1
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Mandler MD, Maligireddy SS, Guiblet WM, Fitzsimmons CM, McDonald KS, Warrell DL, Batista PJ. The modification landscape of Pseudomonas aeruginosa tRNAs. RNA (NEW YORK, N.Y.) 2024; 30:1025-1040. [PMID: 38684317 PMCID: PMC11251520 DOI: 10.1261/rna.080004.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 04/09/2024] [Indexed: 05/02/2024]
Abstract
RNA modifications have a substantial impact on tRNA function, with modifications in the anticodon loop contributing to translational fidelity and modifications in the tRNA core impacting structural stability. In bacteria, tRNA modifications are crucial for responding to stress and regulating the expression of virulence factors. Although tRNA modifications are well-characterized in a few model organisms, our knowledge of tRNA modifications in human pathogens, such as Pseudomonas aeruginosa, remains limited. Here, we leveraged two orthogonal approaches to build a reference landscape of tRNA modifications in Escherichia coli, which enabled us to identify similar modifications in P. aeruginosa Our analysis supports a substantial degree of conservation between the two organisms, while also uncovering potential sites of tRNA modification in P. aeruginosa tRNAs that are not present in E. coli The mutational signature at one of these sites, position 46 of tRNAGln1(UUG) is dependent on the P. aeruginosa homolog of TapT, the enzyme responsible for the 3-(3-amino-3-carboxypropyl) uridine (acp3U) modification. Identifying which modifications are present on different tRNAs will uncover the pathways impacted by the different tRNA-modifying enzymes, some of which play roles in determining virulence and pathogenicity.
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Affiliation(s)
- Mariana D Mandler
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Siddhardha S Maligireddy
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Wilfried M Guiblet
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Christina M Fitzsimmons
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Kayla S McDonald
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Delayna L Warrell
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Pedro J Batista
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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2
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Davis WJH, Drummond CJ, Diermeier S, Reid G. The Potential Links between lncRNAs and Drug Tolerance in Lung Adenocarcinoma. Genes (Basel) 2024; 15:906. [PMID: 39062685 PMCID: PMC11276205 DOI: 10.3390/genes15070906] [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: 05/31/2024] [Revised: 07/09/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
Lung cancer patients treated with targeted therapies frequently respond well but invariably relapse due to the development of drug resistance. Drug resistance is in part mediated by a subset of cancer cells termed "drug-tolerant persisters" (DTPs), which enter a dormant, slow-cycling state that enables them to survive drug exposure. DTPs also exhibit stem cell-like characteristics, broad epigenetic reprogramming, altered metabolism, and a mutagenic phenotype mediated by adaptive mutability. While several studies have characterised the transcriptional changes that lead to the altered phenotypes exhibited in DTPs, these studies have focused predominantly on protein coding changes. As long non-coding RNAs (lncRNAs) are also implicated in the phenotypes altered in DTPs, it is likely that they play a role in the biology of drug tolerance. In this review, we outline how lncRNAs may contribute to the key characteristics of DTPs, their potential roles in tolerance to targeted therapies, and the emergence of genetic resistance in lung adenocarcinoma.
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Affiliation(s)
- William J. H. Davis
- Department of Pathology, Dunedin School of Medicine, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; (W.J.H.D.); (C.J.D.)
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag, Auckland 1023, New Zealand
| | - Catherine J. Drummond
- Department of Pathology, Dunedin School of Medicine, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; (W.J.H.D.); (C.J.D.)
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag, Auckland 1023, New Zealand
| | - Sarah Diermeier
- Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand;
- Amaroq Therapeutics, Auckland 1010, New Zealand
| | - Glen Reid
- Department of Pathology, Dunedin School of Medicine, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; (W.J.H.D.); (C.J.D.)
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag, Auckland 1023, New Zealand
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3
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Wang Y, Wang S, Meng Z, Liu XM, Mao Y. Determinant of m6A regional preference by transcriptional dynamics. Nucleic Acids Res 2024; 52:3510-3521. [PMID: 38452220 DOI: 10.1093/nar/gkae169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/21/2024] [Accepted: 02/27/2024] [Indexed: 03/09/2024] Open
Abstract
N6-Methyladenosine (m6A) is the most abundant chemical modification occurring on eukaryotic mRNAs, and has been reported to be involved in almost all stages of mRNA metabolism. The distribution of m6A sites is notably asymmetric along mRNAs, with a strong preference toward the 3' terminus of the transcript. How m6A regional preference is shaped remains incompletely understood. In this study, by performing m6A-seq on chromatin-associated RNAs, we found that m6A regional preference arises during transcription. Nucleosome occupancy is remarkedly increased in the region downstream of m6A sites, suggesting an intricate interplay between m6A methylation and nucleosome-mediated transcriptional dynamics. Notably, we found a remarkable slowdown of Pol-II movement around m6A sites. In addition, inhibiting Pol-II movement increases nearby m6A methylation levels. By analyzing massively parallel assays for m6A, we found that RNA secondary structures inhibit m6A methylation. Remarkably, the m6A sites associated with Pol-II pausing tend to be embedded within RNA secondary structures. These results suggest that Pol-II pausing could affect the accessibility of m6A motifs to the methyltransferase complex and subsequent m6A methylation by mediating RNA secondary structure. Overall, our study reveals a crucial role of transcriptional dynamics in the formation of m6A regional preference.
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Affiliation(s)
- Yalan Wang
- Department of Neurology of The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Shen Wang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Zhen Meng
- Department of Neurology of The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiao-Min Liu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Yuanhui Mao
- Department of Neurology of The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
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4
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Ziesel A, Jabbari H. Unveiling hidden structural patterns in the SARS-CoV-2 genome: Computational insights and comparative analysis. PLoS One 2024; 19:e0298164. [PMID: 38574063 PMCID: PMC10994416 DOI: 10.1371/journal.pone.0298164] [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: 10/06/2023] [Accepted: 01/19/2024] [Indexed: 04/06/2024] Open
Abstract
SARS-CoV-2, the causative agent of COVID-19, is known to exhibit secondary structures in its 5' and 3' untranslated regions, along with the frameshifting stimulatory element situated between ORF1a and 1b. To identify additional regions containing conserved structures, we utilized a multiple sequence alignment with related coronaviruses as a starting point. We applied a computational pipeline developed for identifying non-coding RNA elements. Our pipeline employed three different RNA structural prediction approaches. We identified forty genomic regions likely to harbor structures, with ten of them showing three-way consensus substructure predictions among our predictive utilities. We conducted intracomparisons of the predictive utilities within the pipeline and intercomparisons with four previously published SARS-CoV-2 structural datasets. While there was limited agreement on the precise structure, different approaches seemed to converge on regions likely to contain structures in the viral genome. By comparing and combining various computational approaches, we can predict regions most likely to form structures, as well as a probable structure or ensemble of structures. These predictions can be used to guide surveillance, prophylactic measures, or therapeutic efforts. Data and scripts employed in this study may be found at https://doi.org/10.5281/zenodo.8298680.
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Affiliation(s)
- Alison Ziesel
- Department of Biomedical Engineering, University of Alberta, Edmonton, Alberta, Canada
| | - Hosna Jabbari
- Department of Biomedical Engineering, University of Alberta, Edmonton, Alberta, Canada
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5
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Price JL, Ziv O, Pinckert ML, Lim A, Miska EA. rnaCrosslinkOO: an object-oriented R package for the analysis of RNA structural data generated by RNA crosslinking experiments. Bioinformatics 2024; 40:btae193. [PMID: 38597883 PMCID: PMC11060868 DOI: 10.1093/bioinformatics/btae193] [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: 11/30/2023] [Revised: 03/06/2024] [Accepted: 04/08/2024] [Indexed: 04/11/2024] Open
Abstract
SUMMARY RNA (ribonucleic acid) molecules have secondary and tertiary structures in vivo which play a crucial role in cellular processes such as the regulation of gene expression, RNA processing and localization. The ability to investigate these structures will enhance our understanding of their function and contribute to the diagnosis and treatment of diseases caused by RNA dysregulation. However, there are no mature pipelines or packages for processing and analyzing complex in vivo RNA structural data. Here, we present rnaCrosslinkOO (RNA Crosslink Object-Oriented), a novel software package for the comprehensive analysis of data derived from the COMRADES (Crosslinking of Matched RNA and Deep Sequencing) method. rnaCrosslinkOO offers a comprehensive pipeline from raw sequencing reads to the identification and comparison of RNA structural features. It includes read processing and alignment, clustering of duplexes, data exploration, folding and comparisons of RNA structures. rnaCrosslinkOO also enables comparisons between conditions, the identification of inter-RNA interactions, and the incorporation of reactivity data to improve structure prediction. AVAILABILITY AND IMPLEMENTATION rnaCrosslinkOO is freely available to noncommercial users and implemented in R, with the source code and documentation accessible at https://CRAN.R-project.org/package=rnaCrosslinkOO. The software is supported on Linux, macOS, and Windows platforms.
