), which participates in and regulates many important biological activities, such as tissue development and stem cell differentiation. Due to an improved understanding of m6A, researchers have discovered that the biological function of m6A can be linked to many stages of mRNA metabolism and that m6A can regulate a variety of complex biological processes. In addition to its location on mammalian mRNAs, m6A has been identified on viral transcripts. m6A also plays important roles in the life cycle of many viruses and in viral replication in host cells. In this review, we briefly introduce the detection methods of m6A, the m6A-related proteins, and the functions of m6A. We also summarize the effects of m6A-related proteins on viral replication and infection. We hope that this review provides researchers with some insights for elucidating the complex mechanisms of the epitranscriptome related to viruses, and provides information for further study of the mechanisms of other modified nucleobases acting on processes such as viral replication. We also anticipate that this review can stimulate collaborative research from different fields, such as chemistry, biology, and medicine, and promote the development of antiviral drugs and vaccines.
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Affiliation(s)
- Yafen Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China.
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
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20
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Lin SH, Chien CH, Chang KP, Lu MF, Chen YT, Chu YW. SaBrcada: Survival Intervals Prediction for Breast Cancer Patients by Dimension Raising and Age Stratification. Cancers (Basel) 2023; 15:3690. [PMID: 37509351 PMCID: PMC10378351 DOI: 10.3390/cancers15143690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/03/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
(1) Background: Breast cancer is the second leading cause of cancer death among women. The accurate prediction of survival intervals will help physicians make informed decisions about treatment strategies or the use of palliative care. (2) Methods: Gene expression is predictive and correlates to patient prognosis. To establish a reliable prediction tool, we collected a total of 1187 RNA-seq data points from breast cancer patients (median age 58 years) in Fragments Per Kilobase Million (FPKM) format from the TCGA database. Among them, we selected 144 patients with date of death information to establish the SaBrcada-AD dataset. We first normalized the SaBrcada-AD dataset to TPM to build the survival prediction model SaBrcada. After normalization and dimension raising, we used the differential gene expression data to test eight different deep learning architectures. Considering the effect of age on prognosis, we also performed a stratified random sampling test on all ages between the lower and upper quartiles of patient age, 48 and 69 years; (3) Results: Stratifying by age 61, the performance of SaBrcada built by GoogLeNet was improved to a highest accuracy of 0.798. We also built a free website tool to provide five predicted survival periods: within six months, six months to one year, one to three years, three to five years, or over five years, for clinician reference. (4) Conclusions: We built the prediction model, SaBrcada, and the website tool of the same name for breast cancer survival analysis. Through these models and tools, clinicians will be provided with survival interval information as a basis for formulating precision medicine.
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Affiliation(s)
- Shih-Huan Lin
- Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Ching-Hsuan Chien
- Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Kai-Po Chang
- Department of Pathology, China Medical University Hospital, Taichung 404327, Taiwan
| | - Min-Fang Lu
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 40227, Taiwan
| | - Yu-Ting Chen
- Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 40227, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
| | - Yen-Wei Chu
- Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 40227, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
- Institute of Molecular Biology, National Chung Hsing University, Taichung 40227, Taiwan
- Smart Sustainable New Agriculture Research Center (SMARTer), Taichung 40227, Taiwan
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21
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Lu D, Lu J, Liu Q, Zhang Q. Emerging role of the RNA-editing enzyme ADAR1 in stem cell fate and function. Biomark Res 2023; 11:61. [PMID: 37280687 DOI: 10.1186/s40364-023-00503-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 05/13/2023] [Indexed: 06/08/2023] Open
Abstract
Stem cells are critical for organism development and the maintenance of tissue homeostasis. Recent studies focusing on RNA editing have indicated how this mark controls stem cell fate and function in both normal and malignant states. RNA editing is mainly mediated by adenosine deaminase acting on RNA 1 (ADAR1). The RNA editing enzyme ADAR1 converts adenosine in a double-stranded RNA (dsRNA) substrate into inosine. ADAR1 is a multifunctional protein that regulate physiological processes including embryonic development, cell differentiation, and immune regulation, and even apply to the development of gene editing technologies. In this review, we summarize the structure and function of ADAR1 with a focus on how it can mediate distinct functions in stem cell self-renewal and differentiation. Targeting ADAR1 has emerged as a potential novel therapeutic strategy in both normal and dysregulated stem cell contexts.
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Affiliation(s)
- Di Lu
- The Biotherapy Center, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Jianxi Lu
- The Biotherapy Center, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Qiuli Liu
- The Biotherapy Center, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China.
| | - Qi Zhang
- The Biotherapy Center, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China.
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22
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de Morree A, Rando TA. Regulation of adult stem cell quiescence and its functions in the maintenance of tissue integrity. Nat Rev Mol Cell Biol 2023; 24:334-354. [PMID: 36922629 PMCID: PMC10725182 DOI: 10.1038/s41580-022-00568-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2022] [Indexed: 03/18/2023]
Abstract
Adult stem cells are important for mammalian tissues, where they act as a cell reserve that supports normal tissue turnover and can mount a regenerative response following acute injuries. Quiescent stem cells are well established in certain tissues, such as skeletal muscle, brain, and bone marrow. The quiescent state is actively controlled and is essential for long-term maintenance of stem cell pools. In this Review, we discuss the importance of maintaining a functional pool of quiescent adult stem cells, including haematopoietic stem cells, skeletal muscle stem cells, neural stem cells, hair follicle stem cells, and mesenchymal stem cells such as fibro-adipogenic progenitors, to ensure tissue maintenance and repair. We discuss the molecular mechanisms that regulate the entry into, maintenance of, and exit from the quiescent state in mice. Recent studies revealed that quiescent stem cells have a discordance between RNA and protein levels, indicating the importance of post-transcriptional mechanisms, such as alternative polyadenylation, alternative splicing, and translation repression, in the control of stem cell quiescence. Understanding how these mechanisms guide stem cell function during homeostasis and regeneration has important implications for regenerative medicine.
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Affiliation(s)
- Antoine de Morree
- Department of Neurology and Neurological Science, Stanford University School of Medicine, Stanford, CA, USA.
- Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.
| | - Thomas A Rando
- Department of Neurology and Neurological Science, Stanford University School of Medicine, Stanford, CA, USA.
- Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA.
- Center for Tissue Regeneration, Repair, and Restoration, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA.
- Broad Stem Cell Research Center, University of California, Los Angeles, Los Angeles, CA, USA.
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23
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Liu Y, Yang D, Liu T, Chen J, Yu J, Yi P. N6-methyladenosine-mediated gene regulation and therapeutic implications. Trends Mol Med 2023; 29:454-467. [PMID: 37068987 DOI: 10.1016/j.molmed.2023.03.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 03/11/2023] [Accepted: 03/20/2023] [Indexed: 04/19/2023]
Abstract
N6-methyladenosine (m6A) RNA methylation is the most abundant form of mRNA modification in eukaryotes and is at the front line of biological and biomedical research. This dynamic and reversible m6A RNA modification determines the fates of modified RNA molecules at the post-transcriptional level, affecting almost all important biological processes. Notably, m6A is also involved in chromatin and transcriptional regulation, while m6A dysregulation is implicated in various diseases. Here, we review current knowledge of post-transcriptional and transcriptional regulatory mechanisms involving m6A modification. We also discuss their involvement in the occurrence and development of diseases, including cancer, as well as potential theranostic targets, in hope of facilitating the translation of preclinical findings to the clinic.
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Affiliation(s)
- Yujiao Liu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, China
| | - Dan Yang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, China
| | - Tao Liu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, China
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope, Los Angeles, CA 91010, USA
| | - Jianhua Yu
- Hematologic Malignancies Research Institute, City of Hope National Medical Center, Los Angeles, CA 91010, USA; Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA 91010, USA.
| | - Ping Yi
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, China.
