1
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Cai X, Wang H, Han Y, Huang H, Qian P. The essential roles of small non-coding RNAs and RNA modifications in normal and malignant hematopoiesis. Front Mol Biosci 2023; 10:1176416. [PMID: 37065445 PMCID: PMC10102602 DOI: 10.3389/fmolb.2023.1176416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 03/23/2023] [Indexed: 04/03/2023] Open
Abstract
Hematopoietic stem cells (HSCs) developing from mesoderm during embryogenesis are important for the blood circulatory system and immune system. Many factors such as genetic factors, chemical exposure, physical radiation, and viral infection, can lead to the dysfunction of HSCs. Hematological malignancies (involving leukemia, lymphoma, and myeloma) were diagnosed in more than 1.3 million people globally in 2021, taking up 7% of total newly-diagnosed cancer patients. Although many treatments like chemotherapy, bone marrow transplantation, and stem cell transplantation have been applied in clinical therapeutics, the average 5-year survival rate for leukemia, lymphoma, and myeloma is about 65%, 72%, and 54% respectively. Small non-coding RNAs play key roles in a variety of biological processes, including cell division and proliferation, immunological response and cell death. With the development of technologies in high-throughput sequencing and bioinformatic analysis, there is emerging research about modifications on small non-coding RNAs, as well as their functions in hematopoiesis and related diseases. In this study, we summarize the updated information of small non-coding RNAs and RNA modifications in normal and malignant hematopoiesis, which sheds lights into the future application of HSCs into the treatment of blood diseases.
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Affiliation(s)
- Xinyi Cai
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Hui Wang
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Yingli Han
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - He Huang
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Pengxu Qian
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
- *Correspondence: Pengxu Qian,
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2
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Dayie TK, Olenginski LT, Taiwo KM. Isotope Labels Combined with Solution NMR Spectroscopy Make Visible the Invisible Conformations of Small-to-Large RNAs. Chem Rev 2022; 122:9357-9394. [PMID: 35442658 PMCID: PMC9136934 DOI: 10.1021/acs.chemrev.1c00845] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Indexed: 02/07/2023]
Abstract
RNA is central to the proper function of cellular processes important for life on earth and implicated in various medical dysfunctions. Yet, RNA structural biology lags significantly behind that of proteins, limiting mechanistic understanding of RNA chemical biology. Fortunately, solution NMR spectroscopy can probe the structural dynamics of RNA in solution at atomic resolution, opening the door to their functional understanding. However, NMR analysis of RNA, with only four unique ribonucleotide building blocks, suffers from spectral crowding and broad linewidths, especially as RNAs grow in size. One effective strategy to overcome these challenges is to introduce NMR-active stable isotopes into RNA. However, traditional uniform labeling methods introduce scalar and dipolar couplings that complicate the implementation and analysis of NMR measurements. This challenge can be circumvented with selective isotope labeling. In this review, we outline the development of labeling technologies and their application to study biologically relevant RNAs and their complexes ranging in size from 5 to 300 kDa by NMR spectroscopy.
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Affiliation(s)
- Theodore K. Dayie
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Lukasz T. Olenginski
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Kehinde M. Taiwo
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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3
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LeBlanc RM, Mesleh MF. A drug discovery toolbox for Nuclear Magnetic Resonance (NMR) characterization of ligands and their targets. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021; 37:51-60. [PMID: 34895655 DOI: 10.1016/j.ddtec.2020.11.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 11/22/2020] [Accepted: 11/27/2020] [Indexed: 10/22/2022]
Abstract
Information about the structure, dynamics, and ligand-binding properties of biomolecules can be derived from Nuclear Magnetic Resonance (NMR) spectroscopy and provides valuable information for drug discovery. A multitude of experimental approaches provides a wealth of information that can be tailored to the system of interest. Methods to study the behavior of ligands upon target binding enable the identification of weak binders in a robust manner that is critical for the identification of truly novel binding interactions. This is particularly important for challenging targets. Observing the solution behavior of biomolecules yields information about their structure, dynamics, and interactions. This review describes the breadth of approaches that are available, many of which are under-utilized in a drug-discovery environment, and focuses on recent advances that continue to emerge.
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Affiliation(s)
- Regan M LeBlanc
- Structural Biology and Biophysics, Vertex Pharmaceuticals Inc., Boston, MA, 02210, United States
| | - Michael F Mesleh
- Structural Biology and Biophysics, Vertex Pharmaceuticals Inc., Boston, MA, 02210, United States.
