1
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Zhao M, Guo J, Chen Z, Wang F. A disposable electrochemical magnetic immunosensor for the rapid and sensitive detection of 5-formylcytosine and 5-carboxylcytosine in DNA. Biosens Bioelectron 2024; 262:116547. [PMID: 38968775 DOI: 10.1016/j.bios.2024.116547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/28/2024] [Accepted: 07/01/2024] [Indexed: 07/07/2024]
Abstract
5-formylcytosine (5 fC) and 5-carboxylcytosine (5caC) serve as key intermediates in DNA demethylation process with significant implications for gene regulation and disease progression. In this study, we introduce a novel electrochemical sensing platform specifically designed for the sensitive and selective detection of 5 fC and 5caC in DNA. Protein A-modified magnetic beads (ProtA-MBs) coupled with specific antibodies facilitate the immunorecognition and enrichment of these modified bases. Signal amplification is achieved through several chemical reactions involving the interaction between N3-kethonaxl and guanine, copper-free click chemistry for the attachment of dibenzocyclooctyne (DBCO)-Biotin, and the subsequent recognition by streptavidin-conjugated horseradish peroxidase (SA-HRP). The assay's readout is performed on a disposable laser-induced graphene (LIG) electrode, modified with the bead-antibody-DNA complex in a magnetic field, and analyzed using differential pulse voltammetry in a system employing hydroquinone (HQ) as the redox mediator and H2O2 as the substrate. This immunosensor displayed excellent sensitivity, with detection limits of 14.8 fM for 5 fC across a 0.1-1000 pM linear range and 87.4 fM for 5caC across a 0.5-5000 pM linear range, and maintained high selectivity even in the presence of interferences from other DNA modifications. Successful application in quantifying 5 fC and 5caC in genomic DNA from cell extracts, with recovery rates between 97.7% to 102.9%, underscores its potential for clinical diagnostics. N3-kethoxal was used for the first time in an electrochemical sensor. This work not only broadens the toolkit for detecting DNA modifications but also provides a fresh impetus for the development of point-of-care testing (POCT) technologies.
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Affiliation(s)
- Mei Zhao
- School of Pharmaceutical Sciences, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), Wuhan University, Wuhan, 430071, China
| | - Jingyi Guo
- School of Pharmaceutical Sciences, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), Wuhan University, Wuhan, 430071, China
| | - Zilin Chen
- School of Pharmaceutical Sciences, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), Wuhan University, Wuhan, 430071, China
| | - Fang Wang
- School of Pharmaceutical Sciences, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), Wuhan University, Wuhan, 430071, China.
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2
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Chatterjee S, Xiao L, Zhong W, Feng S, Kool ET. Selective Arylation of RNA 2'-OH Groups via S NAr Reaction with Trialkylammonium Heterocycles. Angew Chem Int Ed Engl 2024; 63:e202403496. [PMID: 38625814 DOI: 10.1002/anie.202403496] [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: 02/19/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 04/18/2024]
Abstract
Small-molecule reactions at the 2'-OH groups of RNA enable useful applications for transcriptome technology and biology. To date, all reactions have involved carbonyl acylation and mechanistically related sulfonylation, limiting the types of modifications and properties that can be achieved. Here we report that electron-deficient heteroaryl species selectively react with 2'-OH groups of RNA in water via SNAr chemistry. In particular, trialkyl-ammonium (TAA)-activated aromatic heterocycles, prepared in one step from aryl chloride precursors, give high conversions to aryl ether adducts with RNAs in aqueous buffer in ~2-3 h. Remarkably, a TAA triazine previously used only for reaction with carboxylic acids, shows unprecedented selectivity for RNA over water, reacting rapidly with 2'-OH groups while exhibiting a half-life in water of >10 days. We further show that a triazine aryl species can be used as a probe at trace-level yields to map RNA structure in vitro. Finally, we prepare a number of functionalized trialkylammonium triazine reagents and show that they can be used to covalently label RNA efficiently for use in vitro and in living cells. This direct arylation chemistry offers a simple and distinct structural scaffold for post-synthetic RNA modification, with potential utility in multiple applications in transcriptome research.
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Affiliation(s)
| | - Lu Xiao
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Wenrui Zhong
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Sheng Feng
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
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3
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Bose E, Xiong S, Jones AN. Probing RNA structure and dynamics using nanopore and next generation sequencing. J Biol Chem 2024; 300:107317. [PMID: 38677514 PMCID: PMC11145556 DOI: 10.1016/j.jbc.2024.107317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 04/29/2024] Open
Abstract
It has become increasingly evident that the structures RNAs adopt are conformationally dynamic; the various structured states that RNAs sample govern their interactions with other nucleic acids, proteins, and ligands to regulate a myriad of biological processes. Although several biophysical approaches have been developed and used to study the dynamic landscape of structured RNAs, technical limitations have limited their application to all classes of RNA due to variable size and flexibility. Recent advances combining chemical probing experiments with next-generation- and direct sequencing have emerged as an alternative approach to exploring the conformational dynamics of RNA. In this review, we provide a methodological overview of the sequencing-based techniques used to study RNA conformational dynamics. We discuss how different techniques have enabled us to better understand the propensity of RNAs from a variety of different classes to sample multiple conformational states. Finally, we present examples of the ways these techniques have reshaped how we think about RNA structure.
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Affiliation(s)
- Emma Bose
- Department of Chemistry, New York University, New York, New York, USA
| | - Shengwei Xiong
- Department of Chemistry, New York University, New York, New York, USA
| | - Alisha N Jones
- Department of Chemistry, New York University, New York, New York, USA.
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4
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Li T, Cheng C, Liu J. Chemical and Enzyme-Mediated Chemical Reactions for Studying Nucleic Acids and Their Modifications. Chembiochem 2024:e202400220. [PMID: 38742371 DOI: 10.1002/cbic.202400220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 05/16/2024]
Abstract
Nucleic acids are genetic information-carrying molecules inside cells. Apart from basic nucleotide building blocks, there exist various naturally occurring chemical modifications on nucleobase and ribose moieties, which greatly increase the encoding complexity of nuclei acids, contribute to the alteration of nucleic acid structures, and play versatile regulation roles in gene expression. To study the functions of certain nucleic acids in various biological contexts, robust tools to specifically label and identify these macromolecules and their modifications, and to illuminate their structures are highly necessary. In this review, we summarize recent technique advances of using chemical and enzyme-mediated chemical reactions to study nucleic acids and their modifications and structures. By highlighting the chemical principles of these techniques, we aim to present a perspective on the advancement of the field as well as to offer insights into developing specific chemical reactions and precise enzyme catalysis utilized for nucleic acids and their modifications.
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Affiliation(s)
- Tengwei Li
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058, Zhejiang Province, China
| | - Chongguang Cheng
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058, Zhejiang Province, China
| | - Jianzhao Liu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058, Zhejiang Province, China
- Life Sciences Institute, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058, Zhejiang Province, China
- State Key Laboratory of Transvascular Implantation Devices, Hangzhou, 310009, Zhejiang Province, China
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5
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Hoskins I, Rao S, Tante C, Cenik C. Integrated multiplexed assays of variant effect reveal determinants of catechol-O-methyltransferase gene expression. Mol Syst Biol 2024; 20:481-505. [PMID: 38355921 PMCID: PMC11066095 DOI: 10.1038/s44320-024-00018-9] [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: 11/01/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/16/2024] Open
Abstract
Multiplexed assays of variant effect are powerful methods to profile the consequences of rare variants on gene expression and organismal fitness. Yet, few studies have integrated several multiplexed assays to map variant effects on gene expression in coding sequences. Here, we pioneered a multiplexed assay based on polysome profiling to measure variant effects on translation at scale, uncovering single-nucleotide variants that increase or decrease ribosome load. By combining high-throughput ribosome load data with multiplexed mRNA and protein abundance readouts, we mapped the cis-regulatory landscape of thousands of catechol-O-methyltransferase (COMT) variants from RNA to protein and found numerous coding variants that alter COMT expression. Finally, we trained machine learning models to map signatures of variant effects on COMT gene expression and uncovered both directional and divergent impacts across expression layers. Our analyses reveal expression phenotypes for thousands of variants in COMT and highlight variant effects on both single and multiple layers of expression. Our findings prompt future studies that integrate several multiplexed assays for the readout of gene expression.
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Affiliation(s)
- Ian Hoskins
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Shilpa Rao
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Charisma Tante
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Can Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA.
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6
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Oleynikov M, Jaffrey SR. RNA tertiary structure and conformational dynamics revealed by BASH MaP. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.11.589009. [PMID: 38645201 PMCID: PMC11030352 DOI: 10.1101/2024.04.11.589009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The functional effects of an RNA can arise from complex three-dimensional folds known as tertiary structures. However, predicting the tertiary structure of an RNA and whether an RNA adopts distinct tertiary conformations remains challenging. To address this, we developed BASH MaP, a single-molecule dimethyl sulfate (DMS) footprinting method and DAGGER, a computational pipeline, to identify alternative tertiary structures adopted by different molecules of RNA. BASH MaP utilizes potassium borohydride to reveal the chemical accessibility of the N7 position of guanosine, a key mediator of tertiary structures. We used BASH MaP to identify diverse conformational states and dynamics of RNA G-quadruplexes, an important RNA tertiary motif, in vitro and in cells. BASH MaP and DAGGER analysis of the fluorogenic aptamer Spinach reveals that it adopts alternative tertiary conformations which determine its fluorescence states. BASH MaP thus provides an approach for structural analysis of RNA by revealing previously undetectable tertiary structures.