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24
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Wu C, Huang X, Li M, Wang Z, Zhang Y, Tian B. Crosstalk between circRNAs and the PI3K/AKT and/or MEK/ERK signaling pathways in digestive tract malignancy progression. Future Oncol 2023; 18:4525-4538. [PMID: 36891896 DOI: 10.2217/fon-2022-0429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023] Open
Abstract
Evidence indicates that circular RNAs (circRNAs) may play an important role in regulating gene expression by binding to miRNAs through miRNA response elements. circRNAs are formed by back-splicing and have a covalently closed structure. The biogenesis of circRNAs also appears to be regulated by certain cell-specific and/or gene-specific mechanisms, and thus some circRNAs are tissue specific and tumor-expression specific. Furthermore, the high stability and tissue specificity of circRNAs may be of value for early diagnosis, survival prediction and precision medicine. This review summarizes current knowledge regarding the classification and functions of circRNAs and the role of circRNAs in regulating the PI3K/AKT and/or MEK/ERK signaling pathways in digestive tract malignancy tumors.
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Affiliation(s)
- Chao Wu
- Department of General Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China.,Department of Pancreatic Surgery, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, Sichuan Province, China
| | - Xing Huang
- Department of Pancreatic Surgery, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, Sichuan Province, China
| | - Mao Li
- Department of Pancreatic Surgery, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, Sichuan Province, China
| | - Zihe Wang
- Department of Pancreatic Surgery, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, Sichuan Province, China
| | - Yi Zhang
- Department of Pancreatic Surgery, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, Sichuan Province, China
| | - Bole Tian
- Department of Pancreatic Surgery, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, Sichuan Province, China
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25
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Huang Y, Gao BQ, Meng Q, Yang LZ, Ma XK, Wu H, Pan YH, Yang L, Li D, Chen LL. CRISPR-dCas13-tracing reveals transcriptional memory and limited mRNA export in developing zebrafish embryos. Genome Biol 2023; 24:15. [PMID: 36658633 PMCID: PMC9854193 DOI: 10.1186/s13059-023-02848-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 01/04/2023] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Understanding gene transcription and mRNA-protein (mRNP) dynamics in single cells in a multicellular organism has been challenging. The catalytically dead CRISPR-Cas13 (dCas13) system has been used to visualize RNAs in live cells without genetic manipulation. We optimize this system to track developmentally expressed mRNAs in zebrafish embryos and to understand features of endogenous transcription kinetics and mRNP export. RESULTS We report that zygotic microinjection of purified CRISPR-dCas13-fluorescent proteins and modified guide RNAs allows single- and dual-color tracking of developmentally expressed mRNAs in zebrafish embryos from zygotic genome activation (ZGA) until early segmentation period without genetic manipulation. Using this approach, we uncover non-synchronized de novo transcription between inter-alleles, synchronized post-mitotic re-activation in pairs of alleles, and transcriptional memory as an extrinsic noise that potentially contributes to synchronized post-mitotic re-activation. We also reveal rapid dCas13-engaged mRNP movement in the nucleus with a corralled and diffusive motion, but a wide varying range of rate-limiting mRNP export, which can be shortened by Alyref and Nxf1 overexpression. CONCLUSIONS This optimized dCas13-based toolkit enables robust spatial-temporal tracking of endogenous mRNAs and uncovers features of transcription and mRNP motion, providing a powerful toolkit for endogenous RNA visualization in a multicellular developmental organism.
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Affiliation(s)
- Youkui Huang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China
| | - Bao-Qing Gao
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Quan Meng
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Liang-Zhong Yang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China
| | - Xu-Kai Ma
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Hao Wu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China
| | - Yu-Hang Pan
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China
| | - Li Yang
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Dong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
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26
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Wang G, Heij LR, Liu D, Dahl E, LANG SA, Ulmer TF, LUEDDE T, Neumann UP, Bednarsch J. The Role of Single-Nucleotide Polymorphisms in Cholangiocarcinoma: A Systematic Review. Cancers (Basel) 2022; 14:cancers14235969. [PMID: 36497451 PMCID: PMC9739277 DOI: 10.3390/cancers14235969] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Single-nucleotide polymorphisms (SNPs) play an essential role in various malignancies, but their role in cholangiocarcinoma (CCA) remains to be elucidated. Therefore, the purpose of this systematic review was to evaluate the association between SNPs and CCA, focusing on tumorigenesis and prognosis. A systematic literature search was carried out using PubMed, Embase, Web of Science and the Cochrane database for the association between SNPs and CCA, including literature published between January 2000 and April 2022. This systematic review compiles 43 SNPs in 32 genes associated with CCA risk, metastatic progression and overall prognosis based on 34 studies. Susceptibility to CCA was associated with SNPs in genes related to inflammation (PTGS2/COX2, IL6, IFNG/IFN-γ, TNF/TNF-α), DNA repair (ERCC1, MTHFR, MUTYH, XRCC1, OGG1), detoxification (NAT1, NAT2 and ABCC2), enzymes (SERPINA1, GSTO1, APOBEC3A, APOBEC3B), RNA (HOTAIR) and membrane-based proteins (EGFR, GAB1, KLRK1/NKG2D). Overall oncological prognosis was also related to SNPs in eight genes (GNB3, NFE2L2/NRF2, GALNT14, EGFR, XRCC1, EZH2, GNAS, CXCR1). Our findings indicate that multiple SNPs play different roles at various stages of CCA and might serve as biomarkers guiding treatment and allowing oncological risk assessment. Considering the differences in SNP detection methods, patient ethnicity and corresponding environmental factors, more large-scale multicentric investigations are needed to fully determine the potential of SNP analysis for CCA susceptibility prediction and prognostication.
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Affiliation(s)
- Guanwu Wang
- Department of Surgery and Transplantation, University Hospital RWTH Aachen, 52074 Aachen, Germany
| | - Lara Rosaline Heij
- Department of Surgery and Transplantation, University Hospital RWTH Aachen, 52074 Aachen, Germany
- Institute of Pathology, University Hospital RWTH Aachen, 52074 Aachen, Germany
- NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, 6211 LK Maastricht, The Netherlands
- Department of Pathology, Erasmus Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands
| | - Dong Liu
- Department of Surgery and Transplantation, University Hospital RWTH Aachen, 52074 Aachen, Germany
| | - Edgar Dahl
- Institute of Pathology, University Hospital RWTH Aachen, 52074 Aachen, Germany
| | - Sven Arke LANG
- Department of Surgery and Transplantation, University Hospital RWTH Aachen, 52074 Aachen, Germany
| | - Tom Florian Ulmer
- Department of Surgery and Transplantation, University Hospital RWTH Aachen, 52074 Aachen, Germany
| | - Tom LUEDDE
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Heinrich Heine University Duesseldorf, 40225 Duesseldorf, Germany
| | - Ulf Peter Neumann
- Department of Surgery and Transplantation, University Hospital RWTH Aachen, 52074 Aachen, Germany
- Department of Surgery, Maastricht University Medical Center (MUMC), 6229 HX Maastricht, The Netherlands
| | - Jan Bednarsch
- Department of Surgery and Transplantation, University Hospital RWTH Aachen, 52074 Aachen, Germany
- Correspondence:
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Chou YJ, Lin CC, Hsu YC, Syu JL, Tseng LM, Chiu JH, Lo JF, Lin CH, Fu SL. Andrographolide suppresses the malignancy of triple-negative breast cancer by reducing THOC1-promoted cancer stem cell characteristics. Biochem Pharmacol 2022; 206:115327. [PMID: 36330949 DOI: 10.1016/j.bcp.2022.115327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/11/2022] [Accepted: 10/19/2022] [Indexed: 12/14/2022]
Abstract
Triple-negative breast cancers (TNBCs) are difficult to cure and currently lack of effective treatment strategies. Cancer stem cells (CSCs) are highly associated with the poor clinical outcome of TNBCs. Thoc1 is a core component of the THO complex (THOC) that regulates the elongation, processing and nuclear export of mRNA. The function of thoc1 in TNBC and whether Thoc1 serves as a drug target are poorly understood. In this study, we demonstrated that thoc1 expression is elevated in TNBC cell lines and human TNBC patient tissues. Knockdown of thoc1 decreased cancer stem cell populations, reduced mammosphere formation, impaired THOC function, and downregulated the expression of stemness-related proteins. Moreover, the thoc1-knockdown 4T1 cells showed less lung metastasis in an orthotopic breast cancer mouse model. Overexpression of Thoc1 promoted TNBC malignancy and the mRNA export of stemness-related genes. Furthermore, treatment of TNBC cells with the natural compound andrographolide reduced the expression of Thoc1 expression, impaired homeostasis of THOC, suppressed CSC properties, and delayed tumor growth in a 4T1-implanted orthotopic mouse model. Andrographolide also reduced the activity of NF-κB, an upstream transcriptional regulator of Thoc1. Notably, thoc1 overexpression attenuates andrographolide-suppressed cellular proliferation. Altogether, our results demonstrate that THOC1 promotes cancer stem cell characteristics of TNBC, and andrographolide is a potential natural compound for eliminating CSCs of TNBCs by downregulating the NF-κB-thoc1 axis.