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4
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Götze M, Sarnowski CP, de Vries T, Knörlein A, Allain FHT, Hall J, Aebersold R, Leitner A. Single Nucleotide Resolution RNA-Protein Cross-Linking Mass Spectrometry: A Simple Extension of the CLIR-MS Workflow. Anal Chem 2021; 93:14626-14634. [PMID: 34714631 PMCID: PMC8581962 DOI: 10.1021/acs.analchem.1c02384] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
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RNA–protein
interactions mediate many intracellular processes.
CLIR-MS (cross-linking of isotope-labeled RNA and tandem mass spectrometry)
allows the identification of RNA–protein interaction sites
at single nucleotide/amino acid resolution in a single experiment.
Using isotopically labeled RNA segments for UV-light-induced cross-linking
generates characteristic isotope patterns that constrain the sequence
database searches, increasing spatial resolution. Whereas the use
of segmentally isotopically labeled RNA is effective, it is technically
involved and not applicable in some settings, e.g., in cell or tissue
samples. Here we introduce an extension of the CLIR-MS workflow that
uses unlabeled RNA during cross-linking and subsequently adds an isotopic
label during sample preparation for MS analysis. After RNase and protease
digests of a cross-linked complex, the nucleic acid part of a peptide–RNA
conjugate is labeled using the enzyme T4 polynucleotide kinase and
a 1:1 mixture of heavy 18O4-γ-ATP and
light ATP. In this simple, one-step reaction, three heavy oxygen atoms
are transferred from the γ-phosphate to the 5′-end of
the RNA, introducing an isotopic shift of 6.01 Da that is detectable
by mass spectrometry. We applied this approach to the RNA recognition
motif (RRM) of the protein FOX1 in complex with its cognate binding
substrate, FOX-binding element (FBE) RNA. We also labeled a single
phosphate within an RNA and unambiguously determined the cross-linking
site of the FOX1-RRM binding to FBE at single residue resolution on
the RNA and protein level and used differential ATP labeling for relative
quantification based on isotope dilution. Data are available via ProteomeXchange
with the identifier PXD024010.
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Affiliation(s)
- Michael Götze
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zürich 8093, Switzerland
| | - Chris P Sarnowski
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zürich 8093, Switzerland
| | - Tebbe de Vries
- Department of Biology, Institute of Biochemistry, ETH Zürich, Zürich 8093, Switzerland
| | - Anna Knörlein
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, Zürich 8093, Switzerland
| | - Frédéric H-T Allain
- Department of Biology, Institute of Biochemistry, ETH Zürich, Zürich 8093, Switzerland
| | - Jonathan Hall
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, Zürich 8093, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zürich 8093, Switzerland
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zürich 8093, Switzerland
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5
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Synthesis of atom-specific nucleobase and ribose labeled uridine phosphoramidite for NMR analysis of large RNAs. MONATSHEFTE FUR CHEMIE 2021. [DOI: 10.1007/s00706-021-02851-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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6
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Amalric A, Bastide A, Attina A, Choquet A, Vialaret J, Lehmann S, David A, Hirtz C. Quantifying RNA modifications by mass spectrometry: a novel source of biomarkers in oncology. Crit Rev Clin Lab Sci 2021; 59:1-18. [PMID: 34473579 DOI: 10.1080/10408363.2021.1958743] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Despite significant progress in targeted therapies, cancer recurrence remains a major cause of mortality worldwide. Identification of accurate biomarkers, through molecular profiling in healthy and cancer patient samples, will improve diagnosis and promote personalized medicine. While genetic and epigenetic alterations of DNA are currently exploited as cancer biomarkers, their robustness is limited by tumor heterogeneity. Recently, cancer-associated changes in RNA marks have emerged as a promising source of diagnostic and prognostic biomarkers. RNA epigenetics (also known as epitranscriptomics) is an emerging field in which at least 150 chemical modifications in all types of RNA (mRNA, tRNA, lncRNA, rRNA, and microRNA) have been detected. These modifications fine-tune gene expression in both physiological and pathological processes. A growing number of studies have established links between specific modified nucleoside levels in solid/liquid biopsies, and cancer onset and progression. In this review, we highlight the potential role of epitranscriptomic markers in refining cancer diagnosis and/or prognosis. RNA modification patterns may contain important information for establishing an initial diagnosis, monitoring disease evolution, and predicting response to treatment. Furthermore, recent developments in mass spectrometry allow reliable quantification of RNA marks in solid biopsies and biological fluids. We discuss the great potential of mass spectrometry for identifying epitranscriptomic biomarker signatures in cancer diagnosis. While there are various methods to quantify modified nucleosides, most are unable to detect and quantify more than one type of RNA modification at a time. Mass spectrometry analyses, especially GC-MS/MS and LC-MS/MS, overcome this limitation and simultaneously detect modified nucleosides by multiple reaction monitoring. Indeed, several groups are currently validating mass spectrometry methods that quantify several nucleosides at one time in liquid biopsies. The challenge now is to exploit these powerful analytical tools to establish epitranscriptomic signatures that should open new perspectives in personalized medicine. This review summarizes the growing clinical field of analysis of RNA modifications and discusses pre-analytical and analytical approaches, focusing in particular on the development of new mass spectrometry tools and their clinical applications.
