1
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Kim J. Circular RNAs: Novel Players in Cancer Mechanisms and Therapeutic Strategies. Int J Mol Sci 2024; 25:10121. [PMID: 39337606 PMCID: PMC11432211 DOI: 10.3390/ijms251810121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2024] [Revised: 09/19/2024] [Accepted: 09/19/2024] [Indexed: 09/30/2024] Open
Abstract
Circular RNAs (circRNAs) are a novel class of noncoding RNAs that have emerged as pivotal players in gene regulation. Our understanding of circRNAs has greatly expanded over the last decade, with studies elucidating their biology and exploring their therapeutic applications. In this review, we provide an overview of the current understanding of circRNA biogenesis, outline their mechanisms of action in cancer, and assess their clinical potential as biomarkers. Furthermore, we discuss circRNAs as a potential therapeutic strategy, including recent advances in circRNA production and translation, along with proof-of-concept preclinical studies of cancer vaccines.
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Affiliation(s)
- Jimi Kim
- Department of Life Sciences, Gachon University, Seongnam 13120, Republic of Korea;
- Department of Health Science and Technology, GAIHST, Lee Gil Ya Cancer and Diabetes Institute, Incheon 21999, Republic of Korea
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Li S, Chu Y, Guo X, Mao C, Xiao SJ. Circular RNA oligonucleotides: enzymatic synthesis and scaffolding for nanoconstruction. NANOSCALE HORIZONS 2024. [PMID: 39042106 DOI: 10.1039/d4nh00236a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
We report the efficient synthesis of monomeric circular RNAs (circRNAs) in the size range of 16-44 nt with a novel DNA dumbbell splinting plus T4 DNA ligation strategy. Such a DNA dumbbell splinting strategy was developed by one group among ours recently for near-quantitative conversion of short linear DNAs into monomeric circular ones. Furthermore, using the 44 nt circRNA as scaffold strands, we constructed hybrid RNA:DNA and pure RNA:RNA double crossover tiles and their assemblies of nucleic acid nanotubes and flat arrays.
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Affiliation(s)
- Shijie Li
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, Jiangsu, China
| | - Yanxin Chu
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, Jiangsu, China
| | - Xin Guo
- Bruker (Beijing) Scientific Technology Co. Ltd, China
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA.
| | - Shou-Jun Xiao
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, Jiangsu, China
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Sharma NK, Dwivedi P, Bhushan R, Maurya PK, Kumar A, Dakal TC. Engineering circular RNA for molecular and metabolic reprogramming. Funct Integr Genomics 2024; 24:117. [PMID: 38918231 DOI: 10.1007/s10142-024-01394-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 06/10/2024] [Accepted: 06/17/2024] [Indexed: 06/27/2024]
Abstract
The role of messenger RNA (mRNA) in biological systems is extremely versatile. However, it's extremely short half-life poses a fundamental restriction on its application. Moreover, the translation efficiency of mRNA is also limited. On the contrary, circular RNAs, also known as circRNAs, are a common and stable form of RNA found in eukaryotic cells. These molecules are synthesized via back-splicing. Both synthetic circRNAs and certain endogenous circRNAs have the potential to encode proteins, hence suggesting the potential of circRNA as a gene expression machinery. Herein, we aim to summarize all engineering aspects that allow exogenous circular RNA (circRNA) to prolong the time that proteins are expressed from full-length RNA signals. This review presents a systematic engineering approach that have been devised to efficiently assemble circRNAs and evaluate several aspects that have an impact on protein production derived from. We have also reviewed how optimization of the key components of circRNAs, including the topology of vector, 5' and 3' untranslated sections, entrance site of the internal ribosome, and engineered aptamers could be efficiently impacting the translation machinery for molecular and metabolic reprogramming. Collectively, molecular and metabolic reprogramming present a novel way of regulating distinctive cellular features, for instance growth traits to neoplastic cells, and offer new possibilities for therapeutic inventions.
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Affiliation(s)
- Narendra Kumar Sharma
- Department of Bioscience and Biotechnology, Banasthali Vidyapith (Deemed University), P.O. Banasthali Vidyapith Distt. Tonk, Rajasthan, 304 022, India.
| | - Pragya Dwivedi
- Department of Bioscience and Biotechnology, Banasthali Vidyapith (Deemed University), P.O. Banasthali Vidyapith Distt. Tonk, Rajasthan, 304 022, India
| | - Ravi Bhushan
- Department of Zoology, M.S. College, Motihari, Bihar, India
| | - Pawan Kumar Maurya
- Department of Biochemistry, Central University of Haryana, Mahendergarh, 123031, Haryana, India
| | - Abhishek Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, Karnataka, India
- Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Tikam Chand Dakal
- Genome and Computational Biology Lab, Department of Biotechnology, Mohanlal Sukhadia University, Udaipur, Rajasthan, 313001, India.
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He W, Zhang X, Zou Y, Li J, Chang L, He YC, Jin Q, Ye J. Effective synthesis of circRNA via a thermostable T7 RNA polymerase variant as the catalyst. Front Bioeng Biotechnol 2024; 12:1356354. [PMID: 38655387 PMCID: PMC11035883 DOI: 10.3389/fbioe.2024.1356354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/04/2024] [Indexed: 04/26/2024] Open
Abstract
Introduction Circular RNAs (circRNAs) are endogenous noncoding RNAs (ncRNAs) with transcriptional lengths ranging from hundreds to thousands. circRNAs have attracted attention owing to their stable structure and ability to treat complicated diseases. Our objective was to create a one-step reaction for circRNA synthesis using wild-type T7 RNA polymerase as the catalyst. However, T7 RNA polymerase is thermally unstable, and we streamlined circRNA synthesis via consensus and folding free energy calculations for hotspot selection. Because of the thermal instability, the permuted intron and exon (PIE) method for circRNA synthesis is conducted via tandem catalysis with a transcription reaction at a low temperature and linear RNA precursor cyclization at a high temperature. Methods To streamline the process, a multisite mutant T7 RNA polymerase (S430P, N433T, S633P, F849I, F880Y, and G788A) with significantly improved thermostability was constructed, and G788A was used. Results The resulting mutant exhibited stable activity at 45°C for over an hour, enabling the implementation of a one-pot transcription and cyclization reaction. The simplified circRNA production process demonstrated an efficiency comparable to that of the conventional two-step reaction, with a cyclization rate exceeding 95% and reduced production of immunostimulatory dsRNA byproducts.
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Affiliation(s)
- Wei He
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- Vazyme Biotech Co., Ltd, Nanjing, China
| | | | | | - Ji Li
- Vazyme Biotech Co., Ltd, Nanjing, China
| | - Le Chang
- Vazyme Biotech Co., Ltd, Nanjing, China
| | - Yu-Cai He
- School of Pharmacy, Changzhou University, Changzhou, China
| | | | - Jianren Ye
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
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Janvier A, Hayek H, Alghoul F, Gross L, Allmang C, Martin F, Eriani G. Purification of In Vivo or In Vitro-Assembled RNA-Protein Complexes by RNA Centric Methods. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 3234:17-29. [PMID: 38507197 DOI: 10.1007/978-3-031-52193-5_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Throughout their entire life cycle, RNAs are associated with RNA-binding proteins (RBPs), forming ribonucleoprotein (RNP) complexes with highly dynamic compositions and very diverse functions in RNA metabolism, including splicing, translational regulation, ribosome assembly. Many RNPs remain poorly characterized due to the challenges inherent in their purification and subsequent biochemical characterization. Therefore, developing methods to isolate specific RNA-protein complexes is an important initial step toward understanding their function. Many elegant methodologies have been developed to isolate RNPs. This chapter describes different approaches and methods devised for RNA-specific purification of a target RNP. We focused on general methods for selecting RNPs that target a given RNA under conditions favourable for the copurification of associated factors including RNAs and protein components of the RNP.
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Affiliation(s)
- Aurélie Janvier
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Hassan Hayek
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Fatima Alghoul
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Lauriane Gross
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Christine Allmang
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Franck Martin
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Gilbert Eriani
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France.
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Kim YS, Kim DH, An D, Lim Y, Seo YJ, Kim HK, Kang HY. The RNA ligation method using modified splint DNAs significantly improves the efficiency of circular RNA synthesis. Anim Cells Syst (Seoul) 2023; 27:208-218. [PMID: 37808549 PMCID: PMC10552601 DOI: 10.1080/19768354.2023.2265165] [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: 08/03/2023] [Accepted: 09/20/2023] [Indexed: 10/10/2023] Open
Abstract
Circular RNA (circRNA) is a non-coding RNA with a covalently closed loop structure and usually more stable than messenger RNA (mRNA). However, coding sequences (CDSs) following an internal ribosome entry site (IRES) in circRNAs can be translated, and this property has been recently utilized to produce proteins as novel therapeutic tools. However, it is difficult to produce large proteins from circRNAs because of the low circularization efficiency of lengthy RNAs. In this study, we report that we successfully synthesized circRNAs with the splint DNA ligation method using RNA ligase 1 and the splint DNAs, which contain complementary sequences to both ends of precursor linear RNAs. This method results in more efficient circularization than the conventional enzymatic method that does not use the splint DNAs, easily generating circRNAs that express relatively large proteins, including IgG heavy and light chains. Longer splint DNA (42 nucleotide) is more effective in circularization. Also, the use of splint DNAs with an adenine analog, 2,6-diaminopurine (DAP), increase the circularization efficiency presumably by strengthening the interaction between the splint DNAs and the precursor RNAs. The splint DNA ligation method requires 5 times more splint DNA than the precursor RNA to efficiently produce circRNAs, but our modified splint DNA ligation method can produce circRNAs using the amount of splint DNA which is equal to that of the precursor RNA. Our modified splint DNA ligation method will help develop novel therapeutic tools using circRNAs, to treat various diseases and to develop human and veterinary vaccines.
