1
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Małecka EM, Woodson SA. RNA compaction and iterative scanning for small RNA targets by the Hfq chaperone. Nat Commun 2024; 15:2069. [PMID: 38453956 PMCID: PMC10920880 DOI: 10.1038/s41467-024-46316-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/18/2024] [Indexed: 03/09/2024] Open
Abstract
RNA-guided enzymes must quickly search a vast sequence space for their targets. This search is aided by chaperones such as Hfq, a protein that mediates regulation by bacterial small RNAs (sRNAs). How RNA binding proteins enhance this search is little known. Using single-molecule Förster resonance energy transfer, we show that E. coli Hfq performs a one-dimensional scan in which compaction of the target RNA delivers sRNAs to sites distant from the location of Hfq recruitment. We also show that Hfq can transfer an sRNA between different target sites in a single mRNA, favoring the most stable duplex. We propose that compaction and segmental transfer, combined with repeated cycles of base pairing, enable the kinetic selection of optimal sRNA targets. Finally, we show that RNA compaction and sRNA transfer require conserved arginine patches. We suggest that arginine patches are a widespread strategy for enabling the movement of RNA across protein surfaces.
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Affiliation(s)
- Ewelina M Małecka
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St.,5, Baltimore, MD, 21218, USA.
- Laboratory of Single-Molecule Biophysics, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, Warsaw, 02-109, Poland.
| | - Sarah A Woodson
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St.,5, Baltimore, MD, 21218, USA.
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2
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Paudel B, Jeong SY, Martinez CP, Rickman A, Haluck-Kangas A, Bartom ET, Fredriksen K, Affaneh A, Kessler JA, Mazzulli JR, Murmann AE, Rogalski E, Geula C, Ferreira A, Heckmann BL, Green DR, Sadleir KR, Vassar R, Peter ME. Death Induced by Survival gene Elimination (DISE) correlates with neurotoxicity in Alzheimer's disease and aging. Nat Commun 2024; 15:264. [PMID: 38238311 PMCID: PMC10796375 DOI: 10.1038/s41467-023-44465-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 12/13/2023] [Indexed: 01/22/2024] Open
Abstract
Alzheimer's disease (AD) is characterized by progressive neurodegeneration, but the specific events that cause cell death remain poorly understood. Death Induced by Survival gene Elimination (DISE) is a cell death mechanism mediated by short (s) RNAs acting through the RNA-induced silencing complex (RISC). DISE is thus a form of RNA interference, in which G-rich 6mer seed sequences in the sRNAs (position 2-7) target hundreds of C-rich 6mer seed matches in genes essential for cell survival, resulting in the activation of cell death pathways. Here, using Argonaute precipitation and RNAseq (Ago-RP-Seq), we analyze RISC-bound sRNAs to quantify 6mer seed toxicity in several model systems. In mouse AD models and aging brain, in induced pluripotent stem cell-derived neurons from AD patients, and in cells exposed to Aβ42 oligomers, RISC-bound sRNAs show a shift to more toxic 6mer seeds compared to controls. In contrast, in brains of "SuperAgers", humans over age 80 who have superior memory performance, RISC-bound sRNAs are shifted to more nontoxic 6mer seeds. Cells depleted of nontoxic sRNAs are sensitized to Aβ42-induced cell death, and reintroducing nontoxic RNAs is protective. Altogether, the correlation between DISE and Aβ42 toxicity suggests that increasing the levels of nontoxic miRNAs in the brain or blocking the activity of toxic RISC-bound sRNAs could ameliorate neurodegeneration.
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Affiliation(s)
- Bidur Paudel
- Department of Medicine/Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Si-Yeon Jeong
- Department of Medicine/Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Ministry of Food and Drug Safety, Pharmaceutical Safety Bureau, Pharmaceutical Policy Division 187, Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do, Republic of Korea
| | - Carolina Pena Martinez
- USF Health Byrd Alzheimer's Center and Neuroscience Institute; Department of Molecular Medicine, Morsani College of Medicine, Tampa, FL, 33613, USA
| | - Alexis Rickman
- USF Health Byrd Alzheimer's Center and Neuroscience Institute; Department of Molecular Medicine, Morsani College of Medicine, Tampa, FL, 33613, USA
| | - Ashley Haluck-Kangas
- Department of Medicine/Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Elizabeth T Bartom
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Department of Preventive Medicine/Division of Biostatistics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Kristina Fredriksen
- Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Amira Affaneh
- Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - John A Kessler
- Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Joseph R Mazzulli
- Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Andrea E Murmann
- Department of Medicine/Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Emily Rogalski
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Healthy Aging & Alzheimer's Research Care (HAARC) Center, Department of Neurology, The University of Chicago, Chicago, IL, 60637, USA
| | - Changiz Geula
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Adriana Ferreira
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Bradlee L Heckmann
- USF Health Byrd Alzheimer's Center and Neuroscience Institute; Department of Molecular Medicine, Morsani College of Medicine, Tampa, FL, 33613, USA
| | - Douglas R Green
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Katherine R Sadleir
- Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Robert Vassar
- Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Marcus E Peter
- Department of Medicine/Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
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3
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Zhen X, Xu X, Ye L, Xie S, Huang Z, Yang S, Wang Y, Li J, Long F, Ouyang S. Structural basis of antiphage immunity generated by a prokaryotic Argonaute-associated SPARSA system. Nat Commun 2024; 15:450. [PMID: 38200015 PMCID: PMC10781750 DOI: 10.1038/s41467-023-44660-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 12/26/2023] [Indexed: 01/12/2024] Open
Abstract
Argonaute (Ago) proteins are ubiquitous across all kingdoms of life. Eukaryotic Agos (eAgos) use small RNAs to recognize transcripts for RNA silencing in eukaryotes. In contrast, the functions of prokaryotic counterparts (pAgo) are less well known. Recently, short pAgos in conjunction with the associated TIR or Sir2 (SPARTA or SPARSA) were found to serve as antiviral systems to combat phage infections. Herein, we present the cryo-EM structures of nicotinamide adenine dinucleotide (NAD+)-bound SPARSA with and without nucleic acids at resolutions of 3.1 Å and 3.6 Å, respectively. Our results reveal that the APAZ (Analogue of PAZ) domain and the short pAgo form a featured architecture similar to the long pAgo to accommodate nucleic acids. We further identified the key residues for NAD+ binding and elucidated the structural basis for guide RNA and target DNA recognition. Using structural comparisons, molecular dynamics simulations, and biochemical experiments, we proposed a putative mechanism for NAD+ hydrolysis in which an H186 loop mediates nucleophilic attack by catalytic water molecules. Overall, our study provides mechanistic insight into the antiphage role of the SPARSA system.
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Affiliation(s)
- Xiangkai Zhen
- Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Xiaolong Xu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China Wuhan University, Wuhan, 430071, China
| | - Le Ye
- Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Song Xie
- College of Chemistry, Fuzhou University, 350116, Fuzhou, China
| | - Zhijie Huang
- Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Sheng Yang
- Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Yanhui Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China Wuhan University, Wuhan, 430071, China
| | - Jinyu Li
- College of Chemistry, Fuzhou University, 350116, Fuzhou, China.
| | - Feng Long
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China Wuhan University, Wuhan, 430071, China.
| | - Songying Ouyang
- Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China.
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4
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Gao L, Behrens A, Rodschinka G, Forcelloni S, Wani S, Strasser K, Nedialkova DD. Selective gene expression maintains human tRNA anticodon pools during differentiation. Nat Cell Biol 2024; 26:100-112. [PMID: 38191669 PMCID: PMC10791582 DOI: 10.1038/s41556-023-01317-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 11/16/2023] [Indexed: 01/10/2024]
Abstract
Transfer RNAs are essential for translating genetic information into proteins. The human genome contains hundreds of predicted tRNA genes, many in multiple copies. How their expression is regulated to control tRNA repertoires is unknown. Here we combined quantitative tRNA profiling and chromatin immunoprecipitation with sequencing to measure tRNA expression following the differentiation of human induced pluripotent stem cells into neuronal and cardiac cells. We find that tRNA transcript levels vary substantially, whereas tRNA anticodon pools, which govern decoding rates, are more stable among cell types. Mechanistically, RNA polymerase III transcribes a wide range of tRNA genes in human induced pluripotent stem cells but on differentiation becomes constrained to a subset we define as housekeeping tRNAs. This shift is mediated by decreased mTORC1 signalling, which activates the RNA polymerase III repressor MAF1. Our data explain how tRNA anticodon pools are buffered to maintain decoding speed across cell types and reveal that mTORC1 drives selective tRNA expression during differentiation.
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Affiliation(s)
- Lexi Gao
- Mechanisms of Protein Biogenesis, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Andrew Behrens
- Mechanisms of Protein Biogenesis, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Geraldine Rodschinka
- Mechanisms of Protein Biogenesis, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sergio Forcelloni
- Mechanisms of Protein Biogenesis, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sascha Wani
- Mechanisms of Protein Biogenesis, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Katrin Strasser
- Mechanisms of Protein Biogenesis, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Danny D Nedialkova
- Mechanisms of Protein Biogenesis, Max Planck Institute of Biochemistry, Martinsried, Germany.
- Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich, Garching, Germany.
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5
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Liu F, Chen Z, Zhang S, Wu K, Bei C, Wang C, Chao Y. In vivo RNA interactome profiling reveals 3'UTR-processed small RNA targeting a central regulatory hub. Nat Commun 2023; 14:8106. [PMID: 38062076 PMCID: PMC10703908 DOI: 10.1038/s41467-023-43632-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023] Open
Abstract
Small noncoding RNAs (sRNAs) are crucial regulators of gene expression in bacteria. Acting in concert with major RNA chaperones such as Hfq or ProQ, sRNAs base-pair with multiple target mRNAs and form large RNA-RNA interaction networks. To systematically investigate the RNA-RNA interactome in living cells, we have developed a streamlined in vivo approach iRIL-seq (intracellular RIL-seq). This generic approach is highly robust, illustrating the dynamic sRNA interactomes in Salmonella enterica across multiple stages of growth. We have identified the OmpD porin mRNA as a central regulatory hub that is targeted by a dozen sRNAs, including FadZ cleaved from the conserved 3'UTR of fadBA mRNA. Both ompD and FadZ are activated by CRP, constituting a type I incoherent feed-forward loop in the fatty acid metabolism pathway. Altogether, we have established an approach to profile RNA-RNA interactomes in live cells, highlighting the complexity of RNA regulatory hubs and RNA networks.
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Affiliation(s)
- Fang Liu
- Microbial RNA Systems Biology Unit, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China
- The Center for Microbes, Development and Health (CMDH), Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Ziying Chen
- Microbial RNA Systems Biology Unit, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200033, China
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center & Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Shuo Zhang
- Microbial RNA Systems Biology Unit, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China
- The Center for Microbes, Development and Health (CMDH), Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kejing Wu
- Microbial RNA Systems Biology Unit, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China
- The Center for Microbes, Development and Health (CMDH), Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Cheng Bei
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200033, China
| | - Chuan Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200033, China.
| | - Yanjie Chao
- Microbial RNA Systems Biology Unit, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China.
- The Center for Microbes, Development and Health (CMDH), Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China.
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6
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Zhang Y, Shi J, Chen Q. Towards the understanding of "Herbal RNA Code" for traditional medicine. Cell Res 2023; 33:900-901. [PMID: 37479856 PMCID: PMC10709395 DOI: 10.1038/s41422-023-00851-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2023] Open
Affiliation(s)
- Ying Zhang
- The Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China.
| | - Junchao Shi
- Molecular Medicine Program, Department of Human Genetics, and Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA.
- Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China.
| | - Qi Chen
- Molecular Medicine Program, Department of Human Genetics, and Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
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7
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Camara-Wilpert S, Mayo-Muñoz D, Russel J, Fagerlund RD, Madsen JS, Fineran PC, Sørensen SJ, Pinilla-Redondo R. Bacteriophages suppress CRISPR-Cas immunity using RNA-based anti-CRISPRs. Nature 2023; 623:601-607. [PMID: 37853129 PMCID: PMC10651486 DOI: 10.1038/s41586-023-06612-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 09/05/2023] [Indexed: 10/20/2023]
Abstract
Many bacteria use CRISPR-Cas systems to combat mobile genetic elements, such as bacteriophages and plasmids1. In turn, these invasive elements have evolved anti-CRISPR proteins to block host immunity2,3. Here we unveil a distinct type of CRISPR-Cas Inhibition strategy that is based on small non-coding RNA anti-CRISPRs (Racrs). Racrs mimic the repeats found in CRISPR arrays and are encoded in viral genomes as solitary repeat units4. We show that a prophage-encoded Racr strongly inhibits the type I-F CRISPR-Cas system by interacting specifically with Cas6f and Cas7f, resulting in the formation of an aberrant Cas subcomplex. We identified Racr candidates for almost all CRISPR-Cas types encoded by a diverse range of viruses and plasmids, often in the genetic context of other anti-CRISPR genes5. Functional testing of nine candidates spanning the two CRISPR-Cas classes confirmed their strong immune inhibitory function. Our results demonstrate that molecular mimicry of CRISPR repeats is a widespread anti-CRISPR strategy, which opens the door to potential biotechnological applications6.
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Affiliation(s)
| | - David Mayo-Muñoz
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand
| | - Jakob Russel
- Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Robert D Fagerlund
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand
| | - Jonas S Madsen
- Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.
- Genetics Otago, University of Otago, Dunedin, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand.
- Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand.
| | - Søren J Sørensen
- Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Rafael Pinilla-Redondo
- Section of Microbiology, University of Copenhagen, Copenhagen, Denmark.