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7
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Xie R, Li W, Ge Y, Zhou Y, Xiao G, Zhao Q, Han Y, Li Y, Chen G. Late-stage guanine C8-H alkylation of nucleosides, nucleotides, and oligonucleotides via photo-mediated Minisci reaction. Nat Commun 2024; 15:2549. [PMID: 38514662 PMCID: PMC10957873 DOI: 10.1038/s41467-024-46671-4] [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: 05/31/2023] [Accepted: 02/26/2024] [Indexed: 03/23/2024] Open
Abstract
Chemically modified nucleosi(ti)des and functional oligonucleotides (ONs, including therapeutic oligonucleotides, aptamer, nuclease, etc.) have been identified playing an essential role in the areas of medicinal chemistry, chemical biology, biotechnology, and nanotechnology. Introduction of functional groups into the nucleobases of ONs mostly relies on the laborious de novo chemical synthesis. Due to the importance of nucleosides modification and aforementioned limitations of functionalizing ONs, herein, we describe a highly efficient site-selective alkylation at the C8-position of guanines in guanosine (together with its analogues), GMP, GDP, and GTP, as well as late-stage functionalization of dinucleotides and single-strand ONs (including ssDNA and RNA) through photo-mediated Minisci reaction. Addition of catechol to assist the formation of alkyl radicals via in situ generated boronic acid catechol ester derivatives (BACED) markedly enhances the yields especially for the reaction of less stable primary alkyl radicals, and is the key to success for the post-synthetic alkylation of ONs. This method features excellent chemoselectivity, no necessity for pre-protection, wide range of substrate scope, various free radical precursors, and little strand lesion. Downstream applications in disease treatment and diagnosis, or as biochemical probes to study biological processes after linking with suitable fluorescent compounds are expected.
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Affiliation(s)
- Ruoqian Xie
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, People's Republic of China
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Wanlu Li
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, People's Republic of China
| | - Yuhua Ge
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, People's Republic of China.
| | - Yutong Zhou
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Key Laboratory of Green and High-End Utilization of Salt Lake Resources, Chinese Academy of Sciences, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining, 810008, Qinghai, People's Republic of China
| | - Guolan Xiao
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Qin Zhao
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Yunxi Han
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Yangyan Li
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Gang Chen
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
- Key Laboratory of Green and High-End Utilization of Salt Lake Resources, Chinese Academy of Sciences, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining, 810008, Qinghai, People's Republic of China.
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8
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An H, Wang X, Li J, Sun H, Zhu S, Ge J, Han L, Shen B, Wang Q. KAS-seq profiling captures transcription dynamics during oocyte maturation. J Ovarian Res 2024; 17:23. [PMID: 38267939 PMCID: PMC10807090 DOI: 10.1186/s13048-023-01342-8] [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: 11/03/2023] [Accepted: 12/31/2023] [Indexed: 01/26/2024] Open
Abstract
In fully grown oocytes, the genome is considered to be globally transcriptionally silenced. However, this conclusion is primarily derived from the results obtained through immunofluorescence staining or inferred from the highly condensed state of chromosomes, lacking more direct evidence. Here, by using a kethoxal-assisted single-stranded DNA sequencing (KAS-seq) approach, we investigated the landscape of single-strand DNA (ssDNA) throughout the genome and provided a readout of the activity and dynamics of transcription during oocyte meiotic maturation. In non-surrounded nucleolus (NSN) oocytes, we observed a robust KAS-seq signal, indicating the high transcriptional activity. In surrounded nucleolus (SN) oocytes, the presence of ssDNA still persists although the KAS-seq signal was relatively weak, suggesting the presence of transcription. Accompanying with the meiotic resumption, the transcriptional activity gradually decreased, and global repression was detected in matured oocytes. Moreover, we preformed the integrative genomics analysis to dissect the transcriptional dynamics during mouse oocyte maturation. In sum, the present study delineates the detailed transcriptional activity during mammalian oocyte maturation.
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Affiliation(s)
- Huiqing An
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 101 Longmian Rd, Nanjing, 211166, China
| | - Xiuwan Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 101 Longmian Rd, Nanjing, 211166, China
| | - Jiashuo Li
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 101 Longmian Rd, Nanjing, 211166, China
| | - Hongzheng Sun
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 101 Longmian Rd, Nanjing, 211166, China
| | - Shuai Zhu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 101 Longmian Rd, Nanjing, 211166, China
| | - Juan Ge
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 101 Longmian Rd, Nanjing, 211166, China
| | - Longsen Han
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 101 Longmian Rd, Nanjing, 211166, China
| | - Bin Shen
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 101 Longmian Rd, Nanjing, 211166, China
| | - Qiang Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 101 Longmian Rd, Nanjing, 211166, China.
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.
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9
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Wu T, Cheng AY, Zhang Y, Xu J, Wu J, Wen L, Li X, Liu B, Dou X, Wang P, Zhang L, Fei J, Li J, Ouyang Z, He C. KARR-seq reveals cellular higher-order RNA structures and RNA-RNA interactions. Nat Biotechnol 2024:10.1038/s41587-023-02109-8. [PMID: 38238480 DOI: 10.1038/s41587-023-02109-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 12/15/2023] [Indexed: 02/12/2024]
Abstract
RNA fate and function are affected by their structures and interactomes. However, how RNA and RNA-binding proteins (RBPs) assemble into higher-order structures and how RNA molecules may interact with each other to facilitate functions remain largely unknown. Here we present KARR-seq, which uses N3-kethoxal labeling and multifunctional chemical crosslinkers to covalently trap and determine RNA-RNA interactions and higher-order RNA structures inside cells, independent of local protein binding to RNA. KARR-seq depicts higher-order RNA structure and detects widespread intermolecular RNA-RNA interactions with high sensitivity and accuracy. Using KARR-seq, we show that translation represses mRNA compaction under native and stress conditions. We determined the higher-order RNA structures of respiratory syncytial virus (RSV) and vesicular stomatitis virus (VSV) and identified RNA-RNA interactions between the viruses and the host RNAs that potentially regulate viral replication.
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Affiliation(s)
- Tong Wu
- Department of Chemistry, University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, Chicago, IL, USA
| | - Anthony Youzhi Cheng
- Department of Genetics and Genome Sciences and Institute for Systems Genomics, University of Connecticut, Farmington, CT, USA
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts, Amherst, MA, USA
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Yuexiu Zhang
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Jiayu Xu
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Jinjun Wu
- Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | - Li Wen
- Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | - Xiao Li
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Bei Liu
- Department of Chemistry, University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, Chicago, IL, USA
| | - Xiaoyang Dou
- Department of Chemistry, University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, Chicago, IL, USA
| | - Pingluan Wang
- Department of Chemistry, University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, Chicago, IL, USA
| | - Linda Zhang
- Department of Chemistry, University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, Chicago, IL, USA
| | - Jingyi Fei
- Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | - Jianrong Li
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Zhengqing Ouyang
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts, Amherst, MA, USA.
| | - Chuan He
- Department of Chemistry, University of Chicago, Chicago, IL, USA.
- Howard Hughes Medical Institute, Chicago, IL, USA.
- Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.
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10
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Xiao L, Fang L, Kool ET. 2'-OH as a universal handle for studying intracellular RNAs. Cell Chem Biol 2024; 31:110-124. [PMID: 37992716 PMCID: PMC10841764 DOI: 10.1016/j.chembiol.2023.10.022] [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: 07/06/2023] [Revised: 09/28/2023] [Accepted: 10/29/2023] [Indexed: 11/24/2023]
Abstract
RNA plays pivotal roles in most cellular processes, serving as both the traditional carrier of genetic information and as a key regulator of cellular functions. The advent of chemical technologies has contributed critically to the analysis of cellular RNA structures, functions, and interactions. Many of these methods and molecules involve the utilization of chemically reactive handles in RNAs, either introduced externally or inherent within the polymer itself. Among these handles, the 2'-hydroxyl (2'-OH) group has emerged as an exceptionally well-suited and general chemical moiety for the modification and profiling of RNAs in intracellular studies. In this review, we provide an overview of the recent advancements in intracellular applications of acylation at the 2'-OH group of RNA. We outline progress made in probing RNA structure and interactomes, controlling RNA function, RNA imaging, and analyzing RNA-small molecule interactions, all achieved in living cells through this simple chemical handle on the biopolymer.
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Affiliation(s)
- Lu Xiao
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Linglan Fang
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA.
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11
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Shioi R, Xiao L, Fang L, Kool ET. Efficient post-synthesis incorporation and conjugation of reactive ketones in RNA via 2'-acylation. Chem Commun (Camb) 2023; 60:232-235. [PMID: 38054242 PMCID: PMC10745195 DOI: 10.1039/d3cc05123d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Despite the broad utility of ketones in bioconjugation, few methods exist to introduce them into RNA. Here we develop highly reactive 2'-OH acylating reagents containing strained-ring ketones, and employ them as versatile labeling handles for RNA.
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Affiliation(s)
- Ryuta Shioi
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
| | - Lu Xiao
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
| | - Linglan Fang
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
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12
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Hoskins I, Rao S, Tante C, Cenik C. Integrated multiplexed assays of variant effect reveal cis-regulatory determinants of catechol- O-methyltransferase gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.02.551517. [PMID: 38014045 PMCID: PMC10680568 DOI: 10.1101/2023.08.02.551517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Multiplexed assays of variant effect are powerful methods to profile the consequences of rare variants on gene expression and organismal fitness. Yet, few studies have integrated several multiplexed assays to map variant effects on gene expression in coding sequences. Here, we pioneered a multiplexed assay based on polysome profiling to measure variant effects on translation at scale, uncovering single-nucleotide variants that increase and decrease ribosome load. By combining high-throughput ribosome load data with multiplexed mRNA and protein abundance readouts, we mapped the cis-regulatory landscape of thousands of catechol-O-methyltransferase (COMT) variants from RNA to protein and found numerous coding variants that alter COMT expression. Finally, we trained machine learning models to map signatures of variant effects on COMT gene expression and uncovered both directional and divergent impacts across expression layers. Our analyses reveal expression phenotypes for thousands of variants in COMT and highlight variant effects on both single and multiple layers of expression. Our findings prompt future studies that integrate several multiplexed assays for the readout of gene expression.