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Affiliation(s)
- Yoon-Seob Kim
- Drug Discovery Center, NuclixBio, Seoul, Republic of Korea
| | - Do-Hyung Kim
- Drug Discovery Center, NuclixBio, Seoul, Republic of Korea
| | - Daegi An
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Younghyun Lim
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Young-Jin Seo
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Hak Kyun Kim
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Ho-Young Kang
- Drug Discovery Center, NuclixBio, Seoul, Republic of Korea
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7
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Zhou W, Jiang L, Liao S, Wu F, Yang G, Hou L, Liu L, Pan X, Jia W, Zhang Y. Vaccines' New Era-RNA Vaccine. Viruses 2023; 15:1760. [PMID: 37632102 PMCID: PMC10458896 DOI: 10.3390/v15081760] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
RNA vaccines, including conventional messenger RNA (mRNA) vaccines, circular RNA (circRNA) vaccines, and self-amplifying RNA (saRNA) vaccines, have ushered in a promising future and revolutionized vaccine development. The success of mRNA vaccines in combating the COVID-19 pandemic caused by the SARS-CoV-2 virus that emerged in 2019 has highlighted the potential of RNA vaccines. These vaccines possess several advantages, such as high efficacy, adaptability, simplicity in antigen design, and the ability to induce both humoral and cellular immunity. They also offer rapid and cost-effective manufacturing, flexibility to target emerging or mutant pathogens and a potential approach for clearing immunotolerant microbes by targeting bacterial or parasitic survival mechanisms. The self-adjuvant effect of mRNA-lipid nanoparticle (LNP) formulations or circular RNA further enhances the potential of RNA vaccines. However, some challenges need to be addressed. These include the technology's immaturity, high research expenses, limited duration of antibody response, mRNA instability, low efficiency of circRNA cyclization, and the production of double-stranded RNA as a side product. These factors hinder the widespread adoption and utilization of RNA vaccines, particularly in developing countries. This review provides a comprehensive overview of mRNA, circRNA, and saRNA vaccines for infectious diseases while also discussing their development, current applications, and challenges.
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Affiliation(s)
- Wenshuo Zhou
- CNBG-Virogin Biotech (Shanghai) Co., Ltd., Shanghai 201800, China; (W.Z.); (L.J.); (S.L.); (F.W.); (G.Y.); (L.H.); (L.L.); (X.P.); (W.J.)
| | - Linglei Jiang
- CNBG-Virogin Biotech (Shanghai) Co., Ltd., Shanghai 201800, China; (W.Z.); (L.J.); (S.L.); (F.W.); (G.Y.); (L.H.); (L.L.); (X.P.); (W.J.)
| | - Shimiao Liao
- CNBG-Virogin Biotech (Shanghai) Co., Ltd., Shanghai 201800, China; (W.Z.); (L.J.); (S.L.); (F.W.); (G.Y.); (L.H.); (L.L.); (X.P.); (W.J.)
| | - Feifei Wu
- CNBG-Virogin Biotech (Shanghai) Co., Ltd., Shanghai 201800, China; (W.Z.); (L.J.); (S.L.); (F.W.); (G.Y.); (L.H.); (L.L.); (X.P.); (W.J.)
| | - Guohuan Yang
- CNBG-Virogin Biotech (Shanghai) Co., Ltd., Shanghai 201800, China; (W.Z.); (L.J.); (S.L.); (F.W.); (G.Y.); (L.H.); (L.L.); (X.P.); (W.J.)
| | - Li Hou
- CNBG-Virogin Biotech (Shanghai) Co., Ltd., Shanghai 201800, China; (W.Z.); (L.J.); (S.L.); (F.W.); (G.Y.); (L.H.); (L.L.); (X.P.); (W.J.)
| | - Lan Liu
- CNBG-Virogin Biotech (Shanghai) Co., Ltd., Shanghai 201800, China; (W.Z.); (L.J.); (S.L.); (F.W.); (G.Y.); (L.H.); (L.L.); (X.P.); (W.J.)
| | - Xinping Pan
- CNBG-Virogin Biotech (Shanghai) Co., Ltd., Shanghai 201800, China; (W.Z.); (L.J.); (S.L.); (F.W.); (G.Y.); (L.H.); (L.L.); (X.P.); (W.J.)
| | - William Jia
- CNBG-Virogin Biotech (Shanghai) Co., Ltd., Shanghai 201800, China; (W.Z.); (L.J.); (S.L.); (F.W.); (G.Y.); (L.H.); (L.L.); (X.P.); (W.J.)
- Shanghai-Virogin Biotech Co., Ltd., Shanghai 201800, China
| | - Yuntao Zhang
- CNBG-Virogin Biotech (Shanghai) Co., Ltd., Shanghai 201800, China; (W.Z.); (L.J.); (S.L.); (F.W.); (G.Y.); (L.H.); (L.L.); (X.P.); (W.J.)
- Sinopharm Group China National Biotech Group (CNBG) Co., Ltd., Beijing 100124, China
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8
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Wee LM, Tong AB, Florez Ariza AJ, Cañari-Chumpitaz C, Grob P, Nogales E, Bustamante CJ. A trailing ribosome speeds up RNA polymerase at the expense of transcript fidelity via force and allostery. Cell 2023; 186:1244-1262.e34. [PMID: 36931247 PMCID: PMC10135430 DOI: 10.1016/j.cell.2023.02.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 11/14/2022] [Accepted: 02/06/2023] [Indexed: 03/18/2023]
Abstract
In prokaryotes, translation can occur on mRNA that is being transcribed in a process called coupling. How the ribosome affects the RNA polymerase (RNAP) during coupling is not well understood. Here, we reconstituted the E. coli coupling system and demonstrated that the ribosome can prevent pausing and termination of RNAP and double the overall transcription rate at the expense of fidelity. Moreover, we monitored single RNAPs coupled to ribosomes and show that coupling increases the pause-free velocity of the polymerase and that a mechanical assisting force is sufficient to explain the majority of the effects of coupling. Also, by cryo-EM, we observed that RNAPs with a terminal mismatch adopt a backtracked conformation, while a coupled ribosome allosterically induces these polymerases toward a catalytically active anti-swiveled state. Finally, we demonstrate that prolonged RNAP pausing is detrimental to cell viability, which could be prevented by polymerase reactivation through a coupled ribosome.
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Affiliation(s)
- Liang Meng Wee
- QB3-Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA
| | - Alexander B Tong
- QB3-Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Alfredo Jose Florez Ariza
- QB3-Berkeley, Berkeley, CA, USA; Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, USA
| | - Cristhian Cañari-Chumpitaz
- QB3-Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA
| | - Patricia Grob
- QB3-Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Eva Nogales
- QB3-Berkeley, Berkeley, CA, USA; Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Carlos J Bustamante
- QB3-Berkeley, Berkeley, CA, USA; Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California Berkeley, Berkeley, CA, USA; Department of Physics, University of California Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA; Kavli Energy Nanoscience Institute, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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9
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Huang K, Fang X. A review on recent advances in methods for site-directed spin labeling of long RNAs. Int J Biol Macromol 2023; 239:124244. [PMID: 37001783 DOI: 10.1016/j.ijbiomac.2023.124244] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 01/12/2023] [Accepted: 03/15/2023] [Indexed: 03/31/2023]
Abstract
RNAs are important biomolecules that play essential roles in various cellular processes and are crucially linked with many human diseases. The key to elucidate the mechanisms underlying their biological functions and develop RNA-based therapeutics is to investigate RNA structure and dynamics and their connections to function in detail using a variety of approaches. Magnetic resonance techniques including paramagnetic nuclear magnetic resonance (NMR) and electron magnetic resonance (EPR) spectroscopies have proved to be powerful tools to gain insights into such properties. The prerequisites for paramagnetic NMR and EPR studies on RNAs are to achieve site-specific spin labeling of the intrinsically diamagnetic RNAs, which however is not trivial, especially for long ones. In this review, we present some covalent labeling strategies that allow site-specific introduction of electron spins to long RNAs. Generally, these strategies include assembly of long RNAs via enzymatic ligation of short oligonucleotides, co- and post-transcriptional site-specific labeling empowered with the unnatural base pair system, and direct enzymatic functionalization of natural RNAs. We introduce a few case studies to discuss the advantages and limitations of each strategy, and to provide a vision for the future development.
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10
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Jouravleva K, Golovenko D, Demo G, Dutcher RC, Hall TMT, Zamore PD, Korostelev AA. Structural basis of microRNA biogenesis by Dicer-1 and its partner protein Loqs-PB. Mol Cell 2022; 82:4049-4063.e6. [PMID: 36182693 PMCID: PMC9637774 DOI: 10.1016/j.molcel.2022.09.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/24/2022] [Accepted: 08/31/2022] [Indexed: 12/22/2022]
Abstract
In animals and plants, Dicer enzymes collaborate with double-stranded RNA-binding domain (dsRBD) proteins to convert precursor-microRNAs (pre-miRNAs) into miRNA duplexes. We report six cryo-EM structures of Drosophila Dicer-1 that show how Dicer-1 and its partner Loqs‑PB cooperate (1) before binding pre-miRNA, (2) after binding and in a catalytically competent state, (3) after nicking one arm of the pre-miRNA, and (4) following complete dicing and initial product release. Our reconstructions suggest that pre-miRNA binds a rare, open conformation of the Dicer‑1⋅Loqs‑PB heterodimer. The Dicer-1 dsRBD and three Loqs‑PB dsRBDs form a tight belt around the pre-miRNA, distorting the RNA helix to place the scissile phosphodiester bonds in the RNase III active sites. Pre-miRNA cleavage shifts the dsRBDs and partially closes Dicer-1, which may promote product release. Our data suggest a model for how the Dicer‑1⋅Loqs‑PB complex affects a complete cycle of pre-miRNA recognition, stepwise endonuclease cleavage, and product release.