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Affiliation(s)
- Jonathan L Price
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, United Kingdom
| | - Omer Ziv
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, United Kingdom
- Eleven Therapeutics, Cambridge, CB2 0RE, United Kingdom
| | - Malte L Pinckert
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, United Kingdom
| | - Andrew Lim
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, United Kingdom
| | - Eric A Miska
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, United Kingdom
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6
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Yang R, Pan M, Guo J, Huang Y, Zhang QC, Deng T, Wang J. Mapping of the influenza A virus genome RNA structure and interactions reveals essential elements of viral replication. Cell Rep 2024; 43:113833. [PMID: 38416642 DOI: 10.1016/j.celrep.2024.113833] [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: 05/31/2023] [Revised: 12/04/2023] [Accepted: 02/02/2024] [Indexed: 03/01/2024] Open
Abstract
Influenza A virus (IAV) represents a constant public health threat. The single-stranded, segmented RNA genome of IAV is replicated in host cell nuclei as a series of 8 ribonucleoprotein complexes (vRNPs) with RNA structures known to exert essential function to support viral replication. Here, we investigate RNA secondary structures and RNA interactions networks of the IAV genome and construct an in vivo structure model for each of the 8 IAV genome segments. Our analyses reveal an overall in vivo and in virio resemblance of the IAV genome conformation but also wide disparities among long-range and intersegment interactions. Moreover, we identify a long-range RNA interaction that exerts an essential role in genome packaging. Disrupting this structure displays reduced infectivity, attenuating virus pathogenicity in mice. Our findings characterize the in vivo RNA structural landscape of the IAV genome and reveal viral RNA structures that can be targeted to develop antiviral interventions.
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Affiliation(s)
- Rui Yang
- The State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Minglei Pan
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Jiamei Guo
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yong Huang
- The State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qiangfeng Cliff Zhang
- The State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Tao Deng
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China; CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Jianwei Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China; Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China.
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7
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Xu Q, Bao X, Lin Z, Tang L, He LN, Ren J, Zuo Z, Hu K. AStruct: detection of allele-specific RNA secondary structure in structuromic probing data. BMC Bioinformatics 2024; 25:91. [PMID: 38429654 PMCID: PMC11264973 DOI: 10.1186/s12859-024-05704-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 02/14/2024] [Indexed: 03/03/2024] Open
Abstract
BACKGROUND Uncovering functional genetic variants from an allele-specific perspective is of paramount importance in advancing our understanding of gene regulation and genetic diseases. Recently, various allele-specific events, such as allele-specific gene expression, allele-specific methylation, and allele-specific binding, have been explored on a genome-wide scale due to the development of high-throughput sequencing methods. RNA secondary structure, which plays a crucial role in multiple RNA-associated processes like RNA modification, translation and splicing, has emerged as an essential focus of relevant research. However, tools to identify genetic variants associated with allele-specific RNA secondary structures are still lacking. RESULTS Here, we develop a computational tool called 'AStruct' that enables us to detect allele-specific RNA secondary structure (ASRS) from RT-stop based structuromic probing data. AStruct shows robust performance in both simulated datasets and public icSHAPE datasets. We reveal that single nucleotide polymorphisms (SNPs) with higher AStruct scores are enriched in coding regions and tend to be functional. These SNPs are highly conservative, have the potential to disrupt sites involved in m6A modification or protein binding, and are frequently associated with disease. CONCLUSIONS AStruct is a tool dedicated to invoke allele-specific RNA secondary structure events at heterozygous SNPs in RT-stop based structuromic probing data. It utilizes allelic variants, base pairing and RT-stop information under different cell conditions to detect dynamic and functional ASRS. Compared to sequence-based tools, AStruct considers dynamic cell conditions and outperforms in detecting functional variants. AStruct is implemented in JAVA and is freely accessible at: https://github.com/canceromics/AStruct .
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Affiliation(s)
- Qingru Xu
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510060, China
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Xiaoqiong Bao
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510060, China
| | - Zhuobin Lin
- Guangdong Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Lin Tang
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510060, China
| | - Li-Na He
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510060, China
| | - Jian Ren
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510060, China
| | - Zhixiang Zuo
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510060, China.
| | - Kunhua Hu
- Guangdong Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.
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8
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Fitzsimmons CM, Mandler MD, Lunger JC, Chan D, Maligireddy S, Schmiechen A, Gamage S, Link C, Jenkins L, Chan K, Andresson T, Crooks D, Meier J, Linehan W, Batista P. Rewiring of RNA methylation by the oncometabolite fumarate in renal cell carcinoma. NAR Cancer 2024; 6:zcae004. [PMID: 38328795 PMCID: PMC10849186 DOI: 10.1093/narcan/zcae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 01/09/2024] [Accepted: 01/16/2024] [Indexed: 02/09/2024] Open
Abstract
Metabolic reprogramming is a hallmark of cancer that facilitates changes in many adaptive biological processes. Mutations in the tricarboxylic acid cycle enzyme fumarate hydratase (FH) lead to fumarate accumulation and cause hereditary leiomyomatosis and renal cell cancer (HLRCC). HLRCC is a rare, inherited disease characterized by the development of non-cancerous smooth muscle tumors of the uterus and skin, and an increased risk of an aggressive form of kidney cancer. Fumarate has been shown to inhibit 2-oxoglutarate-dependent dioxygenases (2OGDDs) involved in the hydroxylation of HIF1α, as well as in DNA and histone demethylation. However, the link between fumarate accumulation and changes in RNA post-transcriptional modifications has not been defined. Here, we determine the consequences of fumarate accumulation on the activity of different members of the 2OGDD family targeting RNA modifications. By evaluating multiple RNA modifications in patient-derived HLRCC cell lines, we show that mutation of FH selectively affects the levels of N6-methyladenosine (m6A), while the levels of 5-formylcytosine (f5C) in mitochondrial tRNA are unaffected. This supports the hypothesis of a differential impact of fumarate accumulation on distinct RNA demethylases. The observation that metabolites modulate specific subsets of RNA-modifying enzymes offers new insights into the intersection between metabolism and the epitranscriptome.
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Affiliation(s)
- Christina M Fitzsimmons
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mariana D Mandler
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Judith C Lunger
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dalen Chan
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Siddhardha S Maligireddy
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexandra C Schmiechen
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Supuni Thalalla Gamage
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Courtney Link
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Lisa M Jenkins
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - King Chan
- Protein Characterization Laboratory, Research Technology Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21701, USA
| | - Thorkell Andresson
- Protein Characterization Laboratory, Research Technology Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21701, USA
| | - Daniel R Crooks
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jordan L Meier
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pedro J Batista
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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9
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Jolley EA, Bevilacqua PC. Single-cell probing of RNA structure. Nat Methods 2024; 21:377-378. [PMID: 38321343 DOI: 10.1038/s41592-024-02178-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Affiliation(s)
- Elizabeth A Jolley
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Philip C Bevilacqua
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA.
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, USA.
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
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10
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Mandler MD, Maligireddy SS, Guiblet WM, Fitzsimmons CM, McDonald KS, Warrell DL, Batista PJ. The modification landscape of P. aeruginosa tRNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.21.581370. [PMID: 38529508 PMCID: PMC10962704 DOI: 10.1101/2024.02.21.581370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
RNA modifications have a substantial impact on tRNA function, with modifications in the anticodon loop contributing to translational fidelity and modifications in the tRNA core impacting structural stability. In bacteria, tRNA modifications are crucial for responding to stress and regulating the expression of virulence factors. Although tRNA modifications are well-characterized in a few model organisms, our knowledge of tRNA modifications in human pathogens, such as Pseudomonas aeruginosa, remains limited. Here we leveraged two orthogonal approaches to build a reference landscape of tRNA modifications in E. coli, which enabled us to identify similar modifications in P. aeruginosa. Our analysis revealed a substantial degree of conservation between the two organisms, while also uncovering potential sites of tRNA modification in P. aeruginosa tRNAs that are not present in E. coli. The mutational signature at one of these sites, position 46 of tRNAGln1(UUG) is dependent on the P. aeruginosa homolog of TapT, the enzyme responsible for the 3-(3-amino-3-carboxypropyl) uridine (acp3U) modification. Identifying which modifications are present on different tRNAs will uncover the pathways impacted by the different tRNA modifying enzymes, some of which play roles in determining virulence and pathogenicity.