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.
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8
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Vetter L, Bajalan A, Ahamed MT, Scasso C, Shafeeq S, Andersson B, Ribacke U. Starvation induces changes in abundance and small RNA cargo of extracellular vesicles released from Plasmodium falciparum infected red blood cells. Sci Rep 2023; 13:18423. [PMID: 37891207 PMCID: PMC10611735 DOI: 10.1038/s41598-023-45590-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/21/2023] [Indexed: 10/29/2023] Open
Abstract
The lethal malaria parasite Plasmodium falciparum needs to constantly respond and adapt to changes within the human host in order to survive and transmit. One such change is composed of nutritional limitation, which is augmented with increased parasite loads and intimately linked to severe disease development. Extracellular vesicles released from infected red blood cells have been proposed as important mediators of disease pathogenesis and intercellular communication but whether important for the parasite response to nutritional availability is unknown. Therefore, we investigated the abundance and small RNA cargo of extracellular vesicles released upon short-term nutritional starvation of P. falciparum in vitro cultures. We show that primarily ring-stage parasite cultures respond to glucose and amino acid deprivation with an increased release of extracellular vesicles. Small RNA sequencing of these extracellular vesicles further revealed human miRNAs and parasitic tRNA fragments as the main constituent biotypes. Short-term starvations led to alterations in the transcriptomic profile, most notably in terms of the over-represented biotypes. These data suggest a potential role for extracellular vesicles released from P. falciparum infected red blood cells in the response to nutritional perturbations, their potential as prognostic biomarkers and point towards an evolutionary conserved role among protozoan parasites.
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Affiliation(s)
- Leonie Vetter
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solnavägen 9, SE-17165, Solna, Sweden
| | - Amanj Bajalan
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solnavägen 9, SE-17165, Solna, Sweden
| | - Mohammad Tanvir Ahamed
- Department of Learning, Informatics, Management and Ethics, Karolinska Institutet, Tomtebodavägen 18, SE-17177, Solna, Sweden
| | - Caterina Scasso
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solnavägen 9, SE-17165, Solna, Sweden
| | - Sulman Shafeeq
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solnavägen 9, SE-17165, Solna, Sweden
| | - Björn Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 9, SE-17165, Solna, Sweden
| | - Ulf Ribacke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solnavägen 9, SE-17165, Solna, Sweden.
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, SE-75237, Uppsala, Sweden.
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9
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Liao T, Gan M, Lei Y, Wang Y, Chen L, Shen L, Zhu L. Dynamic changes in the transcriptome of tRNA-derived small RNAs related with fat metabolism. Sci Data 2023; 10:703. [PMID: 37838754 PMCID: PMC10576826 DOI: 10.1038/s41597-023-02624-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 10/09/2023] [Indexed: 10/16/2023] Open
Abstract
The prevalence of obesity and overweight is steadily rising, posing a significant global challenge for humanity. The fundamental cause of obesity and overweight lies in the abnormal accumulation of adipose tissue. While numerous regulatory factors related to fat deposition have been identified in previous studies, a considerable number of regulatory mechanisms remain unknown. tRNA-derived small RNAs (tsRNAs), a novel class of non-coding RNAs, have emerged as significant regulators in various biological processes. In this study, we obtained small RNA sequencing data from subcutaneous white adipose tissue and omental white adipose tissue of lean and obese pigs. In addition, we similarly obtained tsRNAs profiles from scapular brown adipose tissue (BAT), inguinal white adipose tissue (iWAT) and epigonadal white adipose tissue (eWAT) of normal mice. Finally, we successfully identified a large number of expressed tsRNAs in each tissue type and identified tsRNAs conserved in different adipose tissues of pigs and mice. These datasets will be a valuable resource for elucidating the epigenetic mechanisms of fat deposition.
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Affiliation(s)
- Tianci Liao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mailin Gan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuhang Lei
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yan Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lei Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Linyuan Shen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China.
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Li Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China.
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
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10
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Price IF, Wagner JA, Pastore B, Hertz HL, Tang W. C. elegans germ granules sculpt both germline and somatic RNAome. Nat Commun 2023; 14:5965. [PMID: 37749091 PMCID: PMC10520050 DOI: 10.1038/s41467-023-41556-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 09/08/2023] [Indexed: 09/27/2023] Open
Abstract
Germ granules are membrane-less organelles essential for small RNA biogenesis and germline development. Among the conserved properties of germ granules is their association with the nuclear membrane. Recent studies demonstrated that LOTUS domain proteins, EGGD-1 and EGGD-2 (also known as MIP-1 and MIP-2 respectively), promote the formation of perinuclear germ granules in C. elegans. This finding presents a unique opportunity to evaluate the significance of perinuclear localization of germ granules. Here we show that loss of eggd-1 causes the coalescence of germ granules and formation of abnormal cytoplasmic aggregates. Impairment of perinuclear granules affects certain germline classes of small RNAs including Piwi-interacting RNAs. Transcriptome profiling reveals overexpression of spermatogenic and cuticle-related genes in eggd-1 hermaphrodites. We further demonstrate that disruption of germ granules activates HLH-30-mediated transcriptional program in somatic tissues. Collectively, our findings underscore the essential role of EGGD-1 in germ granule organization and reveal an unexpected germ granule-to-soma communication.
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Affiliation(s)
- Ian F Price
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, 43210, USA
| | - Jillian A Wagner
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Benjamin Pastore
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, 43210, USA
| | - Hannah L Hertz
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Wen Tang
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA.
- Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA.
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11
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Lai H, Feng N, Zhai Q. Discovery of the major 15-30 nt mammalian small RNAs, their biogenesis and function. Nat Commun 2023; 14:5796. [PMID: 37723159 PMCID: PMC10507107 DOI: 10.1038/s41467-023-41554-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 09/08/2023] [Indexed: 09/20/2023] Open
Abstract
Small RNAs (sRNAs) within 15-30 nt such as miRNA, tsRNA, srRNA with 3'-OH have been identified. However, whether these sRNAs are the major 15-30 nt sRNAs is still unknown. Here we show about 90% mammalian sRNAs within 15-30 nt end with 2',3'-cyclic phosphate (3'-cP). TANT-seq was developed to simultaneously profile sRNAs with 3'-cP (sRNA-cPs) and sRNA-OHs, and huge amount of sRNA-cPs were detected. Surprisingly, sRNA-cPs and sRNA-OHs usually have distinct sequences. The data from TANT-seq were validated by a novel method termed TE-qPCR, and Northern blot. Furthermore, we found that Angiogenin and RNase 4 contribute to the biogenesis of sRNA-cPs. Moreover, much more sRNA-cPs than sRNA-OHs bind to Ago2, and can regulate gene expression. Particularly, snR-2-cP regulates Bcl2 by targeting to its 3'UTR dependent on Ago2, and subsequently regulates apoptosis. In addition, sRNA-cPs can guide the cleavage of target RNAs in Ago2 complex as miRNAs without the requirement of 3'-cP. Our discovery greatly expands the repertoire of mammalian sRNAs, and provides strategies and powerful tools towards further investigation of sRNA-cPs.
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Affiliation(s)
- Hejin Lai
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ning Feng
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qiwei Zhai
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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12
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He TT, Xu YF, Li X, Wang X, Li JY, Ou-Yang D, Cheng HS, Li HY, Qin J, Huang Y, Wang HY. A linear and circular dual-conformation noncoding RNA involved in oxidative stress tolerance in Bacillus altitudinis. Nat Commun 2023; 14:5722. [PMID: 37714854 PMCID: PMC10504365 DOI: 10.1038/s41467-023-41491-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 09/06/2023] [Indexed: 09/17/2023] Open
Abstract
Circular RNAs have been extensively studied in eukaryotes, but their presence and/or biological functionality in bacteria are unclear. Here, we show that a regulatory noncoding RNA (DucS) exists in both linear and circular conformation in Bacillus altitudinis. The linear forms promote B. altitudinis tolerance to H2O2 stress, partly through increased translation of a stress-responsive gene, htrA. The 3' end sequences of the linear forms are crucial for RNA circularization, and formation of circular forms can decrease the levels of the regulatory linear cognates. Bioinformatic analysis of available RNA-seq datasets from 30 bacterial species revealed multiple circular RNA candidates, distinct from DucS, for all the examined species. Experiments testing for the presence of selected circular RNA candidates in four species successfully validated 7 out of 9 candidates from B. altitudinis and 4 out of 5 candidates from Bacillus paralicheniformis; However, none of the candidates tested for Bacillus subtilis and Escherichia coli were detected. Our work identifies a dual-conformation regulatory RNA in B. altitutidinis, and indicates that circular RNAs exist in diverse bacteria. However, circularization of specific RNAs does not seem to be conserved across species, and the circularization mechanisms and biological functionality of the circular forms remain unclear.
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Affiliation(s)
- Ting-Ting He
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Yun-Fan Xu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Xiang Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Xia Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Jie-Yu Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Dan Ou-Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Han-Sen Cheng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Hao-Yang Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Jia Qin
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Yu Huang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Hai-Yan Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China.
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13
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Abstract
U6 snRNA is a catalytic RNA responsible for pre-mRNA splicing reactions and undergoes various post-transcriptional modifications during its maturation process. The 3'-oligouridylation of U6 snRNA by the terminal uridylyltransferase, TUT1, provides the Lsm-binding site in U6 snRNA for U4/U6 di-snRNP formation and this ensures pre-mRNA splicing. Here, we present the crystal structure of human TUT1 (hTUT1) complexed with U6 snRNA, representing the post-uridylation of U6 snRNA by hTUT1. The N-terminal ZF-RRM and catalytic palm clamp the single-stranded AUA motif between the 5'-short stem and the 3'-telestem of U6 snRNA, and the ZF-RRM specifically recognizes the AUA motif. The ZF and the fingers hold the telestem, and the 3'-end of U6 snRNA is placed in the catalytic pocket of the palm for oligouridylation. The oligouridylation of U6 snRNA depends on the internal four-adenosine tract in the 5'-part of the telestem of U6 snRNA, and hTUT1 adds uridines until the internal adenosine tract can form base-pairs with the 3'-oligouridine tract. Together, the recognition of the specific structure and sequence of U6 snRNA by the multi-domain TUT1 protein and the intrinsic sequence and structure of U6 snRNA ensure the oligouridylation of U6 snRNA.
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Affiliation(s)
- Seisuke Yamashita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Kozo Tomita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan.
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14
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Du J, Kageyama SI, Yamashita R, Tanaka K, Okumura M, Motegi A, Hojo H, Nakamura M, Hirata H, Sunakawa H, Kotani D, Yano T, Kojima T, Hamaya Y, Kojima M, Nakamura Y, Suzuki A, Suzuki Y, Tsuchihara K, Akimoto T. Transposable elements potentiate radiotherapy-induced cellular immune reactions via RIG-I-mediated virus-sensing pathways. Commun Biol 2023; 6:818. [PMID: 37543704 PMCID: PMC10404237 DOI: 10.1038/s42003-023-05080-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 06/28/2023] [Indexed: 08/07/2023] Open
Abstract
Radiotherapy (RT) plus immunotherapy is a promising modality; however, the therapeutic effects are insufficient, and the molecular mechanism requires clarification to further develop combination therapies. Here, we found that the RNA virus sensor pathway dominantly regulates the cellular immune response in NSCLC and ESCC cell lines. Notably, transposable elements (TEs), especially long terminal repeats (LTRs), functioned as key ligands for the RNA virus sensor RIG-I, and the mTOR-LTR-RIG-I axis induced the cellular immune response and dendritic cell and macrophage infiltration after irradiation. Moreover, RIG-I-dependent immune activation was observed in ESCC patient tissue. scRNA sequencing and spatial transcriptome analysis revealed that radiotherapy induced the expression of LTRs, and the RNA virus sensor pathway in immune and cancer cells; this pathway was also found to mediate tumour conversion to an immunological hot state. Here, we report the upstream and ligand of the RNA virus sensor pathway functions in irradiated cancer tissues.
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Affiliation(s)
- Junyan Du
- Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Shun-Ichiro Kageyama
- Division of Radiation Oncology and Particle Therapy, National Cancer Center Hospital East, Chiba, Japan.