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Affiliation(s)
- Karina Jouravleva
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Dmitrij Golovenko
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Gabriel Demo
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA; Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 62500, Czech Republic
| | - Robert C Dutcher
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, USA.
| | - Phillip D Zamore
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA; Howard Hughes Medical Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
| | - Andrei A Korostelev
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
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11
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Liu X, Zhang Y, Zhou S, Dain L, Mei L, Zhu G. Circular RNA: An emerging frontier in RNA therapeutic targets, RNA therapeutics, and mRNA vaccines. J Control Release 2022; 348:84-94. [PMID: 35649485 PMCID: PMC9644292 DOI: 10.1016/j.jconrel.2022.05.043] [Citation(s) in RCA: 107] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 05/17/2022] [Accepted: 05/25/2022] [Indexed: 12/13/2022]
Abstract
Circular RNAs (circRNA) is a class of natural (biogenic) or synthetic closed RNA without 5' or 3' ends. Meanwhile, their unique covalently-closed structures of circRNA prevent RNA degradation by exonucleases, thereby empowering them with high pharmaceutical stability and biostability relative to current standard-of-care linear mRNA. Natural circRNA can be non-coding RNAs as well as protein-coding RNA, the latter of which was recently discovered. The physiological functions of biogenic circRNAs, which largely remain elusive, include protein and gene sponges, cell activity modulators, and protein translation. The discovery that the circRNA levels can be correlated with some human diseases empowers circRNA with the potential as a novel type of disease biomarkers and a noncanonical class of therapeutic targets. Recently, synthetic circRNA have been engineered to explore their applications as a novel class of mRNA therapeutics and vaccines. In this review, we will discuss the current understanding of the biogenesis and physiological functions of natural circRNAs, the approaches to circRNA synthesis, and current research in the exploration of endogenous circRNAs as novel therapeutic targets and testing circRNAs as an emerging class of RNA therapeutics and vaccines.
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Affiliation(s)
- Xiang Liu
- Department of Pharmaceutics and Center for Pharmaceutical Engineering and Sciences, School of Pharmacy, Institute for Structural Biology and Drug Discovery, The Developmental Therapeutics Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Yu Zhang
- Department of Pharmaceutics and Center for Pharmaceutical Engineering and Sciences, School of Pharmacy, Institute for Structural Biology and Drug Discovery, The Developmental Therapeutics Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Shurong Zhou
- Department of Pharmaceutics and Center for Pharmaceutical Engineering and Sciences, School of Pharmacy, Institute for Structural Biology and Drug Discovery, The Developmental Therapeutics Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Lauren Dain
- Department of Pharmaceutics and Center for Pharmaceutical Engineering and Sciences, School of Pharmacy, Institute for Structural Biology and Drug Discovery, The Developmental Therapeutics Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Lei Mei
- Department of Pharmaceutics and Center for Pharmaceutical Engineering and Sciences, School of Pharmacy, Institute for Structural Biology and Drug Discovery, The Developmental Therapeutics Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Guizhi Zhu
- Department of Pharmaceutics and Center for Pharmaceutical Engineering and Sciences, School of Pharmacy, Institute for Structural Biology and Drug Discovery, The Developmental Therapeutics Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA.
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12
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Zhou H, Li Y, Gan Y, Wang R. Total RNA Synthesis and its Covalent Labeling Innovation. Top Curr Chem (Cham) 2022; 380:16. [PMID: 35218412 DOI: 10.1007/s41061-022-00371-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/24/2022] [Indexed: 12/16/2022]
Abstract
RNA plays critical roles in a wide range of physiological processes. For example, it is well known that RNA plays an important role in regulating gene expression, cell proliferation, and differentiation, and many other chemical and biological processes. However, the research community still suffers from limited approaches that can be applied to readily visualize a specific RNA-of-interest (ROI). Several methods can be used to track RNAs; these rely mainly on biological properties, namely, hybridization, aptamer, reporter protein, and protein binding. With respect to covalent approaches, very few cases have been reported. Happily, several new methods for efficient labeling studies of ROIs have been demonstrated successfully in recent years. Additionally, methods employed for the detection of ROIs by RNA modifying enzymes have also proved feasible. Several approaches, namely, phosphoramidite chemistry, in vitro transcription reactions, co-transcription reactions, chemical post-modification, RNA modifying enzymes, ligation, and other methods targeted at RNA labeling have been revealed in the past decades. To illustrate the most recent achievements, this review aims to summarize the most recent research in the field of synthesis of RNAs-of-interest bearing a variety of unnatural nucleosides, the subsequent RNA labeling research via biocompatible ligation, and beyond.
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Affiliation(s)
- Hongling Zhou
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yuanyuan Li
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Youfang Gan
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Rui Wang
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China. .,Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Huazhong University of Science and Technology, Wuhan, 430030, China. .,Key Laboratory of Natural Product and Resource, Shanghai Institute of Organic Chemistry, Shanghai, 230030, China.
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13
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Blümler A, Schwalbe H, Heckel A. Solid‐Phase‐Supported Chemoenzymatic Synthesis of a Light‐Activatable tRNA Derivative. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202111613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Anja Blümler
- Institute for Organic Chemistry and Chemical Biology Goethe University Frankfurt am Main Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology Goethe University Frankfurt am Main Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance BMRZ Goethe University Frankfurt am Main Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology Goethe University Frankfurt am Main Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
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14
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Blümler A, Schwalbe H, Heckel A. Solid-Phase-Supported Chemoenzymatic Synthesis of a Light-Activatable tRNA Derivative. Angew Chem Int Ed Engl 2022; 61:e202111613. [PMID: 34738704 PMCID: PMC9299214 DOI: 10.1002/anie.202111613] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Indexed: 12/14/2022]
Abstract
Herein, we present a multi-cycle chemoenzymatic synthesis of modified RNA with simplified solid-phase handling to overcome size limitations of RNA synthesis. It combines the advantages of classical chemical solid-phase synthesis and enzymatic synthesis using magnetic streptavidin beads and biotinylated RNA. Successful introduction of light-controllable RNA nucleotides into the tRNAMet sequence was confirmed by gel electrophoresis and mass spectrometry. The methods tolerate modifications in the RNA phosphodiester backbone and allow introductions of photocaged and photoswitchable nucleotides as well as photocleavable strand breaks and fluorophores.
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Affiliation(s)
- Anja Blümler
- Institute for Organic Chemistry and Chemical BiologyGoethe University Frankfurt am MainMax-von-Laue-Strasse 760438Frankfurt/MainGermany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical BiologyGoethe University Frankfurt am MainMax-von-Laue-Strasse 760438Frankfurt/MainGermany
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance BMRZGoethe University Frankfurt am MainMax-von-Laue-Strasse 760438Frankfurt/MainGermany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical BiologyGoethe University Frankfurt am MainMax-von-Laue-Strasse 760438Frankfurt/MainGermany
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15
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Analysis of the conformational space and dynamics of RNA helicases by single-molecule FRET in solution and on surfaces. Methods Enzymol 2022; 673:251-310. [DOI: 10.1016/bs.mie.2022.03.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Obi P, Chen YG. The design and synthesis of circular RNAs. Methods 2021; 196:85-103. [PMID: 33662562 PMCID: PMC8670866 DOI: 10.1016/j.ymeth.2021.02.020] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 12/13/2022] Open
Abstract
Circular RNAs (circRNAs) are a novel class of RNAs distinguished by their single-stranded, covalently-closed topology. Although initially perceived as rare byproducts of aberrant splicing, circRNAs are now recognized as ubiquitously expressed and functionally significant. These discoveries have led to a growing need for ways to model circRNAs in living cells to advance our understanding of their biogenesis, regulation, and function, and to adopt them as new technologies for application within research and medicine. In this review, we provide an updated summary of approaches used to produce circRNAs in vitro and in vivo, the latter of which has grown considerably in recent years. Given increased interest in the unique functions carried out by individual circRNAs, we further dedicate a section on how to customize synthesized circRNAs for specific biological roles. We focus on the most common applications, including designing circRNAs for protein delivery, to target miRNAs and proteins, to act as fluorescent reporters, and to modulate cellular immunity.
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Affiliation(s)
- Prisca Obi
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Y Grace Chen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
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17
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Depmeier H, Hoffmann E, Bornewasser L, Kath‐Schorr S. Strategies for Covalent Labeling of Long RNAs. Chembiochem 2021; 22:2826-2847. [PMID: 34043861 PMCID: PMC8518768 DOI: 10.1002/cbic.202100161] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 05/26/2021] [Indexed: 12/17/2022]
Abstract
The introduction of chemical modifications into long RNA molecules at specific positions for visualization, biophysical investigations, diagnostic and therapeutic applications still remains challenging. In this review, we present recent approaches for covalent internal labeling of long RNAs. Topics included are the assembly of large modified RNAs via enzymatic ligation of short synthetic oligonucleotides and synthetic biology approaches preparing site-specifically modified RNAs via in vitro transcription using an expanded genetic alphabet. Moreover, recent approaches to employ deoxyribozymes (DNAzymes) and ribozymes for RNA labeling and RNA methyltransferase based labeling strategies are presented. We discuss the potentials and limits of the individual methods, their applicability for RNAs with several hundred to thousands of nucleotides in length and indicate future directions in the field.
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Affiliation(s)
- Hannah Depmeier
- University of CologneDepartment of ChemistryGreinstr. 450939CologneGermany
| | - Eva Hoffmann
- University of CologneDepartment of ChemistryGreinstr. 450939CologneGermany
| | - Lisa Bornewasser
- University of CologneDepartment of ChemistryGreinstr. 450939CologneGermany
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18
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Olenginski LT, Taiwo KM, LeBlanc RM, Dayie TK. Isotope-Labeled RNA Building Blocks for NMR Structure and Dynamics Studies. Molecules 2021; 26:5581. [PMID: 34577051 PMCID: PMC8466439 DOI: 10.3390/molecules26185581] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/05/2021] [Accepted: 09/07/2021] [Indexed: 01/19/2023] Open
Abstract
RNA structural research lags behind that of proteins, preventing a robust understanding of RNA functions. NMR spectroscopy is an apt technique for probing the structures and dynamics of RNA molecules in solution at atomic resolution. Still, RNA analysis by NMR suffers from spectral overlap and line broadening, both of which worsen for larger RNAs. Incorporation of stable isotope labels into RNA has provided several solutions to these challenges. In this review, we summarize the benefits and limitations of various methods used to obtain isotope-labeled RNA building blocks and how they are used to prepare isotope-labeled RNA for NMR structure and dynamics studies.