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Affiliation(s)
- Mariana D Mandler
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health
| | - Siddhardha S Maligireddy
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health
| | - Wilfried M Guiblet
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health
| | - Christina M Fitzsimmons
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health
| | - Kayla S McDonald
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health
| | - Delayna L Warrell
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institues of Health
| | - Pedro J Batista
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health
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11
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Sharma H, Valentine MNZ, Toki N, Sueki HN, Gustincich S, Takahashi H, Carninci P. Decryption of sequence, structure, and functional features of SINE repeat elements in SINEUP non-coding RNA-mediated post-transcriptional gene regulation. Nat Commun 2024; 15:1400. [PMID: 38383605 PMCID: PMC10881587 DOI: 10.1038/s41467-024-45517-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/26/2024] [Indexed: 02/23/2024] Open
Abstract
RNA structure folding largely influences RNA regulation by providing flexibility and functional diversity. In silico and in vitro analyses are limited in their ability to capture the intricate relationships between dynamic RNA structure and RNA functional diversity present in the cell. Here, we investigate sequence, structure and functional features of mouse and human SINE-transcribed retrotransposons embedded in SINEUPs long non-coding RNAs, which positively regulate target gene expression post-transcriptionally. In-cell secondary structure probing reveals that functional SINEs-derived RNAs contain conserved short structure motifs essential for SINEUP-induced translation enhancement. We show that SINE RNA structure dynamically changes between the nucleus and cytoplasm and is associated with compartment-specific binding to RBP and related functions. Moreover, RNA-RNA interaction analysis shows that the SINE-derived RNAs interact directly with ribosomal RNAs, suggesting a mechanism of translation regulation. We further predict the architecture of 18 SINE RNAs in three dimensions guided by experimental secondary structure data. Overall, we demonstrate that the conservation of short key features involved in interactions with RBPs and ribosomal RNA drives the convergent function of evolutionarily distant SINE-transcribed RNAs.
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Affiliation(s)
- Harshita Sharma
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Matthew N Z Valentine
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Naoko Toki
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Hiromi Nishiyori Sueki
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | | | - Hazuki Takahashi
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.
| | - Piero Carninci
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.
- Human Technopole, Milan, 20157, Italy.
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12
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Allouche D, De Bisschop G, Saaidi A, Hardouin P, du Moutier FXL, Ponty Y, Bruno S. RNA Secondary Structure Modeling Following the IPANEMAP Workflow. Methods Mol Biol 2024; 2726:85-104. [PMID: 38780728 DOI: 10.1007/978-1-0716-3519-3_4] [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] [Indexed: 05/25/2024]
Abstract
The structure of RNA molecules and their complexes are crucial for understanding biology at the molecular level. Resolving these structures holds the key to understanding their manifold structure-mediated functions ranging from regulating gene expression to catalyzing biochemical processes. Predicting RNA secondary structure is a prerequisite and a key step to accurately model their three dimensional structure. Although dedicated modelling software are making fast and significant progresses, predicting an accurate secondary structure from the sequence remains a challenge. Their performance can be significantly improved by the incorporation of experimental RNA structure probing data. Many different chemical and enzymatic probes have been developed; however, only one set of quantitative data can be incorporated as constraints for computer-assisted modelling. IPANEMAP is a recent workflow based on RNAfold that can take into account several quantitative or qualitative data sets to model RNA secondary structure. This chapter details the methods for popular chemical probing (DMS, CMCT, SHAPE-CE, and SHAPE-Map) and the subsequent analysis and structure prediction using IPANEMAP.
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Affiliation(s)
- Delphine Allouche
- CiTCOM, Cibles Thérapeutiques et conception de médicaments, UMR8038 CNRS, Université de PARIS, Paris, France
- Sanofi mRNA center of excellence 1541, Marcy-l'Etoile, France
| | - Grégoire De Bisschop
- CiTCOM, Cibles Thérapeutiques et conception de médicaments, UMR8038 CNRS, Université de PARIS, Paris, France
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada
| | - Afaf Saaidi
- Georgia Institute of Technology, School of Mathematics, Atlanta, GA, USA
| | - Pierre Hardouin
- CiTCOM, Cibles Thérapeutiques et conception de médicaments, UMR8038 CNRS, Université de PARIS, Paris, France
| | | | - Yann Ponty
- CNRS UMR 7161, LIX, Ecole Polytechnique, Palaiseau, France.
| | - Sargueil Bruno
- CiTCOM, Cibles Thérapeutiques et conception de médicaments, UMR8038 CNRS, Université de PARIS, Paris, France.
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13
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Fang L, Kool ET. Reactivity-based RNA profiling for analyzing transcriptome interactions of small molecules in human cells. STAR Protoc 2023; 4:102670. [PMID: 37917579 PMCID: PMC10643522 DOI: 10.1016/j.xpro.2023.102670] [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: 07/17/2023] [Revised: 09/06/2023] [Accepted: 10/05/2023] [Indexed: 11/04/2023] Open
Abstract
Protein-targeted small-molecule drugs may unintentionally bind intracellular RNA, contributing to drug toxicity. Moreover, new drugs are actively sought for intentionally targeting RNA. Here, we present a protocol to globally profile RNA-drug interactions in human cells using acylating probes and next-generation sequencing. We describe steps for cell culture, target acylation, library preparation, and sequencing. Detailed bioinformatic analyses identify drug-binding RNA loci in ∼16,000 poly(A)+ human transcripts. This streamlined workflow identifies RNA-drug interactions at single-nucleotide resolution, revealing widespread transcriptome interactions of drugs. For complete details on the use and execution of this protocol, please refer to Fang et al.1.
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Affiliation(s)
- Linglan Fang
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Eric T Kool
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA.
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14
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Nagorska A, Zaucker A, Lambert F, Inman A, Toral-Perez S, Gorodkin J, Wan Y, Smutny M, Sampath K. Translational control of furina by an RNA regulon is important for left-right patterning, heart morphogenesis and cardiac valve function. Development 2023; 150:dev201657. [PMID: 38032088 PMCID: PMC10730018 DOI: 10.1242/dev.201657] [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: 01/30/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023]
Abstract
Heart development is a complex process that requires asymmetric positioning of the heart, cardiac growth and valve morphogenesis. The mechanisms controlling heart morphogenesis and valve formation are not fully understood. The pro-convertase FurinA functions in heart development across vertebrates. How FurinA activity is regulated during heart development is unknown. Through computational analysis of the zebrafish transcriptome, we identified an RNA motif in a variant FurinA transcript harbouring a long 3' untranslated region (3'UTR). The alternative 3'UTR furina isoform is expressed prior to organ positioning. Somatic deletions in the furina 3'UTR lead to embryonic left-right patterning defects. Reporter localisation and RNA-binding assays show that the furina 3'UTR forms complexes with the conserved RNA-binding translational repressor, Ybx1. Conditional ybx1 mutant embryos show premature and increased Furin reporter expression, abnormal cardiac morphogenesis and looping defects. Mutant ybx1 hearts have an expanded atrioventricular canal, abnormal sino-atrial valves and retrograde blood flow from the ventricle to the atrium. This is similar to observations in humans with heart valve regurgitation. Thus, the furina 3'UTR element/Ybx1 regulon is important for translational repression of FurinA and regulation of heart development.
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Affiliation(s)
- Agnieszka Nagorska
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Andreas Zaucker
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Finnlay Lambert
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A*STAR, Singapore 138672
| | - Angus Inman
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Sara Toral-Perez
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Jan Gorodkin
- Center for non-coding RNAs in Technology and Health, Department of Veterinary and Animal Sciences, Faculty for Health and Medical Sciences, University of Copenhagen, Grønnega °rdsvej 3, 1870 Frederiksberg C, Denmark
| | - Yue Wan
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A*STAR, Singapore 138672
| | - Michael Smutny
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
- Centre for Mechanochemical Cell Biology, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Karuna Sampath
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
- Centre for Mechanochemical Cell Biology, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
- Centre for Early Life, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
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15
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Zhu H, Yang Y, Wang Y, Wang F, Huang Y, Chang Y, Wong KC, Li X. Dynamic characterization and interpretation for protein-RNA interactions across diverse cellular conditions using HDRNet. Nat Commun 2023; 14:6824. [PMID: 37884495 PMCID: PMC10603054 DOI: 10.1038/s41467-023-42547-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 10/13/2023] [Indexed: 10/28/2023] Open
Abstract
RNA-binding proteins play crucial roles in the regulation of gene expression, and understanding the interactions between RNAs and RBPs in distinct cellular conditions forms the basis for comprehending the underlying RNA function. However, current computational methods pose challenges to the cross-prediction of RNA-protein binding events across diverse cell lines and tissue contexts. Here, we develop HDRNet, an end-to-end deep learning-based framework to precisely predict dynamic RBP binding events under diverse cellular conditions. Our results demonstrate that HDRNet can accurately and efficiently identify binding sites, particularly for dynamic prediction, outperforming other state-of-the-art models on 261 linear RNA datasets from both eCLIP and CLIP-seq, supplemented with additional tissue data. Moreover, we conduct motif and interpretation analyses to provide fresh insights into the pathological mechanisms underlying RNA-RBP interactions from various perspectives. Our functional genomic analysis further explores the gene-human disease associations, uncovering previously uncharacterized observations for a broad range of genetic disorders.
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Affiliation(s)
- Haoran Zhu
- School of Artificial Intelligence, Jilin University, 130012, Changchun, China
| | - Yuning Yang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Yunhe Wang
- School of Artificial Intelligence, Hebei University of Technology, Tianjin, China
| | - Fuzhou Wang
- Department of Computer Science, City University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Yujian Huang
- College of Computer Science and Cyber Security, Chengdu University of Technology, 610059, Chengdu, China
| | - Yi Chang
- School of Artificial Intelligence, Jilin University, 130012, Changchun, China
| | - Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, Hong Kong, Hong Kong SAR.
| | - Xiangtao Li
- School of Artificial Intelligence, Jilin University, 130012, Changchun, China.