- Department of Radiation Oncology, National Cancer Center Hospital East, Chiba, Japan.
| | - Riu Yamashita
- Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Kosuke Tanaka
- Division of Cancer Immunology, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Masayuki Okumura
- Division of Radiation Oncology and Particle Therapy, National Cancer Center Hospital East, Chiba, Japan
| | - Atsushi Motegi
- Division of Radiation Oncology and Particle Therapy, National Cancer Center Hospital East, Chiba, Japan
| | - Hidehiro Hojo
- Division of Radiation Oncology and Particle Therapy, National Cancer Center Hospital East, Chiba, Japan
| | - Masaki Nakamura
- Division of Radiation Oncology and Particle Therapy, National Cancer Center Hospital East, Chiba, Japan
| | - Hidenari Hirata
- Division of Radiation Oncology and Particle Therapy, National Cancer Center Hospital East, Chiba, Japan
| | - Hironori Sunakawa
- Department of Gastroenterology and Endoscopy, National Cancer Center Hospital East, Chiba, Japan
| | - Daisuke Kotani
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Tomonori Yano
- Department of Gastroenterology and Endoscopy, National Cancer Center Hospital East, Chiba, Japan
| | - Takashi Kojima
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Yamato Hamaya
- Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Motohiro Kojima
- Division of Pathology, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Yuka Nakamura
- Division of Pathology, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Ayako Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Katsuya Tsuchihara
- Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Tetsuo Akimoto
- Division of Radiation Oncology and Particle Therapy, National Cancer Center Hospital East, Chiba, Japan
- Department of Radiation Oncology, National Cancer Center Hospital East, Chiba, Japan
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15
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Di Fazio A, Gullerova M. An old friend with a new face: tRNA-derived small RNAs with big regulatory potential in cancer biology. Br J Cancer 2023; 128:1625-1635. [PMID: 36759729 PMCID: PMC10133234 DOI: 10.1038/s41416-023-02191-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 02/11/2023] Open
Abstract
Transfer RNAs (tRNAs) are small non-coding RNAs (sncRNAs) essential for protein translation. Emerging evidence suggests that tRNAs can also be processed into smaller fragments, tRNA-derived small RNAs (tsRNAs), a novel class of sncRNAs with powerful applications and high biological relevance to cancer. tsRNAs biogenesis is heterogeneous and involves different ribonucleases, such as Angiogenin and Dicer. For many years, tsRNAs were thought to be just degradation products. However, accumulating evidence shows their roles in gene expression: either directly via destabilising the mRNA or the ribosomal machinery, or indirectly via regulating the expression of ribosomal components. Furthermore, tsRNAs participate in various biological processes linked to cancer, including apoptosis, cell cycle, immune response, and retroviral insertion into the human genome. It is emerging that tsRNAs have significant therapeutic potential. Endogenous tsRNAs can be used as cancer biomarkers, while synthetic tsRNAs and antisense oligonucleotides can be employed to regulate gene expression. In this review, we are recapitulating the regulatory roles of tsRNAs, with a focus on cancer biology.
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Affiliation(s)
- Arianna Di Fazio
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK.
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16
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Jia X, Pan Z, Yuan Y, Luo B, Luo Y, Mukherjee S, Jia G, Liu L, Ling X, Yang X, Miao Z, Wei X, Bujnicki JM, Zhao K, Su Z. Structural basis of sRNA RsmZ regulation of Pseudomonas aeruginosa virulence. Cell Res 2023; 33:328-330. [PMID: 36828938 PMCID: PMC10066318 DOI: 10.1038/s41422-023-00786-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 02/06/2023] [Indexed: 02/26/2023] Open
Affiliation(s)
- Xinyu Jia
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zhiling Pan
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yang Yuan
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, Sichuan, China
| | - Bingnan Luo
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yongbo Luo
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Sunandan Mukherjee
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109, Warsaw, Poland
| | - Guowen Jia
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Liu Liu
- Department of Conservative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Xiaobin Ling
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiting Yang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, Sichuan, China
| | - Zhichao Miao
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, Guangdong, China
| | - Xiawei Wei
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109, Warsaw, Poland
| | - Kelei Zhao
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, Sichuan, China.
| | - Zhaoming Su
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
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17
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Zhu J, Mao S, Zhen N, Zhu G, Bian Z, Xie Y, Tang X, Ding M, Wu H, Ma J, Zhu Y, Sun F, Pan Q. SNORA14A inhibits hepatoblastoma cell proliferation by regulating SDHB-mediated succinate metabolism. Cell Death Dis 2023; 9:36. [PMID: 36717552 PMCID: PMC9886955 DOI: 10.1038/s41420-023-01325-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 01/06/2023] [Accepted: 01/11/2023] [Indexed: 01/31/2023]
Abstract
Hepatoblastoma (HB) is the most common paediatric liver malignancy. Dysregulation of small nucleolar RNAs (snoRNAs) is a critical inducer of tumour initiation and progression. However, the association between snoRNAs and HB remains unknown. Here, we conducted snoRNA expression profiling in HB by snoRNA sequencing and identified a decreased level of SNORA14A, a box H/ACA snoRNA, in HB tissues. Low expression of SNORA14A was correlated with PRETEXT stage and metastasis in patients. Functionally, overexpression of SNORA14A suppressed HB cell proliferation and triggered cell apoptosis and G2/M phase arrest. Mechanistically, SNORA14A overexpression promoted the processing and maturation of the 18 S ribosomal RNA (rRNA) precursor to increase succinate dehydrogenase subunit B (SDHB) protein levels. In accordance with SNORA14A downregulation, SDHB protein expression was significantly reduced in HB tissues and cells, accompanied by abnormal accumulation of succinate. Overexpression of SDHB showed antiproliferative and proapoptotic effects and the capacity to induce G2/M phase arrest, while succinate dose-dependently stimulated HB cell growth. Furthermore, the inhibition of SNORA14A in HB malignant phenotypes was mediated by SDHB upregulation-induced reduction of cellular succinate levels. Therefore, the SNORA14A/18 S rRNA/SDHB axis suppresses HB progression by preventing cellular accumulation of the oncometabolite succinate and provides promising prognostic biomarkers and novel therapeutic targets for HB.
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Affiliation(s)
- Jiabei Zhu
- grid.16821.3c0000 0004 0368 8293Department of Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China ,Shanghai Key Laboratory of Clinical Molecular Diagnostics for Paediatrics, Shanghai, 200127 China
| | - Siwei Mao
- grid.16821.3c0000 0004 0368 8293Department of Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China ,Shanghai Key Laboratory of Clinical Molecular Diagnostics for Paediatrics, Shanghai, 200127 China
| | - Ni Zhen
- grid.16821.3c0000 0004 0368 8293Department of Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Guoqing Zhu
- grid.16821.3c0000 0004 0368 8293Department of Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Zhixuan Bian
- grid.16821.3c0000 0004 0368 8293Department of Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Yi Xie
- grid.16821.3c0000 0004 0368 8293Department of Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Xiaochen Tang
- grid.16821.3c0000 0004 0368 8293Department of Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Miao Ding
- grid.16821.3c0000 0004 0368 8293Department of Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Han Wu
- grid.16821.3c0000 0004 0368 8293Department of Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Ji Ma
- grid.16821.3c0000 0004 0368 8293Department of Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Yizhun Zhu
- grid.259384.10000 0000 8945 4455State Key Laboratory of Quality Research in Chinese Medicine and School of Pharmacy, Macau University of Science and Technology, Macau, 999078 China
| | - Fenyong Sun
- grid.412538.90000 0004 0527 0050Department of Laboratory Medicine, Shanghai Tenth People’s Hospital of Tongji University, Shanghai, 200072 China
| | - Qiuhui Pan
- grid.16821.3c0000 0004 0368 8293Department of Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China ,Shanghai Key Laboratory of Clinical Molecular Diagnostics for Paediatrics, Shanghai, 200127 China ,grid.415626.20000 0004 4903 1529Sanya Women and Children’s Hospital Managed by Shanghai Children’s Medical Center, Sanya, 572000 China
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18
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Petroni E, Esnault C, Tetreault D, Dale RK, Storz G, Adams PP. Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogen B. burgdorferi. bioRxiv 2023:2023.01.04.522626. [PMID: 36712141 PMCID: PMC9881889 DOI: 10.1101/2023.01.04.522626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Transcription termination is an essential and dynamic process that can tune gene expression in response to diverse molecular signals. Yet, the genomic positions, molecular mechanisms, and regulatory consequences of termination have only been studied thoroughly in model bacteria. We employed complementary RNA-seq approaches to map RNA ends for the transcriptome of the spirochete Borrelia burgdorferi - the etiological agent of Lyme disease. By systematically mapping B. burgdorferi RNA ends at single nucleotide resolution, we delineated complex gene arrangements and operons and mapped untranslated regions (UTRs) and small RNAs (sRNAs). We experimentally tested modes of B. burgdorferi transcription termination and compared our findings to observations in E. coli , P. aeruginosa , and B. subtilis . We discovered 63% of B. burgdorferi RNA 3' ends map upstream or internal to open reading frames (ORFs), suggesting novel mechanisms of regulation. Northern analysis confirmed the presence of stable 5' derived RNAs from mRNAs encoding gene products involved in the unique infectious cycle of B. burgdorferi . We suggest these RNAs resulted from premature termination and regulatory events, including forms of cis- acting regulation. For example, we documented that the polyamine spermidine globally influences the generation of truncated mRNAs. In one case, we showed that high spermidine concentrations increased levels of RNA fragments derived from an mRNA encoding a spermidine import system, with a concomitant decrease in levels of the full- length mRNA. Collectively, our findings revealed new insight into transcription termination and uncovered an abundance of potential RNA regulators.
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Affiliation(s)
- Emily Petroni
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Caroline Esnault
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Daniel Tetreault
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Ryan K. Dale
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Philip P. Adams
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA.,Postdoctoral Research Associate Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD 20892, USA.,Independent Research Scholar Program, Intramural Research Program, National Institutes of Health, Bethesda, MD 20892, USA.,correspondence:
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19
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Kärkkäinen E, Heikkinen S, Tengström M, Kosma VM, Mannermaa A, Hartikainen JM. Expression profiles of small non-coding RNAs in breast cancer tumors characterize clinicopathological features and show prognostic and predictive potential. Sci Rep 2022; 12:22614. [PMID: 36585466 PMCID: PMC9803687 DOI: 10.1038/s41598-022-26954-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 12/22/2022] [Indexed: 12/31/2022] Open
Abstract
Precision medicine approaches are required for more effective therapies for cancer. As small non-coding RNAs (sncRNAs) have recently been suggested as intriguing candidates for cancer biomarkers and have shown potential also as novel therapeutic targets, we aimed at profiling the non-miRNA sncRNAs in a large sample set to evaluate their role in invasive breast cancer (BC). We used small RNA sequencing and 195 fresh-frozen invasive BC and 22 benign breast tissue samples to identify significant associations of small nucleolar RNAs, small nuclear RNAs, and miscellaneous RNAs with the clinicopathological features and patient outcome of BC. Ninety-six and five sncRNAs significantly distinguished (Padj < 0.01) invasive local BC from benign breast tissue and metastasized BC from invasive local BC, respectively. Furthermore, 69 sncRNAs significantly associated (Padj < 0.01) with the tumor grade, hormone receptor status, subtype, and/or tumor histology. Additionally, 42 sncRNAs were observed as candidates for prognostic markers and 29 for predictive markers for radiotherapy and/or tamoxifen response (P < 0.05). We discovered the clinical relevance of sncRNAs from each studied RNA type. By introducing new sncRNA biomarker candidates for invasive BC and validating the potential of previously described ones, we have guided the way for further research that is warranted for providing novel insights into BC biology.
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Affiliation(s)
- Emmi Kärkkäinen
- grid.9668.10000 0001 0726 2490School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, and Translational Cancer Research Area, University of Eastern Finland, Yliopistonranta 1 C, 70210 Kuopio, Finland
| | - Sami Heikkinen
- grid.9668.10000 0001 0726 2490School of Medicine, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland ,grid.9668.10000 0001 0726 2490School of Medicine, Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Maria Tengström
- grid.9668.10000 0001 0726 2490School of Medicine, Institute of Clinical Medicine, Oncology, and Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland ,grid.410705.70000 0004 0628 207XCancer Center, Kuopio University Hospital, Kuopio, Finland
| | - Veli-Matti Kosma
- grid.9668.10000 0001 0726 2490School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, and Translational Cancer Research Area, University of Eastern Finland, Yliopistonranta 1 C, 70210 Kuopio, Finland ,grid.410705.70000 0004 0628 207XDepartment of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Arto Mannermaa
- grid.9668.10000 0001 0726 2490School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, and Translational Cancer Research Area, University of Eastern Finland, Yliopistonranta 1 C, 70210 Kuopio, Finland ,grid.410705.70000 0004 0628 207XDepartment of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Jaana M. Hartikainen
- grid.9668.10000 0001 0726 2490School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, and Translational Cancer Research Area, University of Eastern Finland, Yliopistonranta 1 C, 70210 Kuopio, Finland
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20
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Neeb ZT, Ritter AJ, Chauhan LV, Katzman S, Lipkin WI, Mishra N, Sanford JR. A potential role for SARS-CoV-2 small viral RNAs in targeting host microRNAs and modulating gene expression. Sci Rep 2022; 12:21694. [PMID: 36522444 PMCID: PMC9753033 DOI: 10.1038/s41598-022-26135-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease (COVID-19) in humans, with symptoms ranging from mild to severe, including fatality. The molecular mechanisms surrounding the effects of viral infection on the host RNA machinery remain poorly characterized. We used a comparative transcriptomics approach to investigate the effects of SARS-CoV-2 infection on the host mRNA and sRNA expression machinery in a human lung epithelial cell line (Calu-3) and an African green monkey kidney cell line (Vero-E6). Upon infection, we observed global changes in host gene expression and differential expression of dozens of host miRNAs, many with known links to viral infection and immune response. Additionally, we discovered an expanded landscape of more than a hundred SARS-CoV-2-derived small viral RNAs (svRNAs) predicted to interact with differentially expressed host mRNAs and miRNAs. svRNAs are derived from distinct regions of the viral genome and sequence signatures suggest they are produced by a non-canonical biogenesis pathway. 52 of the 67 svRNAs identified in Calu-3 cells are predicted to interact with differentially expressed miRNAs, with many svRNAs having multiple targets. Accordingly, we speculate that these svRNAs may play a role in SARS-CoV-2 propagation by modulating post-transcriptional gene regulation, and that methods for antagonizing them may have therapeutic value.
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Affiliation(s)
- Zachary T Neeb
- Department of Molecular, Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Alexander J Ritter
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Lokendra V Chauhan
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Sol Katzman
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Nischay Mishra
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA.
| | - Jeremy R Sanford
- Department of Molecular, Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA, USA.