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Affiliation(s)
- Yi-Ju Chou
- Program in Molecular Medicine, School of Life Sciences, National Yang Ming Chiao Tung University and Academia Sinica, Taipei 11221, Taiwan
| | - Ching-Cheng Lin
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Ya-Chi Hsu
- Institute of Traditional Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Jia-Ling Syu
- Institute of Traditional Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Ling-Ming Tseng
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Jen-Hwey Chiu
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Jeng-Fan Lo
- Institute of Oral Biology, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Chao-Hsiung Lin
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Shu-Ling Fu
- Program in Molecular Medicine, School of Life Sciences, National Yang Ming Chiao Tung University and Academia Sinica, Taipei 11221, Taiwan; Institute of Traditional Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan.
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28
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Tissue dissociation for single-cell and single-nuclei RNA sequencing for low amounts of input material. Front Zool 2022; 19:27. [DOI: 10.1186/s12983-022-00472-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 10/27/2022] [Indexed: 11/15/2022] Open
Abstract
Abstract
Background
Recent technological advances opened the opportunity to simultaneously study gene expression for thousands of individual cells on a genome-wide scale. The experimental accessibility of such single-cell RNA sequencing (scRNAseq) approaches allowed gaining insights into the cell type composition of heterogeneous tissue samples of animal model systems and emerging models alike. A major prerequisite for a successful application of the method is the dissociation of complex tissues into individual cells, which often requires large amounts of input material and harsh mechanical, chemical and temperature conditions. However, the availability of tissue material may be limited for small animals, specific organs, certain developmental stages or if samples need to be acquired from collected specimens. Therefore, we evaluated different dissociation protocols to obtain single cells from small tissue samples of Drosophila melanogaster eye-antennal imaginal discs.
Results
We show that a combination of mechanical and chemical dissociation resulted in sufficient high-quality cells. As an alternative, we tested protocols for the isolation of single nuclei, which turned out to be highly efficient for fresh and frozen tissue samples. Eventually, we performed scRNAseq and single-nuclei RNA sequencing (snRNAseq) to show that the best protocols for both methods successfully identified relevant cell types. At the same time, snRNAseq resulted in less artificial gene expression that is caused by rather harsh dissociation conditions needed to obtain single cells for scRNAseq. A direct comparison of scRNAseq and snRNAseq data revealed that both datasets share biologically relevant genes among the most variable genes, and we showed differences in the relative contribution of the two approaches to identified cell types.
Conclusion
We present two dissociation protocols that allow isolating single cells and single nuclei, respectively, from low input material. Both protocols resulted in extraction of high-quality RNA for subsequent scRNAseq or snRNAseq applications. If tissue availability is limited, we recommend the snRNAseq procedure of fresh or frozen tissue samples as it is perfectly suited to obtain thorough insights into cellular diversity of complex tissue.
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29
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Akinlalu AO, Njoku PC, Nzekwe CV, Oni RO, Fojude T, Faniyi AJ, Olagunju AS. Recent developments in the significant effect of mRNA modification (M6A) in glioblastoma and esophageal cancer. SCIENTIFIC AFRICAN 2022. [DOI: 10.1016/j.sciaf.2022.e01347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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30
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Tingey M, Yang W. Unraveling docking and initiation of mRNA export through the nuclear pore complex. Bioessays 2022; 44:e2200027. [PMID: 35754154 PMCID: PMC9308666 DOI: 10.1002/bies.202200027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 05/18/2022] [Accepted: 06/03/2022] [Indexed: 11/07/2022]
Abstract
The nuclear export of mRNA through the nuclear pore complex (NPC) is a process required for the healthy functioning of human cells, making it a critical area of research. However, the geometries of mRNA and the NPC are well below the diffraction limit of light microscopy, thereby presenting significant challenges in evaluating the discrete interactions and dynamics involved in mRNA nuclear export through the native NPC. Recent advances in biotechnology and single-molecule super-resolution light microscopy have enabled researchers to gain granular insight into the specific contributions made by discrete nucleoporins in the nuclear basket of the NPC to the export of mRNA. Specifically, by expanding upon the docking step facilitated by the protein TPR in the nuclear basket as well as identifying NUP153 as being the primary nuclear basket protein initiating export through the central channel of the NPC.
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Affiliation(s)
- Mark Tingey
- Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
| | - Weidong Yang
- Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
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31
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Deng Q, Chen A, Qiu H, Zhou T. Analysis of a non-Markov transcription model with nuclear RNA export and RNA nuclear retention. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022; 19:8426-8451. [PMID: 35801472 DOI: 10.3934/mbe.2022392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Transcription involves gene activation, nuclear RNA export (NRE) and RNA nuclear retention (RNR). All these processes are multistep and biochemical. A multistep reaction process can create memories between reaction events, leading to non-Markovian kinetics. This raises an unsolved issue: how does molecular memory affect stochastic transcription in the case that NRE and RNR are simultaneously considered? To address this issue, we analyze a non-Markov model, which considers multistep activation, multistep NRE and multistep RNR can interpret many experimental phenomena. In order to solve this model, we introduce an effective transition rate for each reaction. These effective transition rates, which explicitly decode the effect of molecular memory, can transform the original non-Markov issue into an equivalent Markov one. Based on this technique, we derive analytical results, showing that molecular memory can significantly affect the nuclear and cytoplasmic mRNA mean and noise. In addition to the results providing insights into the role of molecular memory in gene expression, our modeling and analysis provide a paradigm for studying more complex stochastic transcription processes.
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Affiliation(s)
- Qiqi Deng
- Guangdong Province Key Laboratory of Computational Science, School of Mathematics, Sun Yat-sen University, Guangzhou 510275, China
| | - Aimin Chen
- School of Mathematics and Statistics, Henan University, Kaifeng 475004, China
| | - Huahai Qiu
- School of Mathematical and Physical Sciences, Wuhan Textile University, Wuhan 430200, China
| | - Tianshou Zhou
- Guangdong Province Key Laboratory of Computational Science, School of Mathematics, Sun Yat-sen University, Guangzhou 510275, China
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32
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Sellin M, Berg S, Hagen P, Zhang J. The molecular mechanism and challenge of targeting XPO1 in treatment of relapsed and refractory myeloma. Transl Oncol 2022; 22:101448. [PMID: 35660848 PMCID: PMC9166471 DOI: 10.1016/j.tranon.2022.101448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 04/14/2022] [Accepted: 05/06/2022] [Indexed: 11/29/2022] Open
Abstract
Significant progress has been made on the treatment of MM during past two decades. Acquired drug-resistance continues to drive early relapse in primary refractory MM. XPO1 over-expression and cargo mislocalization are associated with drug-resistance. XPO1 inhibitor selinexor restores drug sensitivity to subsets of RR-MM cells.