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16
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Tang Z, Hegde S, Hao S, Selvaraju M, Qiu J, Wang J. Chemical-guided SHAPE sequencing (cgSHAPE-seq) informs the binding site of RNA-degrading chimeras targeting SARS-CoV-2 5' untranslated region. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.03.535453. [PMID: 37066172 PMCID: PMC10103992 DOI: 10.1101/2023.04.03.535453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
One of the hallmarks of RNA viruses is highly structured untranslated regions (UTRs) in their genomes. These conserved RNA structures are often essential for viral replication, transcription, or translation. In this report, we discovered and optimized a new type of coumarin derivatives, such as C30 and C34, which bind to a four-way RNA helix called SL5 in the 5' UTR of the SARS-CoV-2 RNA genome. To locate the binding site, we developed a novel sequencing-based method namely cgSHAPE-seq, in which the acylating chemical probe was directed to crosslink with the 2'-OH groups of ribose at the ligand binding site. This crosslinked RNA could then create read-through mutations during reverse transcription (i.e., primer extension) at single-nucleotide resolution to uncover the acylation locations. cgSHAPE-seq unambiguously determined that a bulged G in SL5 was the primary binding site of C30 in the SARS-CoV-2 5' UTR, which was validated through mutagenesis and in vitro binding experiments. C30 was further used as a warhead in RNA-degrading chimeras to reduce viral RNA expression levels. We demonstrated that replacing the acylating moiety in the cgSHAPE probe with ribonuclease L recruiter (RLR) moieties yielded RNA degraders active in the in vitro RNase L degradation assay and SARS-CoV-2 5' UTR expressing cells. We further explored another RLR conjugation site on the E ring of C30/C34 and discovered improved RNA degradation activities in vitro and in cells. The optimized RNA-degrading chimera C64 inhibited live virus replication in lung epithelial carcinoma cells.
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Affiliation(s)
- Zhichao Tang
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS, USA
| | - Shalakha Hegde
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS, USA
| | - Siyuan Hao
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS, USA
| | | | - Jianming Qiu
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Jingxin Wang
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS, USA
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17
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Zhu YJ, Liao ML, Dong YW. Exploring the adaptability of the secondary structure of mRNA to temperature in intertidal snails based on SHAPE experiments. J Exp Biol 2023; 226:jeb246544. [PMID: 37767692 DOI: 10.1242/jeb.246544] [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: 08/16/2023] [Accepted: 09/22/2023] [Indexed: 09/29/2023]
Abstract
RNA-based thermal regulation is an important strategy for organisms to cope with temperature changes. Inhabiting the intertidal rocky shore, a key interface of the ocean, atmosphere and terrestrial environments, intertidal species have developed variable thermal adaptation mechanisms; however, adaptions at the RNA level remain largely uninvestigated. To examine the relationship between mRNA structural stability and species distribution, in the present study, the secondary structure of cytosolic malate dehydrogenase (cMDH) mRNA of Echinolittorina malaccana, Echinolittorina radiata and Littorina brevicula was determined using selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE), and the change in folding free energy of formation (ΔGfold) was calculated. The results showed that ΔGfold increased as the temperature increased. The difference in ΔGfold (ΔΔGfold) between two specific temperatures (25 versus 0°C, 37 versus 0°C and 57 versus 0°C) differed among the three species, and the ΔΔGfold value of E. malaccana was significantly lower than those of E. radiata and L. brevicula. The number of stems of cMDH mRNA of the snails decreased with increasing temperature, and the breakpoint temperature of E. malaccana was the highest among these. The number of loops was also reduced with increasing temperature, while the length of the loop structure increased accordingly. Consequently, these structural changes can potentially affect the translational efficiency of mRNA. These results imply that there were interspecific differences in the thermal stability of RNA secondary structures in intertidal snails, and these differences may be related to snail distribution.
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Affiliation(s)
- Ya-Jie Zhu
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao 266003, PR China
| | - Ming-Ling Liao
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao 266003, PR China
| | - Yun-Wei Dong
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao 266003, PR China
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18
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Fullenkamp CR, Schneekloth JS. RNA as an off-target for FDA-approved drugs. Nat Chem 2023; 15:1329-1331. [PMID: 37697037 DOI: 10.1038/s41557-023-01330-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Affiliation(s)
| | - John S Schneekloth
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, USA.
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19
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Fang L, Velema WA, Lee Y, Xiao L, Mohsen MG, Kietrys AM, Kool ET. Pervasive transcriptome interactions of protein-targeted drugs. Nat Chem 2023; 15:1374-1383. [PMID: 37653232 DOI: 10.1038/s41557-023-01309-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 07/27/2023] [Indexed: 09/02/2023]
Abstract
The off-target toxicity of drugs targeted to proteins imparts substantial health and economic costs. Proteome interaction studies can reveal off-target effects with unintended proteins; however, little attention has been paid to intracellular RNAs as potential off-targets that may contribute to toxicity. To begin to assess this, we developed a reactivity-based RNA profiling methodology and applied it to uncover transcriptome interactions of a set of Food and Drug Administration-approved small-molecule drugs in vivo. We show that these protein-targeted drugs pervasively interact with the human transcriptome and can exert unintended biological effects on RNA functions. In addition, we show that many off-target interactions occur at RNA loci associated with protein binding and structural changes, allowing us to generate hypotheses to infer the biological consequences of RNA off-target binding. The results suggest that rigorous characterization of drugs' transcriptome interactions may help assess target specificity and potentially avoid toxicity and clinical failures.
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Affiliation(s)
- Linglan Fang
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Willem A Velema
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Yujeong Lee
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Lu Xiao
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | | | - Anna M Kietrys
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA, USA.
- Sarafan ChEM-H Institute, Stanford University, Stanford, CA, USA.
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20
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Yu G, Liu Y, Li Z, Deng S, Wu Z, Zhang X, Chen W, Yang J, Chen X, Yang JR. Genome-wide probing of eukaryotic nascent RNA structure elucidates cotranscriptional folding and its antimutagenic effect. Nat Commun 2023; 14:5853. [PMID: 37730811 PMCID: PMC10511511 DOI: 10.1038/s41467-023-41550-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 09/08/2023] [Indexed: 09/22/2023] Open
Abstract
The transcriptional intermediates of RNAs fold into secondary structures with multiple regulatory roles, yet the details of such cotranscriptional RNA folding are largely unresolved in eukaryotes. Here, we present eSPET-seq (Structural Probing of Elongating Transcripts in eukaryotes), a method to assess the cotranscriptional RNA folding in Saccharomyces cerevisiae. Our study reveals pervasive structural transitions during cotranscriptional folding and overall structural similarities between nascent and mature RNAs. Furthermore, a combined analysis with genome-wide R-loop and mutation rate approximations provides quantitative evidence for the antimutator effect of nascent RNA folding through competitive inhibition of the R-loops, known to facilitate transcription-associated mutagenesis. Taken together, we present an experimental evaluation of cotranscriptional folding in eukaryotes and demonstrate the antimutator effect of nascent RNA folding. These results suggest genome-wide coupling between the processing and transmission of genetic information through RNA folding.
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Affiliation(s)
- Gongwang Yu
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Yao Liu
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Zizhang Li
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Shuyun Deng
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Zhuoxing Wu
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Xiaoyu Zhang
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Wenbo Chen
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Junnan Yang
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Xiaoshu Chen
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, 510080, China
| | - Jian-Rong Yang
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, 510080, China.
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21
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Horlacher M, Cantini G, Hesse J, Schinke P, Goedert N, Londhe S, Moyon L, Marsico A. A systematic benchmark of machine learning methods for protein-RNA interaction prediction. Brief Bioinform 2023; 24:bbad307. [PMID: 37635383 PMCID: PMC10516373 DOI: 10.1093/bib/bbad307] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 06/15/2023] [Accepted: 07/18/2023] [Indexed: 08/29/2023] Open
Abstract
RNA-binding proteins (RBPs) are central actors of RNA post-transcriptional regulation. Experiments to profile-binding sites of RBPs in vivo are limited to transcripts expressed in the experimental cell type, creating the need for computational methods to infer missing binding information. While numerous machine-learning based methods have been developed for this task, their use of heterogeneous training and evaluation datasets across different sets of RBPs and CLIP-seq protocols makes a direct comparison of their performance difficult. Here, we compile a set of 37 machine learning (primarily deep learning) methods for in vivo RBP-RNA interaction prediction and systematically benchmark a subset of 11 representative methods across hundreds of CLIP-seq datasets and RBPs. Using homogenized sample pre-processing and two negative-class sample generation strategies, we evaluate methods in terms of predictive performance and assess the impact of neural network architectures and input modalities on model performance. We believe that this study will not only enable researchers to choose the optimal prediction method for their tasks at hand, but also aid method developers in developing novel, high-performing methods by introducing a standardized framework for their evaluation.