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Affiliation(s)
- Ian Hoskins
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Shilpa Rao
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Charisma Tante
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Can Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
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13
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Xue X, Wang Z, Wang Y, Zhou X. Disease Diagnosis Based on Nucleic Acid Modifications. ACS Chem Biol 2023; 18:2114-2127. [PMID: 37527510 DOI: 10.1021/acschembio.3c00251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Nucleic acid modifications include a wide range of epigenetic and epitranscriptomic factors and impact a wide range of nucleic acids due to their profound influence on biological inheritance, growth, and metabolism. The recently developed methods of mapping and characterizing these modifications have promoted their discovery as well as large-scale studies in eukaryotes, especially in humans. Because of these pioneering strategies, nucleic acid modifications have been shown to have a great impact on human disorders such as cancer. Therefore, whether nucleic acid modifications could become a new type of biomarker remains an open question. In this review, we briefly look back at classical nucleic acid modifications and then focus on the progress made in investigating these modifications as diagnostic biomarkers in clinical therapy and present our perspective on their development prospects.
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Affiliation(s)
- Xiaochen Xue
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Zhiying Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
- Department of Chemistry, College of Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Yafen Wang
- School of Public Health, Wuhan University, Wuhan 430071, China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
- Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
- Cross Research Institute of Zhongnan Hospital, Wuhan University, Wuhan 430071, China
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14
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Xiao L, Fang L, Kool ET. RNA Infrastructure Profiling Illuminates Transcriptome Structure in Crowded Spaces. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.09.561413. [PMID: 37873487 PMCID: PMC10592667 DOI: 10.1101/2023.10.09.561413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
RNAs can fold into compact three-dimensional structures, and most RNAs undergo protein interactions in the cell. These compact and occluded environments can block the ability of structure-probing agents to provide useful data about the folding and modification of the underlying RNA. The development of probes that can analyze structure in crowded settings, and differentiate the proximity of interactions, can shed new light on RNA biology. To this end, here we employ 2'-OH-reactive probes that are small enough to access folded RNA structure underlying many close molecular contacts within cells, providing considerably broader coverage for intracellular RNA structural analysis. We compare reverse transcriptase stops in RNA-Seq data from probes of small and standard size to assess RNA-protein proximity and evaluate solvent-exposed tunnels adjacent to RNA. The data are analyzed first with structurally characterized complexes (human 18S and 28S RNA), and then applied transcriptome-wide to polyadenylated transcripts in HEK293 cells. In our transcriptome profile, the smallest probe acetylimidazole (AcIm) yields 80% greater structural coverage than larger conventional reagent NAIN3, providing enhanced structural information in hundreds of transcripts. We further show that acetyl probes provide superior signals for identifying m6A modification sites in transcripts, and provide information regarding methylation sites that are inaccessible to a larger standard probe. RNA infrastructure profiling (RISP) enables enhanced analysis of transcriptome structure, modification, and interactions in living cells, especially in spatially crowded settings.
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Affiliation(s)
- Lu Xiao
- Department of Chemistry, Stanford University, Stanford, CA 94305, United States
| | - Linglan Fang
- Department of Chemistry, Stanford University, Stanford, CA 94305, United States
| | - Eric T. Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, United States
- Sarafan ChEM-H Institute, Stanford University, Stanford, CA 94305, United States
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15
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Herbert A. Flipons and small RNAs accentuate the asymmetries of pervasive transcription by the reset and sequence-specific microcoding of promoter conformation. J Biol Chem 2023; 299:105140. [PMID: 37544644 PMCID: PMC10474125 DOI: 10.1016/j.jbc.2023.105140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/25/2023] [Accepted: 07/31/2023] [Indexed: 08/08/2023] Open
Abstract
The role of alternate DNA conformations such as Z-DNA in the regulation of transcription is currently underappreciated. These structures are encoded by sequences called flipons, many of which are enriched in promoter and enhancer regions. Through a change in their conformation, flipons provide a tunable mechanism to mechanically reset promoters for the next round of transcription. They act as actuators that capture and release energy to ensure that the turnover of the proteins at promoters is optimized to cell state. Likewise, the single-stranded DNA formed as flipons cycle facilitates the docking of RNAs that are able to microcode promoter conformations and canalize the pervasive transcription commonly observed in metazoan genomes. The strand-specific nature of the interaction between RNA and DNA likely accounts for the known asymmetry of epigenetic marks present on the histone tetramers that pair to form nucleosomes. The role of these supercoil-dependent processes in promoter choice and transcriptional interference is reviewed. The evolutionary implications are examined: the resilience and canalization of flipon-dependent gene regulation is contrasted with the rapid adaptation enabled by the spread of flipon repeats throughout the genome. Overall, the current findings underscore the important role of flipons in modulating the readout of genetic information and how little we know about their biology.
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Affiliation(s)
- Alan Herbert
- Discovery Division, InsideOutBio, Charlestown, Massachusetts, USA.
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16
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Xiang Y, Huang W, Tan L, Chen T, He Y, Irving PS, Weeks KM, Zhang QC, Dong X. Pervasive downstream RNA hairpins dynamically dictate start-codon selection. Nature 2023; 621:423-430. [PMID: 37674078 PMCID: PMC10499604 DOI: 10.1038/s41586-023-06500-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 07/31/2023] [Indexed: 09/08/2023]
Abstract
Translational reprogramming allows organisms to adapt to changing conditions. Upstream start codons (uAUGs), which are prevalently present in mRNAs, have crucial roles in regulating translation by providing alternative translation start sites1-4. However, what determines this selective initiation of translation between conditions remains unclear. Here, by integrating transcriptome-wide translational and structural analyses during pattern-triggered immunity in Arabidopsis, we found that transcripts with immune-induced translation are enriched with upstream open reading frames (uORFs). Without infection, these uORFs are selectively translated owing to hairpins immediately downstream of uAUGs, presumably by slowing and engaging the scanning preinitiation complex. Modelling using deep learning provides unbiased support for these recognizable double-stranded RNA structures downstream of uAUGs (which we term uAUG-ds) being responsible for the selective translation of uAUGs, and allows the prediction and rational design of translating uAUG-ds. We found that uAUG-ds-mediated regulation can be generalized to human cells. Moreover, uAUG-ds-mediated start-codon selection is dynamically regulated. After immune challenge in plants, induced RNA helicases that are homologous to Ded1p in yeast and DDX3X in humans resolve these structures, allowing ribosomes to bypass uAUGs to translate downstream defence proteins. This study shows that mRNA structures dynamically regulate start-codon selection. The prevalence of this RNA structural feature and the conservation of RNA helicases across kingdoms suggest that mRNA structural remodelling is a general feature of translational reprogramming.
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Affiliation(s)
- Yezi Xiang
- Department of Biology, Duke University, Durham, NC, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC, USA
| | - Wenze Huang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Beijing Frontier Research Center for Biological Structures, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Lianmei Tan
- Department of Pharmacology and Cancer Biology, Duke Medical Center, Duke University, Durham, NC, USA
| | - Tianyuan Chen
- Department of Biology, Duke University, Durham, NC, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC, USA
| | - Yang He
- Department of Biology, Duke University, Durham, NC, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC, USA
| | - Patrick S Irving
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Beijing Frontier Research Center for Biological Structures, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Xinnian Dong
- Department of Biology, Duke University, Durham, NC, USA.
- Howard Hughes Medical Institute, Duke University, Durham, NC, USA.
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17
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Umerenkov D, Herbert A, Konovalov D, Danilova A, Beknazarov N, Kokh V, Fedorov A, Poptsova M. Z-flipon variants reveal the many roles of Z-DNA and Z-RNA in health and disease. Life Sci Alliance 2023; 6:e202301962. [PMID: 37164635 PMCID: PMC10172764 DOI: 10.26508/lsa.202301962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/25/2023] [Accepted: 04/28/2023] [Indexed: 05/12/2023] Open
Abstract
Identifying roles for Z-DNA remains challenging given their dynamic nature. Here, we perform genome-wide interrogation with the DNABERT transformer algorithm trained on experimentally identified Z-DNA forming sequences (Z-flipons). The algorithm yields large performance enhancements (F1 = 0.83) over existing approaches and implements computational mutagenesis to assess the effects of base substitution on Z-DNA formation. We show Z-flipons are enriched in promoters and telomeres, overlapping quantitative trait loci for RNA expression, RNA editing, splicing, and disease-associated variants. We cross-validate across a number of orthogonal databases and define BZ junction motifs. Surprisingly, many effects we delineate are likely mediated through Z-RNA formation. A shared Z-RNA motif is identified in SCARF2, SMAD1, and CACNA1 transcripts, whereas other motifs are present in noncoding RNAs. We provide evidence for a Z-RNA fold that promotes adaptive immunity through alternative splicing of KRAB domain zinc finger proteins. An analysis of OMIM and presumptive gnomAD loss-of-function datasets reveals an overlap of Z-flipons with disease-causing variants in 8.6% and 2.9% of Mendelian disease genes, respectively, greatly extending the range of phenotypes mapped to Z-flipons.
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Affiliation(s)
| | - Alan Herbert
- Laboratory of Bioinformatics, Faculty of Computer Science, HSE University, Moscow, Russia
- InsideOutBio, Charlestown, MA, USA
| | - Dmitrii Konovalov
- Laboratory of Bioinformatics, Faculty of Computer Science, HSE University, Moscow, Russia
| | - Anna Danilova
- Laboratory of Bioinformatics, Faculty of Computer Science, HSE University, Moscow, Russia
| | - Nazar Beknazarov
- Laboratory of Bioinformatics, Faculty of Computer Science, HSE University, Moscow, Russia
| | | | - Aleksandr Fedorov
- Laboratory of Bioinformatics, Faculty of Computer Science, HSE University, Moscow, Russia
| | - Maria Poptsova
- Laboratory of Bioinformatics, Faculty of Computer Science, HSE University, Moscow, Russia
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18
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Feng Y, He Z, Luo Z, Sperti FR, Valverde IE, Zhang W, Monchaud D. Side-by-side comparison of G-quadruplex (G4) capture efficiency of the antibody BG4 versus the small-molecule ligands TASQs. iScience 2023; 26:106846. [PMID: 37250775 PMCID: PMC10212998 DOI: 10.1016/j.isci.2023.106846] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/20/2023] [Accepted: 05/04/2023] [Indexed: 05/31/2023] Open
Abstract
The search for G-quadruplex (G4)-forming sequences across the genome is motivated by their involvement in key cellular processes and their putative roles in dysregulations underlying human genetic diseases. Sequencing-based methods have been developed to assess the prevalence of DNA G4s genome wide, including G4-seq to detect G4s in purified DNA (in vitro) using the G4 stabilizer PDS, and G4 chromatin immunoprecipitation sequencing (G4 ChIP-seq) to detect G4s in in situ fixed chromatin (in vivo) using the G4-specific antibody BG4. We recently reported on G4-RNA precipitation and sequencing (G4RP-seq) to assess the in vivo prevalence of RNA G4 landscapes transcriptome wide using the small molecule BioTASQ. Here, we apply this technique for mapping DNA G4s in plants (rice) and compare the efficiency of this new technique, G4-DNA precipitation and sequencing, G4DP-seq, to that of BG4-DNA-IP-seq that we developed for mapping of DNA G4s in rice using BG4. By doing so, we compare the G4 capture ability of small-sized ligands (BioTASQ and BioCyTASQ) versus the antibody BG4.