Multiple myeloma (MM) treatment regimens have vastly improved since the introduction of immunomodulators, proteasome inhibitors, and anti-CD38 monoclonal antibodies; however, MM is considered an incurable disease due to inevitable relapse and acquired drug resistance. Understanding the molecular mechanism by which drug resistance is acquired will help create novel strategies to prevent relapse and help develop novel therapeutics to treat relapsed/refractory (RR)-MM patients. Currently, only homozygous deletion/mutation of TP53 gene due to “double-hits” on Chromosome 17p region is consistently associated with a poor prognosis. The exciting discovery of XPO1 overexpression and mislocalization of its cargos in the RR-MM cells has led to a novel treatment options. Clinical studies have demonstrated that the XPO1 inhibitor selinexor can restore sensitivity of RR-MM to PIs and dexamethasone. We will elaborate on the problems of MM treatment strategies and discuss the mechanism and challenges of using XPO1 inhibitors in RR-MM therapies while deliberating potential solutions.
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Affiliation(s)
- Mark Sellin
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Loyola University Chicago, USA
| | - Stephanie Berg
- Loyola University Chicago, Department of Cancer Biology and Internal Medicine, Cardinal Bernardin Cancer Center, Stritch School of Medicine, Maywood, IL, USA.
| | - Patrick Hagen
- Department of Medicine, Division of Hematology/Oncology, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL USA
| | - Jiwang Zhang
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, USA
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33
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Smith LK, Parmenter T, Kleinschmidt M, Kusnadi EP, Kang J, Martin CA, Lau P, Patel R, Lorent J, Papadopoli D, Trigos A, Ward T, Rao AD, Lelliott EJ, Sheppard KE, Goode D, Hicks RJ, Tiganis T, Simpson KJ, Larsson O, Blythe B, Cullinane C, Wickramasinghe VO, Pearson RB, McArthur GA. Adaptive translational reprogramming of metabolism limits the response to targeted therapy in BRAF V600 melanoma. Nat Commun 2022; 13:1100. [PMID: 35232962 PMCID: PMC8888590 DOI: 10.1038/s41467-022-28705-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 02/07/2022] [Indexed: 12/26/2022] Open
Abstract
Despite the success of therapies targeting oncogenes in cancer, clinical outcomes are limited by residual disease that ultimately results in relapse. This residual disease is often characterized by non-genetic adaptive resistance, that in melanoma is characterised by altered metabolism. Here, we examine how targeted therapy reprograms metabolism in BRAF-mutant melanoma cells using a genome-wide RNA interference (RNAi) screen and global gene expression profiling. Using this systematic approach we demonstrate post-transcriptional regulation of metabolism following BRAF inhibition, involving selective mRNA transport and translation. As proof of concept we demonstrate the RNA processing kinase U2AF homology motif kinase 1 (UHMK1) associates with mRNAs encoding metabolism proteins and selectively controls their transport and translation during adaptation to BRAF-targeted therapy. UHMK1 inactivation induces cell death by disrupting therapy induced metabolic reprogramming, and importantly, delays resistance to BRAF and MEK combination therapy in multiple in vivo models. We propose selective mRNA processing and translation by UHMK1 constitutes a mechanism of non-genetic resistance to targeted therapy in melanoma by controlling metabolic plasticity induced by therapy. Different adaptive mechanisms have been reported to reduce the efficacy of mutant BRAF inhibition in melanoma. Here, the authors show BRAF inhibition induces the translational regulation of metabolic genes leading to acquired therapy resistance.
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Affiliation(s)
- Lorey K Smith
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia.
| | - Tiffany Parmenter
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia
| | | | - Eric P Kusnadi
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Jian Kang
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Claire A Martin
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Peter Lau
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Riyaben Patel
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Julie Lorent
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - David Papadopoli
- Lady Davis Institute for Medical Research and Gerald Bronfman Department of Oncology, McGill University, Montreal, Canada
| | - Anna Trigos
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Teresa Ward
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Aparna D Rao
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Emily J Lelliott
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Karen E Sheppard
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia.,Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, Australia
| | - David Goode
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Rodney J Hicks
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Tony Tiganis
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Kaylene J Simpson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Ola Larsson
- Lady Davis Institute for Medical Research and Gerald Bronfman Department of Oncology, McGill University, Montreal, Canada
| | - Benjamin Blythe
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Carleen Cullinane
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Vihandha O Wickramasinghe
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Richard B Pearson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia.,Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, Australia
| | - Grant A McArthur
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia. .,Department of Medicine, St. Vincent's Hospital, University of Melbourne, Melbourne, Australia.
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34
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Inoue AH, Domingues PF, Serpeloni M, Hiraiwa PM, Vidal NM, Butterfield ER, Del Pino RC, Ludwig A, Boehm C, Field MC, Ávila AR. Proteomics Uncovers Novel Components of an Interactive Protein Network Supporting RNA Export in Trypanosomes. Mol Cell Proteomics 2022; 21:100208. [PMID: 35091090 PMCID: PMC8938319 DOI: 10.1016/j.mcpro.2022.100208] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 01/15/2022] [Accepted: 01/24/2022] [Indexed: 11/03/2022] Open
Abstract
In trypanosomatids, transcription is polycistronic and all mRNAs are processed by trans-splicing, with export mediated by noncanonical mechanisms. Although mRNA export is central to gene regulation and expression, few orthologs of proteins involved in mRNA export in higher eukaryotes are detectable in trypanosome genomes, necessitating direct identification of protein components. We previously described conserved mRNA export pathway components in Trypanosoma cruzi, including orthologs of Sub2, a component of the TREX complex, and eIF4AIII (previously Hel45), a core component of the exon junction complex (EJC). Here, we searched for protein interactors of both proteins using cryomilling and mass spectrometry. Significant overlap between TcSub2 and TceIF4AIII-interacting protein cohorts suggests that both proteins associate with similar machinery. We identified several interactions with conserved core components of the EJC and multiple additional complexes, together with proteins specific to trypanosomatids. Additional immunoisolations of kinetoplastid-specific proteins both validated and extended the superinteractome, which is capable of supporting RNA processing from splicing through to nuclear export and cytoplasmic events. We also suggest that only proteomics is powerful enough to uncover the high connectivity between multiple aspects of mRNA metabolism and to uncover kinetoplastid-specific components that create a unique amalgam to support trypanosome mRNA maturation.
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Affiliation(s)
| | | | | | | | - Newton Medeiros Vidal
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | | | | | - Adriana Ludwig
- Instituto Carlos Chagas, FIOCRUZ, Curitiba, Paraná, Brazil
| | - Cordula Boehm
- School of Life Sciences, University of Dundee, Dundee, Scotland, UK
| | - Mark C Field
- School of Life Sciences, University of Dundee, Dundee, Scotland, UK; Biology Centre, University of South Bohemia, České Budějovice, Czech Republic.