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21
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Huber M, Lippegaus A, Melamed S, Siemers M, Wucher BR, Hoyos M, Nadell C, Storz G, Papenfort K. An RNA sponge controls quorum sensing dynamics and biofilm formation in Vibrio cholerae. Nat Commun 2022; 13:7585. [PMID: 36482060 DOI: 10.1038/s41467-022-35261-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 11/24/2022] [Indexed: 12/13/2022] Open
Abstract
Small regulatory RNAs (sRNAs) acting in concert with the RNA chaperone Hfq are prevalent in many bacteria and typically act by base-pairing with multiple target transcripts. In the human pathogen Vibrio cholerae, sRNAs play roles in various processes including antibiotic tolerance, competence, and quorum sensing (QS). Here, we use RIL-seq (RNA-interaction-by-ligation-and-sequencing) to identify Hfq-interacting sRNAs and their targets in V. cholerae. We find hundreds of sRNA-mRNA interactions, as well as RNA duplexes formed between two sRNA regulators. Further analysis of these duplexes identifies an RNA sponge, termed QrrX, that base-pairs with and inactivates the Qrr1-4 sRNAs, which are known to modulate the QS pathway. Transcription of qrrX is activated by QrrT, a previously uncharacterized LysR-type transcriptional regulator. Our results indicate that QrrX and QrrT are required for rapid conversion from individual to community behaviours in V. cholerae.
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22
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Kerkhofs K, Garg J, Fafard-Couture É, Abou Elela S, Scott MS, Pearlman RE, Bayfield MA. Altered tRNA processing is linked to a distinct and unusual La protein in Tetrahymena thermophila. Nat Commun 2022; 13:7332. [PMID: 36443289 DOI: 10.1038/s41467-022-34796-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 11/07/2022] [Indexed: 11/29/2022] Open
Abstract
Nascent pre-tRNAs are transcribed by RNA polymerase III and immediately bound by La proteins on the UUU-3'OH sequence, using a tandem arrangement of the La motif and an adjacent RNA recognition motif-1 (RRM1), resulting in protection from 3'-exonucleases and promotion of pre-tRNA folding. The Tetrahymena thermophila protein Mlp1 has been previously classified as a genuine La protein, despite the predicted absence of the RRM1. We find that Mlp1 functions as a La protein through binding of pre-tRNAs, and affects pre-tRNA processing in Tetrahymena thermophila and when expressed in fission yeast. However, unlike in other examined eukaryotes, depletion of Mlp1 results in 3'-trailer stabilization. The 3'-trailers in Tetrahymena thermophila are uniquely short relative to other examined eukaryotes, and 5'-leaders have evolved to disfavour pre-tRNA leader/trailer pairing. Our data indicate that this variant Mlp1 architecture is linked to an altered, novel mechanism of tRNA processing in Tetrahymena thermophila.
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23
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Zhang E, Gao J, Wei Z, Zeng J, Li J, Li G, Liu J. MicroRNA-mediated regulation of lipid metabolism in virus-infected Emiliania huxleyi. ISME J 2022; 16:2457-2466. [PMID: 35869388 PMCID: PMC9561107 DOI: 10.1038/s41396-022-01291-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 06/30/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
The interactions between Emiliania huxleyi and E. huxleyi virus (EhV) regulate marine carbon and sulfur biogeochemical cycles and play a prominent role in global climate change. As a large DNA virus, EhV has developed a novel "virocell metabolism" model to meet its high metabolic needs. Although it has been widely demonstrated that EhV infection can profoundly rewire lipid metabolism, the epigenetic regulatory mechanisms of lipid metabolism are still obscure. MicroRNAs (miRNAs) can regulate biological pathways by targeting hub genes in the metabolic processes. In this study, the transcriptome, lipidome, and miRNAome were applied to investigate the epigenetic regulation of lipid metabolism in E. huxleyi cells during a detailed time course of viral infection. Combined transcriptomic, lipidomic, and physiological experiments revealed reprogrammed lipid metabolism, along with mitochondrial dysfunction and calcium influx through the cell membrane. A total of 69 host miRNAs (including 1 known miRNA) and 7 viral miRNAs were identified, 27 of which were differentially expressed. Bioinformatic prediction revealed that miRNAs involved in the regulation of lipid metabolism and a dual-luciferase reporter assay suggested that phosphatidylinositol 3-kinase (PI3K) gene might be a target of ehx-miR5. Further qPCR and western blot analysis showed a significant negative correlation between the expression of ehx-miR5 and its target gene PI3K, along with the lower activity of its downstream components (p-Akt, p-TOR, SREBP), indicating that lipid metabolism might be regulated by ehx-miR5 through the PI3K-Akt-TOR signaling pathway. Our findings reveal several novel mechanisms of viral strategies to manipulate host lipid metabolism and provide evidence that ehx-miR5 negatively modulates the expression of PI3K and disturbs lipid metabolism in the interactions between E. huxleyi and EhV.
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Affiliation(s)
- Enquan Zhang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Jingjing Gao
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Zehua Wei
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Jun Zeng
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Jian Li
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Guiling Li
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China.
| | - Jingwen Liu
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China.
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24
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Jacquemot L, Vigneron A, Tremblay JÉ, Lovejoy C. Contrasting sea ice conditions shape microbial food webs in Hudson Bay (Canadian Arctic). ISME Commun 2022; 2:104. [PMID: 37938285 PMCID: PMC9723562 DOI: 10.1038/s43705-022-00192-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 10/07/2022] [Accepted: 10/12/2022] [Indexed: 01/07/2023]
Abstract
The transition from ice-covered to open water is a recurring feature of the Arctic and sub-Arctic, but microbial diversity and cascading effects on the microbial food webs is poorly known. Here, we investigated microbial eukaryote, bacterial and archaeal communities in Hudson Bay (sub-Arctic, Canada) under sea-ice cover and open waters conditions. Co-occurrence networks revealed a <3 µm pico‒phytoplankton-based food web under the ice and a >3 µm nano‒microphytoplankton-based food web in the open waters. The ice-edge communities were characteristic of post-bloom conditions with high proportions of the picophytoplankton Micromonas and Bathycoccus. Nano‒ to micro‒phytoplankton and ice associated diatoms were detected throughout the water column, with the sympagic Melosira arctica exclusive to ice-covered central Hudson Bay and Thalassiosira in open northwestern Hudson Bay. Heterotrophic microbial eukaryotes and prokaryotes also differed by ice-state, suggesting a linkage between microbes at depth and surface phytoplankton bloom state. The findings suggest that a longer open water season may favor the establishment of a large phytoplankton-based food web at the subsurface chlorophyll maxima (SCM), increasing carbon export from pelagic diatoms to deeper waters and affect higher trophic levels in the deep Hudson Bay.
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Affiliation(s)
- Loïc Jacquemot
- Département de Biologie, Université Laval, Québec, QC, Canada.
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.
| | - Adrien Vigneron
- Département de Biologie, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | | | - Connie Lovejoy
- Département de Biologie, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
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25
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Li H, You C, Yoshikawa M, Yang X, Gu H, Li C, Cui J, Chen X, Ye N, Zhang J, Wang G. A spontaneous thermo-sensitive female sterility mutation in rice enables fully mechanized hybrid breeding. Cell Res 2022; 32:931-945. [PMID: 36068348 PMCID: PMC9525692 DOI: 10.1038/s41422-022-00711-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 08/08/2022] [Indexed: 11/08/2022] Open
Abstract
Male sterility enables hybrid crop breeding to increase yields and has been extensively studied. But thermo-sensitive female sterility, which is an ideal property that may enable full mechanization in hybrid rice breeding, has rarely been investigated due to the absence of such germplasm. Here we identify the spontaneous thermo-sensitive female sterility 1 (tfs1) mutation that confers complete sterility under regular/high temperature and partial fertility under low temperature as a point mutation in ARGONAUTE7 (AGO7). AGO7 associates with miR390 to form an RNA-Induced Silencing Complex (RISC), which triggers the biogenesis of small interfering RNAs (siRNAs) from TRANS-ACTING3 (TAS3) loci by recruiting SUPPRESSOR OF GENE SILENCING (SGS3) and RNA-DEPENDENT RNA POLYMERASE6 (RDR6) to TAS3 transcripts. These siRNAs are known as tasiR-ARFs as they act in trans to repress auxin response factor genes. The mutant TFS1 (mTFS1) protein is compromised in its ability to load the miR390/miR390* duplex and eject miR390* during RISC formation. Furthermore, tasiR-ARF levels are reduced in tfs1 due to the deficiency in RDR6 but not SGS3 recruitment by mTFS1 RISC under regular/high temperature, while low temperature partially restores mTFS1 function in RDR6 recruitment and tasiR-ARF biogenesis. A miR390 mutant also exhibits female sterility, suggesting that female fertility is controlled by the miR390-AGO7 module. Notably, the tfs1 allele introduced into various elite rice cultivars endows thermo-sensitive female sterility. Moreover, field trials confirm the utility of tfs1 as a restorer line in fully mechanized hybrid rice breeding.
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Affiliation(s)
- Haoxuan Li
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Agriculture, Hunan Agricultural University, Changsha, Hunan, China
| | - Chenjiang You
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Manabu Yoshikawa
- Division of Plant and Microbial Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 2-1-2 Kannondai Tsukuba, Ibaraki, Japan
| | - Xiaoyu Yang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong, China
| | - Haiyong Gu
- The Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Chuanguo Li
- The Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Jie Cui
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA.
| | - Nenghui Ye
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Agriculture, Hunan Agricultural University, Changsha, Hunan, China.
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, Hong Kong, China.
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China.
| | - Guanqun Wang
- Department of Biology, Hong Kong Baptist University, Hong Kong, China.
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China.
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26
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Bao Z, Zhang N, Niu W, Mu M, Zhang X, Hu S, Niu C. Exosomal miR-155-5p derived from glioma stem-like cells promotes mesenchymal transition via targeting ACOT12. Cell Death Dis 2022; 13:725. [PMID: 35986010 DOI: 10.1038/s41419-022-05097-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 07/07/2022] [Accepted: 07/12/2022] [Indexed: 01/21/2023]
Abstract
Tumor-associated exosomes play essential roles in intercellular communication and the foundation of cancer microenvironment in glioma. Many mRNAs, microRNAs (miRNAs) and proteins contained in tumor-associated exosomes can be transferred to recipient cells and contribute to the progression of tumor. Nevertheless, the cellular communication between malignant cells with different heterogeneities or characteristics and resultant tumor progression are still unclear in glioma. Here, we show that exosomes released from glioma stem-like cells (GSCs) contain a significant increasing level of miR-155-5p and could be horizontally transferred to surrounding glioma cells. High expression of miR-155-5p in plasma exosomes from patients was associated with glioma diagnosis and grading. Mechanically, we found that miR-155-5p markedly reduced the expression of acetyl-CoA thioesterase 12 (ACOT12), which played as a tumor suppressor in glioma. Furthermore, mesenchymal transition was significantly promoted in glioma cells treated with GSCs-derived exosomes. In conclusion, GSCs-derived exosomal miR-155-5p play a critical role in glioma progression and facilitating tumor aggressive growth by targeting ACOT12 and promoting mesenchymal transition. Exosomal miR-155-5p is also a potential predictive biomarker for glioma, which may provoke the development of novel diagnostic and therapeutic strategies against glioma.
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27
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He T, Tao W, Zhang LL, Wang BY, Li K, Lu HM, Tang GJ, He YD, Li LY. CircSCAF8 promotes growth and metastasis of prostate cancer through the circSCAF8-miR-140-3p/miR-335-LIF pathway. Cell Death Dis 2022; 13:517. [PMID: 35654787 DOI: 10.1038/s41419-022-04913-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 04/23/2022] [Accepted: 05/04/2022] [Indexed: 02/07/2023]
Abstract
Circular RNAs (circRNAs) have been increasingly linked to cancer progression. However, the detailed biological functions of circRNAs in prostate cancer (PCa) remain unclear. Using high-throughput circRNA sequencing, we previously identified 18 urine extracellular vesicle circRNAs that were increased in patients with PCa compared with those with benign prostatic hyperplasia. Spearman correlation analysis of the expression levels of the 18 circRNAs between the tumor tissue and matched urine extracellular vesicles in 30 PCa patients showed that circSCAF8 had the highest R2 (R2 = 0.635, P < 0.001). The Cox proportional hazards regression model was used to estimate the effect of circSCAF8 on progression-free survival. The in vitro and in vivo functional experiments were implemented to investigate the effects of circSCAF8 on the phenotype of PCa. We found that the knockdown of circSCAF8 in PCa cells suppressed the proliferation, migration, and invasion ability, while overexpression of circSCAF8 had the opposite effects. Similar results were observed in vivo. In a cohort of 85 patients who had undergone radical prostatectomy, circSCAF8 expression in PCa tissues was a powerful predictor of progression-free survival (HR = 2.14, P = 0.022). Mechanistically, circSCAF8 can function by binding to both miR-140-3p and miR-335 to regulate LIF expression and activate the LIF-STAT3 pathway that leads to the growth and metastasis of PCa. Collectively, our findings demonstrate that circSCAF8 contributes to PCa progression through the circSCAF8-miR-140-3p/miR-335-LIF pathway.