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Affiliation(s)
- Yilong Feng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, Nanjing, P.R. China
| | - Zexue He
- State Key Laboratory for Crop Genetics and Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, Nanjing, P.R. China
| | - Zhenyu Luo
- State Key Laboratory for Crop Genetics and Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, Nanjing, P.R. China
| | - Francesco Rota Sperti
- Institut de Chimie Moléculaire, ICMUB CNRS UMR 6302, Université de Bourgogne, Dijon, France
| | - Ibai E. Valverde
- Institut de Chimie Moléculaire, ICMUB CNRS UMR 6302, Université de Bourgogne, Dijon, France
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, Nanjing, P.R. China
| | - David Monchaud
- Institut de Chimie Moléculaire, ICMUB CNRS UMR 6302, Université de Bourgogne, Dijon, France
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19
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Li F, Zhou J. G-quadruplexes from non-coding RNAs. J Mol Med (Berl) 2023:10.1007/s00109-023-02314-7. [PMID: 37069370 DOI: 10.1007/s00109-023-02314-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 03/22/2023] [Accepted: 03/30/2023] [Indexed: 04/19/2023]
Abstract
Non-coding RNAs (ncRNAs) are significant regulators of gene expression in a wide range of biological processes, such as transcription, RNA maturation, or translation. ncRNAs interplay with proteins or other RNAs through not only classical sequence-based mechanisms but also unique higher-order structures such as RNA G-quadruplexes (rG4s). rG4s are predictably formed in guanine-rich sequences and are closely related to various human diseases, such as tumors, neurodegenerative diseases, and infections. This review focuses on the vital role of rG4s in ncRNAs, particularly lncRNAs and miRNAs. We outline the dynamic balance between rG4s and RNA stem-loop/hairpin structures and the interplay between ncRNAs and interactors, thereby modulating gene expression and disease progression. A complete understanding of the biological regulatory role and mechanism of rG4s in ncRNAs affirms the critical importance of folding into the appropriate three-dimensional structure in maintaining or modulating the functions of ncRNAs. It makes them novel therapeutic targets for adjusting potential-G4-containing-ncRNAs-associated diseases.
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Affiliation(s)
- Fangyuan Li
- Department Medical Research Central, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
- Clinical Biobank, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Jiang Zhou
- Beijing National Laboratory for Molecular Sciences, Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
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20
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Zhao R, Fang X, Mai Z, Chen X, Mo J, Lin Y, Xiao R, Bao X, Weng X, Zhou X. Transcriptome-wide identification of single-stranded RNA binding proteins. Chem Sci 2023; 14:4038-4047. [PMID: 37063799 PMCID: PMC10094363 DOI: 10.1039/d3sc00957b] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 03/07/2023] [Indexed: 04/18/2023] Open
Abstract
RNA-protein interactions are precisely regulated by RNA secondary structures in various biological processes. Large-scale identification of proteins that interact with particular RNA structure is important to the RBPome. Herein, a kethoxal assisted single-stranded RNA interactome capture (KASRIC) strategy was developed to globally identify single-stranded RNA binding proteins (ssRBPs). This approach combines RNA secondary structure probing technology with the conventional method of RNA-binding proteins profiling, realizing the transcriptome-wide identification of ssRBPs. Applying KASRIC, we identified 3180 candidate RBPs and 244 candidate ssRBPs in HeLa cells. Importantly, the 244 candidate ssRBPs contained 55 previously reported ssRBPs and 189 novel ssRBPs. Function analysis of the candidate ssRBPs exhibited enrichment in cellular processes related to RNA splicing and RNA degradation. The KASRIC strategy will facilitate the investigation of RNA-protein interactions.
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Affiliation(s)
- Ruiqi Zhao
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University Wuhan Hubei 430072 P. R. China
| | - Xin Fang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University Wuhan Hubei 430072 P. R. China
| | - Zhibiao Mai
- Laboratory of RNA Molecular Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences Guangzhou Guangdong Province 510530 China
| | - Xi Chen
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University Wuhan Hubei 430072 P. R. China
| | - Jing Mo
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University Wuhan Hubei 430072 P. R. China
| | - Yingying Lin
- Laboratory of RNA Molecular Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences Guangzhou Guangdong Province 510530 China
| | - Rui Xiao
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University Wuhan Hubei 430071 China
- TaiKang Center for Life and Medical Sciences, Wuhan University Wuhan Hubei 430071 China
| | - Xichen Bao
- Laboratory of RNA Molecular Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences Guangzhou Guangdong Province 510530 China
| | - Xiaocheng Weng
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University Wuhan Hubei 430072 P. R. China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University Wuhan Hubei 430072 P. R. China
- TaiKang Center for Life and Medical Sciences, Wuhan University Wuhan Hubei 430071 China
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21
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Apostolidi M, Stamatopoulou V. Aberrant splicing in human cancer: An RNA structural code point of view. Front Pharmacol 2023; 14:1137154. [PMID: 36909167 PMCID: PMC9995731 DOI: 10.3389/fphar.2023.1137154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 02/14/2023] [Indexed: 02/25/2023] Open
Abstract
Alternative splicing represents an essential process that occurs widely in eukaryotes. In humans, most genes undergo alternative splicing to ensure transcriptome and proteome diversity reflecting their functional complexity. Over the last decade, aberrantly spliced transcripts due to mutations in cis- or trans-acting splicing regulators have been tightly associated with cancer development, largely drawing scientific attention. Although a plethora of single proteins, ribonucleoproteins, complexed RNAs, and short RNA sequences have emerged as nodal contributors to the splicing cascade, the role of RNA secondary structures in warranting splicing fidelity has been underestimated. Recent studies have leveraged the establishment of novel high-throughput methodologies and bioinformatic tools to shed light on an additional layer of splicing regulation in the context of RNA structural elements. This short review focuses on the most recent available data on splicing mechanism regulation on the basis of RNA secondary structure, emphasizing the importance of the complex RNA G-quadruplex structures (rG4s), and other specific RNA motifs identified as splicing silencers or enhancers. Moreover, it intends to provide knowledge on newly established techniques that allow the identification of RNA structural elements and highlight the potential to develop new RNA-oriented therapeutic strategies against cancer.
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Affiliation(s)
- Maria Apostolidi
- Agilent Laboratories, Agilent Technologies, Santa Clara, CA, United States
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22
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Wu T, Lyu R, He C. spKAS-seq reveals R-loop dynamics using low-input materials by detecting single-stranded DNA with strand specificity. SCIENCE ADVANCES 2022; 8:eabq2166. [PMID: 36449625 PMCID: PMC9710868 DOI: 10.1126/sciadv.abq2166] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 10/13/2022] [Indexed: 05/26/2023]
Abstract
R-loops affect transcription and genome stability. Dysregulation of R-loops is related to human diseases. Genome-wide R-loop mapping typically uses the S9.6 antibody or inactive ribonuclease H, both requiring a large number of cells with varying results observed depending on the approach applied. Here, we present strand-specific kethoxal-assisted single-stranded DNA (ssDNA) sequencing (spKAS-seq) to map R-loops by taking advantage of the presence of a ssDNA in the triplex structure. We show that spKAS-seq detects R-loops and their dynamics at coding sequences, enhancers, and other intergenic regions with as few as 50,000 cells. A joint analysis of R-loops and chromatin-bound RNA binding proteins (RBPs) suggested that R-loops can be RBP binding hotspots on the chromatin.
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Affiliation(s)
- Tong Wu
- Department of Chemistry, University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA
| | - Ruitu Lyu
- Department of Chemistry, University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA
| | - Chuan He
- Department of Chemistry, University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA
- Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
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23
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An atypical RNA quadruplex marks RNAs as vectors for gene silencing. Nat Struct Mol Biol 2022; 29:1113-1121. [PMID: 36352138 PMCID: PMC10092862 DOI: 10.1038/s41594-022-00854-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 09/28/2022] [Indexed: 11/11/2022]
Abstract
The addition of poly(UG) ('pUG') repeats to 3' termini of mRNAs drives gene silencing and transgenerational epigenetic inheritance in the metazoan Caenorhabditis elegans. pUG tails promote silencing by recruiting an RNA-dependent RNA polymerase (RdRP) that synthesizes small interfering RNAs. Here we show that active pUG tails require a minimum of 11.5 repeats and adopt a quadruplex (G4) structure we term the pUG fold. The pUG fold differs from known G4s in that it has a left-handed backbone similar to Z-RNA, no consecutive guanosines in its sequence, and three G quartets and one U quartet stacked non-sequentially. The compact pUG fold binds six potassium ions and brings the RNA ends into close proximity. The biological importance of the pUG fold is emphasized by our observations that porphyrin molecules bind to the pUG fold and inhibit both gene silencing and binding of RdRP. Moreover, specific 7-deaza substitutions that disrupt the pUG fold neither bind RdRP nor induce RNA silencing. These data define the pUG fold as a previously unrecognized RNA structural motif that drives gene silencing. The pUG fold can also form internally within larger RNA molecules. Approximately 20,000 pUG-fold sequences are found in noncoding regions of human RNAs, suggesting that the fold probably has biological roles beyond gene silencing.