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Affiliation(s)
- Marc Horlacher
- Computational Health Center, Helmholtz Center Munich, Germany
- School of Computation, Information and Technology, Technical University Munich (TUM), Germany
| | - Giulia Cantini
- Computational Health Center, Helmholtz Center Munich, Germany
| | - Julian Hesse
- Computational Health Center, Helmholtz Center Munich, Germany
| | - Patrick Schinke
- Computational Health Center, Helmholtz Center Munich, Germany
| | - Nicolas Goedert
- Computational Health Center, Helmholtz Center Munich, Germany
| | | | - Lambert Moyon
- Computational Health Center, Helmholtz Center Munich, Germany
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22
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Papaspyropoulos A, Hazapis O, Altulea A, Polyzou A, Verginis P, Evangelou K, Fousteri M, Papantonis A, Demaria M, Gorgoulis V. Decoding of translation-regulating entities reveals heterogeneous translation deficiency patterns in cellular senescence. Aging Cell 2023; 22:e13893. [PMID: 37547972 PMCID: PMC10497830 DOI: 10.1111/acel.13893] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/04/2023] [Indexed: 08/08/2023] Open
Abstract
Cellular senescence constitutes a generally irreversible proliferation barrier, accompanied by macromolecular damage and metabolic rewiring. Several senescence types have been identified based on the initiating stimulus, such as replicative (RS), stress-induced (SIS) and oncogene-induced senescence (OIS). These senescence subtypes are heterogeneous and often develop subset-specific phenotypes. Reduced protein synthesis is considered a senescence hallmark, but whether this trait pertains to various senescence subtypes and if distinct molecular mechanisms are involved remain largely unknown. Here, we analyze large published or experimentally produced RNA-seq and Ribo-seq datasets to determine whether major translation-regulating entities such as ribosome stalling, the presence of uORFs/dORFs and IRES elements may differentially contribute to translation deficiency in senescence subsets. We show that translation-regulating mechanisms may not be directly relevant to RS, however uORFs are significantly enriched in SIS. Interestingly, ribosome stalling, uORF/dORF patterns and IRES elements comprise predominant mechanisms upon OIS, strongly correlating with Notch pathway activation. Our study provides for the first time evidence that major translation dysregulation mechanisms/patterns occur during cellular senescence, but at different rates depending on the stimulus type. The degree at which those mechanisms accumulate directly correlates with translation deficiency levels. Our thorough analysis contributes to elucidating crucial and so far unknown differences in the translation machinery between senescence subsets.
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Affiliation(s)
- Angelos Papaspyropoulos
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of MedicineNational Kapodistrian University of Athens (NKUA)AthensGreece
- Biomedical Research FoundationAcademy of AthensAthensGreece
| | - Orsalia Hazapis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of MedicineNational Kapodistrian University of Athens (NKUA)AthensGreece
| | - Abdullah Altulea
- European Research Institute for the Biology of Ageing (ERIBA)University Medical Center GroningenGroningenThe Netherlands
| | - Aikaterini Polyzou
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of MedicineNational Kapodistrian University of Athens (NKUA)AthensGreece
| | | | - Konstantinos Evangelou
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of MedicineNational Kapodistrian University of Athens (NKUA)AthensGreece
| | - Maria Fousteri
- Institute for Fundamental Biomedical ResearchBiomedical Sciences Research Center “Alexander Fleming”VariGreece
| | - Argyris Papantonis
- Institute of PathologyUniversity Medical Center GöttingenGöttingenGermany
- Center for Molecular Medicine CologneUniversity of CologneCologneGermany
| | - Marco Demaria
- European Research Institute for the Biology of Ageing (ERIBA)University Medical Center GroningenGroningenThe Netherlands
| | - Vassilis Gorgoulis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of MedicineNational Kapodistrian University of Athens (NKUA)AthensGreece
- Biomedical Research FoundationAcademy of AthensAthensGreece
- Clinical Molecular PathologyMedical School, University of DundeeDundeeUK
- Molecular and Clinical Cancer Sciences, Manchester Cancer Research Centre, Manchester Academic Health Sciences CentreUniversity of ManchesterManchesterUK
- Center for New Biotechnologies and Precision MedicineMedical School, National and Kapodistrian University of AthensAthensGreece
- Faculty of Health and Medical SciencesUniversity of SurreySurreyUK
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23
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How does precursor RNA structure influence RNA processing and gene expression? Biosci Rep 2023; 43:232489. [PMID: 36689327 PMCID: PMC9977717 DOI: 10.1042/bsr20220149] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 01/17/2023] [Accepted: 01/23/2023] [Indexed: 01/24/2023] Open
Abstract
RNA is a fundamental biomolecule that has many purposes within cells. Due to its single-stranded and flexible nature, RNA naturally folds into complex and dynamic structures. Recent technological and computational advances have produced an explosion of RNA structural data. Many RNA structures have regulatory and functional properties. Studying the structure of nascent RNAs is particularly challenging due to their low abundance and long length, but their structures are important because they can influence RNA processing. Precursor RNA processing is a nexus of pathways that determines mature isoform composition and that controls gene expression. In this review, we examine what is known about human nascent RNA structure and the influence of RNA structure on processing of precursor RNAs. These known structures provide examples of how other nascent RNAs may be structured and show how novel RNA structures may influence RNA processing including splicing and polyadenylation. RNA structures can be targeted therapeutically to treat disease.
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24
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Takizawa N. RNA Structure Determination by High-Throughput Structural Analysis. Methods Mol Biol 2023; 2586:217-231. [PMID: 36705907 DOI: 10.1007/978-1-0716-2768-6_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
RNA functions are closely linked with their structures. Therefore, elucidating the secondary structure of RNAs provides crucial information regarding their function. The chemical modification or RNase-mediated digestion of single-stranded RNA has been utilized to experimentally reveal RNA secondary structures. Owing to advances in high-throughput sequencing technology and chemical analysis, RNA structural analyses that enable structural profiling at the transcriptomic scale in living cells have been developed. Here, we provide an overview of the high-throughput RNA structural (HTS) analyses and describe the computational processing steps of recent HTS analysis pipelines: PROBer, BUMHMM, and reactIDR.
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Affiliation(s)
- Naoki Takizawa
- Laboratory of Virology, Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan.
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25
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Yu B, Li P, Zhang QC, Hou L. Differential analysis of RNA structure probing experiments at nucleotide resolution: uncovering regulatory functions of RNA structure. Nat Commun 2022; 13:4227. [PMID: 35869080 PMCID: PMC9307511 DOI: 10.1038/s41467-022-31875-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 07/05/2022] [Indexed: 11/09/2022] Open
Abstract
RNAs perform their function by forming specific structures, which can change across cellular conditions. Structure probing experiments combined with next generation sequencing technology have enabled transcriptome-wide analysis of RNA secondary structure in various cellular conditions. Differential analysis of structure probing data in different conditions can reveal the RNA structurally variable regions (SVRs), which is important for understanding RNA functions. Here, we propose DiffScan, a computational framework for normalization and differential analysis of structure probing data in high resolution. DiffScan preprocesses structure probing datasets to remove systematic bias, and then scans the transcripts to identify SVRs and adaptively determines their lengths and locations. The proposed approach is compatible with most structure probing platforms (e.g., icSHAPE, DMS-seq). When evaluated with simulated and benchmark datasets, DiffScan identifies structurally variable regions at nucleotide resolution, with substantial improvement in accuracy compared with existing SVR detection methods. Moreover, the improvement is robust when tested in multiple structure probing platforms. Application of DiffScan in a dataset of multi-subcellular RNA structurome and a subsequent motif enrichment analysis suggest potential links of RNA structural variation and mRNA abundance, possibly mediated by RNA binding proteins such as the serine/arginine rich splicing factors. This work provides an effective tool for differential analysis of RNA secondary structure, reinforcing the power of structure probing experiments in deciphering the dynamic RNA structurome. The authors present DiffScan, an advanced tool for normalization and differential analysis of RNA structure probing experiments, combining their power in deciphering the dynamic RNA structurome and facilitating the discovery of RNA regulatory functions.
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26
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Pepe G, Appierdo R, Carrino C, Ballesio F, Helmer-Citterich M, Gherardini PF. Artificial intelligence methods enhance the discovery of RNA interactions. Front Mol Biosci 2022; 9:1000205. [PMID: 36275611 PMCID: PMC9585310 DOI: 10.3389/fmolb.2022.1000205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Understanding how RNAs interact with proteins, RNAs, or other molecules remains a challenge of main interest in biology, given the importance of these complexes in both normal and pathological cellular processes. Since experimental datasets are starting to be available for hundreds of functional interactions between RNAs and other biomolecules, several machine learning and deep learning algorithms have been proposed for predicting RNA-RNA or RNA-protein interactions. However, most of these approaches were evaluated on a single dataset, making performance comparisons difficult. With this review, we aim to summarize recent computational methods, developed in this broad research area, highlighting feature encoding and machine learning strategies adopted. Given the magnitude of the effect that dataset size and quality have on performance, we explored the characteristics of these datasets. Additionally, we discuss multiple approaches to generate datasets of negative examples for training. Finally, we describe the best-performing methods to predict interactions between proteins and specific classes of RNA molecules, such as circular RNAs (circRNAs) and long non-coding RNAs (lncRNAs), and methods to predict RNA-RNA or RNA-RBP interactions independently of the RNA type.