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35
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Van Bergen NJ, Bell KM, Carey K, Gear R, Massey S, Murrell EK, Gallacher L, Pope K, Lockhart PJ, Kornberg A, Pais L, Walkiewicz M, Simons C, Wickramasinghe VO, White SM, Christodoulou J. Pathogenic variants in nucleoporin TPR (translocated promoter region, nuclear basket protein) cause severe intellectual disability in humans. Hum Mol Genet 2022; 31:362-375. [PMID: 34494102 PMCID: PMC8825455 DOI: 10.1093/hmg/ddab248] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 08/10/2021] [Accepted: 08/23/2021] [Indexed: 01/16/2023] Open
Abstract
The nuclear pore complex (NPC) is a multi-protein complex that regulates the trafficking of macromolecules between the nucleus and cytoplasm. Genetic variants in components of the NPC have been shown to cause a range of neurological disorders, including intellectual disability and microcephaly. Translocated promoter region, nuclear basket protein (TPR) is a critical scaffolding element of the nuclear facing interior of the NPC. Here, we present two siblings with biallelic variants in TPR who present with a phenotype of microcephaly, ataxia and severe intellectual disability. The variants result in a premature truncation variant, and a splice variant leading to a 12-amino acid deletion respectively. Functional analyses in patient fibroblasts demonstrate significantly reduced TPR levels, and decreased TPR-containing NPC density. A compensatory increase in total NPC levels was observed, and decreased global RNA intensity in the nucleus. The discovery of variants that partly disable TPR function provide valuable insight into this essential protein in human disease, and our findings suggest that TPR variants are the cause of the siblings' neurological disorder.
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Affiliation(s)
- Nicole J Van Bergen
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Katrina M Bell
- Bioinformatics Methods group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, Australia
- Victorian Clinical Genetics Services, Royal Children’s Hospital, VIC, Australia
| | - Kirsty Carey
- RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Russell Gear
- Victorian Clinical Genetics Services, Royal Children’s Hospital, VIC, Australia
| | - Sean Massey
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, Australia
| | - Edward K Murrell
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, Australia
| | - Lyndon Gallacher
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
- Victorian Clinical Genetics Services, Royal Children’s Hospital, VIC, Australia
| | - Kate Pope
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, Australia
| | - Paul J Lockhart
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, Australia
| | - Andrew Kornberg
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
- Neurology Department, Royal Children's Hospital, Melbourne, Australia
- Neurosciences Research, Murdoch Children’s Research Institute, Victoria, Australia
| | - Lynn Pais
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Marzena Walkiewicz
- Translational Genomics Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, Australia
| | - Cas Simons
- Victorian Clinical Genetics Services, Royal Children’s Hospital, VIC, Australia
- Translational Genomics Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, Australia
| | - MCRI Rare Diseases Flagship
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, Australia
- Bioinformatics Methods group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, Australia
- Victorian Clinical Genetics Services, Royal Children’s Hospital, VIC, Australia
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, Australia
- Neurosciences Research, Murdoch Children’s Research Institute, Victoria, Australia
- Translational Genomics Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, Australia
| | - Vihandha O Wickramasinghe
- RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Susan M White
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
- Victorian Clinical Genetics Services, Royal Children’s Hospital, VIC, Australia
| | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
- Discipline of Child & Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
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36
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Nojima T, Proudfoot NJ. Mechanisms of lncRNA biogenesis as revealed by nascent transcriptomics. Nat Rev Mol Cell Biol 2022; 23:389-406. [DOI: 10.1038/s41580-021-00447-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2021] [Indexed: 12/14/2022]
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Sweaad WK, Stefanizzi FM, Chamorro-Jorganes A, Devaux Y, Emanueli C. Relevance of N6-methyladenosine regulators for transcriptome: Implications for development and the cardiovascular system. J Mol Cell Cardiol 2021; 160:56-70. [PMID: 33991529 DOI: 10.1016/j.yjmcc.2021.05.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 05/09/2021] [Accepted: 05/10/2021] [Indexed: 10/21/2022]
Abstract
N6-methyladenosine (m6A) is the most abundant and well-studied internal modification of messenger RNAs among the various RNA modifications in eukaryotic cells. Moreover, it is increasingly recognized to regulate non-coding RNAs. The dynamic and reversible nature of m6A is ensured by the precise and coordinated activity of specific proteins able to insert ("write"), bind ("read") or remove ("erase") the m6A modification from coding and non-coding RNA molecules. Mounting evidence suggests a pivotal role for m6A in prenatal and postnatal development and cardiovascular pathophysiology. In the present review we summarise and discuss the major functions played by m6A RNA methylation and its components particularly referring to the cardiovascular system. We present the methods used to study m6A and the most abundantly methylated RNA molecules. Finally, we highlight the possible involvement of the m6A mark in cardiovascular disease as well as the need for further studies to better describe the mechanisms of action and the potential therapeutic role of this RNA modification.
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Affiliation(s)
- Walid Khalid Sweaad
- National Heart and Lung Institute, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | - Francesca Maria Stefanizzi
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg
| | - Aránzazu Chamorro-Jorganes
- National Heart and Lung Institute, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg
| | - Costanza Emanueli
- National Heart and Lung Institute, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK.
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38
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Niikura M, Fukutomi T, Mitobe J, Kobayashi F. Roles and Cellular Localization of GBP2 and NAB2 During the Blood Stage of Malaria Parasites. Front Cell Infect Microbiol 2021; 11:737457. [PMID: 34604117 PMCID: PMC8479154 DOI: 10.3389/fcimb.2021.737457] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 08/24/2021] [Indexed: 12/03/2022] Open
Abstract
The quality control and export of mRNA by RNA-binding proteins are necessary for the survival of malaria parasites, which have complex life cycles. Nuclear poly(A) binding protein 2 (NAB2), THO complex subunit 4 (THO4), nucleolar protein 3 (NPL3), G-strand binding protein 2 (GBP2) and serine/arginine-rich splicing factor 1 (SR1) are involved in nuclear mRNA export in malaria parasites. However, their roles in asexual and sexual development, and in cellular localization, are not fully understood. In this study using the rodent malaria parasite, Plasmodium berghei, we found that NAB2 and SR1, but not THO4, NPL3 or GBP2, played essential roles in the asexual development of malaria parasites. By contrast, GBP2 but not NPL3 was involved in male and female gametocyte production. THO4 was involved in female gametocyte production, but had a lower impact than GBP2. In this study, we focused on GBP2 and NAB2, which play important roles in the sexual and asexual development of malaria parasites, respectively, and examined their cellular localization. GBP2 localized to both the nucleus and cytoplasm of malaria parasites. Using immunoprecipitation coupled to mass spectrometry (IP-MS), GBP2 interacted with the proteins ALBA4, DOZI, and CITH, which play roles in translational repression. IP-MS also revealed that phosphorylated adapter RNA export protein (PHAX) domain-containing protein, an adaptor protein for exportin-1, also interacted with GBP2, implying that mRNA export occurs via the PHAX domain-containing protein pathway in malaria parasites. Live-cell fluorescence imaging revealed that NAB2 localized at the nuclear periphery. Moreover, IP-MS indicated that NAB2 interacted with transportin. RNA immunoprecipitation coupled to RNA sequencing revealed that NAB2 bound directly to 143 mRNAs, including those encoding 40S and 60S ribosomal proteins. Our findings imply that malaria parasites use an evolutionarily ancient mechanism conserved throughout eukaryotic evolution.