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24
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Chen Y, Onizuka K, Hazemi ME, Nagatsugi F. Reactivity Modulation of Reactive OFF–ON Type G-Quadruplex Alkylating Agents. Bioconjug Chem 2022; 33:2097-2102. [DOI: 10.1021/acs.bioconjchem.2c00458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yutong Chen
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
- Division for the Establishment of Frontier Sciences of Organization for Advanced Studies, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Madoka E. Hazemi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
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25
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Yu H, Qi Y, Yang B, Yang X, Ding Y. G4Atlas: a comprehensive transcriptome-wide G-quadruplex database. Nucleic Acids Res 2022; 51:D126-D134. [PMID: 36243987 PMCID: PMC9825586 DOI: 10.1093/nar/gkac896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/16/2022] [Accepted: 10/03/2022] [Indexed: 01/29/2023] Open
Abstract
RNA G-quadruplex (rG4) is a vital RNA tertiary structure motif that involves the base pairs on both Hoogsteen and Watson-Crick faces of guanines. rG4 is of great importance in the post-transcriptional regulation of gene expression. Experimental technologies have advanced to identify in vitro and in vivo rG4s across diverse transcriptomes. Building on these recent advances, here we present G4Atlas, the first transcriptome-wide G-quadruplex database, in which we have collated, classified, and visualized transcriptome rG4 experimental data, generated from rG4-seq, chemical profiling and ligand-binding methods. Our comprehensive database includes transcriptome-wide rG4s generated from 82 experimental treatments and 238 samples across ten species. In addition, we have also included RNA secondary structure prediction information across both experimentally identified and unidentified rG4s to enable users to display any potential competitive folding between rG4 and RNA secondary structures. As such, G4Atlas will enable users to explore the general functions of rG4s in diverse biological processes. In addition, G4Atlas lays the foundation for further data-driven deep learning algorithms to examine rG4 structural features.
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Affiliation(s)
- Haopeng Yu
- Correspondence may also be addressed to Haopeng Yu. Tel: +44 1603 450214;
| | | | - Bibo Yang
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Xiaofei Yang
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK,National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China,CAS-JIC Center of Excellence for Plant and Microbial Sciences (CEPAMS), Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yiliang Ding
- To whom correspondence should be addressed. Tel: +44 1603 450266; Fax: +44 1603 450045;
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26
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Xiao L, Fang L, Kool ET. Acylation probing of "generic" RNA libraries reveals critical influence of loop constraints on reactivity. Cell Chem Biol 2022; 29:1341-1352.e8. [PMID: 35662395 PMCID: PMC9391288 DOI: 10.1016/j.chembiol.2022.05.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/16/2022] [Accepted: 05/12/2022] [Indexed: 01/08/2023]
Abstract
The reactivity of RNA 2'-OH acylation is broadly useful both in probing structure and in preparing conjugates. To date, this reactivity has been analyzed in limited sets of biological RNA sequences, leaving open questions of how reactivity varies inherently without regard to sequence in structured contexts. We constructed and probed "generic" structured RNA libraries using homogeneous loop sequences, employing deep sequencing to carry out a systematic survey of reactivity. We find a wide range of RNA reactivities among single-stranded sequences, with nearest neighbors playing substantial roles. Remarkably, certain small loops are found to be far more reactive on average (up to 4,000-fold) than single-stranded RNAs, due to conformational constraints that enhance reactivity. Among loops, we observe large variations in reactivity based on size, type, and position. The results lend insights into RNA designs for achieving high-efficiency local conjugation and provide new opportunities to refine structure analysis.
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Affiliation(s)
- Lu Xiao
- Department of Chemistry and ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Linglan Fang
- Department of Chemistry and ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Eric T Kool
- Department of Chemistry and ChEM-H Institute, Stanford University, Stanford, CA 94305, USA.
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27
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Felix AS, Quillin AL, Mousavi S, Heemstra JM. Harnessing Nature's Molecular Recognition Capabilities to Map and Study RNA Modifications. Acc Chem Res 2022; 55:2271-2279. [PMID: 35900335 PMCID: PMC9388579 DOI: 10.1021/acs.accounts.2c00287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
RNA editing or "epitranscriptomic modification" refers to the processing of RNA that occurs after transcription to alter the sequence or structure of the nucleic acid. These chemical alterations can be found on either the ribose sugar or the nucleobase, and although many are "silent" and do not change the Watson-Crick-Franklin code of the RNA, others result in recoding events. More than 170 RNA modifications have been identified so far, each having a specific biological purpose. Additionally, dysregulated RNA editing has been linked to several types of diseases and disorders. As new modifications are discovered and our understanding of their functional impact grows, so does the need for selective methods of identifying and mapping editing sites in the transcriptome.The most common methods for studying RNA modifications rely on antibodies as affinity reagents; however, antibodies can be difficult to generate and often have undesirable off-target binding. More recently, selective chemical labeling has advanced the field by offering techniques that can be used for the detection, enrichment, and quantification of RNA modifications. In our method using acrylamide for inosine labeling, we demonstrated the versatility with which this approach enables pull-down or downstream functionalization with other tags or affinity handles. Although this method did enable the quantitative analysis of A-to-I editing levels, we found that selectivity posed a significant limitation, likely because of the similar reactivity profiles of inosine and pseudouridine or other nucleobases.Seeking to overcome the inherent limitations of antibodies and chemical labeling methods, a more recent approach to studying the epitranscriptome is through the repurposing of proteins and enzymes that recognize modified RNA. Our laboratory has used Endonuclease V, a repair enzyme that cleaves inosine-containing RNAs, and reprogrammed it to instead bind inosine. We first harnessed EndoV to develop a preparative technique for RNA sequencing that we termed EndoVIPER-seq. This method uses EndoV to enrich inosine-edited RNAs, providing better coverage in RNA sequencing and leading to the discovery of previously undetected A-to-I editing sites. We also leveraged EndoV to create a plate-based immunoassay (EndoVLISA) to quantify inosine in cellular RNA. This approach can detect differential A-to-I editing levels across tissue types or disease states while being independent of RNA sequencing, making it cost-effective and high-throughput. By harnessing the molecular recognition capabilities of this enzyme, we show that EndoV can be repurposed as an "anti-inosine antibody" to develop new methods of detecting and enriching inosine from cellular RNA.Nature has evolved a plethora of proteins and enzymes that selectively recognize and act on RNA modifications, and exploiting the affinity of these biomolecules offers a promising new direction for the field of epitranscriptomics.
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Affiliation(s)
- Ansley S. Felix
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Alexandria L. Quillin
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Shikufa Mousavi
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Jennifer M. Heemstra
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
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28
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Xu B, Zhu Y, Cao C, Chen H, Jin Q, Li G, Ma J, Yang SL, Zhao J, Zhu J, Ding Y, Fang X, Jin Y, Kwok CK, Ren A, Wan Y, Wang Z, Xue Y, Zhang H, Zhang QC, Zhou Y. Recent advances in RNA structurome. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1285-1324. [PMID: 35717434 PMCID: PMC9206424 DOI: 10.1007/s11427-021-2116-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/01/2022] [Indexed: 12/27/2022]
Abstract
RNA structures are essential to support RNA functions and regulation in various biological processes. Recently, a range of novel technologies have been developed to decode genome-wide RNA structures and novel modes of functionality across a wide range of species. In this review, we summarize key strategies for probing the RNA structurome and discuss the pros and cons of representative technologies. In particular, these new technologies have been applied to dissect the structural landscape of the SARS-CoV-2 RNA genome. We also summarize the functionalities of RNA structures discovered in different regulatory layers-including RNA processing, transport, localization, and mRNA translation-across viruses, bacteria, animals, and plants. We review many versatile RNA structural elements in the context of different physiological and pathological processes (e.g., cell differentiation, stress response, and viral replication). Finally, we discuss future prospects for RNA structural studies to map the RNA structurome at higher resolution and at the single-molecule and single-cell level, and to decipher novel modes of RNA structures and functions for innovative applications.
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Affiliation(s)
- Bingbing Xu
- MOE Laboratory of Biosystems Homeostasis & Protection, Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yanda Zhu
- MOE Laboratory of Biosystems Homeostasis & Protection, Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Changchang Cao
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hao Chen
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Qiongli Jin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Guangnan Li
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Junfeng Ma
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Siwy Ling Yang
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Jieyu Zhao
- Department of Chemistry, and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Jianghui Zhu
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology and Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Yiliang Ding
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
| | - Xianyang Fang
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Yongfeng Jin
- MOE Laboratory of Biosystems Homeostasis & Protection, Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Chun Kit Kwok
- Department of Chemistry, and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.
- Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China.
| | - Aiming Ren
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China.
| | - Yue Wan
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A*STAR, Singapore, Singapore.
| | - Zhiye Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Yuanchao Xue
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100101, China.
| | - Huakun Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, 130024, China.
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology and Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China.
| | - Yu Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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29
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Liu H, Chu Z, Yang X. A Key Molecular Regulator, RNA G-Quadruplex and Its Function in Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:926953. [PMID: 35783953 PMCID: PMC9242502 DOI: 10.3389/fpls.2022.926953] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
RNA structure plays key roles in plant growth, development, and adaptation. One of the complex RNA structures is the RNA G-quadruplex (RG4) where guanine-rich sequences are folded into two or more layers of G-quartets. Previous computational predictions of RG4 revealed that it is widespread across the whole transcriptomes in many plant species, raising the hypothesis that RG4 is likely to be an important regulatory motif in plants. Recently, with the advances in both high-throughput sequencing and cell imaging technologies, RG4 can be detected in living cells as well as at the genome-wide scale. Here, we provide a comprehensive review of recent developments in new methods for detecting RG4 in plants. We also summarize the new functions of RG4 in regulating plant growth and development. We then discuss the possible role of RG4 in adapting to environmental conditions along with evolutionary perspectives.