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Affiliation(s)
- Lukasz T. Olenginski
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA; (L.T.O.); (K.M.T.); (R.M.L.)
| | - Kehinde M. Taiwo
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA; (L.T.O.); (K.M.T.); (R.M.L.)
| | - Regan M. LeBlanc
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA; (L.T.O.); (K.M.T.); (R.M.L.)
- Vertex Pharmaceuticals, 50 Northern Avenue, Boston, MA 02210, USA
| | - Theodore K. Dayie
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA; (L.T.O.); (K.M.T.); (R.M.L.)
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19
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Detection and Labeling of Small Non-Coding RNAs by Splinted Ligation. Methods Mol Biol 2021. [PMID: 33792872 DOI: 10.1007/978-1-0716-1386-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Discovery and characterization of microRNAs (miRNAs) and other families of small RNAs lead researchers to study their structures/functions and their expression patterns. The splinted ligation method described here is based on nucleic acid hybridization. It is optimized for the direct labeling and quantitative detection of small RNAs. A specific bridge DNA oligonucleotide is used, which is perfectly complementary to both the target small RNA and a labeled ligation nucleic acid. The target RNA is subsequently labeled by ligation, detected by analysis in denaturing conditions, and quantified by phosphorimaging. The protocol does not require any specific material, and the procedure is fast and sensitive.
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20
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Advanced approaches for elucidating structures of large RNAs using NMR spectroscopy and complementary methods. Methods 2020; 183:93-107. [DOI: 10.1016/j.ymeth.2020.01.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/11/2019] [Accepted: 01/16/2020] [Indexed: 11/23/2022] Open
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21
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Zhou L, O'Flaherty DK, Szostak JW. Template-Directed Copying of RNA by Non-enzymatic Ligation. Angew Chem Int Ed Engl 2020; 59:15682-15687. [PMID: 32558121 PMCID: PMC7496532 DOI: 10.1002/anie.202004934] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 06/04/2020] [Indexed: 12/12/2022]
Abstract
The non-enzymatic replication of the primordial genetic material is thought to have enabled the evolution of early forms of RNA-based life. However, the replication of oligonucleotides long enough to encode catalytic functions is problematic due to the low efficiency of template copying with mononucleotides. We show that template-directed ligation can assemble long RNAs from shorter oligonucleotides, which would be easier to replicate. The rate of ligation can be greatly enhanced by employing a 3'-amino group at the 3'-end of each oligonucleotide, in combination with an N-alkyl imidazole organocatalyst. These modifications enable the copying of RNA templates by the multistep ligation of tetranucleotide building blocks, as well as the assembly of long oligonucleotides using short splint oligonucleotides. We also demonstrate the formation of long oligonucleotides inside model prebiotic vesicles, which suggests a potential route to the assembly of artificial cells capable of evolution.
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Affiliation(s)
- Lijun Zhou
- Howard Hughes Medical InstituteDepartment of Molecular BiologyCenter for Computational and Integrative BiologyMassachusetts General HospitalBostonMA02114 (USA), E
| | - Derek K. O'Flaherty
- Howard Hughes Medical InstituteDepartment of Molecular BiologyCenter for Computational and Integrative BiologyMassachusetts General HospitalBostonMA02114 (USA), E
- Present address: Alnylam PharmaceuticalsCambridgeMA02142USA
| | - Jack W. Szostak
- Howard Hughes Medical InstituteDepartment of Molecular BiologyCenter for Computational and Integrative BiologyMassachusetts General HospitalBostonMA02114 (USA), E
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22
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Zhou L, O'Flaherty DK, Szostak JW. Template‐Directed Copying of RNA by Non‐enzymatic Ligation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004934] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Lijun Zhou
- Howard Hughes Medical Institute Department of Molecular Biology Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 (USA), E
| | - Derek K. O'Flaherty
- Howard Hughes Medical Institute Department of Molecular Biology Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 (USA), E
- Present address: Alnylam Pharmaceuticals Cambridge MA 02142 USA
| | - Jack W. Szostak
- Howard Hughes Medical Institute Department of Molecular Biology Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 (USA), E
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23
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Yu F, Zhang Y, Cheng C, Wang W, Zhou Z, Rang W, Yu H, Wei Y, Wu Q, Zhang Y. Poly(A)-seq: A method for direct sequencing and analysis of the transcriptomic poly(A)-tails. PLoS One 2020; 15:e0234696. [PMID: 32544193 PMCID: PMC7297374 DOI: 10.1371/journal.pone.0234696] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 06/02/2020] [Indexed: 12/19/2022] Open
Abstract
Poly(A) tails at the 3' end of eukaryotic messenger RNAs control mRNA stability and translation efficiency. Facilitated by various NGS methods, alternative polyadenylation sites determining the 3'-UTR length of gene transcripts have been extensively studied. However, poly(A) lengths demonstrating dynamic and developmental regulation remain largely unexplored. The recently developed NGS-based methods for genome-wide poly(A) profiling have promoted the study of genom-wide poly(A) dynamics. Here we present a straight forward NGS-method for poly(A) profiling, which applies a direct 3'-end adaptor ligation and the template switching for 5'-end adaptor ligation for cDNA library construction. Poly(A) lengths are directly calculated from base call data using a self-developed pipeline pA-finder. The libraries were directly sequenced from the 3'-UTR regions into the followed poly(A) tails, firstly on NextSeq 500 to produce single-end 300-nt reads, demonstrating the method feasibility and that optimization of the fragmented RNA size for cDNA library construction could detecting longer poly (A) tails. We next applied Poly(A)-seq cDNA libraries containing 40-nt and 120-nt poly(A) tail spike-in RNAs on HiSeq X-ten and NovaSeq 6000 to obtain 150-nt and 250-nt pair-end reads. The sequencing profiles of the spike-in RNAs demonstrated both high accuracy and high quality score in reading poly(A) tails. The poly(A) signal bleeding into the 3' adaptor sequence and a sharp decreased quality score at the junction were observed, allowing the modification of pA-finder to remove homopolymeric signal bleeding. We hope that wide applications of Poly(A)-seq help facilitate the study of the development- and disease-related poly(A) dynamics and regulation, and of the recent emerging mixed tailing regulation.
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Affiliation(s)
- Fengyun Yu
- Laboratory for Genomics Regulation and Human Health, ABLife Inc., Wuhan, PR China
- ABLife BioBigData Instibute, Wuhan, PR China
| | - Yu Zhang
- Center for Genomics Analysis, ABLife Inc., Wuhan, PR China
| | - Chao Cheng
- ABLife BioBigData Instibute, Wuhan, PR China
- Center for Genomics Analysis, ABLife Inc., Wuhan, PR China
| | - Wenqing Wang
- Center for Genomics Analysis, ABLife Inc., Wuhan, PR China
| | - Zisong Zhou
- Center for Genomics Analysis, ABLife Inc., Wuhan, PR China
| | - Wenliang Rang
- Laboratory for Genomics Regulation and Human Health, ABLife Inc., Wuhan, PR China
| | - Han Yu
- Laboratory for Genomics Regulation and Human Health, ABLife Inc., Wuhan, PR China
| | - Yaxun Wei
- Center for Genomics Analysis, ABLife Inc., Wuhan, PR China
| | - Qijia Wu
- Laboratory for Genomics Regulation and Human Health, ABLife Inc., Wuhan, PR China
| | - Yi Zhang
- Laboratory for Genomics Regulation and Human Health, ABLife Inc., Wuhan, PR China
- ABLife BioBigData Instibute, Wuhan, PR China
- Center for Genomics Analysis, ABLife Inc., Wuhan, PR China
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24
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Palumbo CM, Gutierrez-Bujari JM, O'Geen H, Segal DJ, Beal PA. Versatile 3' Functionalization of CRISPR Single Guide RNA. Chembiochem 2020; 21:1633-1640. [PMID: 31943634 PMCID: PMC7323579 DOI: 10.1002/cbic.201900736] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Indexed: 01/06/2023]
Abstract
Specific applications of CRISPR/Cas genome editing systems benefit from chemical modifications of the sgRNA. Herein we describe a versatile and efficient strategy for functionalization of the 3'-end of a sgRNA. An exemplary collection of six chemically modified sgRNAs was prepared containing crosslinkers, a fluorophore and biotin. Modification of the sgRNA 3'-end was broadly tolerated by Streptococcus pyogenes Cas9 in an in vitro DNA cleavage assay. The 3'-biotinylated sgRNA was used as an affinity reagent to identify IGF2BP1, YB1 and hnRNP K as sgRNA-binding proteins present in HEK293T cells. Overall, the modification strategy presented here has the potential to expand on current applications of CRISPR/Cas systems.
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Affiliation(s)
- Cody M Palumbo
- Department of Chemistry, University of California Davis, One Shields Ave., Davis, CA, 95616, USA
| | - Jeton M Gutierrez-Bujari
- Department of Chemistry, University of California Davis, One Shields Ave., Davis, CA, 95616, USA
| | - Henriette O'Geen
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, CA, 95616, USA
| | - David J Segal
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, CA, 95616, USA
| | - Peter A Beal
- Department of Chemistry, University of California Davis, One Shields Ave., Davis, CA, 95616, USA
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25
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Fukuda S, Yan S, Komi Y, Sun M, Gabizon R, Bustamante C. The Biogenesis of SRP RNA Is Modulated by an RNA Folding Intermediate Attained during Transcription. Mol Cell 2019; 77:241-250.e8. [PMID: 31706702 DOI: 10.1016/j.molcel.2019.10.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 08/29/2019] [Accepted: 10/04/2019] [Indexed: 11/16/2022]
Abstract
The signal recognition particle (SRP), responsible for co-translational protein targeting and delivery to cellular membranes, depends on the native long-hairpin fold of its RNA to confer functionality. Since RNA initiates folding during its synthesis, we used high-resolution optical tweezers to follow in real time the co-transcriptional folding of SRP RNA. Surprisingly, SRP RNA folding is robust to transcription rate changes and the presence or absence of its 5'-precursor sequence. The folding pathway also reveals the obligatory attainment of a non-native hairpin intermediate (H1) that eventually rearranges into the native fold. Furthermore, H1 provides a structural platform alternative to the native fold for RNase P to bind and mature SRP RNA co-transcriptionally. Delays in attaining the final native fold are detrimental to the cell, altogether showing that a co-transcriptional folding pathway underpins the proper biogenesis of function-essential SRP RNA.