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Affiliation(s)
- Mamoru Niikura
- Department of Infectious Diseases, Kyorin University School of Medicine, Tokyo, Japan
| | - Toshiyuki Fukutomi
- Department of Pharmacology and Toxicology, Kyorin University School of Medicine, Tokyo, Japan
| | - Jiro Mitobe
- Department of Infectious Diseases, Kyorin University School of Medicine, Tokyo, Japan
| | - Fumie Kobayashi
- Department of Environmental Science, School of Life and Environmental Science, Azabu University, Kanagawa, Japan
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Nuclear export and translation of circular repeat-containing intronic RNA in C9ORF72-ALS/FTD. Nat Commun 2021; 12:4908. [PMID: 34389711 PMCID: PMC8363653 DOI: 10.1038/s41467-021-25082-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 07/16/2021] [Indexed: 12/14/2022] Open
Abstract
C9ORF72 hexanucleotide GGGGCC repeat expansion is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Repeat-containing RNA mediates toxicity through nuclear granules and dipeptide repeat (DPR) proteins produced by repeat-associated non-AUG translation. However, it remains unclear how the intron-localized repeats are exported and translated in the cytoplasm. We use single molecule imaging approach to examine the molecular identity and spatiotemporal dynamics of the repeat RNA. We demonstrate that the spliced intron with G-rich repeats is stabilized in a circular form due to defective lariat debranching. The spliced circular intron, instead of pre-mRNA, serves as the translation template. The NXF1-NXT1 pathway plays an important role in the nuclear export of the circular intron and modulates toxic DPR production. This study reveals an uncharacterized disease-causing RNA species mediated by repeat expansion and demonstrates the importance of RNA spatial localization to understand disease etiology. Hexanucleotide repeat expansion in the intron 1 of the C9ORF72 gene can cause amyotrophic lateral sclerosis (ALS) and frontal temporal dementia (FTD). Here the authors use single molecule imaging to show nuclear export and translation of circular repeat-containing C9ORF72 intronic RNA.
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40
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Kubina J, Geldreich A, Gales JP, Baumberger N, Bouton C, Ryabova LA, Grasser KD, Keller M, Dimitrova M. Nuclear export of plant pararetrovirus mRNAs involves the TREX complex, two viral proteins and the highly structured 5' leader region. Nucleic Acids Res 2021; 49:8900-8922. [PMID: 34370034 PMCID: PMC8421220 DOI: 10.1093/nar/gkab653] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 07/09/2021] [Accepted: 07/22/2021] [Indexed: 11/13/2022] Open
Abstract
In eukaryotes, the major nuclear export pathway for mature mRNAs uses the dimeric receptor TAP/p15, which is recruited to mRNAs via the multisubunit TREX complex, comprising the THO core and different export adaptors. Viruses that replicate in the nucleus adopt different strategies to hijack cellular export factors and achieve cytoplasmic translation of their mRNAs. No export receptors are known in plants, but Arabidopsis TREX resembles the mammalian complex, with a conserved hexameric THO core associated with ALY and UIEF proteins, as well as UAP56 and MOS11. The latter protein is an orthologue of mammalian CIP29. The nuclear export mechanism for viral mRNAs has not been described in plants. To understand this process, we investigated the export of mRNAs of the pararetrovirus CaMV in Arabidopsis and demonstrated that it is inhibited in plants deficient in ALY, MOS11 and/or TEX1. Deficiency for these factors renders plants partially resistant to CaMV infection. Two CaMV proteins, the coat protein P4 and reverse transcriptase P5, are important for nuclear export. P4 and P5 interact and co-localise in the nucleus with the cellular export factor MOS11. The highly structured 5′ leader region of 35S RNAs was identified as an export enhancing element that interacts with ALY1, ALY3 and MOS11 in vitro.
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Affiliation(s)
- Julie Kubina
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Angèle Geldreich
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Jón Pol Gales
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Nicolas Baumberger
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Clément Bouton
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Lyubov A Ryabova
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Klaus D Grasser
- Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, D-93053 Regensburg, Germany
| | - Mario Keller
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Maria Dimitrova
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
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41
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Gondo N, Sakai Y, Zhang Z, Hato Y, Kuzushima K, Phimsen S, Kawashima Y, Kuroda M, Suzuki M, Okada S, Iwata H, Toyama T, Rezano A, Kuwahara K. Increased chemosensitivity via BRCA2-independent DNA damage in DSS1- and PCID2-depleted breast carcinomas. J Transl Med 2021; 101:1048-1059. [PMID: 34031538 DOI: 10.1038/s41374-021-00613-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 05/08/2021] [Accepted: 05/09/2021] [Indexed: 11/09/2022] Open
Abstract
Breast cancer, the most common malignancy among women, is closely associated with mutations in the tumor suppressor gene BRCA. DSS1, a component of the TRanscription-EXport-2 (TREX-2) complex involved in transcription and mRNA nuclear export, stabilizes BRCA2 expression. DSS1 is also related to poor prognosis in patients with breast cancer owing to the induction of chemoresistance. Recently, BRCA2 was shown to be associated with the TREX-2 component PCID2, which prevents DNA:RNA hybrid R-loop formation and transcription-coupled DNA damage. This study aimed to elucidate the involvement of these TREX-2 components and BRCA2 in the chemosensitivity of breast carcinomas. Our results showed that compared with that in normal breast tissues, DSS1 expression was upregulated in human breast carcinoma, whereas PCID2 expression was comparable between normal and malignant tissues. We then compared patient survival time among groups divided by high or low expressions of DSS1, BRCA2, and PCID2. Increased DSS1 expression was significantly correlated with poor prognosis in recurrence-free survival time, whereas no differences were detected in the high and low BRCA2 and PCID2 expression groups. We performed in vitro analyses, including propidium iodide nuclear staining, single-cell gel electrophoresis, and clonogenic survival assays, using breast carcinoma cell lines. The results confirmed that DSS1 depletion significantly increased chemosensitivity, whereas overexpression conferred chemoresistance to breast cancer cell lines; however, BRCA2 expression did not affect chemosensitivity. Similar to DSS1, PCID2 expression was also inversely correlated with chemosensitivity. These results strongly suggest that DSS1 and PCID2 depletion is closely associated with increased chemosensitivity via BRCA2-independent DNA damage. Together with the finding that DSS1 is not highly expressed in normal breast tissues, these results demonstrate that DSS1 depletion confers a druggable trait and may contribute to the development of novel chemotherapeutic strategies to treat DSS1-depleted breast carcinomas independent of BRCA2 mutations.
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Affiliation(s)
- Naomi Gondo
- Division of Immunology, Aichi Cancer Center Research Institute, Nagoya, Japan
- Division of Cellular Oncology, Department of Cancer Genetics, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Breast Oncology, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Yasuhiro Sakai
- Department of Joint Research Laboratory of Clinical Medicine, Fujita Health University School of Medicine, Toyoake, Japan
| | - Zhenhuan Zhang
- Radiation Oncology Department, University of Florida, Gainesville, FL, USA
| | - Yukari Hato
- Department of Breast Surgery, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Kiyotaka Kuzushima
- Division of Immunology, Aichi Cancer Center Research Institute, Nagoya, Japan
- Division of Cellular Oncology, Department of Cancer Genetics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Suchada Phimsen
- Faculty of Medical Science, Department of Biochemistry, Naresuan University, Phitsanulok, Thailand
| | - Yoshiaki Kawashima
- Department of Pathology, Fujita Health University Hospital, Toyoake, Japan
| | - Makoto Kuroda
- Department of Pathology, Fujita Health University Okazaki Medical Center, Okazaki, Japan
| | - Motoshi Suzuki
- Department of Molecular Oncology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Seiji Okada
- Division of Hematopoiesis, Joint Research Center for Retroviral Infection, Kumamoto University, Kumamoto, Japan
| | - Hiroji Iwata
- Department of Breast Oncology, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Tatsuya Toyama
- Department of Breast Surgery, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Andri Rezano
- Division of Cell Biology, Faculty of Medicine, Department of Biomedical Sciences, Universitas Padjadjaran, West Java, Indonesia.
| | - Kazuhiko Kuwahara
- Division of Immunology, Aichi Cancer Center Research Institute, Nagoya, Japan.