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Affiliation(s)
- Haifeng Liu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, China
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Zhaohui Chu
- State Key Laboratory of Hybrid Rice, Hubei Hongshan Laboratory, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiaofei Yang
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science, Shanghai, China
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30
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Jia S, Wang W, Qin S, Xie S, Zhan L, Wei Q, Lu Z, Zhou X, Chen C, Chen K, Yan S, Tan C, Mao Z, Zhou X. The development of an iridium(III) complex functionalized G-quadruplex probe for the stability of G-quadruplex and lifetime image in cytoplasm. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.05.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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31
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Jin Q, Zhang L, Hu S, Wei G, Wang Z. Probing in vivo RNA Structure With Optimized DMS-MaPseq in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:869267. [PMID: 35432393 PMCID: PMC9009289 DOI: 10.3389/fpls.2022.869267] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/08/2022] [Indexed: 05/11/2023]
Abstract
RNA transcripts form various secondary and tertiary structures that have a wide range of regulatory functions. Several methods have been developed to profile in vivo RNA secondary structure in prokaryotes and eukaryotes. These methods, such as dimethyl sulfate (DMS) mutational profiling with high-throughput sequencing (DMS-MaPseq), couple small chemical-mediated RNA modifications with next-generation sequencing. DMS-MaPseq, a powerful method for genome-wide and target-specific RNA secondary structure profiling, has been applied in yeast, mammals, Drosophila, and Arabidopsis thaliana, but not in crops. Here, we used DMS-MaPseq to conduct a target-specific and genome-wide profile of in vivo RNA secondary structure in rice (Oryza sativa). The DMS treatment conditions were optimized for rice leaf and root tissues. To increase the sequencing depth and coverage of low-abundance transcripts in genome-wide DMS-MaPseq, we used streptavidin-biotin depletion to reduce the abundance of highly expressed chloroplast transcripts during library construction. The resulting target-specific and genome-wide rice DMS-MaPseq data were of high quality and reproducibility. Furthermore, we used DMS-MaPseq to profile the in vivo RNA secondary structure of an OsmiR399 target region located at 5'UTR of OsPHO2, which participates in rice phosphate homeostasis. An unfolded RNA structure downstream of miRNA target site was observed in predicted in vivo RNA secondary structure, reminiscence of the TAM (Target Adjacent nucleotide Motif) involved in mRNA structure-mediated regulation in miRNA cleavage. Our study optimized DMS-MaPseq for probing in vivo RNA secondary structure in rice, facilitating the study of RNA structure-mediated regulations in crops.
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Affiliation(s)
| | | | | | | | - Zhiye Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
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32
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Solayman M, Litfin T, Singh J, Paliwal K, Zhou Y, Zhan J. Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives. Brief Bioinform 2022; 23:6554125. [PMID: 35348613 PMCID: PMC9116373 DOI: 10.1093/bib/bbac112] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 12/30/2022] Open
Abstract
Characterizing RNA structures and functions have mostly been focused on 2D, secondary and 3D, tertiary structures. Recent advances in experimental and computational techniques for probing or predicting RNA solvent accessibility make this 1D representation of tertiary structures an increasingly attractive feature to explore. Here, we provide a survey of these recent developments, which indicate the emergence of solvent accessibility as a simple 1D property, adding to secondary and tertiary structures for investigating complex structure–function relations of RNAs.
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Affiliation(s)
- Md Solayman
- Institute for Glycomics, Griffith University, Parklands Dr. Southport, QLD 4222, Australia
| | - Thomas Litfin
- Institute for Glycomics, Griffith University, Parklands Dr. Southport, QLD 4222, Australia
| | - Jaswinder Singh
- Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University, Brisbane, QLD 4111, Australia
| | - Kuldip Paliwal
- Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University, Brisbane, QLD 4111, Australia
| | - Yaoqi Zhou
- Institute for Glycomics, Griffith University, Parklands Dr. Southport, QLD 4222, Australia.,Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China.,Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Jian Zhan
- Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
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33
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Leone D, Pohl R, Hubálek M, Kadeřábková M, Krömer M, Sýkorová V, Hocek M. Glyoxal‐Linked Nucleotides and DNA for Bioconjugations and Crosslinking with Arginine‐Containing Peptides and Proteins. Chemistry 2022; 28:e202104208. [DOI: 10.1002/chem.202104208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Indexed: 12/16/2022]
Affiliation(s)
- Denise‐Liu' Leone
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry Faculty of Science Charles University in Prague Hlavova 8 12843 Prague 2 Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Martin Hubálek
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Marta Kadeřábková
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Matouš Krömer
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry Faculty of Science Charles University in Prague Hlavova 8 12843 Prague 2 Czech Republic
| | - Veronika Sýkorová
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry Faculty of Science Charles University in Prague Hlavova 8 12843 Prague 2 Czech Republic
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34
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Moshitch-Moshkovitz S, Dominissini D, Rechavi G. The epitranscriptome toolbox. Cell 2022; 185:764-776. [PMID: 35245480 DOI: 10.1016/j.cell.2022.02.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/02/2022] [Accepted: 02/03/2022] [Indexed: 12/15/2022]
Abstract
In the last decade, the notion that mRNA modifications are involved in regulation of gene expression was demonstrated in thousands of studies. To date, new technologies and methods allow accurate identification, transcriptome-wide mapping, and functional characterization of a growing number of RNA modifications, providing important insights into the biology of these marks. Most of the methods and approaches were developed for studying m6A, the most prevalent internal mRNA modification. However, unique properties of other RNA modifications stimulated the development of additional approaches. In this technical primer, we will discuss the available tools and approaches for detecting and studying different RNA modifications.
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Affiliation(s)
- Sharon Moshitch-Moshkovitz
- Cancer Research Center, Sheba Medical Center, Tel Hashomer, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; Wohl Institute for Translational Medicine, Sheba Medical Center, Tel Hashomer, Israel
| | - Dan Dominissini
- Cancer Research Center, Sheba Medical Center, Tel Hashomer, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; Wohl Institute for Translational Medicine, Sheba Medical Center, Tel Hashomer, Israel
| | - Gideon Rechavi
- Cancer Research Center, Sheba Medical Center, Tel Hashomer, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; Wohl Institute for Translational Medicine, Sheba Medical Center, Tel Hashomer, Israel.
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35
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KAS-seq: genome-wide sequencing of single-stranded DNA by N 3-kethoxal-assisted labeling. Nat Protoc 2022; 17:402-420. [PMID: 35013616 PMCID: PMC8923001 DOI: 10.1038/s41596-021-00647-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 09/22/2021] [Indexed: 02/03/2023]
Abstract
Transcription and its dynamics are crucial for gene expression regulation. However, very few methods can directly read out transcriptional activity with low-input material and high temporal resolution. This protocol describes KAS-seq, a robust and sensitive approach for capturing genome-wide single-stranded DNA (ssDNA) profiles using N3-kethoxal-assisted labeling. We developed N3-kethoxal, an azido derivative of kethoxal that reacts with deoxyguanosine bases of ssDNA in live cells within 5-10 min at 37 °C, allowing the capture of dynamic changes. Downstream biotinylation of labeled DNA occurs via copper-free click chemistry. Altogether, the KAS-seq procedure involves N3-kethoxal labeling, DNA isolation, biotinylation, fragmentation, affinity pull-down, library preparation, sequencing and bioinformatics analysis. The pre-library construction labeling and enrichment can be completed in as little as 3-4 h and is applicable to both animal tissue and as few as 1,000 cultured cells. Our recent study shows that ssDNA signals measured by KAS-seq simultaneously reveal the dynamics of transcriptionally engaged RNA polymerase (Pol) II, transcribing enhancers, RNA Pol I and Pol III activities and potentially non-canonical DNA structures with high analytical sensitivity. In addition to the experimental protocol, we also introduce here KAS-pipe, a user-friendly integrative data analysis pipeline for KAS-seq.
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36
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Piao M, Li P, Zeng X, Wang XW, Kang L, Zhang J, Wei Y, Zhang S, Tang L, Zhu J, Kwok CK, Hu X, Zhang QC. An ultra low-input method for global RNA structure probing uncovers Regnase-1-mediated regulation in macrophages. FUNDAMENTAL RESEARCH 2022; 2:2-13. [PMID: 38933905 PMCID: PMC11197792 DOI: 10.1016/j.fmre.2021.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/10/2021] [Accepted: 12/20/2021] [Indexed: 11/17/2022] Open
Abstract
To enable diverse functions and precise regulation, an RNA sequence often folds into complex yet distinct structures in different cellular states. Probing RNA in its native environment is essential to uncovering RNA structures of biological contexts. However, current methods generally require large amounts of input RNA and are challenging for physiologically relevant use. Here, we report smartSHAPE, a new RNA structure probing method that requires very low amounts of RNA input due to the largely reduced artefact of probing signals and increased efficiency of library construction. Using smartSHAPE, we showcased the profiling of the RNA structure landscape of mouse intestinal macrophages upon inflammation, and provided evidence that RNA conformational changes regulate immune responses. These results demonstrate that smartSHAPE can greatly expand the scope of RNA structure-based investigations in practical biological systems, and also provide a research paradigm for the study of post-transcriptional regulation.
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Affiliation(s)
- Meiling Piao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Pan Li
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Xiaomin Zeng
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
- Beijing Key Laboratory for Immunological Research on Chronic Diseases, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Xi-Wen Wang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Lan Kang
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
- Beijing Key Laboratory for Immunological Research on Chronic Diseases, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Jinsong Zhang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Yifan Wei
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Shaojun Zhang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Lei Tang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Jianghui Zhu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Chun Kit Kwok
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong, China
- Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
| | - Xiaoyu Hu
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
- Beijing Key Laboratory for Immunological Research on Chronic Diseases, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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37
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Varshney D, Cuesta SM, Herdy B, Abdullah UB, Tannahill D, Balasubramanian S. RNA G-quadruplex structures control ribosomal protein production. Sci Rep 2021; 11:22735. [PMID: 34815422 PMCID: PMC8611094 DOI: 10.1038/s41598-021-01847-6] [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: 07/02/2021] [Accepted: 10/27/2021] [Indexed: 12/13/2022] Open
Abstract
Four-stranded G-quadruplex (G4) structures form from guanine-rich tracts, but the extent of their formation in cellular RNA and details of their role in RNA biology remain poorly defined. Herein, we first delineate the presence of endogenous RNA G4s in the human cytoplasmic transcriptome via the binding sites of G4-interacting proteins, DDX3X (previously published), DHX36 and GRSF1. We demonstrate that a sub-population of these RNA G4s are reliably detected as folded structures in cross-linked cellular lysates using the G4 structure-specific antibody BG4. The 5' UTRs of protein coding mRNAs show significant enrichment in folded RNA G4s, particularly those for ribosomal proteins. Mutational disruption of G4s in ribosomal protein UTRs alleviates translation in vitro, whereas in cells, depletion of G4-resolving helicases or treatment with G4-stabilising small molecules inhibit the translation of ribosomal protein mRNAs. Our findings point to a common mode for translational co-regulation mediated by G4 structures. The results reveal a potential avenue for therapeutic intervention in diseases with dysregulated translation, such as cancer.