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28
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Cui H, Li H, Wu H, Du F, Xie X, Zeng S, Zhang Z, Dong K, Shang L, Jing C, Li L. A novel 3'tRNA-derived fragment tRF-Val promotes proliferation and inhibits apoptosis by targeting EEF1A1 in gastric cancer. Cell Death Dis 2022; 13:471. [PMID: 35585048 PMCID: PMC9117658 DOI: 10.1038/s41419-022-04930-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 05/03/2022] [Accepted: 05/09/2022] [Indexed: 12/14/2022]
Abstract
At present, it is commonly believed that tRFs and tiRNAs are formed by the specific and selective shear of tRNAs under certain pressure stimulation, rather than by random degradation of tRNA. tRFs and tiRNAs have been reported to contribute to the biological process of a variety of human cancers. However, the evidence for the mechanisms of tRFs and tiRNAs in the occurrence and development of gastric cancer (GC) is still insufficient. Here, we aimed to explore the carcinogenic roles of tRFs and tiRNAs in GC with RNA-sequencing technique, and found a novel 3'tRNA-derived fragment tRF-Val was significantly upregulated in GC tissues and cell lines. tRF-Val expression was positively correlated with tumor size and the depth of tumor invasion in GC tissues. Functionally, tRF-Val promoted proliferation and invasion, and inhibited apoptosis in GC cells. Mechanistically, tRF-Val directly bound to the chaperone molecule EEF1A1, mediated its transport into the nucleus and promoted its interaction with MDM2 (a specific p53 E3 ubiquitin ligase), thus inhibiting the downstream molecular pathway of p53 and promoting GC progression. These findings provided a new potential therapeutic target for GC and a new explanation for the occurrence of GC.
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Affiliation(s)
- Huaiping Cui
- grid.27255.370000 0004 1761 1174Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, 250021 Jinan, Shandong China ,grid.460018.b0000 0004 1769 9639Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250021 Jinan, Shandong China ,grid.460018.b0000 0004 1769 9639Shandong Provincial Laboratory of Translational Medicine Engineering for Digestive Tumors, Shandong Provincial Hospital, 250021 Jinan, Shandong China
| | - Han Li
- grid.452422.70000 0004 0604 7301Department of Gastrointestinal Surgery, the First Affiliated Hospital of Shandong First Medical University, Shandong Provincial Qianfoshan Hospital, 250013 Jinan, Shandong China
| | - Hao Wu
- grid.27255.370000 0004 1761 1174Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, 250021 Jinan, Shandong China
| | - Fengying Du
- grid.27255.370000 0004 1761 1174Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, 250021 Jinan, Shandong China
| | - Xiaozhou Xie
- grid.460018.b0000 0004 1769 9639Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250021 Jinan, Shandong China
| | - Shujie Zeng
- grid.27255.370000 0004 1761 1174Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, 250021 Jinan, Shandong China
| | - Zihao Zhang
- grid.27255.370000 0004 1761 1174Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, 250021 Jinan, Shandong China
| | - Kangdi Dong
- grid.460018.b0000 0004 1769 9639Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250021 Jinan, Shandong China
| | - Liang Shang
- grid.27255.370000 0004 1761 1174Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, 250021 Jinan, Shandong China ,grid.460018.b0000 0004 1769 9639Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250021 Jinan, Shandong China ,grid.460018.b0000 0004 1769 9639Shandong Provincial Laboratory of Translational Medicine Engineering for Digestive Tumors, Shandong Provincial Hospital, 250021 Jinan, Shandong China
| | - Changqing Jing
- grid.27255.370000 0004 1761 1174Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, 250021 Jinan, Shandong China ,grid.460018.b0000 0004 1769 9639Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250021 Jinan, Shandong China ,grid.460018.b0000 0004 1769 9639Shandong Provincial Laboratory of Translational Medicine Engineering for Digestive Tumors, Shandong Provincial Hospital, 250021 Jinan, Shandong China
| | - Leping Li
- grid.27255.370000 0004 1761 1174Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, 250021 Jinan, Shandong China ,grid.460018.b0000 0004 1769 9639Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250021 Jinan, Shandong China ,grid.460018.b0000 0004 1769 9639Shandong Provincial Laboratory of Translational Medicine Engineering for Digestive Tumors, Shandong Provincial Hospital, 250021 Jinan, Shandong China
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Roca J, Santiago-Frangos A, Woodson SA. Diversity of bacterial small RNAs drives competitive strategies for a mutual chaperone. Nat Commun 2022; 13:2449. [PMID: 35508531 PMCID: PMC9068810 DOI: 10.1038/s41467-022-30211-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 04/06/2022] [Indexed: 12/17/2022] Open
Abstract
Hundreds of bacterial small RNAs (sRNAs) require the Hfq chaperone to regulate mRNA expression. Hfq is limiting, thus competition among sRNAs for binding to Hfq shapes the proteomes of individual cells. To understand how sRNAs compete for a common partner, we present a single-molecule fluorescence platform to simultaneously visualize binding and release of multiple sRNAs with Hfq. We show that RNA residents rarely dissociate on their own. Instead, clashes between residents and challengers on the same face of Hfq cause rapid exchange, whereas RNAs that recognize different surfaces may cohabit Hfq for several minutes before one RNA departs. The prevalence of these pathways depends on the structure of each RNA and how it interacts with Hfq. We propose that sRNA diversity creates many pairwise interactions with Hfq that allow for distinct biological outcomes: active exchange favors fast regulation whereas co-residence of dissimilar RNAs favors target co-recognition or target exclusion.
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Affiliation(s)
- Jorjethe Roca
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD, 21218, USA
| | - Andrew Santiago-Frangos
- CMDB Program, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD, 21218, USA.,Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, 59717, USA
| | - Sarah A Woodson
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD, 21218, USA.
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30
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Su Z, Monshaugen I, Wilson B, Wang F, Klungland A, Ougland R, Dutta A. TRMT6/61A-dependent base methylation of tRNA-derived fragments regulates gene-silencing activity and the unfolded protein response in bladder cancer. Nat Commun 2022; 13:2165. [PMID: 35444240 PMCID: PMC9021294 DOI: 10.1038/s41467-022-29790-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 03/16/2022] [Indexed: 01/11/2023] Open
Abstract
RNA modifications are important regulatory elements of RNA functions. However, most genome-wide mapping of RNA modifications has focused on messenger RNAs and transfer RNAs, but such datasets have been lacking for small RNAs. Here we mapped N1-methyladenosine (m1A) in the cellular small RNA space. Benchmarked with synthetic m1A RNAs, our workflow identified specific groups of m1A-containing small RNAs, which are otherwise disproportionally under-represented. In particular, 22-nucleotides long 3' tRNA-fragments are highly enriched for TRMT6/61A-dependent m1A located within the seed region. TRMT6/61A-dependent m1A negatively affects gene silencing by tRF-3s. In urothelial carcinoma of the bladder, where TRMT6/61A is over-expressed, higher m1A modification on tRFs is detected, correlated with a dysregulation of tRF targetome. Lastly, TRMT6/61A regulates tRF-3 targets involved in unfolded protein response. Together, our results reveal a mechanism of regulating gene expression via base modification of small RNA.
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Affiliation(s)
- Zhangli Su
- Department of Genetics, University of Alabama, Birmingham, AL, 35233, USA
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, 22901, USA
| | - Ida Monshaugen
- Department of Microbiology, Oslo University Hospital Rikshospitalet, 0372, Oslo, Norway
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0317, Oslo, Norway
- Department of Surgery, Baerum Hospital Vestre Viken Hospital Trust, 1346, Gjettum, Norway
| | - Briana Wilson
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, 22901, USA
| | - Fengbin Wang
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, 22901, USA
| | - Arne Klungland
- Department of Microbiology, Oslo University Hospital Rikshospitalet, 0372, Oslo, Norway
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, P.O. 10 Box 1066 Blindern, 0316, Oslo, Norway
| | - Rune Ougland
- Department of Microbiology, Oslo University Hospital Rikshospitalet, 0372, Oslo, Norway.
- Department of Surgery, Baerum Hospital Vestre Viken Hospital Trust, 1346, Gjettum, Norway.
| | - Anindya Dutta
- Department of Genetics, University of Alabama, Birmingham, AL, 35233, USA.
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, 22901, USA.
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31
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Reshetnyak G, Jacobs JM, Auguy F, Sciallano C, Claude L, Medina C, Perez-Quintero AL, Comte A, Thomas E, Bogdanove A, Koebnik R, Szurek B, Dievart A, Brugidou C, Lacombe S, Cunnac S. An atypical class of non-coding small RNAs is produced in rice leaves upon bacterial infection. Sci Rep 2021; 11:24141. [PMID: 34921170 PMCID: PMC8683429 DOI: 10.1038/s41598-021-03391-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 11/29/2021] [Indexed: 01/18/2023] Open
Abstract
Non-coding small RNAs (sRNA) act as mediators of gene silencing and regulate plant growth, development and stress responses. Early insights into plant sRNAs established a role in antiviral defense and they are now extensively studied across plant-microbe interactions. Here, sRNA sequencing discovered a class of sRNA in rice (Oryza sativa) specifically associated with foliar diseases caused by Xanthomonas oryzae bacteria. Xanthomonas-induced small RNAs (xisRNAs) loci were distinctively upregulated in response to diverse virulent strains at an early stage of infection producing a single duplex of 20-22 nt sRNAs. xisRNAs production was dependent on the Type III secretion system, a major bacterial virulence factor for host colonization. xisRNA loci overlap with annotated transcripts sequences, with about half of them encoding protein kinase domain proteins. A number of the corresponding rice cis-genes have documented functions in immune signaling and xisRNA loci predominantly coincide with the coding sequence of a conserved kinase motif. xisRNAs exhibit features of small interfering RNAs and their biosynthesis depend on canonical components OsDCL1 and OsHEN1. xisRNA induction possibly mediates post-transcriptional gene silencing but they do not broadly suppress cis-genes expression on the basis of mRNA-seq data. Overall, our results identify a group of unusual sRNAs with a potential role in plant-microbe interactions.
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Affiliation(s)
- Ganna Reshetnyak
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Jonathan M Jacobs
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
- Department of Plant Pathology, The Ohio State University, Columbus, OH, 43201, USA
- Infectious Disease Institute, The Ohio State University, Columbus, OH, 43201, USA
| | - Florence Auguy
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Coline Sciallano
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Lisa Claude
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Clemence Medina
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Alvaro L Perez-Quintero
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Aurore Comte
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Emilie Thomas
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Adam Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Ralf Koebnik
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Boris Szurek
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Anne Dievart
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398, Montpellier, France
- CIRAD, UMR AGAP Institut, 34398, Montpellier, France
| | - Christophe Brugidou
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Severine Lacombe
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Sebastien Cunnac
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France.
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32
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Gusachenko ON, Woodford L, Balbirnie-Cumming K, Evans DJ. First come, first served: superinfection exclusion in Deformed wing virus is dependent upon sequence identity and not the order of virus acquisition. ISME J 2021; 15:3704-3713. [PMID: 34193965 PMCID: PMC8630095 DOI: 10.1038/s41396-021-01043-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 02/06/2023]
Abstract
Deformed wing virus (DWV) is the most important globally distributed pathogen of honey bees and, when vectored by the ectoparasite Varroa destructor, is associated with high levels of colony losses. Divergent DWV types may differ in their pathogenicity and are reported to exhibit superinfection exclusion upon sequential infections, an inevitability in a Varroa-infested colony. We used a reverse genetic approach to investigate competition and interactions between genetically distinct or related virus strains, analysing viral load over time, tissue distribution with reporter gene-expressing viruses and recombination between virus variants. Transient competition occurred irrespective of the order of virus acquisition, indicating no directionality or dominance. Over longer periods, the ability to compete with a pre-existing infection correlated with the genetic divergence of the inoculae. Genetic recombination was observed throughout the DWV genome with recombinants accounting for ~2% of the population as determined by deep sequencing. We propose that superinfection exclusion, if it occurs at all, is a consequence of a cross-reactive RNAi response to the viruses involved, explaining the lack of dominance of one virus type over another. A better understanding of the consequences of dual- and superinfection will inform development of cross-protective honey bee vaccines and landscape-scale DWV transmission and evolution.
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Affiliation(s)
- Olesya N. Gusachenko
- grid.11914.3c0000 0001 0721 1626Biomedical Sciences Research Complex, University of St. Andrews, North Haugh, St. Andrews, UK
| | - Luke Woodford
- grid.11914.3c0000 0001 0721 1626Biomedical Sciences Research Complex, University of St. Andrews, North Haugh, St. Andrews, UK
| | - Katharin Balbirnie-Cumming
- grid.11914.3c0000 0001 0721 1626Biomedical Sciences Research Complex, University of St. Andrews, North Haugh, St. Andrews, UK
| | - David J. Evans
- grid.11914.3c0000 0001 0721 1626Biomedical Sciences Research Complex, University of St. Andrews, North Haugh, St. Andrews, UK
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33
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Zhang Y, Ren L, Sun X, Zhang Z, Liu J, Xin Y, Yu J, Jia Y, Sheng J, Hu GF, Zhao R, He B. Angiogenin mediates paternal inflammation-induced metabolic disorders in offspring through sperm tsRNAs. Nat Commun 2021; 12:6673. [PMID: 34845238 DOI: 10.1038/s41467-021-26909-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 10/28/2021] [Indexed: 01/20/2023] Open
Abstract
Paternal environmental inputs can influence various phenotypes in offspring, presenting tremendous implications for basic biology and public health and policy. However, which signals function as a nexus to transmit paternal environmental inputs to offspring remains unclear. Here we show that offspring of fathers with inflammation exhibit metabolic disorders including glucose intolerance and obesity. Deletion of a mouse tRNA RNase, Angiogenin (Ang), abolished paternal inflammation-induced metabolic disorders in offspring. Additionally, Ang deletion prevented the inflammation-induced alteration of 5'-tRNA-derived small RNAs (5'-tsRNAs) expression profile in sperm, which might be essential in composing a sperm RNA 'coding signature' that is needed for paternal epigenetic memory. Microinjection of sperm 30-40 nt RNA fractions (predominantly 5'-tsRNAs) from inflammatory Ang+/+ males but not Ang-/- males resulted in metabolic disorders in the resultant offspring. Moreover, zygotic injection with synthetic 5'-tsRNAs which increased in inflammatory mouse sperm and decreased by Ang deletion partially resembled paternal inflammation-induced metabolic disorders in offspring. Together, our findings demonstrate that Ang-mediated biogenesis of 5'-tsRNAs in sperm contributes to paternal inflammation-induced metabolic disorders in offspring.