- Department of Diagnostic Pathology, Fujita Health University School of Medicine, Toyoake, Japan.
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42
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Mishra A, Kaur JN, McSkimming DI, Hegedűsová E, Dubey AP, Ciganda M, Paris Z, Read LK. Selective nuclear export of mRNAs is promoted by DRBD18 in Trypanosoma brucei. Mol Microbiol 2021; 116:827-840. [PMID: 34146438 DOI: 10.1111/mmi.14773] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 06/04/2021] [Accepted: 06/18/2021] [Indexed: 11/27/2022]
Abstract
Kinetoplastids, including Trypanosoma brucei, control gene expression primarily at the posttranscriptional level. Nuclear mRNA export is an important, but understudied, step in this process. The general heterodimeric export factors, Mex67/Mtr2, function in the export of mRNAs and tRNAs in T. brucei, but RNA binding proteins (RBPs) that regulate export processes by controlling the dynamics of Mex67/Mtr2 ribonucleoprotein formation or transport have not been identified. Here, we report that DRBD18, an essential and abundant T. brucei RBP, associates with Mex67/Mtr2 in vivo, likely through its direct interaction with Mtr2. DRBD18 downregulation results in partial accumulation of poly(A)+ mRNA in the nucleus, but has no effect on the localization of intron-containing or mature tRNAs. Comprehensive analysis of transcriptomes from whole-cell and cytosol in DRBD18 knockdown parasites demonstrates that depletion of DRBD18 leads to impairment of nuclear export of a subset of mRNAs. CLIP experiments reveal the association of DRBD18 with several of these mRNAs. Moreover, DRBD18 knockdown leads to a partial accumulation of the Mex67/Mtr2 export receptors in the nucleus. Taken together, the current study supports a model in which DRBD18 regulates the selective nuclear export of mRNAs by promoting the mobilization of export competent mRNPs to the cytosol through the nuclear pore complex.
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Affiliation(s)
- Amartya Mishra
- Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Jan Naseer Kaur
- Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Daniel I McSkimming
- Bioinformatics and Computational Biology Core, University of Southern Florida, Tampa, FL, USA
| | - Eva Hegedűsová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Ashutosh P Dubey
- Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Martin Ciganda
- Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Zdeněk Paris
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Laurie K Read
- Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
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43
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Lubelsky Y, Zuckerman B, Ulitsky I. High-resolution mapping of function and protein binding in an RNA nuclear enrichment sequence. EMBO J 2021; 40:e106357. [PMID: 33938020 PMCID: PMC8204871 DOI: 10.15252/embj.2020106357] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 03/14/2021] [Accepted: 03/24/2021] [Indexed: 01/04/2023] Open
Abstract
The functions of long RNAs, including mRNAs and long noncoding RNAs (lncRNAs), critically depend on their subcellular localization. The identity of the sequences that dictate subcellular localization and their high-resolution anatomy remain largely unknown. We used a suite of massively parallel RNA assays and libraries containing thousands of sequence variants to pinpoint the functional features within the SIRLOIN element, which dictates nuclear enrichment through hnRNPK recruitment. In addition, we profiled the endogenous SIRLOIN RNA-nucleoprotein complex and identified the nuclear RNA-binding proteins SLTM and SNRNP70 as novel SIRLOIN binders. Taken together, using massively parallel assays, we identified the features that dictate binding of hnRNPK, SLTM, and SNRNP70 to SIRLOIN and found that these factors are jointly required for SIRLOIN activity. Our study thus provides a roadmap for high-throughput dissection of functional sequence elements in long RNAs.
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Affiliation(s)
- Yoav Lubelsky
- Department of Biological RegulationWeizmann Institute of ScienceRehovotIsrael
| | - Binyamin Zuckerman
- Department of Biological RegulationWeizmann Institute of ScienceRehovotIsrael
| | - Igor Ulitsky
- Department of Biological RegulationWeizmann Institute of ScienceRehovotIsrael
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44
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Li Y, Wang M, Yang M, Xiao Y, Jian Y, Shi D, Chen X, Ouyang Y, Kong L, Huang X, Bai J, Hu Y, Lin C, Song L. Nicotine-Induced ILF2 Facilitates Nuclear mRNA Export of Pluripotency Factors to Promote Stemness and Chemoresistance in Human Esophageal Cancer. Cancer Res 2021; 81:3525-3538. [PMID: 33975879 DOI: 10.1158/0008-5472.can-20-4160] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 04/05/2021] [Accepted: 05/07/2021] [Indexed: 11/16/2022]
Abstract
Balancing mRNA nuclear export kinetics with its nuclear decay is critical for mRNA homeostasis control. How this equilibrium is aberrantly disrupted in esophageal cancer to acquire cancer stem cell properties remains unclear. Here we find that the RNA-binding protein interleukin enhancer binding factor 2 (ILF2) is robustly upregulated by nicotine, a major chemical component of tobacco smoke, via activation of JAK2/STAT3 signaling and significantly correlates with poor prognosis in heavy-smoking patients with esophageal cancer. ILF2 bound the THO complex protein THOC4 as a regulatory cofactor to induce selective interactions with pluripotency transcription factor mRNAs to promote their assembly into export-competent messenger ribonucleoprotein complexes. ILF2 facilitated nuclear mRNA export and inhibited hMTR4-mediated exosomal degradation to promote stabilization and expression of SOX2, NANOG, and SALL4, resulting in enhanced stemness and tumor-initiating capacity of esophageal cancer cells. Importantly, inducible depletion of ILF2 significantly increased the therapeutic efficiency of cisplatin and abrogated nicotine-induced chemoresistance in vitro and in vivo. These findings reveal a novel role of ILF2 in nuclear mRNA export and maintenance of cancer stem cells and open new avenues to overcome smoking-mediated chemoresistance in esophageal cancer. SIGNIFICANCE: This study defines a previously uncharacterized role of nicotine-regulated ILF2 in facilitating nuclear mRNA export to promote cancer stemness, suggesting a potential therapeutic strategy against nicotine-induced chemoresistance in esophageal cancer.
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Affiliation(s)
- Yue Li
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Meng Wang
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Muwen Yang
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yunyun Xiao
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yunting Jian
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Dongni Shi
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiangfu Chen
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ying Ouyang
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Lingzhi Kong
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xinjian Huang
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jiewen Bai
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yameng Hu
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Chuyong Lin
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China. .,Guangdong Esophageal Cancer Institute, Guangzhou, China
| | - Libing Song
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China. .,Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences; Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
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45
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McCormack NM, Abera MB, Arnold ES, Gibbs RM, Martin SE, Buehler E, Chen YC, Chen L, Fischbeck KH, Burnett BG. A high-throughput genome-wide RNAi screen identifies modifiers of survival motor neuron protein. Cell Rep 2021; 35:109125. [PMID: 33979606 PMCID: PMC8679797 DOI: 10.1016/j.celrep.2021.109125] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 03/17/2021] [Accepted: 04/22/2021] [Indexed: 11/28/2022] Open
Abstract
Spinal muscular atrophy (SMA) is a debilitating neurological disorder marked by degeneration of spinal motor neurons and muscle atrophy. SMA results from mutations in survival motor neuron 1 (SMN1), leading to deficiency of survival motor neuron (SMN) protein. Current therapies increase SMN protein and improve patient survival but have variable improvements in motor function, making it necessary to identify complementary strategies to further improve disease outcomes. Here, we perform a genome-wide RNAi screen using a luciferase-based activity reporter and identify genes involved in regulating SMN gene expression, RNA processing, and protein stability. We show that reduced expression of Transcription Export complex components increases SMN levels through the regulation of nuclear/cytoplasmic RNA transport. We also show that the E3 ligase, Neurl2, works cooperatively with Mib1 to ubiquitinate and promote SMN degradation. Together, our screen uncovers pathways through which SMN expression is regulated, potentially revealing additional strategies to treat SMA. Treatments for spinal muscular atrophy aim to increase survival motor neuron (SMN) protein. Using a genome-wide RNAi screen, McCormack et al. identify modifiers of SMN expression, including genes that are involved in transcription regulation, RNA processing, and protein stability.