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Affiliation(s)
- Amandine Amalric
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, France.,University of Montpellier, IRMB-PPC, INM, CHU Montpellier, INSERM CNRS, Montpellier, France
| | - Amandine Bastide
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Aurore Attina
- University of Montpellier, IRMB-PPC, INM, CHU Montpellier, INSERM CNRS, Montpellier, France
| | - Armelle Choquet
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Jerome Vialaret
- University of Montpellier, IRMB-PPC, INM, CHU Montpellier, INSERM CNRS, Montpellier, France
| | - Sylvain Lehmann
- University of Montpellier, IRMB-PPC, INM, CHU Montpellier, INSERM CNRS, Montpellier, France
| | - Alexandre David
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, France.,University of Montpellier, IRMB-PPC, INM, CHU Montpellier, INSERM CNRS, Montpellier, France
| | - Christophe Hirtz
- University of Montpellier, IRMB-PPC, INM, CHU Montpellier, INSERM CNRS, Montpellier, France
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7
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Garikipati VNS, Uchida S. Elucidating the Functions of Non-Coding RNAs from the Perspective of RNA Modifications. Noncoding RNA 2021; 7:ncrna7020031. [PMID: 34065036 PMCID: PMC8163165 DOI: 10.3390/ncrna7020031] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/29/2021] [Accepted: 05/05/2021] [Indexed: 12/11/2022] Open
Abstract
It is now commonly accepted that most of the mammalian genome is transcribed as RNA, yet less than 2% of such RNA encode for proteins. A majority of transcribed RNA exists as non-protein-coding RNAs (ncRNAs) with various functions. Because of the lack of sequence homologies among most ncRNAs species, it is difficult to infer the potential functions of ncRNAs by examining sequence patterns, such as catalytic domains, as in the case of proteins. Added to the existing complexity of predicting the functions of the ever-growing number of ncRNAs, increasing evidence suggests that various enzymes modify ncRNAs (e.g., ADARs, METTL3, and METTL14), which has opened up a new field of study called epitranscriptomics. Here, we examine the current status of ncRNA research from the perspective of epitranscriptomics.
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Affiliation(s)
- Venkata Naga Srikanth Garikipati
- Department of Emergency Medicine, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA;
- Dorothy M. Davis Heart Lung and Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Shizuka Uchida
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Frederikskaj 10B, 2. (building C), DK-2450 Copenhagen SV, Denmark
- Correspondence: or
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8
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Rich T, Pan D, Chordia M, Keppel C, Beylin D, Stepanov P, Jung M, Pang D, Grindrod S, Dritschilo A. 18Oxygen Substituted Nucleosides Combined with Proton Beam Therapy: Therapeutic Transmutation In Vitro. Int J Part Ther 2021; 7:11-18. [PMID: 33829069 PMCID: PMC8019575 DOI: 10.14338/ijpt-d-20-00036.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 12/17/2020] [Indexed: 11/21/2022] Open
Abstract
Purpose Proton therapy precisely delivers radiation to cancers to cause damaging strand breaks to cellular DNA, kill malignant cells, and stop tumor growth. Therapeutic protons also generate short-lived activated nuclei of carbon, oxygen, and nitrogen atoms in patients as a result of atomic transmutations that are imaged by positron emission tomography (PET). We hypothesized that the transition of 18O to 18F in an 18O-substituted nucleoside irradiated with therapeutic protons may result in the potential for combined diagnosis and treatment for cancer with proton therapy. Materials and Methods Reported here is a feasibility study with a therapeutic proton beam used to irradiate H218O to a dose of 10 Gy produced by an 85 MeV pristine Bragg peak. PET imaging initiated >45 minutes later showed an 18F decay signal with T1/2 of ∼111 minutes. Results The 18O to 18F transmutation effect on cell survival was tested by exposing SQ20B squamous carcinoma cells to physiologic 18O-thymidine concentrations of 5 μM for 48 hours followed by 1- to 9-Gy graded doses of proton radiation given 24 hours later. Survival analyses show radiation sensitization with a dose modification factor (DMF) of 1.2. Conclusions These data support the idea of therapeutic transmutation in vitro as a biochemical consequence of proton activation of 18O to 18F in substituted thymidine enabling proton radiation enhancement in a cancer cell. 18O-substituted molecules that incorporate into cancer targets may hold promise for improving the therapeutic window of protons and can be evaluated further for postproton therapy PET imaging.