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34
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Sletten AC, Davidson JW, Yagabasan B, Moores S, Schwaiger-Haber M, Fujiwara H, Gale S, Jiang X, Sidhu R, Gelman SJ, Zhao S, Patti GJ, Ory DS, Schaffer JE. Loss of SNORA73 reprograms cellular metabolism and protects against steatohepatitis. Nat Commun 2021; 12:5214. [PMID: 34471131 DOI: 10.1038/s41467-021-25457-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 08/06/2021] [Indexed: 02/07/2023] Open
Abstract
Dyslipidemia and resulting lipotoxicity are pathologic signatures of metabolic syndrome and type 2 diabetes. Excess lipid causes cell dysfunction and induces cell death through pleiotropic mechanisms that link to oxidative stress. However, pathways that regulate the response to metabolic stress are not well understood. Herein, we show that disruption of the box H/ACA SNORA73 small nucleolar RNAs encoded within the small nucleolar RNA hosting gene 3 (Snhg3) causes resistance to lipid-induced cell death and general oxidative stress in cultured cells. This protection from metabolic stress is associated with broad reprogramming of oxidative metabolism that is dependent on the mammalian target of rapamycin signaling axis. Furthermore, we show that knockdown of SNORA73 in vivo protects against hepatic steatosis and lipid-induced oxidative stress and inflammation. Our findings demonstrate a role for SNORA73 in the regulation of metabolism and lipotoxicity.
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35
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Shigematsu M, Kawamura T, Morichika K, Izumi N, Kiuchi T, Honda S, Pliatsika V, Matsubara R, Rigoutsos I, Katsuma S, Tomari Y, Kirino Y. RNase κ promotes robust piRNA production by generating 2',3'-cyclic phosphate-containing precursors. Nat Commun 2021; 12:4498. [PMID: 34301931 PMCID: PMC8302750 DOI: 10.1038/s41467-021-24681-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 07/01/2021] [Indexed: 11/13/2022] Open
Abstract
In animal germlines, PIWI proteins and the associated PIWI-interacting RNAs (piRNAs) protect genome integrity by silencing transposons. Here we report the extensive sequence and quantitative correlations between 2',3'-cyclic phosphate-containing RNAs (cP-RNAs), identified using cP-RNA-seq, and piRNAs in the Bombyx germ cell line and mouse testes. The cP-RNAs containing 5'-phosphate (P-cP-RNAs) identified by P-cP-RNA-seq harbor highly consistent 5'-end positions as the piRNAs and are loaded onto PIWI protein, suggesting their direct utilization as piRNA precursors. We identified Bombyx RNase Kappa (BmRNase κ) as a mitochondria-associated endoribonuclease which produces cP-RNAs during piRNA biogenesis. BmRNase κ-depletion elevated transposon levels and disrupted a piRNA-mediated sex determination in Bombyx embryos, indicating the crucial roles of BmRNase κ in piRNA biogenesis and embryonic development. Our results reveal a BmRNase κ-engaged piRNA biogenesis pathway, in which the generation of cP-RNAs promotes robust piRNA production.
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Affiliation(s)
- Megumi Shigematsu
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Takuya Kawamura
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Keisuke Morichika
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Natsuko Izumi
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-Ku, Tokyo, Japan
| | - Takashi Kiuchi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo, Japan
| | - Shozo Honda
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Venetia Pliatsika
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Ryuma Matsubara
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Isidore Rigoutsos
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Susumu Katsuma
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo, Japan
| | - Yukihide Tomari
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-Ku, Tokyo, Japan
| | - Yohei Kirino
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA.
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36
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Villa JK, Han R, Tsai CH, Chen A, Sweet P, Franco G, Vaezian R, Tkavc R, Daly MJ, Contreras LM. A small RNA regulates pprM, a modulator of pleiotropic proteins promoting DNA repair, in Deinococcus radiodurans under ionizing radiation. Sci Rep 2021; 11:12949. [PMID: 34155239 PMCID: PMC8217566 DOI: 10.1038/s41598-021-91335-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 05/20/2021] [Indexed: 02/05/2023] Open
Abstract
Networks of transcriptional and post-transcriptional regulators are critical for bacterial survival and adaptation to environmental stressors. While transcriptional regulators provide rapid activation and/or repression of a wide-network of genes, post-transcriptional regulators, such as small RNAs (sRNAs), are also important to fine-tune gene expression. However, the mechanisms of sRNAs remain poorly understood, especially in less-studied bacteria. Deinococcus radiodurans is a gram-positive bacterium resistant to extreme levels of ionizing radiation (IR). Although multiple unique regulatory systems (e.g., the Radiation and Desiccation Response (RDR)) have been identified in this organism, the role of post-transcriptional regulators has not been characterized within the IR response. In this study, we have characterized an sRNA, PprS (formerly Dsr2), as a post-transcriptional coordinator of IR recovery in D. radiodurans. PprS showed differential expression specifically under IR and knockdown of PprS resulted in reduced survival and growth under IR, suggesting its importance in regulating post-radiation recovery. We determined a number of potential RNA targets involved in several pathways including translation and DNA repair. Specifically, we confirmed that PprS binds within the coding region to stabilize the pprM (DR_0907) transcript, a RDR modulator. Overall, these results are the first to present an additional layer of sRNA-based control in DNA repair pathways associated with bacterial radioresistance.
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Affiliation(s)
- Jordan K Villa
- Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - Runhua Han
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Chen-Hsun Tsai
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Angela Chen
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Philip Sweet
- Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - Gabriela Franco
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Respina Vaezian
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Rok Tkavc
- Department of Pathology, School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- Department of Microbiology and Immunology, School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Michael J Daly
- Department of Pathology, School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Department of Molecular and Cellular Biology, School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Lydia M Contreras
- Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA.
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA.
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Singh M, Cornes E, Li B, Quarato P, Bourdon L, Dingli F, Loew D, Proccacia S, Cecere G. Translation and codon usage regulate Argonaute slicer activity to trigger small RNA biogenesis. Nat Commun 2021; 12:3492. [PMID: 34108460 PMCID: PMC8190271 DOI: 10.1038/s41467-021-23615-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 05/06/2021] [Indexed: 11/08/2022] Open
Abstract
In the Caenorhabditis elegans germline, thousands of mRNAs are concomitantly expressed with antisense 22G-RNAs, which are loaded into the Argonaute CSR-1. Despite their essential functions for animal fertility and embryonic development, how CSR-1 22G-RNAs are produced remains unknown. Here, we show that CSR-1 slicer activity is primarily involved in triggering the synthesis of small RNAs on the coding sequences of germline mRNAs and post-transcriptionally regulates a fraction of targets. CSR-1-cleaved mRNAs prime the RNA-dependent RNA polymerase, EGO-1, to synthesize 22G-RNAs in phase with translating ribosomes, in contrast to other 22G-RNAs mostly synthesized in germ granules. Moreover, codon optimality and efficient translation antagonize CSR-1 slicing and 22G-RNAs biogenesis. We propose that codon usage differences encoded into mRNA sequences might be a conserved strategy in eukaryotes to regulate small RNA biogenesis and Argonaute targeting.
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Affiliation(s)
- Meetali Singh
- Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, Institut Pasteur, UMR3738, CNRS, Paris, France
| | - Eric Cornes
- Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, Institut Pasteur, UMR3738, CNRS, Paris, France
| | - Blaise Li
- Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, Institut Pasteur, UMR3738, CNRS, Paris, France
- Hub de Bioinformatique et Biostatistique-Département Biologie Computationnelle, Institut Pasteur, Paris, France
| | - Piergiuseppe Quarato
- Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, Institut Pasteur, UMR3738, CNRS, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Loan Bourdon
- Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, Institut Pasteur, UMR3738, CNRS, Paris, France
| | - Florent Dingli
- Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Paris, France
| | - Damarys Loew
- Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Paris, France
| | - Simone Proccacia
- Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, Institut Pasteur, UMR3738, CNRS, Paris, France
- Università di Trento, Trento TN, Italy
| | - Germano Cecere
- Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, Institut Pasteur, UMR3738, CNRS, Paris, France.
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38
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Dika E, Broseghini E, Porcellini E, Lambertini M, Riefolo M, Durante G, Loher P, Roncarati R, Bassi C, Misciali C, Negrini M, Rigoutsos I, Londin E, Patrizi A, Ferracin M. Unraveling the role of microRNA/isomiR network in multiple primary melanoma pathogenesis. Cell Death Dis 2021; 12:473. [PMID: 33980826 PMCID: PMC8115306 DOI: 10.1038/s41419-021-03764-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 04/19/2021] [Accepted: 04/19/2021] [Indexed: 12/16/2022]
Abstract
Malignant cutaneous melanoma (CM) is a potentially lethal form of skin cancer whose worldwide incidence has been constantly increasing over the past decades. During their lifetime, about 8% of CM patients will develop multiple primary melanomas (MPMs), usually at a young age and within 3 years from the first tumor/diagnosis. With the aim of improving our knowledge on MPM biology and pathogenesis, we explored the miRNome of 24 single and multiple primary melanomas, including multiple tumors from the same patient, using a small RNA-sequencing approach. From a supervised analysis, 22 miRNAs were differentially expressed in MPM compared to single CM, including key miRNAs involved in epithelial-mesenchymal transition. The first and second melanoma from the same patient presented a different miRNA profile. Ten miRNAs, including miR-25-3p, 149-5p, 92b-3p, 211-5p, 125a-5p, 125b-5p, 205-5p, 200b-3p, 21-5p, and 146a-5p, were further validated in 47 single and multiple melanoma samples. Pathway enrichment analysis of miRNA target genes revealed a more differentiated and less invasive status of MPMs compared to CMs. Bioinformatic analyses at the miRNA isoform (isomiR) level detected a panel of highly expressed isomiRs belonging to miRNA families implicated in human tumorigenesis, including miR-200, miR-30, and miR-10 family. Moreover, we identified hsa-miR-125a-5p|0|-2 isoform as tenfold over-represented in melanoma than the canonical form and differentially expressed in MPMs arising in the same patient. Target prediction analysis revealed that the miRNA shortening could change the pattern of target gene regulation, specifically in genes implicated in cell adhesion and neuronal differentiation. Overall, we provided a putative and comprehensive characterization of the miRNA/isomiR regulatory network of MPMs, highlighting mechanisms of tumor development and molecular features differentiating this subtype from single melanomas.
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Affiliation(s)
- Emi Dika
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
- Dermatology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Elisabetta Broseghini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Elisa Porcellini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Martina Lambertini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
- Dermatology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Mattia Riefolo
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Giorgio Durante
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Phillipe Loher
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Roberta Roncarati
- Department of Translational Medicine and for Romagna, and "Laboratorio per le Tecnologie delle Terapie Avanzate" (LTTA), University of Ferrara, Ferrara, Italy
- CNR, Institute of Genetics and Biomedical Research, National Research Council of Italy, Milan, Italy
| | - Cristian Bassi
- Department of Translational Medicine and for Romagna, and "Laboratorio per le Tecnologie delle Terapie Avanzate" (LTTA), University of Ferrara, Ferrara, Italy
| | - Cosimo Misciali
- Dermatology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Massimo Negrini
- Department of Translational Medicine and for Romagna, and "Laboratorio per le Tecnologie delle Terapie Avanzate" (LTTA), University of Ferrara, Ferrara, Italy
| | - Isidore Rigoutsos
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Eric Londin
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Annalisa Patrizi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
- Dermatology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Manuela Ferracin
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy.
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Basu P, Elgrably-Weiss M, Hassouna F, Kumar M, Wiener R, Altuvia S. RNA binding of Hfq monomers promotes RelA-mediated hexamerization in a limiting Hfq environment. Nat Commun 2021; 12:2249. [PMID: 33883550 PMCID: PMC8060364 DOI: 10.1038/s41467-021-22553-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 03/20/2021] [Indexed: 02/02/2023] Open
Abstract
The RNA chaperone Hfq, acting as a hexamer, is a known mediator of post-transcriptional regulation, expediting basepairing between small RNAs (sRNAs) and their target mRNAs. However, the intricate details associated with Hfq-RNA biogenesis are still unclear. Previously, we reported that the stringent response regulator, RelA, is a functional partner of Hfq that facilitates Hfq-mediated sRNA-mRNA regulation in vivo and induces Hfq hexamerization in vitro. Here we show that RelA-mediated Hfq hexamerization requires an initial binding of RNA, preferably sRNA to Hfq monomers. By interacting with a Shine-Dalgarno-like sequence (GGAG) in the sRNA, RelA stabilizes the initially unstable complex of RNA bound-Hfq monomer, enabling the attachment of more Hfq subunits to form a functional hexamer. Overall, our study showing that RNA binding to Hfq monomers is at the heart of RelA-mediated Hfq hexamerization, challenges the previous concept that only Hfq hexamers can bind RNA.