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Affiliation(s)
- G Pepe
- Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
- *Correspondence: G Pepe, ; M Helmer-Citterich,
| | - R Appierdo
- Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - C Carrino
- PhD Program in Cellular and Molecular Biology, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - F Ballesio
- PhD Program in Cellular and Molecular Biology, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - M Helmer-Citterich
- Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
- *Correspondence: G Pepe, ; M Helmer-Citterich,
| | - PF Gherardini
- Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
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27
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Bizuayehu TT, Labun K, Jakubec M, Jefimov K, Niazi A, Valen E. Long-read single-molecule RNA structure sequencing using nanopore. Nucleic Acids Res 2022; 50:e120. [PMID: 36166000 PMCID: PMC9723614 DOI: 10.1093/nar/gkac775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/16/2022] [Accepted: 08/29/2022] [Indexed: 12/24/2022] Open
Abstract
RNA molecules can form secondary and tertiary structures that can regulate their localization and function. Using enzymatic or chemical probing together with high-throughput sequencing, secondary structure can be mapped across the entire transcriptome. However, a limiting factor is that only population averages can be obtained since each read is an independent measurement. Although long-read sequencing has recently been used to determine RNA structure, these methods still used aggregate signals across the strands to detect structure. Averaging across the population also means that only limited information about structural heterogeneity across molecules or dependencies within each molecule can be obtained. Here, we present Single-Molecule Structure sequencing (SMS-seq) that combines structural probing with native RNA sequencing to provide non-amplified, structural profiles of individual molecules with novel analysis methods. Our new approach using mutual information enabled single molecule structural interrogation. Each RNA is probed at numerous bases enabling the discovery of dependencies and heterogeneity of structural features. We also show that SMS-seq can capture tertiary interactions, dynamics of riboswitch ligand binding, and mRNA structural features.
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Affiliation(s)
- Teshome Tilahun Bizuayehu
- Computational Biology Unit, Department of Informatics, University of Bergen, Norway
- Sars International Center for Marine Molecular Biology, University of Bergen, Norway
| | - Kornel Labun
- Computational Biology Unit, Department of Informatics, University of Bergen, Norway
| | | | - Kirill Jefimov
- Computational Biology Unit, Department of Informatics, University of Bergen, Norway
| | - Adnan Muhammad Niazi
- Computational Biology Unit, Department of Informatics, University of Bergen, Norway
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28
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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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29
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Yang SL, Ponti RD, Wan Y, Huber RG. Computational and Experimental Approaches to Study the RNA Secondary Structures of RNA Viruses. Viruses 2022; 14:v14081795. [PMID: 36016417 PMCID: PMC9415818 DOI: 10.3390/v14081795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/12/2022] [Accepted: 08/13/2022] [Indexed: 11/16/2022] Open
Abstract
Most pandemics of recent decades can be traced to RNA viruses, including HIV, SARS, influenza, dengue, Zika, and SARS-CoV-2. These RNA viruses impose considerable social and economic burdens on our society, resulting in a high number of deaths and high treatment costs. As these RNA viruses utilize an RNA genome, which is important for different stages of the viral life cycle, including replication, translation, and packaging, studying how the genome folds is important to understand virus function. In this review, we summarize recent advances in computational and high-throughput RNA structure-mapping approaches and their use in understanding structures within RNA virus genomes. In particular, we focus on the genome structures of the dengue, Zika, and SARS-CoV-2 viruses due to recent significant outbreaks of these viruses around the world.
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Affiliation(s)
- Siwy Ling Yang
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore
| | - Riccardo Delli Ponti
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore
| | - Yue Wan
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore
- Correspondence: (Y.W.); (R.G.H.)
| | - Roland G. Huber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore
- Correspondence: (Y.W.); (R.G.H.)
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30
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Lessons Learned and Yet-to-Be Learned on the Importance of RNA Structure in SARS-CoV-2 Replication. Microbiol Mol Biol Rev 2022; 86:e0005721. [PMID: 35862724 PMCID: PMC9491204 DOI: 10.1128/mmbr.00057-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
SARS-CoV-2, the etiological agent responsible for the COVID-19 pandemic, is a member of the virus family Coronaviridae, known for relatively extensive (~30-kb) RNA genomes that not only encode for numerous proteins but are also capable of forming elaborate structures. As highlighted in this review, these structures perform critical functions in various steps of the viral life cycle, ultimately impacting pathogenesis and transmissibility. We examine these elements in the context of coronavirus evolutionary history and future directions for curbing the spread of SARS-CoV-2 and other potential human coronaviruses. While we focus on structures supported by a variety of biochemical, biophysical, and/or computational methods, we also touch here on recent evidence for novel structures in both protein-coding and noncoding regions of the genome, including an assessment of the potential role for RNA structure in the controversial finding of SARS-CoV-2 integration in “long COVID” patients. This review aims to serve as a consolidation of previous works on coronavirus and more recent investigation of SARS-CoV-2, emphasizing the need for improved understanding of the role of RNA structure in the evolution and adaptation of these human viruses.
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31
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Delli Ponti R, Wang J, Wan Y, Huber RG. RNAvigator: A Pipeline to Identify Candidates for Functional RNA Structure Elements. FRONTIERS IN VIROLOGY 2022. [DOI: 10.3389/fviro.2022.878679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Identifying structural elements in long and complex RNAs, such as long non-coding and RNA viruses, can shed light on the functionality and mechanisms of such RNAs. Here we present RNAvigator, a tool able to identify elements of structural importance by using experimental SHAPE data or SHAPE-like predictions in conjunction with stability and entropy assessments. RNAvigator recognizes regions that are the most stable, unambiguous, and structured on RNA molecules, and thus potentially functional. When relying on predictions, RNAvigator uses the CROSS algorithm, a neural network trained on experimental data that achieved an AUC of 0.74 on hepatitis C virus SHAPE-MaP data and which was able to improve the predictive power of Superfold. By using RNAvigator, we can identify known functional regions on the complete hepatitis C virus genome, including the regulatory regions CRE and IRES, and the 3’ UTR of dengue virus, a region known for the presence of structural elements essential for its replication, and functional regions of long non-coding RNAs such as XIST and HOTAIR. We envision that RNAvigator will be a useful tool for studying long and complex RNA molecules using known chemical probing data or, if they are not available, by employing predicted profiles.
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32
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Jurich CP, Brivanlou A, Rouskin S, Yesselman JD. Web-based platform for analysis of RNA folding from high throughput chemical probing data. Nucleic Acids Res 2022; 50:W266-W271. [PMID: 35657086 PMCID: PMC9252807 DOI: 10.1093/nar/gkac435] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/28/2022] [Accepted: 05/13/2022] [Indexed: 11/21/2022] Open
Abstract
RNA structures play critical roles in regulating gene expression across all domains of life and viruses. Chemical probing methods coupled with massively parallel sequencing have revolutionized the RNA structure field by enabling the assessment of many structures in their native, physiological context. Previously, we developed Dimethyl-Sulfate-based Mutational Profiling and Sequencing (DMS-MaPseq), which uses DMS to label the Watson-Crick face of open and accessible adenine and cytosine bases in the RNA. We used this approach to determine the genome-wide structures of HIV-1 and SARS-CoV-2 in infected cells, which permitted uncovering new biology and identifying therapeutic targets. Due to the simplicity and ease of the experimental procedure, DMS-MaPseq has been adopted by labs worldwide. However, bioinformatic analysis remains a substantial hurdle for labs that often lack the necessary infrastructure and computational expertise. Here we present a modern web-based interface that automates the analysis of chemical probing profiles from raw sequencing files (http://rnadreem.org). The availability of a simple web-based platform for DMS-MaPseq analysis will dramatically expand studies of RNA structure and aid in the design of structure-based therapeutics.