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Affiliation(s)
- Shingo Fukuda
- Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, CA, USA; Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Science, Tokyo, Japan; Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan.
| | - Shannon Yan
- Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
| | - Yusuke Komi
- Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, CA, USA; Laboratory for Protein Conformation Diseases, RIKEN Center for Brain Science, Wako, Saitama, Japan
| | - Mingxuan Sun
- Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Ronen Gabizon
- Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, CA, USA
| | - Carlos Bustamante
- Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, Berkeley, CA, USA; Biophysics Graduate Group, University of California, Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA; Department of Physics, University of California, Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA; Kavli Energy Nanoscience Institute, University of California, Berkeley, Berkeley, CA, USA.
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26
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Jones CP, Panja S, Woodson SA, Ferré-D'Amaré AR. Monitoring co-transcriptional folding of riboswitches through helicase unwinding. Methods Enzymol 2019; 623:209-227. [PMID: 31239047 DOI: 10.1016/bs.mie.2019.05.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In the cell, RNAs fold and begin to function as they are being transcribed. In contrast, in the laboratory, RNAs are typically studied after transcription is completed. Co-transcriptional folding can regulate the function of riboswitches and ribozymes and dictate the order of ribonucleoprotein assembly. Methods to observe and investigate RNA folding and activity during transcription are therefore desirable, yet synchronizing RNA polymerases and incorporating labels at specific sites for biophysical studies can be challenging. A recent methodological advance has been to harness highly processive, engineered "super-helicases" to unwind hybrid RNA-DNA duplexes, thereby releasing the RNA 5'-3'. When combined with single-molecule fluorescence detection, RNA folding and concomitant activity can be studied in vitro in a manner that mimics vectorial folding during transcription. Herein, we describe methods for designing and preparing fluorescently labeled RNA-DNA duplex substrates for sequential helicase-dependent RNA folding experiments.
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Affiliation(s)
- Christopher P Jones
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, United States
| | - Subrata Panja
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, United States
| | - Sarah A Woodson
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, United States
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, United States.
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27
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Torres AG, Wulff TF, Rodríguez-Escribà M, Camacho N, Ribas de Pouplana L. Detection of Inosine on Transfer RNAs without a Reverse Transcription Reaction. Biochemistry 2018; 57:5641-5647. [PMID: 30199619 DOI: 10.1021/acs.biochem.8b00718] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Inosine at the "wobble" position (I34) is one of the few essential posttranscriptional modifications in tRNAs (tRNAs). It results from the deamination of adenosine and occurs in bacteria on tRNAArgACG and in eukarya on six or seven additional tRNA substrates. Because inosine is structurally a guanosine analogue, reverse transcriptases recognize it as a guanosine. Most methods used to examine the presence of inosine rely on this phenomenon and detect the modified base as a change in the DNA sequence that results from the reverse transcription reaction. These methods, however, cannot always be applied to tRNAs because reverse transcription can be compromised by the presence of other posttranscriptional modifications. Here we present SL-ID (splinted ligation-based inosine detection), a reverse transcription-free method for detecting inosine based on an I34-dependent specific cleavage of tRNAs by endonuclease V, followed by a splinted ligation and polyacrylamide gel electrophoresis analysis. We show that the method can detect I34 on different tRNA substrates and can be applied to total RNA derived from different species, cell types, and tissues. Here we apply the method to solve previous controversies regarding the modification status of mammalian tRNAArgACG.
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Affiliation(s)
- Adrian G Torres
- Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology , Parc Científic de Barcelona, C/Baldiri Reixac 10 , 08028 Barcelona , Catalonia , Spain
| | - Thomas F Wulff
- Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology , Parc Científic de Barcelona, C/Baldiri Reixac 10 , 08028 Barcelona , Catalonia , Spain
| | - Marta Rodríguez-Escribà
- Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology , Parc Científic de Barcelona, C/Baldiri Reixac 10 , 08028 Barcelona , Catalonia , Spain
| | - Noelia Camacho
- Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology , Parc Científic de Barcelona, C/Baldiri Reixac 10 , 08028 Barcelona , Catalonia , Spain
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology , Parc Científic de Barcelona, C/Baldiri Reixac 10 , 08028 Barcelona , Catalonia , Spain.,Catalan Institution for Research and Advanced Studies (ICREA) , P/Lluis Companys 23 , 08010 Barcelona , Catalonia , Spain
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28
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Liu Y, Holmstrom E, Yu P, Tan K, Zuo X, Nesbitt DJ, Sousa R, Stagno JR, Wang YX. Incorporation of isotopic, fluorescent, and heavy-atom-modified nucleotides into RNAs by position-selective labeling of RNA. Nat Protoc 2018; 13:987-1005. [PMID: 29651055 DOI: 10.1038/nprot.2018.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Site-specific incorporation of labeled nucleotides is an extremely useful synthetic tool for many structural studies (e.g., NMR, electron paramagnetic resonance (EPR), fluorescence resonance energy transfer (FRET), and X-ray crystallography) of RNA. However, specific-position-labeled RNAs >60 nt are not commercially available on a milligram scale. Position-selective labeling of RNA (PLOR) has been applied to prepare large RNAs labeled at desired positions, and all the required reagents are commercially available. Here, we present a step-by-step protocol for the solid-liquid hybrid phase method PLOR to synthesize 71-nt RNA samples with three different modification applications, containing (i) a 13C15N-labeled segment; (ii) discrete residues modified with Cy3, Cy5, or biotin; or (iii) two iodo-U residues. The flexible procedure enables a wide range of downstream biophysical analyses using precisely localized functionalized nucleotides. All three RNAs were obtained in <2 d, excluding time for preparing reagents and optimizing experimental conditions. With optimization, the protocol can be applied to other RNAs with various labeling schemes, such as ligation of segmentally labeled fragments.
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Affiliation(s)
- Yu Liu
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Erik Holmstrom
- JILA, National Institute of Standards and Technology and Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, Colorado, USA
| | - Ping Yu
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Kemin Tan
- Structural Biology Center, Department of Biosciences, Argonne National Laboratory, Argonne, Illinois, USA
| | - Xiaobing Zuo
- Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois, USA
| | - David J Nesbitt
- JILA, National Institute of Standards and Technology and Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, Colorado, USA
| | - Rui Sousa
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas, USA
| | - Jason R Stagno
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
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29
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Liu X, Chen Y, Fierke CA. Inner-Sphere Coordination of Divalent Metal Ion with Nucleobase in Catalytic RNA. J Am Chem Soc 2017; 139:17457-17463. [PMID: 29116782 PMCID: PMC6020041 DOI: 10.1021/jacs.7b08755] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Identification of the function of metal ions and the RNA moieties, particularly nucleobases, that bind metal ions is important in RNA catalysis. Here we combine single-atom and abasic substitutions to probe functions of conserved nucleobases in ribonuclease P (RNase P). Structural and biophysical studies of bacterial RNase P propose direct coordination of metal ions by the nucleobases of conserved uridine and guanosine in helix P4 of the RNA subunit (P RNA). To biochemically probe the function of metal ion interactions, we substituted the universally conserved bulged uridine (U51) in the P4 helix of circularly permuted Bacillus subtilis P RNA with 4-thiouridine, 4-deoxyuridine, and abasic modifications and G378/379 with 2-aminopurine, N7-deazaguanosine, and 6-thioguanosine. The functional group modifications of U51 decrease RNase P-catalyzed phosphodiester bond cleavage 16- to 23-fold, as measured by the single-turnover cleavage rate constant. The activity of the 4-thiouridine RNase P is partially rescued by addition of Cd(II) or Mn(II) ions. This is the first time a metal-rescue experiment provides evidence for inner-sphere divalent metal ion coordination with a nucleobase. Modifications of G379 modestly decrease the cleavage activity of RNase P, suggesting outer-sphere coordination of O6 on G379 to a metal ion. These data provide biochemical evidence for catalytically important interactions of the P4 helix of P RNA with metal ions, demonstrating that the bulged uridine coordinates at least one catalytic metal ion through an inner-sphere interaction. The combination of single-atom and abasic nucleotide substitutions provides a powerful strategy to probe functions of conserved nucleobases in large RNAs.
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Affiliation(s)
- Xin Liu
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Yu Chen
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Carol A. Fierke
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
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30
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Döring J, Hurek T. Arm-specific cleavage and mutation during reverse transcription of 2΄,5΄-branched RNA by Moloney murine leukemia virus reverse transcriptase. Nucleic Acids Res 2017; 45:3967-3984. [PMID: 28160599 PMCID: PMC5399748 DOI: 10.1093/nar/gkx073] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 01/30/2017] [Indexed: 11/14/2022] Open
Abstract
Branchpoint nucleotides of intron lariats induce pausing of DNA synthesis by reverse transcriptases (RTs), but it is not known yet how they direct RT RNase H activity on branched RNA (bRNA). Here, we report the effects of the two arms of bRNA on branchpoint-directed RNA cleavage and mutation produced by Moloney murine leukemia virus (M-MLV) RT during DNA polymerization. We constructed a long-chained bRNA template by splinted-ligation. The bRNA oligonucleotide is chimeric and contains DNA to identify RNA cleavage products by probe hybridization. Unique sequences surrounding the branchpoint facilitate monitoring of bRNA purification by terminal-restriction fragment length polymorphism analysis. We evaluate the M-MLV RT-generated cleavage and mutational patterns. We find that cleavage of bRNA and misprocessing of the branched nucleotide proceed arm-specifically. Bypass of the branchpoint from the 2΄-arm causes single-mismatch errors, whereas bypass from the 3΄-arm leads to deletion mutations. The non-template arm is cleaved when reverse transcription is primed from the 3΄-arm but not from the 2΄-arm. This suggests that RTs flip ∼180° at branchpoints and RNases H cleave the non-template arm depending on its accessibility. Our observed interplay between M-MLV RT and bRNA would be compatible with a bRNA-mediated control of retroviral and related retrotransposon replication.