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Affiliation(s)
- Pallabi Basu
- grid.9619.70000 0004 1937 0538Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University, Hadassah Medical School, Jerusalem, Israel
| | - Maya Elgrably-Weiss
- grid.9619.70000 0004 1937 0538Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University, Hadassah Medical School, Jerusalem, Israel
| | - Fouad Hassouna
- grid.9619.70000 0004 1937 0538Department of Biochemistry and Molecular Biology, IMRIC, The Hebrew University, Hadassah Medical School, Jerusalem, Israel
| | - Manoj Kumar
- grid.9619.70000 0004 1937 0538Department of Biochemistry and Molecular Biology, IMRIC, The Hebrew University, Hadassah Medical School, Jerusalem, Israel
| | - Reuven Wiener
- grid.9619.70000 0004 1937 0538Department of Biochemistry and Molecular Biology, IMRIC, The Hebrew University, Hadassah Medical School, Jerusalem, Israel
| | - Shoshy Altuvia
- grid.9619.70000 0004 1937 0538Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University, Hadassah Medical School, Jerusalem, Israel
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40
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Poddar A, Azam MS, Kayikcioglu T, Bobrovskyy M, Zhang J, Ma X, Labhsetwar P, Fei J, Singh D, Luthey-Schulten Z, Vanderpool CK, Ha T. Effects of individual base-pairs on in vivo target search and destruction kinetics of bacterial small RNA. Nat Commun 2021; 12:874. [PMID: 33558533 DOI: 10.1038/s41467-021-21144-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/11/2021] [Indexed: 01/30/2023] Open
Abstract
Base-pairing interactions mediate many intermolecular target recognition events. Even a single base-pair mismatch can cause a substantial difference in activity but how such changes influence the target search kinetics in vivo is unknown. Here, we use high-throughput sequencing and quantitative super-resolution imaging to probe the mutants of bacterial small RNA, SgrS, and their regulation of ptsG mRNA target. Mutations that disrupt binding of a chaperone protein, Hfq, and are distal to the mRNA annealing region still decrease the rate of target association, kon, and increase the dissociation rate, koff, showing that Hfq directly facilitates sRNA-mRNA annealing in vivo. Single base-pair mismatches in the annealing region reduce kon by 24-31% and increase koff by 14-25%, extending the time it takes to find and destroy the target by about a third. The effects of disrupting contiguous base-pairing are much more modest than that expected from thermodynamics, suggesting that Hfq buffers base-pair disruptions.
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41
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Peltier J, Hamiot A, Garneau JR, Boudry P, Maikova A, Hajnsdorf E, Fortier LC, Dupuy B, Soutourina O. Type I toxin-antitoxin systems contribute to the maintenance of mobile genetic elements in Clostridioides difficile. Commun Biol 2020; 3:718. [PMID: 33247281 PMCID: PMC7699646 DOI: 10.1038/s42003-020-01448-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 11/03/2020] [Indexed: 12/15/2022] Open
Abstract
Toxin-antitoxin (TA) systems are widespread on mobile genetic elements and in bacterial chromosomes. In type I TA, synthesis of the toxin protein is prevented by the transcription of an antitoxin RNA. The first type I TA were recently identified in the human enteropathogen Clostridioides difficile. Here we report the characterization of five additional type I TA within phiCD630-1 (CD0977.1-RCd11, CD0904.1-RCd13 and CD0956.3-RCd14) and phiCD630-2 (CD2889-RCd12 and CD2907.2-RCd15) prophages of C. difficile strain 630. Toxin genes encode 34 to 47 amino acid peptides and their ectopic expression in C. difficile induces growth arrest that is neutralized by antitoxin RNA co-expression. We show that type I TA located within the phiCD630-1 prophage contribute to its stability and heritability. We have made use of a type I TA toxin gene to generate an efficient mutagenesis tool for this bacterium that allowed investigation of the role of these widespread TA in prophage maintenance.
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Affiliation(s)
- Johann Peltier
- Laboratoire Pathogenèse des Bactéries Anaérobies, CNRS-2001, Institut Pasteur, Université de Paris, 75015, Paris, France
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Audrey Hamiot
- Laboratoire Pathogenèse des Bactéries Anaérobies, CNRS-2001, Institut Pasteur, Université de Paris, 75015, Paris, France
- UMR UMET, INRA, CNRS, Univ. Lille 1, 59650, Villeneuve d'Ascq, France
| | - Julian R Garneau
- Faculty of Medicine and Health Sciences, Department of Microbiology and Infectious Diseases, Université de Sherbrooke, 3201 rue Jean Mignault, Sherbrooke, QC, J1E 4K8, Canada
| | - Pierre Boudry
- Laboratoire Pathogenèse des Bactéries Anaérobies, CNRS-2001, Institut Pasteur, Université de Paris, 75015, Paris, France
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette Cedex, France
| | - Anna Maikova
- Laboratoire Pathogenèse des Bactéries Anaérobies, CNRS-2001, Institut Pasteur, Université de Paris, 75015, Paris, France
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 143028, Russia
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, 195251, Russia
| | - Eliane Hajnsdorf
- Institut de Biologie Physico-Chimique, UMR8261, CNRS, Université de Paris, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Louis-Charles Fortier
- Faculty of Medicine and Health Sciences, Department of Microbiology and Infectious Diseases, Université de Sherbrooke, 3201 rue Jean Mignault, Sherbrooke, QC, J1E 4K8, Canada
| | - Bruno Dupuy
- Laboratoire Pathogenèse des Bactéries Anaérobies, CNRS-2001, Institut Pasteur, Université de Paris, 75015, Paris, France
| | - Olga Soutourina
- Laboratoire Pathogenèse des Bactéries Anaérobies, CNRS-2001, Institut Pasteur, Université de Paris, 75015, Paris, France.
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
- Institut Universitaire de France (IUF), Paris, France.
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42
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Capraro A, O'Meally D, Waters SA, Patel HR, Georges A, Waters PD. MicroRNA dynamics during hibernation of the Australian central bearded dragon (Pogona vitticeps). Sci Rep 2020; 10:17854. [PMID: 33082398 PMCID: PMC7576210 DOI: 10.1038/s41598-020-73706-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 09/17/2020] [Indexed: 11/12/2022] Open
Abstract
Hibernation is a physiological state employed by many animals that are exposed to limited food and adverse winter conditions. Controlling tissue-specific and organism wide changes in metabolism and cellular function requires precise regulation of gene expression, including by microRNAs (miRNAs). Here we profile miRNA expression in the central bearded dragon (Pogona vitticeps) using small RNA sequencing of brain, heart, and skeletal muscle from individuals in late hibernation and four days post-arousal. A total of 1295 miRNAs were identified in the central bearded dragon genome; 664 of which were novel to central bearded dragon. We identified differentially expressed miRNAs (DEmiRs) in all tissues and correlated mRNA expression with known and predicted target mRNAs. Functional analysis of DEmiR targets revealed an enrichment of differentially expressed mRNA targets involved in metabolic processes. However, we failed to reveal biologically relevant tissue-specific processes subjected to miRNA-mediated regulation in heart and skeletal muscle. In brain, neuroprotective pathways were identified as potential targets regulated by miRNAs. Our data suggests that miRNAs are necessary for modulating the shift in cellular metabolism during hibernation and regulating neuroprotection in the brain. This study is the first of its kind in a hibernating reptile and provides key insight into this ephemeral phenotype.
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Affiliation(s)
- Alexander Capraro
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, UNSW Sydney, Kensington, NSW, 2052, Australia.
| | - Denis O'Meally
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
- Center for Gene Therapy, Beckman Research Institute of the City of Hope, Duarte, CA, 91010, USA
| | - Shafagh A Waters
- School of Women's & Children's Health, Faculty of Medicine, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Hardip R Patel
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
| | - Paul D Waters
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, UNSW Sydney, Kensington, NSW, 2052, Australia
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43
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Rodrigues AS, Chaves I, Costa BV, Lin YC, Lopes S, Milhinhos A, Van de Peer Y, Miguel CM. Small RNA profiling in Pinus pinaster reveals the transcriptome of developing seeds and highlights differences between zygotic and somatic embryos. Sci Rep 2019; 9:11327. [PMID: 31383905 PMCID: PMC6683148 DOI: 10.1038/s41598-019-47789-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 07/24/2019] [Indexed: 02/07/2023] Open
Abstract
Regulation of seed development by small non-coding RNAs (sRNAs) is an important mechanism controlling a crucial phase of the life cycle of seed plants. In this work, sRNAs from seed tissues (zygotic embryos and megagametophytes) and from somatic embryos of Pinus pinaster were analysed to identify putative regulators of seed/embryo development in conifers. In total, sixteen sRNA libraries covering several developmental stages were sequenced. We show that embryos and megagametophytes express a large population of 21-nt sRNAs and that substantial amounts of 24-nt sRNAs were also detected, especially in somatic embryos. A total of 215 conserved miRNAs, one third of which are conifer-specific, and 212 high-confidence novel miRNAs were annotated. MIR159, MIR171 and MIR394 families were found in embryos, but were greatly reduced in megagametophytes. Other families, like MIR397 and MIR408, predominated in somatic embryos and megagametophytes, suggesting their expression in somatic embryos is associated with in vitro conditions. Analysis of the predicted miRNA targets suggests that miRNA functions are relevant in several processes including transporter activity at the cotyledon-forming stage, and sulfur metabolism across several developmental stages. An important resource for studying conifer embryogenesis is made available here, which may also provide insightful clues for improving clonal propagation via somatic embryogenesis.
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Affiliation(s)
- Andreia S Rodrigues
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. República, 2780-157, Oeiras, Portugal
| | - Inês Chaves
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. República, 2780-157, Oeiras, Portugal
| | - Bruno Vasques Costa
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. República, 2780-157, Oeiras, Portugal
- INESC-ID, Instituto Superior Técnico, Universidade de Lisboa, Rua Alves Redol 9, Lisboa, 1000-029, Portugal
| | - Yao-Cheng Lin
- Biotechnology Center in Southern Taiwan and Agricultural Biotechnology Research Center, Academia Sinica, Tainan, Taiwan
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Susana Lopes
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. República, 2780-157, Oeiras, Portugal
| | - Ana Milhinhos
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. República, 2780-157, Oeiras, Portugal
| | - Yves Van de Peer
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Célia M Miguel
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal.
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. República, 2780-157, Oeiras, Portugal.
- BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal.
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44
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Elliott BA, Ho HT, Ranganathan SV, Vangaveti S, Ilkayeva O, Abou Assi H, Choi AK, Agris PF, Holley CL. Modification of messenger RNA by 2'-O-methylation regulates gene expression in vivo. Nat Commun 2019; 10:3401. [PMID: 31363086 PMCID: PMC6667457 DOI: 10.1038/s41467-019-11375-7] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 07/11/2019] [Indexed: 12/21/2022] Open
Abstract
Epitranscriptomic modifications of mRNA are important regulators of gene expression. While internal 2'-O-methylation (Nm) has been discovered on mRNA, questions remain about its origin and function in cells and organisms. Here, we show that internal Nm modification can be guided by small nucleolar RNAs (snoRNAs), and that these Nm sites can regulate mRNA and protein expression. Specifically, two box C/D snoRNAs (SNORDs) and the 2'-O-methyltransferase fibrillarin lead to Nm modification in the protein-coding region of peroxidasin (Pxdn). The presence of Nm modification increases Pxdn mRNA expression but inhibits its translation, regulating PXDN protein expression and enzyme activity both in vitro and in vivo. Our findings support a model in which snoRNA-guided Nm modifications of mRNA can regulate physiologic gene expression by altering mRNA levels and tuning protein translation.
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Affiliation(s)
- Brittany A Elliott
- Department of Medicine, Duke University Medical Center, Durham, NC, 27705, USA
| | - Hsiang-Ting Ho
- Department of Medicine, Duke University Medical Center, Durham, NC, 27705, USA
| | | | - Sweta Vangaveti
- The RNA Institute, State University of New York, Albany, NY, 12222, USA
| | - Olga Ilkayeva
- Duke Molecular Physiology Institute, Duke University, Durham, NC, 27701, USA
| | - Hala Abou Assi
- Department of Medicine, Duke University Medical Center, Durham, NC, 27705, USA
| | - Alex K Choi
- Department of Medicine, Duke University Medical Center, Durham, NC, 27705, USA
| | - Paul F Agris
- Department of Medicine, Duke University Medical Center, Durham, NC, 27705, USA
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Zhong F, Hu Z, Jiang K, Lei B, Wu Z, Yuan G, Luo H, Dong C, Tang B, Zheng C, Yang S, Zeng Y, Guo Z, Yu S, Su H, Zhang G, Qiu X, Tomlinson S, He S. Complement C3 activation regulates the production of tRNA-derived fragments Gly-tRFs and promotes alcohol-induced liver injury and steatosis. Cell Res 2019; 29:548-561. [PMID: 31076642 PMCID: PMC6796853 DOI: 10.1038/s41422-019-0175-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 04/12/2019] [Indexed: 12/23/2022] Open
Abstract
Complement is known to play a role in alcoholic fatty liver disease (AFLD), but the underlying mechanisms are poorly understood, thereby constraining the development of a rational approach for therapeutic intervention in the complement system. C3 deficiency has been shown to impart protective effects against ethanol-induced hepatic steatosis and inflammation. Here we demonstrate a protection effect in wild-type mice by treatment with CR2-Crry, a specific inhibitor of C3 activation. The expression of glycine transfer (t) RNA-derived fragments (Gly-tRFs) is upregulated in ethanol-fed mice and inhibition of Gly-tRFs in vivo decreases chronic ethanol feeding-induced hepatosteatosis without affecting inflammation. The expression of Gly-tRF was downregulated in C3-deficient or CR2-Crry-treated mice, but not in C5-deficient mice; Gly-tRF expression was restored by the C3 activation products C3a or Asp (C3a-des-Arg) via the regulation of CYP2E1. Transcriptome profiling of hepatic tissues showed that Gly-tRF inhibitors upregulate the expression of sirtuin1 (Sirt1) and subsequently affect downstream lipogenesis and β-oxidation pathways. Mechanistically, Gly-tRF interacts with AGO3 to downregulate Sirt1 expression via sequence complementarity in the 3' UTR. Notably, the expression levels of C3d, CYP2E1 and Gly-tRF are upregulated, whereas Sirt1 is decreased in AFLD patients compared to healthy controls. Collectively, our findings suggest that C3 activation products contribute to hepatosteatosis by regulating the expression of Gly-tRF. Complement inhibition at the C3 activation step and treatment with Gly-tRF inhibitors may be potential and precise therapeutic approaches for AFLD.