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Affiliation(s)
- Tyvin Rich
- The University of Virginia, Radiation Oncology and Diagnostic Radiology, Charlottesville, VA, USA.,Georgetown University, Radiation Medicine, Washington, DC, USA.,Shuttle Pharmaceuticals, Inc, Rockville, MD, USA.,Hampton University Proton Therapy Institute, Hampton, VA, USA
| | - Dongfeng Pan
- The University of Virginia, Radiology and Medical Imaging, Charlottesville, VA, USA
| | - Mahendra Chordia
- The University of Virginia, Radiology and Medical Imaging, Charlottesville, VA, USA
| | - Cynthia Keppel
- Hampton University Proton Therapy Institute, Hampton, VA, USA.,Thomas Jefferson National Accelerator Facility, Newport News, VA, USA
| | | | | | - Mira Jung
- Georgetown University, Radiation Medicine, Washington, DC, USA
| | - Dalong Pang
- Georgetown University, Radiation Medicine, Washington, DC, USA
| | | | - Anatoly Dritschilo
- Georgetown University, Radiation Medicine, Washington, DC, USA.,Shuttle Pharmaceuticals, Inc, Rockville, MD, USA
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9
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Mouhand A, Pasi M, Catala M, Zargarian L, Belfetmi A, Barraud P, Mauffret O, Tisné C. Overview of the Nucleic-Acid Binding Properties of the HIV-1 Nucleocapsid Protein in Its Different Maturation States. Viruses 2020; 12:v12101109. [PMID: 33003650 PMCID: PMC7601788 DOI: 10.3390/v12101109] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/23/2020] [Accepted: 09/26/2020] [Indexed: 12/17/2022] Open
Abstract
HIV-1 Gag polyprotein orchestrates the assembly of viral particles. Its C-terminus consists of the nucleocapsid (NC) domain that interacts with nucleic acids, and p1 and p6, two unstructured regions, p6 containing the motifs to bind ALIX, the cellular ESCRT factor TSG101 and the viral protein Vpr. The processing of Gag by the viral protease subsequently liberates NCp15 (NC-p1-p6), NCp9 (NC-p1) and NCp7, NCp7 displaying the optimal chaperone activity of nucleic acids. This review focuses on the nucleic acid binding properties of the NC domain in the different maturation states during the HIV-1 viral cycle.
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Affiliation(s)
- Assia Mouhand
- Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (IBPC), 75005 Paris, France; (A.M.); (M.C.); (P.B.)
| | - Marco Pasi
- Laboratoire de Biologie et de Pharmacologie Appliquée (LBPA), UMR 8113 CNRS, Institut D’Alembert, École Normale Supérieure Paris-Saclay, Université Paris-Saclay, 4, Avenue des Sciences, 91190 Gif sur Yvette, France; (M.P.); (L.Z.); (A.B.)
| | - Marjorie Catala
- Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (IBPC), 75005 Paris, France; (A.M.); (M.C.); (P.B.)
| | - Loussiné Zargarian
- Laboratoire de Biologie et de Pharmacologie Appliquée (LBPA), UMR 8113 CNRS, Institut D’Alembert, École Normale Supérieure Paris-Saclay, Université Paris-Saclay, 4, Avenue des Sciences, 91190 Gif sur Yvette, France; (M.P.); (L.Z.); (A.B.)