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Affiliation(s)
- Nikki M McCormack
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, F. Edward Hébert School of Medicine, Bethesda, MD 20814, USA
| | - Mahlet B Abera
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, F. Edward Hébert School of Medicine, Bethesda, MD 20814, USA
| | - Eveline S Arnold
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20892, USA
| | - Rebecca M Gibbs
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20892, USA
| | - Scott E Martin
- Functional Genomics Lab, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20850, USA
| | - Eugen Buehler
- Functional Genomics Lab, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20850, USA
| | - Yu-Chi Chen
- Functional Genomics Lab, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20850, USA
| | - Lu Chen
- Functional Genomics Lab, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20850, USA
| | - Kenneth H Fischbeck
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20892, USA
| | - Barrington G Burnett
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, F. Edward Hébert School of Medicine, Bethesda, MD 20814, USA.
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46
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A CRISPR/Cas13a-powered catalytic electrochemical biosensor for successive and highly sensitive RNA diagnostics. Biosens Bioelectron 2021; 178:113027. [DOI: 10.1016/j.bios.2021.113027] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 01/08/2021] [Accepted: 01/20/2021] [Indexed: 12/20/2022]
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47
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Tziortzouda P, Van Den Bosch L, Hirth F. Triad of TDP43 control in neurodegeneration: autoregulation, localization and aggregation. Nat Rev Neurosci 2021; 22:197-208. [PMID: 33654312 DOI: 10.1038/s41583-021-00431-1] [Citation(s) in RCA: 110] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2021] [Indexed: 01/31/2023]
Abstract
Cytoplasmic aggregation of TAR DNA-binding protein 43 (TDP43; also known as TARDBP or TDP-43) is a key pathological feature of several neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). TDP43 typically resides in the nucleus but can shuttle between the nucleus and the cytoplasm to exert its multiple functions, which include regulation of the splicing, trafficking and stabilization of RNA. Cytoplasmic mislocalization and nuclear loss of TDP43 have both been associated with ALS and FTD, suggesting that calibrated levels and correct localization of TDP43 - achieved through an autoregulatory loop and tightly controlled nucleocytoplasmic transport - safeguard its normal function. Furthermore, TDP43 can undergo phase transitions, including its dispersion into liquid droplets and its accumulation into irreversible cytoplasmic aggregates. Thus, autoregulation, nucleocytoplasmic transport and phase transition are all part of an intrinsic control system regulating the physiological levels and localization of TDP43, and together are essential for the cellular homeostasis that is affected in neurodegenerative disease.
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Affiliation(s)
- Paraskevi Tziortzouda
- Department of Neurosciences, Leuven Brain Institute (LBI), KU Leuven, Leuven, Belgium
- Laboratory of Neurobiology, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium
| | - Ludo Van Den Bosch
- Department of Neurosciences, Leuven Brain Institute (LBI), KU Leuven, Leuven, Belgium.
- Laboratory of Neurobiology, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.
| | - Frank Hirth
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.
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Wu G, Schmid M, Rib L, Polak P, Meola N, Sandelin A, Jensen TH. A Two-Layered Targeting Mechanism Underlies Nuclear RNA Sorting by the Human Exosome. Cell Rep 2021; 30:2387-2401.e5. [PMID: 32075771 DOI: 10.1016/j.celrep.2020.01.068] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 12/09/2019] [Accepted: 01/22/2020] [Indexed: 12/14/2022] Open
Abstract
Degradation of transcripts in human nuclei is primarily facilitated by the RNA exosome. To obtain substrate specificity, the exosome is aided by adaptors; in the nucleoplasm, those adaptors are the nuclear exosome-targeting (NEXT) complex and the poly(A) (pA) exosome-targeting (PAXT) connection. How these adaptors guide exosome targeting remains enigmatic. Employing high-resolution 3' end sequencing, we demonstrate that NEXT substrates arise from heterogenous and predominantly pA- 3' ends often covering kilobase-wide genomic regions. In contrast, PAXT targets harbor well-defined pA+ 3' ends defined by canonical pA site use. Irrespective of this clear division, NEXT and PAXT act redundantly in two ways: (1) regional redundancy, where the majority of exosome-targeted transcription units produce NEXT- and PAXT-sensitive RNA isoforms, and (2) isoform redundancy, where the PAXT connection ensures fail-safe decay of post-transcriptionally polyadenylated NEXT targets. In conjunction, this provides a two-layered targeting mechanism for efficient nuclear sorting of the human transcriptome.
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Affiliation(s)
- Guifen Wu
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
| | - Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
| | - Leonor Rib
- The Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen, Denmark
| | - Patrik Polak
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
| | - Nicola Meola
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
| | - Albin Sandelin
- The Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark.
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Abstract
The subcellular localization of RNAs correlates with their function and how they are regulated. Most protein-coding mRNAs are exported into the cytoplasm for protein synthesis, while some mRNA species, long noncoding RNAs, and some regulatory element-associated unstable transcripts tend to be retained in the nucleus, where they function as a regulatory unit and/or are regulated by nuclear surveillance pathways. While the mechanisms regulating mRNA export and localization have been well summarized, the mechanisms governing nuclear retention of RNAs, especially of noncoding RNAs, are seldomly reviewed. In this review, we summarize recent advances in the mechanistic study of RNA nuclear retention, especially for noncoding RNAs, from the angle of cis-acting elements embedded in RNA transcripts and their interaction with trans-acting factors. We also try to illustrate the general principles of RNA nuclear retention and we discuss potential areas for future investigation.
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Affiliation(s)
- Chong Tong
- Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yafei Yin
- Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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50
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MINFLUX nanometer-scale 3D imaging and microsecond-range tracking on a common fluorescence microscope. Nat Commun 2021; 12:1478. [PMID: 33674570 PMCID: PMC7935904 DOI: 10.1038/s41467-021-21652-z] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 02/04/2021] [Indexed: 12/13/2022] Open
Abstract
The recently introduced minimal photon fluxes (MINFLUX) concept pushed the resolution of fluorescence microscopy to molecular dimensions. Initial demonstrations relied on custom made, specialized microscopes, raising the question of the method’s general availability. Here, we show that MINFLUX implemented with a standard microscope stand can attain 1–3 nm resolution in three dimensions, rendering fluorescence microscopy with molecule-scale resolution widely applicable. Advances, such as synchronized electro-optical and galvanometric beam steering and a stabilization that locks the sample position to sub-nanometer precision with respect to the stand, ensure nanometer-precise and accurate real-time localization of individually activated fluorophores. In our MINFLUX imaging of cell- and neurobiological samples, ~800 detected photons suffice to attain a localization precision of 2.2 nm, whereas ~2500 photons yield precisions <1 nm (standard deviation). We further demonstrate 3D imaging with localization precision of ~2.4 nm in the focal plane and ~1.9 nm along the optic axis. Localizing with a precision of <20 nm within ~100 µs, we establish this spatio-temporal resolution in single fluorophore tracking and apply it to the diffusion of single labeled lipids in lipid-bilayer model membranes. Minimal photon fluxes (MINFLUX) has enabled molecule-scale resolution in fluorescence microscopy but this had not been shown in standard, broadly applicable microscopy platforms. Here the authors report a solution to allow normal fluorescence microscopy while also providing 1-3 nm 3D resolution.
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