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Affiliation(s)
- Fudi Zhong
- Division of Hepatobiliary Surgery, the First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Zhigao Hu
- Division of Hepatobiliary Surgery, the First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Laboratory of Liver Injury and Repair, Nanning, Guangxi, China
| | - Keqing Jiang
- Division of Hepatobiliary Surgery, the First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Biao Lei
- Division of Hepatobiliary Surgery, the First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Zhan Wu
- Division of Hepatobiliary Surgery, the First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Guandou Yuan
- Division of Hepatobiliary Surgery, the First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Hongliang Luo
- Division of Hepatobiliary Surgery, the First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Chunqiang Dong
- Division of Hepatobiliary Surgery, the First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Bo Tang
- Division of Hepatobiliary Surgery, the First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Chaowen Zheng
- Laboratory of Liver Injury and Repair, Nanning, Guangxi, China
| | - Shuai Yang
- Laboratory of Liver Injury and Repair, Nanning, Guangxi, China
| | - Yonglian Zeng
- Division of Hepatobiliary Surgery, the First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Zhenya Guo
- Division of Hepatobiliary Surgery, the First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Shuiping Yu
- Division of Hepatobiliary Surgery, the First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Huizhao Su
- Division of Hepatobiliary Surgery, the First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Guo Zhang
- Department of Gastroenterology, the People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China
| | - Xiaoqiang Qiu
- Laboratory of Liver Injury and Repair, Nanning, Guangxi, China
| | - Stephen Tomlinson
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC, USA
| | - Songqing He
- Division of Hepatobiliary Surgery, the First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China.
- Laboratory of Liver Injury and Repair, Nanning, Guangxi, China.
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46
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Perumal K, Reddy R. The 3' end formation in small RNAs. Gene Expr 2018; 10:59-78. [PMID: 11868988 PMCID: PMC5977532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Small RNAs are a major class of RNAs along with transfer RNAs, ribosomal RNAs, and messenger RNAs. They vary in size from less than 100 nucleotides to several thousand nucleotides and have been identified and characterized both in prokaryotes and eukaryotes. Small RNAs participate in a variety of cellular functions including regulating RNA synthesis, RNA processing, guiding modifications in RNA, and in transport of proteins. Small RNAs are generated by a series of posttranscriptional processing steps following transcription. While RNA 5' end structure, 5' cap formation, and RNA processing mechanisms have been fairly well characterized, the 3' end processing is poorly understood. Recent data point to an emerging theme in small RNAs metabolism in which the 3' end processing is mediated by the exosome, a large multienzyme complex. In addition to removal of nucleotides by the exosome, there is simultaneous rebuilding of the 3' end of some small RNA by adenylation and/or uridylation. This review presents a picture of both degradative and rebuilding reactions operative on the 3' end of some small RNA molecules in prokaryotes and eukaryotes.
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Affiliation(s)
- Karthika Perumal
- Department of Pharmacology, Baylor College of Medicine, Houston, TX 77030
| | - Ram Reddy
- Department of Pharmacology, Baylor College of Medicine, Houston, TX 77030
- Address correspondence to Ram Reddy, Ph.D., Department of Pharmacology, Baylor College of Medicine, Houston, TX 77030. Tel: (713) 798-7906; Fax: (713) 798-3145; E-mail:
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47
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Richard MMS, Gratias A, Thareau V, Kim KD, Balzergue S, Joets J, Jackson SA, Geffroy V. Genomic and epigenomic immunity in common bean: the unusual features of NB-LRR gene family. DNA Res 2018; 25:161-172. [PMID: 29149287 PMCID: PMC5909424 DOI: 10.1093/dnares/dsx046] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 10/26/2017] [Indexed: 12/20/2022] Open
Abstract
In plants, a key class of genes comprising most of disease resistance (R) genes encodes Nucleotide-binding leucine-rich repeat (NL) proteins. Access to common bean (Phaseolus vulgaris) genome sequence provides unparalleled insight into the organization and evolution of this large gene family (∼400 NL) in this important crop. As observed in other plant species, most common bean NL are organized in cluster of genes. However, a particularity of common bean is that these clusters are often located in subtelomeric regions close to terminal knobs containing the satellite DNA khipu. Phylogenetically related NL are spread between different chromosome ends, suggesting frequent exchanges between non-homologous chromosomes. NL peculiar location, in proximity to heterochromatic regions, led us to study their DNA methylation status using a whole-genome cytosine methylation map. In common bean, NL genes displayed an unusual body methylation pattern since half of them are methylated in the three contexts, reminiscent of the DNA methylation pattern of repeated sequences. Moreover, 90 NL were also abundantly targeted by 24 nt siRNA, with 90% corresponding to methylated NL genes. This suggests the existence of a transcriptional gene silencing mechanism of NL through the RdDM (RNA-directed DNA methylation) pathway in common bean that has not been described in other plant species.
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Affiliation(s)
- Manon M S Richard
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Univ Paris-Saclay, Univ Paris-Sud, Univ Evry, Univ Paris-Diderot, Sorbone Paris-Cité, 91405 Orsay, France
| | - Ariane Gratias
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Univ Paris-Saclay, Univ Paris-Sud, Univ Evry, Univ Paris-Diderot, Sorbone Paris-Cité, 91405 Orsay, France
| | - Vincent Thareau
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Univ Paris-Saclay, Univ Paris-Sud, Univ Evry, Univ Paris-Diderot, Sorbone Paris-Cité, 91405 Orsay, France
| | - Kyung Do Kim
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA
| | - Sandrine Balzergue
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Univ Paris-Saclay, Univ Paris-Sud, Univ Evry, Univ Paris-Diderot, Sorbone Paris-Cité, 91405 Orsay, France
- IRHS, INRA, AGROCAMPUS-Ouest, Université d’Angers, SFR 4207 QUASAV, 49071 Beaucouzé cedex, France
| | - Johann Joets
- GQE – Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA
| | - Valérie Geffroy
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Univ Paris-Saclay, Univ Paris-Sud, Univ Evry, Univ Paris-Diderot, Sorbone Paris-Cité, 91405 Orsay, France
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48
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Abstract
MicroRNAs (miRNAs) are a family of small, noncoding RNA molecules that negatively regulate protein expression either by inhibiting initiation of the translation of mRNA or by inducing the degradation of mRNA molecules. Accumulating evidence suggests that miRNA-mediated repression of protein expression is of paramount importance in a broad range of physiologic and pathologic conditions. In particular, miRNA-induced dysregulation of molecular processes involved in inflammatory pathways has been shown to contribute to the development of chronic inflammatory diseases. In this review, first of all we provide an overview of miRNA biogenesis, the main mechanisms of action and the miRNA profiling tools currently available. Then, we summarize the available evidence supporting a specific role for miRNAs in the pathobiology of periodontitis. Based on a review of available data on the differential expression of miRNAs in gingival tissues in states of periodontal health and disease, we address specific roles for miRNAs in molecular and cellular pathways causally linked to periodontitis. Our review points to several lines of evidence suggesting the involvement of miRNAs in periodontal tissue homeostasis and pathology. Although the intricate regulatory networks affected by miRNA function are still incompletely mapped, further utilization of systems biology tools is expected to enhance our understanding of the pathobiology of periodontitis.
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Affiliation(s)
- Moritz Kebschull
- Associate Professor of Dental Medicine, Consultant, Department of Periodontology, Operative and Preventive Dentistry, University of Bonn, Welschnonnenstr. 17, 53111 Bonn, Germany, Tel: +49-228-28722-007,
| | - Panos N. Papapanou
- Professor of Dental Medicine, Director, Division of Periodontics, Chair, Section of Oral and Diagnostic Sciences, Columbia University College of Dental Medicine, 630 West 168 Street, PH-7E-110, New York, NY 10032, USA, Tel: +1-212-342-3008, Fax: +1-212-305-9313,
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49
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Song Q, Chen ZJ. Epigenetic and developmental regulation in plant polyploids. Curr Opin Plant Biol 2015; 24:101-9. [PMID: 25765928 PMCID: PMC4395545 DOI: 10.1016/j.pbi.2015.02.007] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Revised: 02/18/2015] [Accepted: 02/18/2015] [Indexed: 05/18/2023]
Abstract
Polyploidy or whole-genome duplication occurs in some animals and many flowering plants, including many important crops such as wheat, cotton and oilseed rape. The prevalence of polyploidy in the plant kingdom suggests it as an important evolutionary feature for plant speciation and crop domestication. Studies of natural and synthetic polyploids have revealed rapid and dynamic changes in genomic structure and gene expression after polyploid formation. Growing evidence suggests that epigenetic modifications can alter homoeologous gene expression and reprogram gene expression networks, which allows polyploids to establish new cytotypes, grow vigorously and promote adaptation in local environments. Sequence and gene expression changes in polyploids have been well documented and reviewed elsewhere. This review is focused on developmental regulation and epigenetic changes including DNA methylation and histone modifications in polyploids.
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Affiliation(s)
- Qingxin Song
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712, USA
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712, USA; State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
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50
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Castellano L, Rizzi E, Krell J, Di Cristina M, Galizi R, Mori A, Tam J, De Bellis G, Stebbing J, Crisanti A, Nolan T. The germline of the malaria mosquito produces abundant miRNAs, endo-siRNAs, piRNAs and 29-nt small RNAs. BMC Genomics 2015; 16:100. [PMID: 25766668 PMCID: PMC4345017 DOI: 10.1186/s12864-015-1257-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 01/19/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Small RNAs include different classes essential for endogenous gene regulation and cellular defence against genomic parasites. However, a comprehensive analysis of the small RNA pathways in the germline of the mosquito Anopheles gambiae has never been performed despite their potential relevance to reproductive capacity in this malaria vector. RESULTS We performed small RNA deep sequencing during larval and adult gonadogenesis and find that they predominantly express four classes of regulatory small RNAs. We identified 45 novel miRNA precursors some of which were sex-biased and gonad-enriched , nearly doubling the number of previously known miRNA loci. We also determine multiple genomic clusters of 24-30 nt Piwi-interacting RNAs (piRNAs) that map to transposable elements (TEs) and 3'UTR of protein coding genes. Unusually, many TEs and the 3'UTR of some endogenous genes produce an abundant peak of 29-nt small RNAs with piRNA-like characteristics. Moreover, both sense and antisense piRNAs from TEs in both Anopheles gambiae and Drosophila melanogaster reveal novel features of piRNA sequence bias. We also discovered endogenous small interfering RNAs (endo-siRNAs) that map to overlapping transcripts and TEs. CONCLUSIONS This is the first description of the germline miRNome in a mosquito species and should prove a valuable resource for understanding gene regulation that underlies gametogenesis and reproductive capacity. We also provide the first evidence of a piRNA pathway that is active against transposons in the germline and our findings suggest novel piRNA sequence bias. The contribution of small RNA pathways to germline TE regulation and genome defence in general is an important finding for approaches aimed at manipulating mosquito populations through the use of selfish genetic elements.
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Affiliation(s)
- Leandro Castellano
- Division of Oncology, Department of Surgery and Cancer, Imperial Centre for Translational and Experimental Medicine, Imperial College, London, UK.
| | - Ermanno Rizzi
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche (ITB-CNR), Segrate, Milan, Italy.
| | - Jonathan Krell
- Division of Oncology, Department of Surgery and Cancer, Imperial Centre for Translational and Experimental Medicine, Imperial College, London, UK.
| | - Manlio Di Cristina
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy.
| | - Roberto Galizi
- Department of Life Sciences, South Kensington Campus, Imperial College London, London, SW7 2AZ, United Kingdom.
| | - Ayako Mori
- Department of Life Sciences, South Kensington Campus, Imperial College London, London, SW7 2AZ, United Kingdom.
| | - Janis Tam
- Department of Life Sciences, South Kensington Campus, Imperial College London, London, SW7 2AZ, United Kingdom.
| | - Gianluca De Bellis
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche (ITB-CNR), Segrate, Milan, Italy.
| | - Justin Stebbing
- Division of Oncology, Department of Surgery and Cancer, Imperial Centre for Translational and Experimental Medicine, Imperial College, London, UK.
| | - Andrea Crisanti
- Department of Life Sciences, South Kensington Campus, Imperial College London, London, SW7 2AZ, United Kingdom.
- Dipartimento di Medicina Sperimentale Via Gambuli, Centro di Genomica Funzionale, University of Perugia, 06132, Perugia, Italy.
| | - Tony Nolan
- Department of Life Sciences, South Kensington Campus, Imperial College London, London, SW7 2AZ, United Kingdom.
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