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Affiliation(s)
- Dhaval Varshney
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Sergio Martinez Cuesta
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Data Sciences and Quantitative Biology, Discovery Sciences, AstraZeneca, Cambridge, UK
| | - Barbara Herdy
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Ummi Binti Abdullah
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - David Tannahill
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Shankar Balasubramanian
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
- School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0SP, UK.
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38
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Chan D, Feng C, England WE, Wyman D, Flynn R, Wang X, Shi Y, Mortazavi A, Spitale R. Diverse functional elements in RNA predicted transcriptome-wide by orthogonal RNA structure probing. Nucleic Acids Res 2021; 49:11868-11882. [PMID: 34634799 PMCID: PMC8599799 DOI: 10.1093/nar/gkab885] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/15/2021] [Accepted: 09/20/2021] [Indexed: 01/02/2023] Open
Abstract
RNA molecules can fold into complex structures and interact with trans-acting factors to control their biology. Recent methods have been focused on developing novel tools to measure RNA structure transcriptome-wide, but their utility to study and predict RNA-protein interactions or RNA processing has been limited thus far. Here, we extend these studies with the first transcriptome-wide mapping method for cataloging RNA solvent accessibility, icLASER. By combining solvent accessibility (icLASER) with RNA flexibility (icSHAPE) data, we efficiently predict RNA-protein interactions transcriptome-wide and catalog RNA polyadenylation sites by RNA structure alone. These studies showcase the power of designing novel chemical approaches to studying RNA biology. Further, our study exemplifies merging complementary methods to measure RNA structure inside cells and its utility for predicting transcriptome-wide interactions that are critical for control of and regulation by RNA structure. We envision such approaches can be applied to studying different cell types or cells under varying conditions, using RNA structure and footprinting to characterize cellular interactions and processing involving RNA.
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Affiliation(s)
- Dalen Chan
- Department of Pharmaceutical Sciences, University of California, Irvine. Irvine, CA 92697, USA
| | - Chao Feng
- Department of Pharmaceutical Sciences, University of California, Irvine. Irvine, CA 92697, USA
| | - Whitney E England
- Department of Pharmaceutical Sciences, University of California, Irvine. Irvine, CA 92697, USA
| | - Dana Wyman
- Department of Developmental and Cellular Biology, University of California, Irvine. Irvine, CA 92697, USA
| | - Ryan A Flynn
- Stem Cell Program, Boston Children’s Hospital, Boston, MA, USA and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Xiuye Wang
- Department Microbiology and Molecular Genetics, University of California, Irvine. Irvine, CA 92697, USA
| | - Yongsheng Shi
- Department Microbiology and Molecular Genetics, University of California, Irvine. Irvine, CA 92697, USA
| | - Ali Mortazavi
- Department of Developmental and Cellular Biology, University of California, Irvine. Irvine, CA 92697, USA
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California, Irvine. Irvine, CA 92697, USA
- Department of Chemistry, University of California, Irvine. Irvine, CA 92697, USA
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39
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Gong J, Xu K, Ma Z, Lu ZJ, Zhang QC. A deep learning method for recovering missing signals in transcriptome-wide RNA structure profiles from probing experiments. NAT MACH INTELL 2021. [DOI: 10.1038/s42256-021-00412-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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40
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He X, Yuan J, Wang Y. G3BP1 binds to guanine quadruplexes in mRNAs to modulate their stabilities. Nucleic Acids Res 2021; 49:11323-11336. [PMID: 34614161 PMCID: PMC8565330 DOI: 10.1093/nar/gkab873] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 09/12/2021] [Accepted: 10/04/2021] [Indexed: 12/21/2022] Open
Abstract
RNA guanine quadruplexes (rG4) assume important roles in post-transcriptional regulations of gene expression, which are often modulated by rG4-binding proteins. Hence, understanding the biological functions of rG4s requires the identification and functional characterizations of rG4-recognition proteins. By employing a bioinformatic approach based on the analysis of overlap between peaks obtained from rG4-seq analysis and those detected in >230 eCLIP-seq datasets for RNA-binding proteins generated from the ENCODE project, we identified a large number of candidate rG4-binding proteins. We showed that one of these proteins, G3BP1, is able to bind directly to rG4 structures with high affinity and selectivity, where the binding entails its C-terminal RGG domain and is further enhanced by its RRM domain. Additionally, our seCLIP-Seq data revealed that pyridostatin, a small-molecule rG4 ligand, could displace G3BP1 from mRNA in cells, with the most pronounced effects being observed for the 3′-untranslated regions (3′-UTR) of mRNAs. Moreover, luciferase reporter assay results showed that G3BP1 positively regulates mRNA stability through its binding with rG4 structures. Together, we identified a number of candidate rG4-binding proteins and validated that G3BP1 can bind directly with rG4 structures and regulate the stabilities of mRNAs.
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Affiliation(s)
- Xiaomei He
- Department of Chemistry, University of California, Riverside, CA 92521-0403, USA
| | - Jun Yuan
- Department of Chemistry, University of California, Riverside, CA 92521-0403, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, CA 92521-0403, USA
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41
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Manigrasso J, Marcia M, De Vivo M. Computer-aided design of RNA-targeted small molecules: A growing need in drug discovery. Chem 2021. [DOI: 10.1016/j.chempr.2021.05.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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42
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Radecki P, Uppuluri R, Deshpande K, Aviran S. Accurate detection of RNA stem-loops in structurome data reveals widespread association with protein binding sites. RNA Biol 2021; 18:521-536. [PMID: 34606413 PMCID: PMC8677038 DOI: 10.1080/15476286.2021.1971382] [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] [Indexed: 10/31/2022] Open
Abstract
RNA molecules are known to fold into specific structures which often play a central role in their functions and regulation. In silico folding of RNA transcripts, especially when assisted with structure profiling (SP) data, is capable of accurately elucidating relevant structural conformations. However, such methods scale poorly to the swaths of SP data generated by transcriptome-wide experiments, which are becoming more commonplace and advancing our understanding of RNA structure and its regulation at global and local levels. This has created a need for tools capable of rapidly deriving structural assessments from SP data in a scalable manner. One such tool we previously introduced that aims to process such data is patteRNA, a statistical learning algorithm capable of rapidly mining big SP datasets for structural elements. Here, we present a reformulation of patteRNA's pattern recognition scheme that sees significantly improved precision without major compromises to computational overhead. Specifically, we developed a data-driven logistic classifier which interprets patteRNA's statistical characterizations of SP data in addition to local sequence properties as measured with a nearest neighbour thermodynamic model. Application of the classifier to human structurome data reveals a marked association between detected stem-loops and RNA binding protein (RBP) footprints. The results of our application demonstrate that upwards of 30% of RBP footprints occur within loops of stable stem-loop elements. Overall, our work arrives at a rapid and accurate method for automatically detecting families of RNA structure motifs and demonstrates the functional relevance of identifying them transcriptome-wide.
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Affiliation(s)
- Pierce Radecki
- Biomedical Engineering Department and Genome Center, University of California, Davis, CA, USA
| | - Rahul Uppuluri
- Biomedical Engineering Department and Genome Center, University of California, Davis, CA, USA
| | - Kaustubh Deshpande
- Biomedical Engineering Department and Genome Center, University of California, Davis, CA, USA
| | - Sharon Aviran
- Biomedical Engineering Department and Genome Center, University of California, Davis, CA, USA
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43
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Gilmer O, Quignon E, Jousset AC, Paillart JC, Marquet R, Vivet-Boudou V. Chemical and Enzymatic Probing of Viral RNAs: From Infancy to Maturity and Beyond. Viruses 2021; 13:1894. [PMID: 34696322 PMCID: PMC8537439 DOI: 10.3390/v13101894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 11/17/2022] Open
Abstract
RNA molecules are key players in a variety of biological events, and this is particularly true for viral RNAs. To better understand the replication of those pathogens and try to block them, special attention has been paid to the structure of their RNAs. Methods to probe RNA structures have been developed since the 1960s; even if they have evolved over the years, they are still in use today and provide useful information on the folding of RNA molecules, including viral RNAs. The aim of this review is to offer a historical perspective on the structural probing methods used to decipher RNA structures before the development of the selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) methodology and to show how they have influenced the current probing techniques. Actually, these technological breakthroughs, which involved advanced detection methods, were made possible thanks to the development of next-generation sequencing (NGS) but also to the previous works accumulated in the field of structural RNA biology. Finally, we will also discuss how high-throughput SHAPE (hSHAPE) paved the way for the development of sophisticated RNA structural techniques.
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Affiliation(s)
| | | | | | | | - Roland Marquet
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR9002, F-67000 Strasbourg, France; (O.G.); (E.Q.); (A.-C.J.); (J.-C.P.)
| | - Valérie Vivet-Boudou
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR9002, F-67000 Strasbourg, France; (O.G.); (E.Q.); (A.-C.J.); (J.-C.P.)