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Affiliation(s)
- Jessica Döring
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), University of Bremen, PO Box 330440, D-28334 Bremen, Germany
| | - Thomas Hurek
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), University of Bremen, PO Box 330440, D-28334 Bremen, Germany
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31
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Raine A, Manlig E, Wahlberg P, Syvänen AC, Nordlund J. SPlinted Ligation Adapter Tagging (SPLAT), a novel library preparation method for whole genome bisulphite sequencing. Nucleic Acids Res 2017; 45:e36. [PMID: 27899585 PMCID: PMC5389478 DOI: 10.1093/nar/gkw1110] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 10/31/2016] [Indexed: 01/22/2023] Open
Abstract
Sodium bisulphite treatment of DNA combined with next generation sequencing (NGS) is a powerful combination for the interrogation of genome-wide DNA methylation profiles. Library preparation for whole genome bisulphite sequencing (WGBS) is challenging due to side effects of the bisulphite treatment, which leads to extensive DNA damage. Recently, a new generation of methods for bisulphite sequencing library preparation have been devised. They are based on initial bisulphite treatment of the DNA, followed by adaptor tagging of single stranded DNA fragments, and enable WGBS using low quantities of input DNA. In this study, we present a novel approach for quick and cost effective WGBS library preparation that is based on splinted adaptor tagging (SPLAT) of bisulphite-converted single-stranded DNA. Moreover, we validate SPLAT against three commercially available WGBS library preparation techniques, two of which are based on bisulphite treatment prior to adaptor tagging and one is a conventional WGBS method.
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Affiliation(s)
- Amanda Raine
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Sweden
| | - Erika Manlig
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Sweden
| | - Per Wahlberg
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Sweden
| | - Ann-Christine Syvänen
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Sweden
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32
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Pendleton KE, Chen B, Liu K, Hunter OV, Xie Y, Tu BP, Conrad NK. The U6 snRNA m 6A Methyltransferase METTL16 Regulates SAM Synthetase Intron Retention. Cell 2017; 169:824-835.e14. [PMID: 28525753 DOI: 10.1016/j.cell.2017.05.003] [Citation(s) in RCA: 700] [Impact Index Per Article: 100.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 03/16/2017] [Accepted: 04/28/2017] [Indexed: 12/15/2022]
Abstract
Maintenance of proper levels of the methyl donor S-adenosylmethionine (SAM) is critical for a wide variety of biological processes. We demonstrate that the N6-adenosine methyltransferase METTL16 regulates expression of human MAT2A, which encodes the SAM synthetase expressed in most cells. Upon SAM depletion by methionine starvation, cells induce MAT2A expression by enhanced splicing of a retained intron. Induction requires METTL16 and its methylation substrate, a vertebrate conserved hairpin (hp1) in the MAT2A 3' UTR. Increasing METTL16 occupancy on the MAT2A 3' UTR is sufficient to induce efficient splicing. We propose that, under SAM-limiting conditions, METTL16 occupancy on hp1 increases due to inefficient enzymatic turnover, which promotes MAT2A splicing. We further show that METTL16 is the long-unknown methyltransferase for the U6 spliceosomal small nuclear RNA (snRNA). These observations suggest that the conserved U6 snRNA methyltransferase evolved an additional function in vertebrates to regulate SAM homeostasis.
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Affiliation(s)
- Kathryn E Pendleton
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Beibei Chen
- Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kuanqing Liu
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Olga V Hunter
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yang Xie
- Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Benjamin P Tu
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nicholas K Conrad
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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33
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Yadav DK, Lukavsky PJ. NMR solution structure determination of large RNA-protein complexes. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 97:57-81. [PMID: 27888840 DOI: 10.1016/j.pnmrs.2016.10.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/04/2016] [Accepted: 10/04/2016] [Indexed: 06/06/2023]
Abstract
Structure determination of RNA-protein complexes is essential for our understanding of the multiple layers of RNA-mediated posttranscriptional regulation of gene expression. Over the past 20years, NMR spectroscopy became a key tool for structural studies of RNA-protein interactions. Here, we review the progress being made in NMR structure determination of large ribonucleoprotein assemblies. We discuss approaches for the design of RNA-protein complexes for NMR structural studies, established and emerging isotope and segmental labeling schemes suitable for large RNPs and how to gain distance restraints from NOEs, PREs and EPR and orientational information from RDCs and SAXS/SANS in such systems. The new combination of NMR measurements with MD simulations and its potential will also be discussed. Application and combination of these various methods for structure determination of large RNPs will be illustrated with three large RNA-protein complexes (>40kDa) and other interesting complexes determined in the past six and a half years.
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Affiliation(s)
- Deepak Kumar Yadav
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic
| | - Peter J Lukavsky
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic.
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34
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Abstract
RNA with site-specific modification is a useful tool for RNA biology studies. However, generating kilobase (kb) -long RNA with internal modification at a site distant from RNA termini remains challenging. Here we report an enhanced splint ligation technique, proximal disruptor aided ligation (ProDAL), which allows adequate efficiency toward this purpose. The key to our approach is using multiple DNA oligonucleotides, 'proximal disruptors', to target the RNA substrate sequence next to the ligation site. The binding of disruptors helps to free the ligation site from intramolecular RNA basepairing, and consequently promotes more efficient formation of the pre-ligation complex and a higher overall ligation yield. We used naturally occurring 1.0 kb renilla and 1.9 kb firefly luciferase mRNA sequences to test the efficacy of our approach. ProDAL yielded 9-14% efficiency for the ligation between two RNA substrates, both of which were between 414 and 1313 nucleotides (nt) long. ProDAL also allowed similarly high efficiency for generating kb-long RNA with site-specific internal modification by a simple three-part ligation between two long RNA substrates and a modification-carrying RNA oligonucleotide. In comparison, classical splint ligation yielded a significantly lower efficiency of 0-2% in all cases. We expect that ProDAL will benefit studies involving kb-long RNAs, including translation, long non-coding RNAs, RNA splicing and modification, and large ribonucleoprotein complexes.
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Affiliation(s)
- Alexander Zhovmer
- a Molecular Biology Program , Memorial Sloan Kettering Cancer Center , New York , USA
| | - Xiaohui Qu
- a Molecular Biology Program , Memorial Sloan Kettering Cancer Center , New York , USA
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35
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Liu Y, Sousa R, Wang YX. Specific labeling: An effective tool to explore the RNA world. Bioessays 2015; 38:192-200. [DOI: 10.1002/bies.201500119] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yu Liu
- Protein-Nucleic Acid Interaction Section; Structural Biophysics Laboratory; Center for Cancer Research; National Cancer Institute; National Institutes of Health; Frederick MD USA
| | - Rui Sousa
- Department of Biochemistry; University of Texas Health Science Center; San Antonio TX USA
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section; Structural Biophysics Laboratory; Center for Cancer Research; National Cancer Institute; National Institutes of Health; Frederick MD USA
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36
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Detection and labeling of small non-coding RNAs by splinted ligation. Methods Mol Biol 2015; 1296:65-72. [PMID: 25791591 DOI: 10.1007/978-1-4939-2547-6_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Discovery and characterization of microRNAs (miRNAs) and other families of small RNAs lead researchers to study their structures/functions and their expression patterns. The splinted ligation method described here is based on nucleic acid hybridization. It is optimized for the direct labeling and quantitative detection of small RNAs. A specific bridge DNA oligonucleotide is used, which is perfectly complementary to both the target small RNA and a labeled ligation nucleic acid. The target RNA is subsequently labeled by ligation, detected by analysis in denaturing conditions, and quantified by phosphorimaging. The protocol doesn't require any specific material, and the procedure is fast and sensitive.
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37
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Selvam S, Yu Z, Mao H. Exploded view of higher order G-quadruplex structures through click-chemistry assisted single-molecule mechanical unfolding. Nucleic Acids Res 2015; 44:45-55. [PMID: 26626151 PMCID: PMC4705664 DOI: 10.1093/nar/gkv1326] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 11/12/2015] [Indexed: 02/02/2023] Open
Abstract
Due to the long-range nature of high-order interactions between distal components in a biomolecule, transition dynamics of tertiary structures is often too complex to profile using conventional methods. Inspired by the exploded view in mechanical drawing, here, we used laser tweezers to mechanically dissect high-order DNA structures into two constituting G-quadruplexes in the promoter of the human telomerase reverse transcriptase (hTERT) gene. Assisted with click-chemistry coupling, we sandwiched one G-quadruplex with two dsDNA handles while leaving the other unit free. Mechanical unfolding through these handles revealed transition dynamics of the targeted quadruplex in a native environment, which is named as native mechanical segmentation (NMS). Comparison between unfolding of an NMS construct and that of truncated G-quadruplex constructs revealed a quadruplex-quadruplex interaction with 2 kcal/mol stabilization energy. After mechanically targeting the two G-quadruplexes together, the same interaction was observed during the first unfolding step. The unfolding then proceeded through disrupting the weaker G-quadruplex at the 5'-end, followed by the stronger G-quadruplex at the 3'-end via various intermediates. Such a pecking order in unfolding well reflects the hierarchical nature of nucleic acid structures. With surgery-like precisions, we anticipate this NMS approach offers unprecedented perspective to decipher dynamic transitions in complex biomacromolecules.