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Affiliation(s)
| | - Amir Brivanlou
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Silvi Rouskin
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Joseph D Yesselman
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
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33
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Qi Y, Zhang Y, Mu Q, Zheng G, Zhang M, Chen B, Huang J, Ma C, Wang X. RNA Secondary Structurome Revealed Distinct Thermoregulation in Plasmodium falciparum. Front Cell Dev Biol 2022; 9:766532. [PMID: 35059397 PMCID: PMC8763798 DOI: 10.3389/fcell.2021.766532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 11/19/2021] [Indexed: 11/13/2022] Open
Abstract
The development of Plasmodium parasites, a causative agent of malaria, requests two hosts and the completion of 11 different parasite stages during development. Therefore, an efficient and fast response of parasites to various complex environmental changes, such as ambient temperature, pH, ions, and nutrients, is essential for parasite development and survival. Among many of these environmental changes, temperature is a decisive factor for parasite development and pathogenesis, including the thermoregulation of rRNA expression, gametogenesis, and parasite sequestration in cerebral malaria. However, the exact mechanism of how Plasmodium parasites rapidly respond and adapt to temperature change remains elusive. As a fundamental and pervasive regulator of gene expression, RNA structure can be a specific mechanism for fine tuning various biological processes. For example, dynamic and temperature-dependent changes in RNA secondary structures can control the expression of different gene programs, as shown by RNA thermometers. In this study, we applied the in vitro and in vivo transcriptomic-wide secondary structurome approach icSHAPE to measure parasite RNA structure changes with temperature alteration at single-nucleotide resolution for ring and trophozoite stage parasites. Among 3,000 probed structures at different temperatures, our data showed structural changes in the global transcriptome, such as S-type rRNA, HRPII gene, and the erythrocyte membrane protein family. When the temperature drops from 37°C to 26°C, most of the genes in the trophozoite stage cause significantly more changes to the RNA structure than the genes in the ring stage. A multi-omics analysis of transcriptome data from RNA-seq and RNA structure data from icSHAPE reveals that the specific RNA secondary structure plays a significant role in the regulation of transcript expression for parasites in response to temperature changes. In addition, we identified several RNA thermometers (RNATs) that responded quickly to temperature changes. The possible thermo-responsive RNAs in Plasmodium falciparum were further mapped. To this end, we identified dynamic and temperature-dependent RNA structural changes in the P. falciparum transcriptome and performed a comprehensive characterization of RNA secondary structures over the course of temperature stress in blood stage development. These findings not only contribute to a better understanding of the function of the RNA secondary structure but may also provide novel targets for efficient vaccines or drugs.
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Affiliation(s)
- Yanwei Qi
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Yuhong Zhang
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Quankai Mu
- Department of Immunogenetics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Guixing Zheng
- Department of Blood Transfusion, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Mengxin Zhang
- The Third Clinical School, Guangzhou Medical University, Guangzhou, China
| | - Bingxia Chen
- The Third Clinical School, Guangzhou Medical University, Guangzhou, China
| | - Jun Huang
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Changling Ma
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Xinhua Wang
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
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34
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Wei J, Chen S, Zong L, Gao X, Li Y. Protein-RNA interaction prediction with deep learning: structure matters. Brief Bioinform 2022; 23:bbab540. [PMID: 34929730 PMCID: PMC8790951 DOI: 10.1093/bib/bbab540] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/14/2021] [Accepted: 11/22/2021] [Indexed: 12/11/2022] Open
Abstract
Protein-RNA interactions are of vital importance to a variety of cellular activities. Both experimental and computational techniques have been developed to study the interactions. Because of the limitation of the previous database, especially the lack of protein structure data, most of the existing computational methods rely heavily on the sequence data, with only a small portion of the methods utilizing the structural information. Recently, AlphaFold has revolutionized the entire protein and biology field. Foreseeably, the protein-RNA interaction prediction will also be promoted significantly in the upcoming years. In this work, we give a thorough review of this field, surveying both the binding site and binding preference prediction problems and covering the commonly used datasets, features and models. We also point out the potential challenges and opportunities in this field. This survey summarizes the development of the RNA-binding protein-RNA interaction field in the past and foresees its future development in the post-AlphaFold era.
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Affiliation(s)
- Junkang Wei
- Department of Computer Science and Engineering (CSE), The Chinese
University of Hong Kong (CUHK), 999077, Hong Kong SAR, China
| | - Siyuan Chen
- Computational Bioscience Research Center (CBRC),
King Abdullah University of Science and Technology (KAUST),
23955-6900, Thuwal, Saudi Arabia
| | - Licheng Zong
- Department of Computer Science and Engineering (CSE), The Chinese
University of Hong Kong (CUHK), 999077, Hong Kong SAR, China
| | - Xin Gao
- Computational Bioscience Research Center (CBRC),
King Abdullah University of Science and Technology (KAUST),
23955-6900, Thuwal, Saudi Arabia
| | - Yu Li
- Department of Computer Science and Engineering (CSE), The Chinese
University of Hong Kong (CUHK), 999077, Hong Kong SAR, China
- The CUHK Shenzhen Research Institute, Hi-Tech Park, 518057,
Shenzhen, China
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35
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Arnoldi M, Zarantonello G, Espinoza S, Gustincich S, Di Leva F, Biagioli M. Design and Delivery of SINEUP: A New Modular Tool to Increase Protein Translation. Methods Mol Biol 2022; 2434:63-87. [PMID: 35213010 PMCID: PMC9703201 DOI: 10.1007/978-1-0716-2010-6_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
SINEUP is a new class of long non-coding RNAs (lncRNAs) which contain an inverted Short Interspersed Nuclear Element (SINE) B2 element (invSINEB2) necessary to specifically upregulate target gene translation. Originally identified in the mouse AS-Uchl1 (antisense Ubiquitin carboxyl-terminal esterase L1) locus, natural SINEUP molecules are oriented head to head to their sense protein coding, target gene (Uchl1, in this example). Peculiarly, SINEUP is able to augment, in a specific and controlled way, the expression of the target protein, with no alteration of target mRNA levels. SINEUP is characterized by a modular structure with the Binding Domain (BD) providing specificity to the target transcript and an effector domain (ED)-containing the invSINEB2 element-able to promote the loading to the heavy polysomes of the target mRNA. Since the understanding of its modular structure in the endogenous AS-Uchl1 ncRNA, synthetic SINEUP molecules have been developed by creating a specific BD for the gene of interest and placing it upstream the invSINEB2 ED. Synthetic SINEUP is thus a novel molecular tool that potentially may be used for any industrial or biomedical application to enhance protein production, also as possible therapeutic strategy in haploinsufficiency-driven disorders.Here, we describe a detailed protocol to (1) design a specific BD directed to a gene of interest and (2) assemble and clone it with the ED to obtain a functional SINEUP molecule. Then, we provide guidelines to efficiently deliver SINEUP into mammalian cells and evaluate its ability to effectively upregulate target protein translation.
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Affiliation(s)
- Michele Arnoldi
- Neuroepigenetics Laboratory, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Giulia Zarantonello
- Neuroepigenetics Laboratory, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Stefano Espinoza
- Central RNA Laboratory, Istituto Italiano di Tecnologia, Genova, Italy
| | - Stefano Gustincich
- Central RNA Laboratory, Istituto Italiano di Tecnologia, Genova, Italy
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Francesca Di Leva
- Neuroepigenetics Laboratory, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy.
- Institute for Biomedicine, Eurac Research, Bolzano, Italy.
| | - Marta Biagioli
- Neuroepigenetics Laboratory, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy.
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36
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Wang J, Zhang T, Yu Z, Tan WT, Wen M, Shen Y, Lambert FRP, Huber RG, Wan Y. Genome-wide RNA structure changes during human neurogenesis modulate gene regulatory networks. Mol Cell 2021; 81:4942-4953.e8. [PMID: 34655516 DOI: 10.1016/j.molcel.2021.09.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 08/01/2021] [Accepted: 09/24/2021] [Indexed: 11/18/2022]
Abstract
The distribution, dynamics, and function of RNA structures in human development are under-explored. Here, we systematically assayed RNA structural dynamics and their relationship with gene expression, translation, and decay during human neurogenesis. We observed that the human ESC transcriptome is globally more structurally accessible than differentiated cells and undergoes extensive RNA structure changes, particularly in the 3' UTR. Additionally, RNA structure changes during differentiation are associated with translation and decay. We observed that RBP and miRNA binding is associated with RNA structural changes during early neuronal differentiation, and splicing is associated during later neuronal differentiation. Furthermore, our analysis suggests that RBPs are major factors in structure remodeling and co-regulate additional RBPs and miRNAs through structure. We demonstrated an example of this by showing that PUM2-induced structure changes on LIN28A enable miR-30 binding. This study deepens our understanding of the widespread and complex role of RNA-based gene regulation during human development.
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Affiliation(s)
- Jiaxu Wang
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore
| | - Tong Zhang
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore
| | - Zhang Yu
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore
| | - Wen Ting Tan
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore
| | - Ming Wen
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore
| | - Yang Shen
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore
| | - Finnlay R P Lambert
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore; Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Roland G Huber
- Bioinformatics Institute, A(∗)STAR, Singapore 138671, Singapore
| | - Yue Wan
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore; Department of Biochemistry, National University of Singapore, Singapore 117596, Singapore.
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37
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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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38
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De Bisschop G, Allouche D, Frezza E, Masquida B, Ponty Y, Will S, Sargueil B. Progress toward SHAPE Constrained Computational Prediction of Tertiary Interactions in RNA Structure. Noncoding RNA 2021; 7:71. [PMID: 34842779 PMCID: PMC8628965 DOI: 10.3390/ncrna7040071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 01/04/2023] Open
Abstract
As more sequencing data accumulate and novel puzzling genetic regulations are discovered, the need for accurate automated modeling of RNA structure increases. RNA structure modeling from chemical probing experiments has made tremendous progress, however accurately predicting large RNA structures is still challenging for several reasons: RNA are inherently flexible and often adopt many energetically similar structures, which are not reliably distinguished by the available, incomplete thermodynamic model. Moreover, computationally, the problem is aggravated by the relevance of pseudoknots and non-canonical base pairs, which are hardly predicted efficiently. To identify nucleotides involved in pseudoknots and non-canonical interactions, we scrutinized the SHAPE reactivity of each nucleotide of the 188 nt long lariat-capping ribozyme under multiple conditions. Reactivities analyzed in the light of the X-ray structure were shown to report accurately the nucleotide status. Those that seemed paradoxical were rationalized by the nucleotide behavior along molecular dynamic simulations. We show that valuable information on intricate interactions can be deduced from probing with different reagents, and in the presence or absence of Mg2+. Furthermore, probing at increasing temperature was remarkably efficient at pointing to non-canonical interactions and pseudoknot pairings. The possibilities of following such strategies to inform structure modeling software are discussed.