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44
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Radecki P, Uppuluri R, Aviran S. Rapid structure-function insights via hairpin-centric analysis of big RNA structure probing datasets. NAR Genom Bioinform 2021; 3:lqab073. [PMID: 34447931 PMCID: PMC8384053 DOI: 10.1093/nargab/lqab073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 07/14/2021] [Accepted: 08/03/2021] [Indexed: 12/23/2022] Open
Abstract
The functions of RNA are often tied to its structure, hence analyzing structure is of significant interest when studying cellular processes. Recently, large-scale structure probing (SP) studies have enabled assessment of global structure-function relationships via standard data summarizations or local folding. Here, we approach structure quantification from a hairpin-centric perspective where putative hairpins are identified in SP datasets and used as a means to capture local structural effects. This has the advantage of rapid processing of big (e.g. transcriptome-wide) data as RNA folding is circumvented, yet it captures more information than simple data summarizations. We reformulate a statistical learning algorithm we previously developed to significantly improve precision of hairpin detection, then introduce a novel nucleotide-wise measure, termed the hairpin-derived structure level (HDSL), which captures local structuredness by accounting for the presence of likely hairpin elements. Applying HDSL to data from recent studies recapitulates, strengthens and expands on their findings which were obtained by more comprehensive folding algorithms, yet our analyses are orders of magnitude faster. These results demonstrate that hairpin detection is a promising avenue for global and rapid structure-function analysis, furthering our understanding of RNA biology and the principal features which drive biological insights from SP data.
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Affiliation(s)
- Pierce Radecki
- Biomedical Engineering Department and Genome Center, University of California at Davis, Davis, CA 95616, USA
| | - Rahul Uppuluri
- Biomedical Engineering Department and Genome Center, University of California at Davis, Davis, CA 95616, USA
| | - Sharon Aviran
- Biomedical Engineering Department and Genome Center, University of California at Davis, Davis, CA 95616, USA
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45
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Lyu K, Chow EYC, Mou X, Chan TF, Kwok CK. RNA G-quadruplexes (rG4s): genomics and biological functions. Nucleic Acids Res 2021; 49:5426-5450. [PMID: 33772593 PMCID: PMC8191793 DOI: 10.1093/nar/gkab187] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/02/2021] [Accepted: 03/24/2021] [Indexed: 02/07/2023] Open
Abstract
G-quadruplexes (G4s) are non-classical DNA or RNA secondary structures that have been first observed decades ago. Over the years, these four-stranded structural motifs have been demonstrated to have significant regulatory roles in diverse biological processes, but challenges remain in detecting them globally and reliably. Compared to DNA G4s (dG4s), the study of RNA G4s (rG4s) has received less attention until recently. In this review, we will summarize the innovative high-throughput methods recently developed to detect rG4s on a transcriptome-wide scale, highlight the many novel and important functions of rG4 being discovered in vivo across the tree of life, and discuss the key biological questions to be addressed in the near future.
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Affiliation(s)
- Kaixin Lyu
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Eugene Yui-Ching Chow
- School of Life Sciences, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Xi Mou
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Ting-Fung Chan
- School of Life Sciences, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.,Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
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46
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Wang XW, Liu CX, Chen LL, Zhang QC. RNA structure probing uncovers RNA structure-dependent biological functions. Nat Chem Biol 2021; 17:755-766. [PMID: 34172967 DOI: 10.1038/s41589-021-00805-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 04/23/2021] [Indexed: 01/22/2023]
Abstract
RNA molecules fold into complex structures that enable their diverse functions in cells. Recent revolutionary innovations in transcriptome-wide RNA structural probing of living cells have ushered in a new era in understanding RNA functions. Here, we summarize the latest technological advances for probing RNA secondary structures and discuss striking discoveries that have linked RNA regulation and biological processes through interrogation of RNA structures. In particular, we highlight how different long noncoding RNAs form into distinct secondary structures that determine their modes of interactions with protein partners to realize their unique functions. These dynamic structures mediate RNA regulatory functions through altering interactions with proteins and other RNAs. We also outline current methodological hurdles and speculate about future directions for development of the next generation of RNA structure-probing technologies of higher sensitivity and resolution, which could then be applied in increasingly physiologically relevant studies.
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Affiliation(s)
- Xi-Wen Wang
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology and Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China.,Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Chu-Xiao Liu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China. .,School of Life Science and Technology, ShanghaiTech University, Shanghai, China. .,School of Life Sciences, Hangzhou Institute for Advanced Study, University of the Chinese Academy of Sciences, Hangzhou, China.
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology and Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China. .,Tsinghua-Peking Center for Life Sciences, Beijing, China.
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47
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Luo QJ, Zhang J, Li P, Wang Q, Zhang Y, Roy-Chaudhuri B, Xu J, Kay MA, Zhang QC. RNA structure probing reveals the structural basis of Dicer binding and cleavage. Nat Commun 2021; 12:3397. [PMID: 34099665 PMCID: PMC8184798 DOI: 10.1038/s41467-021-23607-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 05/03/2021] [Indexed: 01/27/2023] Open
Abstract
It is known that an RNA's structure determines its biological function, yet current RNA structure probing methods only capture partial structure information. The ability to measure intact (i.e., full length) RNA structures will facilitate investigations of the functions and regulation mechanisms of small RNAs and identify short fragments of functional sites. Here, we present icSHAPE-MaP, an approach combining in vivo selective 2'-hydroxyl acylation and mutational profiling to probe intact RNA structures. We further showcase the RNA structural landscape of substrates bound by human Dicer based on the combination of RNA immunoprecipitation pull-down and icSHAPE-MaP small RNA structural profiling. We discover distinct structural categories of Dicer substrates in correlation to both their binding affinity and cleavage efficiency. And by tertiary structural modeling constrained by icSHAPE-MaP RNA structural data, we find the spatial distance measuring as an influential parameter for Dicer cleavage-site selection.
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Affiliation(s)
- Qing-Jun Luo
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Jinsong Zhang
- Ministry of Education Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Pan Li
- Ministry of Education Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Qing Wang
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Faculty of Preventive Medicine, A Key Laboratory of Guangzhou Environmental Pollution and Risk Assessment, School of Public Health, Sun Yat-Sen University, Guangzhou, China
| | - Yue Zhang
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Freenome Holdings Inc., South San Francisco, CA, USA
| | - Biswajoy Roy-Chaudhuri
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Impossible Foods Inc., Redwood City, CA, USA
| | - Jianpeng Xu
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Mark A Kay
- Department of Pediatrics, Stanford University, Stanford, CA, USA.
- Department of Genetics, Stanford University, Stanford, CA, USA.
| | - Qiangfeng Cliff Zhang
- Ministry of Education Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
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48
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Multi-omics annotation of human long non-coding RNAs. Biochem Soc Trans 2021; 48:1545-1556. [PMID: 32756901 DOI: 10.1042/bst20191063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/05/2020] [Accepted: 07/07/2020] [Indexed: 12/12/2022]
Abstract
LncRNAs (long non-coding RNAs) are pervasively transcribed in the human genome and also extensively involved in a variety of essential biological processes and human diseases. The comprehensive annotation of human lncRNAs is of great significance in navigating the functional landscape of the human genome and deepening the understanding of the multi-featured RNA world. However, the unique characteristics of lncRNAs as well as their enormous quantity have complicated and challenged the annotation of lncRNAs. Advances in high-throughput sequencing technologies give rise to a large volume of omics data that are generated at an unprecedented rate and scale, providing possibilities in the identification, characterization and functional annotation of lncRNAs. Here, we review the recent important discoveries of human lncRNAs through analysis of various omics data and summarize specialized lncRNA database resources. Moreover, we highlight the multi-omics integrative analysis as a powerful strategy to efficiently discover and characterize the functional lncRNAs and elucidate their potential molecular mechanisms.
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49
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Cao J, Xue Y. Characteristic chemical probing patterns of loop motifs improve prediction accuracy of RNA secondary structures. Nucleic Acids Res 2021; 49:4294-4307. [PMID: 33849076 PMCID: PMC8096282 DOI: 10.1093/nar/gkab250] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 03/24/2021] [Accepted: 04/10/2021] [Indexed: 12/14/2022] Open
Abstract
RNA structures play a fundamental role in nearly every aspect of cellular physiology and pathology. Gaining insights into the functions of RNA molecules requires accurate predictions of RNA secondary structures. However, the existing thermodynamic folding models remain less accurate than desired, even when chemical probing data, such as selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) reactivities, are used as restraints. Unlike most SHAPE-directed algorithms that only consider SHAPE restraints for base pairing, we extract two-dimensional structural features encoded in SHAPE data and establish robust relationships between characteristic SHAPE patterns and loop motifs of various types (hairpin, internal, and bulge) and lengths (2-11 nucleotides). Such characteristic SHAPE patterns are closely related to the sugar pucker conformations of loop residues. Based on these patterns, we propose a computational method, SHAPELoop, which refines the predicted results of the existing methods, thereby further improving their prediction accuracy. In addition, SHAPELoop can provide information about local or global structural rearrangements (including pseudoknots) and help researchers to easily test their hypothesized secondary structures.
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Affiliation(s)
- Jingyi Cao
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China
| | - Yi Xue
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China
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50
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England WE, Garfio CM, Spitale RC. Chemical Approaches To Analyzing RNA Structure Transcriptome-Wide. Chembiochem 2021; 22:1114-1121. [PMID: 32737940 PMCID: PMC8769560 DOI: 10.1002/cbic.202000340] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/27/2020] [Indexed: 11/09/2022]
Abstract
RNA molecules can fold into complex two- and three-dimensional shapes that are critical for their function. Chemical probes have long been utilized to interrogate RNA structure and are now considered invaluable resources in the goal of relating structure to function. Recently, the power of deep sequencing and careful chemical probe design have merged, permitting researchers to obtain a holistic understanding of how RNA structure can be utilized to control RNA biology transcriptome-wide. Within this review, we outline the recent advancements in chemical probe design for interrogating RNA structures inside cells and discuss the recent advances in our understanding of RNA biology through the lens of chemical probing.
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Affiliation(s)
- Whitney E England
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Chely M Garfio
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
- Department of Developmental and Cellular Biology, University of California, Irvine, Irvine, CA 92697, USA
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
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