| | - Anissa Belfetmi
- Laboratoire de Biologie et de Pharmacologie Appliquée (LBPA), UMR 8113 CNRS, Institut D’Alembert, École Normale Supérieure Paris-Saclay, Université Paris-Saclay, 4, Avenue des Sciences, 91190 Gif sur Yvette, France; (M.P.); (L.Z.); (A.B.)
| | - Pierre Barraud
- Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (IBPC), 75005 Paris, France; (A.M.); (M.C.); (P.B.)
| | - Olivier Mauffret
- Laboratoire de Biologie et de Pharmacologie Appliquée (LBPA), UMR 8113 CNRS, Institut D’Alembert, École Normale Supérieure Paris-Saclay, Université Paris-Saclay, 4, Avenue des Sciences, 91190 Gif sur Yvette, France; (M.P.); (L.Z.); (A.B.)
- Correspondence: (O.M.); (C.T.)
| | - Carine Tisné
- Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (IBPC), 75005 Paris, France; (A.M.); (M.C.); (P.B.)
- Correspondence: (O.M.); (C.T.)
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10
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Chemo-enzymatic synthesis of [2-13C, 7-15 N]-ATP for facile NMR analysis of RNA. MONATSHEFTE FUR CHEMIE 2020. [DOI: 10.1007/s00706-020-02667-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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11
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Zhang X, Li M, Liu Y. Optimization and characterization of position-selective labelling of RNA (PLOR) for diverse RNA and DNA sequences. RNA Biol 2020; 17:1009-1017. [PMID: 32249673 DOI: 10.1080/15476286.2020.1749797] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Modifications of short RNAs at specific sites can be achieved commercially by solid-phase chemical synthesis method. However, labelling long RNAs is still challenging for the routine methods. Position-selective Labelling of RNA (PLOR) is a hybrid phase transcription method that allows to label RNAs at desired sites with great flexibility and decent efficiency. In principle, PLOR is a promising method for synthesis of long modified RNAs that are unable to be generated by solid-phase chemical synthesis and other methods. However, as a recently developed method, PLOR has been only applied to label a 71nt and a 104nt RNA, and the limited sequence applications of PLOR may hinder its potential usages. To extend PLOR to more RNAs, we tested the PLOR performances for various RNA sequences. Considering that the controlled transcriptional pauses at the initiation stage in PLOR may lead to different preferences on RNA sequences from in vitro transcription method, we here focused on identifying the effects of the 5'-end and initiated lengths of RNA on PLOR. In addition, our work demonstrated that PLOR efficiencies also varied with linker sizes of DNA templates. This work can facilitate PLOR to be the choice of synthesizing long modified RNAs for more users in the near future.
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Affiliation(s)
- Xiaoyu Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University , Shanghai, P. R. China
| | - Mengyang Li
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University , Shanghai, P. R. China
| | - Yu Liu
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University , Shanghai, P. R. China
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12
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Solid-Phase Chemical Synthesis of Stable Isotope-Labeled RNA to Aid Structure and Dynamics Studies by NMR Spectroscopy. Molecules 2019; 24:molecules24193476. [PMID: 31557861 PMCID: PMC6804060 DOI: 10.3390/molecules24193476] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 09/22/2019] [Accepted: 09/23/2019] [Indexed: 02/05/2023] Open
Abstract
RNA structure and dynamic studies by NMR spectroscopy suffer from chemical shift overlap and line broadening, both of which become worse as RNA size increases. Incorporation of stable isotope labels into RNA has provided several solutions to these limitations. Nevertheless, the only method to circumvent the problem of spectral overlap completely is the solid-phase chemical synthesis of RNA with labeled RNA phosphoramidites. In this review, we summarize the practical aspects of this methodology for NMR spectroscopy studies of RNA. These types of investigations lie at the intersection of chemistry and biophysics and highlight the need for collaborative efforts to tackle the integrative structural biology problems that exist in the RNA world. Finally, examples of RNA structure and dynamic studies using labeled phosphoramidites are highlighted.
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13
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Affiliation(s)
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
| | - Matthias J Feige
- Center for Integrated Protein Science Munich at the Department of Chemistry and Institute for Advanced Study, Technical University of Munich, D-85748 Garching, Germany
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