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Affiliation(s)
- Sangeetha Selvam
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Zhongbo Yu
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
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38
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Duss O, Diarra Dit Konté N, Allain FHT. Cut and paste RNA for nuclear magnetic resonance, paramagnetic resonance enhancement, and electron paramagnetic resonance structural studies. Methods Enzymol 2015; 565:537-62. [PMID: 26577744 DOI: 10.1016/bs.mie.2015.05.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
RNA is a crucial regulator involved in most molecular processes of life. Understanding its function at the molecular level requires high-resolution structural information. However, the dynamic nature of RNA complicates structure determination because crystallization is often not possible or can result in crystal-packing artifacts resulting in nonnative structures. To study RNA and its complexes in solution, we described an approach in which large multi-domain RNA or protein-RNA complex structures can be determined at high resolution from isolated domains determined by nuclear magnetic resonance (NMR) spectroscopy, and then constructing the entire macromolecular structure using electron paramagnetic resonance (EPR) long-range distance constraints. Every step in this structure determination approach requires different types of isotope or spin-labeled RNAs. Here, we present a simple modular RNA cut and paste approach including protocols to generate (1) small isotopically labeled RNAs (<10 nucleotides) for NMR structural studies, which cannot be obtained by standard protocols, (2) large segmentally isotope and/or spin-labeled RNAs for diamagnetic NMR and paramagnetic relaxation enhancement NMR, and (3) large spin-labeled RNAs for pulse EPR spectroscopy.
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Affiliation(s)
- Olivier Duss
- Institute for Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland.
| | | | - Frédéric H-T Allain
- Institute for Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland.
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39
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Kahlscheuer ML, Widom J, Walter NG. Single-Molecule Pull-Down FRET to Dissect the Mechanisms of Biomolecular Machines. Methods Enzymol 2015; 558:539-570. [PMID: 26068753 PMCID: PMC4886477 DOI: 10.1016/bs.mie.2015.01.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Spliceosomes are multimegadalton RNA-protein complexes responsible for the faithful removal of noncoding segments (introns) from pre-messenger RNAs (pre-mRNAs), a process critical for the maturation of eukaryotic mRNAs for subsequent translation by the ribosome. Both the spliceosome and ribosome, as well as many other RNA and DNA processing machineries, contain central RNA components that endow biomolecular complexes with precise, sequence-specific nucleic acid recognition, and versatile structural dynamics. Single-molecule fluorescence (or Förster) resonance energy transfer (smFRET) microscopy is a powerful tool for the study of local and global conformational changes of both simple and complex biomolecular systems involving RNA. The integration of biochemical tools such as immunoprecipitation with advanced methods in smFRET microscopy and data analysis has opened up entirely new avenues toward studying the mechanisms of biomolecular machines isolated directly from complex biological specimens, such as cell extracts. Here, we detail the general steps for using prism-based total internal reflection fluorescence microscopy in exemplary single-molecule pull-down FRET studies of the yeast spliceosome and discuss the broad application potential of this technique.
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Affiliation(s)
- Matthew L Kahlscheuer
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Julia Widom
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA.
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40
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Abraham Punnoose J, Cui Y, Koirala D, Yangyuoru PM, Ghimire C, Shrestha P, Mao H. Interaction of G-quadruplexes in the full-length 3' human telomeric overhang. J Am Chem Soc 2014; 136:18062-9. [PMID: 25438191 DOI: 10.1021/ja510079u] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The 3' human telomeric overhang provides ample opportunities for the formation and interaction of G-quadruplexes, which have shown impacts on many biological functions including telomerase activities in the telomere region. However, in the few investigations on DNA constructs that approach to the full length of the human telomeric overhang, the presence of higher-order quadruplex-quadruplex interactions is still a subject of debate. Herein, we employed dynamic splint ligation (DSL) to prepare a DNA construct, 5'-(TTAGGG)24 or 24G, which has the length comparable to the full stretch of 3' human telomeric overhang. Using mechanical unfolding assays in laser tweezers, we observed a minor population (∼5%) of higher-order interactions between G-quadruplexes, while the majority of the quadruplexes follow the bead-on-a-string model. Analyses on the noninteracting G-quadruplexes in the 24G construct showed features similar to those of the stand-alone G-quadruplexes in the 5'-(TTAGGG)4 (4G) construct. As each 24G construct contains as many as six G-quadruplexes, this method offers increased throughput for the time-consuming mechanical unfolding experiments of non-B DNA structures.
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Affiliation(s)
- Jibin Abraham Punnoose
- Department of Chemistry and Biochemistry, Kent State University , Kent, Ohio 44242, United States
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41
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Esquiaqui JM, Sherman EM, Ionescu SA, Ye JD, Fanucci GE. Characterizing the dynamics of the leader-linker interaction in the glycine riboswitch with site-directed spin labeling. Biochemistry 2014; 53:3526-8. [PMID: 24849816 PMCID: PMC4059530 DOI: 10.1021/bi500404b] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Site-directed
spin labeling with continuous wave electron paramagnetic
resonance (EPR) spectroscopy was utilized to characterize dynamic
features of the kink–turn motif formed through a leader–linker
interaction in the Vibrio cholerae glycine riboswitch.
Efficient incorporation of spin-labels into select sites within the
phosphate backbone of the leader–linker region proceeded via
splinted ligation of chemically synthesized spin-labeled oligonucleotides
to in vitro transcribed larger RNA fragments. The
resultant nitroxide EPR line shapes have spectral characteristics
consistent with a kink–turn motif and reveal differential backbone
dynamics that are modulated by the presence of magnesium, potassium,
and glycine.
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Affiliation(s)
- Jackie M Esquiaqui
- Department of Chemistry, University of Florida , P.O. Box 117200, Gainesville, Florida 32611, United States
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42
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Soundararajan HC, Bullock SL. The influence of dynein processivity control, MAPs, and microtubule ends on directional movement of a localising mRNA. eLife 2014; 3:e01596. [PMID: 24737859 PMCID: PMC3985186 DOI: 10.7554/elife.01596] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Many cellular constituents travel along microtubules in association with multiple copies of motor proteins. How the activity of these motors is regulated during cargo sorting is poorly understood. In this study, we address this issue using a novel in vitro assay for the motility of localising Drosophila mRNAs bound to native dynein-dynactin complexes. High precision tracking reveals that individual RNPs within a population undergo either diffusive, or highly processive, minus end-directed movements along microtubules. RNA localisation signals stimulate the processive movements, with regulation of dynein-dynactin’s activity rather than its total copy number per RNP, responsible for this effect. Our data support a novel mechanism for multi-motor translocation based on the regulation of dynein processivity by discrete cargo-associated features. Studying the in vitro responses of RNPs to microtubule-associated proteins (MAPs) and microtubule ends provides insights into how an RNA population could navigate the cytoskeletal network and become anchored at its destination in cells. DOI:http://dx.doi.org/10.7554/eLife.01596.001 For a cell to do its job, the different components inside it need to be moved to different locations. This is achieved by an elaborate cellular transport system. To move a component to where it needs to be, motor proteins bind to it, often with the assistance of other ‘accessory’ proteins. This cargo-motor complex then moves along a network of tracks within the cell. Viruses also exploit this transport system in order to be trafficked to specific parts of the cell during their life cycles. Many cargos are moved along microtubule tracks. Multiple microtubule motor proteins often attach to the same cargo, but it is unclear how they work together during transport. Previous studies have attempted to address this issue by attaching motor proteins to artificial cargoes, such as synthetic beads. However, these experiments did not include some of the accessory proteins that are thought to play a role during transport within the living cell. Soundararajan and Bullock have now examined how complexes containing multiple motors bound to accessory proteins move molecules of messenger RNA to specific sites within cells. By visualising fruit fly mRNA moving along microtubules attached to a glass surface, the transport process can be studied in detail. It appears that the complexes travel using one of two methods: they either diffuse along the microtubules, which they can do in either direction, or they power themselves along the microtubules, which they can only do in one direction. Although previous experiments with artificial cargos suggested that the number of motors in the complex determines the likelihood of one-way traffic, it appears that one or more accessory proteins are actually in control during mRNA transport. Soundararajan and Bullock also documented how the mRNA-motor complexes react to roadblocks and dead-ends on the microtubule highway. Rather than letting go of the microtubule upon such an encounter, the complexes can reverse back down the track. This behaviour may help them to find a new route to their destination. DOI:http://dx.doi.org/10.7554/eLife.01596.002
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43
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Holmstrom ED, Nesbitt DJ. Single-molecule fluorescence resonance energy transfer studies of the human telomerase RNA pseudoknot: temperature-/urea-dependent folding kinetics and thermodynamics. J Phys Chem B 2014; 118:3853-63. [PMID: 24617561 PMCID: PMC4030807 DOI: 10.1021/jp501893c] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Indexed: 02/06/2023]
Abstract
The ribonucleoprotein telomerase is an RNA-dependent DNA polymerase that catalyzes the repetitive addition of a short, species-specific, DNA sequence to the ends of linear eukaryotic chromosomes. The single RNA component of telomerase contains both the template sequence for DNA synthesis and a functionally critical pseudoknot motif, which can also exist as a less stable hairpin. Here we use a minimal version of the human telomerase RNA pseudoknot to study this hairpin-pseudoknot structural equilibrium using temperature-controlled single-molecule fluorescence resonance energy transfer (smFRET) experiments. The urea dependence of these experiments aids in determination of the folding kinetics and thermodynamics. The wild-type pseudoknot behavior is compared and contrasted to a mutant pseudoknot sequence implicated in a genetic disorder-dyskeratosis congenita. These findings clearly identify that this 2nt noncomplementary mutation destabilizes the folding of the wild-type pseudoknot by substantially reducing the folding rate constant (≈ 400-fold) while only nominally increasing the unfolding rate constant (≈ 5-fold). Furthermore, the urea dependence of the equilibrium and rate constants is used to develop a free energy landscape for this unimolecular equilibrium and propose details about the structure of the transition state. Finally, the urea-dependent folding experiments provide valuable physical insights into the mechanism for destabilization of RNA pseudoknots by such chemical denaturants.
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Affiliation(s)
- Erik D. Holmstrom
- JILA, University of Colorado and National
Institute of Standards and Technology, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0440, United States
| | - David J. Nesbitt
- JILA, University of Colorado and National
Institute of Standards and Technology, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0440, United States
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44
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Haugner JC, Seelig B. Universal labeling of 5'-triphosphate RNAs by artificial RNA ligase enzyme with broad substrate specificity. Chem Commun (Camb) 2014; 49:7322-4. [PMID: 23851643 DOI: 10.1039/c3cc44454f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
An artificial RNA ligase specific to RNA with a 5'-triphosphate (PPP-RNA) exhibits broad sequence specificity on model substrates and secondary siRNAs with direct applications in the identification of PPP-RNAs through sequencing.
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Affiliation(s)
- John C Haugner
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Ave, Saint Paul, MN 55108, USA
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45
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Chaulk SG, Xu Z, Glover MJN, Fahlman RP. MicroRNA miR-92a-1 biogenesis and mRNA targeting is modulated by a tertiary contact within the miR-17~92 microRNA cluster. Nucleic Acids Res 2014; 42:5234-44. [PMID: 24520115 PMCID: PMC4005684 DOI: 10.1093/nar/gku133] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
While functional mature microRNAs (miRNAs) are small ∼22 base oligonucleotides that target specific mRNAs, miRNAs are initially expressed as long transcripts (pri-miRNAs) that undergo sequential processing to yield the mature miRNAs. We have previously reported that the pri-miR-17∼92 cluster adopts a compact globular folded structure that internalizes a 3' core domain resulting in reduced miRNA maturation and subsequent mRNA targeting. Using a site-specific photo-cross-linker we have identified a tertiary contact within the 3' core domain of the pri-miRNA between a non-miRNA stem-loop and the pre-miR-19b hairpin. This tertiary contact is involved in the formation of the compact globular fold of the cluster while its disruption enhances miR-92a expression and mRNA targeting. We propose that this tertiary contact serves as a molecular scaffold to restrict expression of the proposed antiangiogenic miR-92a, allowing for the overall pro-angiogenic effect of miR-17∼92 expression.
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Affiliation(s)
- Steven G Chaulk
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada and Department of Oncology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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46
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Fukunaga R, Colpan C, Han BW, Zamore PD. Inorganic phosphate blocks binding of pre-miRNA to Dicer-2 via its PAZ domain. EMBO J 2014; 33:371-84. [PMID: 24488111 DOI: 10.1002/embj.201387176] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
In Drosophila, Dicer-1 produces microRNAs (miRNAs) from pre-miRNAs, whereas Dicer-2 generates small interfering RNAs from long double-stranded RNA (dsRNA), a process that requires ATP hydrolysis. We previously showed that inorganic phosphate inhibits Dicer-2 cleavage of pre-miRNAs, but not long dsRNAs. Here, we report that phosphate-dependent substrate discrimination by Dicer-2 reflects dsRNA substrate length. Efficient processing by Dicer-2 of short dsRNA requires a 5' terminal phosphate and a two-nucleotide, 3' overhang, but does not require ATP. Phosphate inhibits cleavage of such short substrates. In contrast, cleavage of longer dsRNA requires ATP but no specific end structure: phosphate does not inhibit cleavage of these substrates. Mutation of a pair of conserved arginine residues in the Dicer-2 PAZ domain blocked cleavage of short, but not long, dsRNA. We propose that inorganic phosphate occupies a PAZ domain pocket required to bind the 5' terminal phosphate of short substrates, blocking their use and restricting pre-miRNA processing in flies to Dicer-1. Our study helps explain how a small molecule can alter the substrate specificity of a nucleic acid processing enzyme.
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Affiliation(s)
- Ryuya Fukunaga
- Howard Hughes Medical Institute RNA Therapeutics Institute University of Massachusetts Medical School, Worcester, MA, USA
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47
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Esquiaqui JM, Sherman EM, Ye JD, Fanucci GE. Site-directed spin-labeling strategies and electron paramagnetic resonance spectroscopy for large riboswitches. Methods Enzymol 2014; 549:287-311. [PMID: 25432754 DOI: 10.1016/b978-0-12-801122-5.00013-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Genetic regulation effected by RNA riboswitches is governed by ligand-induced structural reorganization with modulation of RNA conformation and dynamics. Characterization of the conformational states of riboswitches in the presence or absence of salts and ligands is important for understanding how interconversion of riboswitch RNA folding states influences function. The methodology of site-directed spin labeling (SDSL) coupled with electron paramagnetic resonance (EPR) spectroscopy is suitable for such studies, wherein site-specific incorporation of a nitroxide radical spin probe allows for local dynamics and conformational changes to be investigated. This chapter reviews a strategy for SDSL-EPR studies of large riboswitches and uses the full length 232 nucleotide (nt) kink-turn motif-containing Vibrio cholerae (VC) glycine riboswitch as an example. Spin-labeling strategies and the challenges of incorporating spin labels into large riboswitches are reviewed and the approach to overcome these challenges is described. Results are subsequently presented illustrating changes in dynamics within the labeled region of the VC glycine riboswitch as observed using SDSL-EPR.
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Affiliation(s)
- Jackie M Esquiaqui
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Eileen M Sherman
- Department of Chemistry, University of Central Florida, Orlando, Florida, USA
| | - Jing-Dong Ye
- Department of Chemistry, University of Central Florida, Orlando, Florida, USA.
| | - Gail E Fanucci
- Department of Chemistry, University of Florida, Gainesville, Florida, USA.
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48
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Graifer D, Karpova G. General approach for introduction of various chemical labels in specific RNA locations based on insertion of amino linkers. Molecules 2013; 18:14455-69. [PMID: 24287984 PMCID: PMC6269657 DOI: 10.3390/molecules181214455] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 11/12/2013] [Accepted: 11/18/2013] [Indexed: 01/06/2023] Open
Abstract
Introduction of reporter groups at designed RNA sites is a widely accepted approach to gain information about the molecular environment of RNAs in their complexes with other biopolymers formed during various cellular processes. A general approach to obtain RNAs bearing diverse reporter groups at designed locations is based on site-specific insertion of groups containing primary aliphatic amine functions (amino linkers) with their subsequent selective derivatization by appropriate chemicals. This article is a brief review on methods for site-specific introduction of amino linkers in different RNAs. These methods comprise: (i) incorporation of a nucleoside carrying an amino-linker or a function that can be substituted with it into oligoribonucleotides in the course of their chemical synthesis; (ii) assembly of amino linker-containing RNAs from short synthetic fragments via their ligation; (iii) synthesis of amino linker-modified RNAs using T7 RNA polymerase; (iv) insertion of amino linkers into unmodified RNAs at functional groups of a certain type such as the 5'-phosphates and N7 of guanosine residues and (v) introduction of an amino linker into long highly structured RNAs exploiting an approach based on sequence-specific modification of nucleic acids. Particular reporter groups used for derivatization of amino linker-containing RNAs together with types of RNA derivatives obtained and fields of their application are presented.
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Affiliation(s)
- Dmitri Graifer
- Laboratory of Ribosome Structure and Functions, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospect Lavrentieva 8, Novosibirsk 630090, Russia.
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49
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Lohman GJS, Zhang Y, Zhelkovsky AM, Cantor EJ, Evans TC. Efficient DNA ligation in DNA-RNA hybrid helices by Chlorella virus DNA ligase. Nucleic Acids Res 2013; 42:1831-44. [PMID: 24203707 PMCID: PMC3919565 DOI: 10.1093/nar/gkt1032] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Single-stranded DNA molecules (ssDNA) annealed to an RNA splint are notoriously poor substrates for DNA ligases. Herein we report the unexpectedly efficient ligation of RNA-splinted DNA by Chlorella virus DNA ligase (PBCV-1 DNA ligase). PBCV-1 DNA ligase ligated ssDNA splinted by RNA with kcat ≈ 8 x 10(-3) s(-1) and K(M) < 1 nM at 25 °C under conditions where T4 DNA ligase produced only 5'-adenylylated DNA with a 20-fold lower kcat and a K(M) ≈ 300 nM. The rate of ligation increased with addition of Mn(2+), but was strongly inhibited by concentrations of NaCl >100 mM. Abortive adenylylation was suppressed at low ATP concentrations (<100 µM) and pH >8, leading to increased product yields. The ligation reaction was rapid for a broad range of substrate sequences, but was relatively slower for substrates with a 5'-phosphorylated dC or dG residue on the 3' side of the ligation junction. Nevertheless, PBCV-1 DNA ligase ligated all sequences tested with 10-fold less enzyme and 15-fold shorter incubation times than required when using T4 DNA ligase. Furthermore, this ligase was used in a ligation-based detection assay system to show increased sensitivity over T4 DNA ligase in the specific detection of a target mRNA.
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Affiliation(s)
- Gregory J S Lohman
- DNA Enzymes Division, New England BioLabs, Inc., Ipswich, MA 01938-2723, USA, RNA Biology Division, New England BioLabs, Inc., Ipswich, MA 01938-2723, USA and Applications Development, New England BioLabs, Inc., Ipswich, MA 01938-2723, USA
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50
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Shcherbakova I, Hoskins AA, Friedman LJ, Serebrov V, Corrêa IR, Xu MQ, Gelles J, Moore MJ. Alternative spliceosome assembly pathways revealed by single-molecule fluorescence microscopy. Cell Rep 2013; 5:151-65. [PMID: 24075986 DOI: 10.1016/j.celrep.2013.08.026] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 07/18/2013] [Accepted: 08/15/2013] [Indexed: 12/28/2022] Open
Abstract
Removal of introns from nascent transcripts (pre-mRNAs) by the spliceosome is an essential step in eukaryotic gene expression. Previous studies have suggested that the earliest steps in spliceosome assembly in yeast are highly ordered and the stable recruitment of U1 small nuclear ribonucleoprotein particle (snRNP) to the 5' splice site necessarily precedes recruitment of U2 snRNP to the branch site to form the "prespliceosome." Here, using colocalization single-molecule spectroscopy to follow initial spliceosome assembly on eight different S. cerevisiae pre-mRNAs, we demonstrate that active yeast spliceosomes can form by both U1-first and U2-first pathways. Both assembly pathways yield prespliceosomes functionally equivalent for subsequent U5·U4/U6 tri-snRNP recruitment and for intron excision. Although fractional flux through the two pathways varies on different introns, both are operational on all introns studied. Thus, multiple pathways exist for assembling functional spliceosomes. These observations provide insight into the mechanisms of cross-intron coordination of initial spliceosome assembly.
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Affiliation(s)
- Inna Shcherbakova
- Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA
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