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Affiliation(s)
- Grégoire De Bisschop
- Université de Paris, CNRS, UMR 8038/CiTCoM, F-75006 Paris, France; (G.D.B.); (D.A.); (E.F.)
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
| | - Delphine Allouche
- Université de Paris, CNRS, UMR 8038/CiTCoM, F-75006 Paris, France; (G.D.B.); (D.A.); (E.F.)
- Institut Necker-Enfants Malades (INEM), Inserm U1151, 156 rue de Vaugirard, CEDEX 15, 75015 Paris, France
| | - Elisa Frezza
- Université de Paris, CNRS, UMR 8038/CiTCoM, F-75006 Paris, France; (G.D.B.); (D.A.); (E.F.)
| | - Benoît Masquida
- Université de Strasbourg, CNRS UMR7156 GMGM, 67084 Strasbourg, France;
| | - Yann Ponty
- Ecole Polytechnique, CNRS UMR 7161, LIX, 91120 Palaiseau, France; (Y.P.); (S.W.)
| | - Sebastian Will
- Ecole Polytechnique, CNRS UMR 7161, LIX, 91120 Palaiseau, France; (Y.P.); (S.W.)
| | - Bruno Sargueil
- Université de Paris, CNRS, UMR 8038/CiTCoM, F-75006 Paris, France; (G.D.B.); (D.A.); (E.F.)
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39
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Corley M, Flynn RA, Blue SM, Yee BA, Chang HY, Yeo GW. fSHAPE, fSHAPE-eCLIP, and SHAPE-eCLIP probe transcript regions that interact with specific proteins. STAR Protoc 2021; 2:100762. [PMID: 34485935 PMCID: PMC8406031 DOI: 10.1016/j.xpro.2021.100762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) structure probing techniques characterize the secondary structure of RNA molecules, which influence their functions and interactions. A variation of SHAPE, footprinting SHAPE (fSHAPE), probes RNA in the presence and absence of protein to identify RNA bases that hydrogen-bond with protein. SHAPE or fSHAPE coupled with enhanced crosslinking and immunoprecipitation (SHAPE-eCLIP or fSHAPE-eCLIP) pulls down RNAs bound by any protein of interest and returns their structure or protein interaction information, respectively. Here, we describe detailed protocols for SHAPE-eCLIP and fSHAPE-eCLIP and an analysis protocol for fSHAPE. For complete details on the use and execution of these protocols, please refer to Corley et al. (2020).
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Affiliation(s)
- Meredith Corley
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Ryan A. Flynn
- Stem Cell Program, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Steven M. Blue
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Brian A. Yee
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Howard Y. Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Gene W. Yeo
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA
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40
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Williams AM, Poudyal RR, Bevilacqua PC. Long Tracts of Guanines Drive Aggregation of RNA G-Quadruplexes in the Presence of Spermine. Biochemistry 2021; 60:2715-2726. [PMID: 34448586 DOI: 10.1021/acs.biochem.1c00467] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
G-Quadruplexes (GQs) are compact, stable structures in DNA and RNA comprised of two or more tiers of quartets whose G-rich motif of tracts of two or more G's occurs commonly within genomes and transcriptomes. While thermodynamically stable in vitro, these structures remain difficult to study in vivo. One approach to understanding GQ in vivo behavior is to test whether conditions and molecules found in cells facilitate their folding. Polyamines are biogenic polycations that interact with RNA. Among common polyamines, spermine contains the highest charge and is found in eukaryotes, making it a good candidate for association with high-charge density nucleic acid structures like GQs. Using a variety of techniques, including ultraviolet-detected thermal denaturation, circular dichroism, size exclusion chromatography, and confocal microscopy, on an array of quadruplex sequence variants, we find that eukaryotic biological concentrations of spermine induce microaggregation of three-tiered G-rich sequences, but not of purely two-tiered structures, although higher spermine concentrations induce aggregation of even these. The formation of microaggregates can also be induced by addition of as little as a single G to a two-tiered structure; moreover, they form at biological temperatures, are sensitive to salt, and can form in the presence of at least some flanking sequence. Notably, GQ aggregation is not observed under prokaryotic-like conditions of no spermine and higher NaCl concentrations. The sequence, polyamine, and salt specificity of microaggregation reported herein have implications for the formation and stability of G-rich nucleic acid aggregates in vivo and for functional roles for understudied GQ sequences with only two quadruplex tiers.
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Affiliation(s)
- Allison M Williams
- Department of Biochemistry, Microbiology, and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Raghav R Poudyal
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Philip C Bevilacqua
- Department of Biochemistry, Microbiology, and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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41
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Pezoulas VC, Hazapis O, Lagopati N, Exarchos TP, Goules AV, Tzioufas AG, Fotiadis DI, Stratis IG, Yannacopoulos AN, Gorgoulis VG. Machine Learning Approaches on High Throughput NGS Data to Unveil Mechanisms of Function in Biology and Disease. Cancer Genomics Proteomics 2021; 18:605-626. [PMID: 34479914 PMCID: PMC8441762 DOI: 10.21873/cgp.20284] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/21/2021] [Accepted: 08/03/2021] [Indexed: 12/13/2022] Open
Abstract
In this review, the fundamental basis of machine learning (ML) and data mining (DM) are summarized together with the techniques for distilling knowledge from state-of-the-art omics experiments. This includes an introduction to the basic mathematical principles of unsupervised/supervised learning methods, dimensionality reduction techniques, deep neural networks architectures and the applications of these in bioinformatics. Several case studies under evaluation mainly involve next generation sequencing (NGS) experiments, like deciphering gene expression from total and single cell (scRNA-seq) analysis; for the latter, a description of all recent artificial intelligence (AI) methods for the investigation of cell sub-types, biomarkers and imputation techniques are described. Other areas of interest where various ML schemes have been investigated are for providing information regarding transcription factors (TF) binding sites, chromatin organization patterns and RNA binding proteins (RBPs), while analyses on RNA sequence and structure as well as 3D dimensional protein structure predictions with the use of ML are described. Furthermore, we summarize the recent methods of using ML in clinical oncology, when taking into consideration the current omics data with pharmacogenomics to determine personalized treatments. With this review we wish to provide the scientific community with a thorough investigation of main novel ML applications which take into consideration the latest achievements in genomics, thus, unraveling the fundamental mechanisms of biology towards the understanding and cure of diseases.
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Affiliation(s)
- Vasileios C Pezoulas
- Unit of Medical Technology and Intelligent Information Systems, University of Ioannina, Ioannina, Greece
| | - Orsalia Hazapis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Nefeli Lagopati
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
- Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Themis P Exarchos
- Unit of Medical Technology and Intelligent Information Systems, Department of Materials Science and Engineering, University of Ioannina, Ioannina, Greece
- Department of Informatics, Ionian University, Corfu, Greece
| | - Andreas V Goules
- Department of Pathophysiology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Athanasios G Tzioufas
- Department of Pathophysiology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimitrios I Fotiadis
- Unit of Medical Technology and Intelligent Information Systems, University of Ioannina, Ioannina, Greece
| | - Ioannis G Stratis
- Department of Mathematics, National and Kapodistrian University of Athens, Athens, Greece
| | - Athanasios N Yannacopoulos
- Department of Statistics, and Stochastic Modelling and Applications Laboratory, Athens University of Economics and Business (AUEB), Athens, Greece;
| | - Vassilis G Gorgoulis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece;
- Biomedical Research Foundation of the Academy of Athens, Athens, Greece
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, Manchester Cancer Research Centre, NIHR Manchester Biomedical Research Centre, University of Manchester, Manchester, U.K
- Center for New Biotechnologies and Precision Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece
- Faculty of Health and Medical Sciences, University of Surrey, Surrey, U.K
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42
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Zhang LS, Xiong QP, Perez SP, Liu C, Wei J, Le C, Zhang L, Harada BT, Dai Q, Feng X, Hao Z, Wang Y, Dong X, Hu L, Wang ED, Pan T, Klungland A, Liu RJ, He C. ALKBH7-mediated demethylation regulates mitochondrial polycistronic RNA processing. Nat Cell Biol 2021; 23:684-691. [PMID: 34253897 PMCID: PMC8716185 DOI: 10.1038/s41556-021-00709-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 06/07/2021] [Indexed: 02/06/2023]
Abstract
Members of the mammalian AlkB family are known to mediate nucleic acid demethylation1,2. ALKBH7, a mammalian AlkB homologue, localizes in mitochondria and affects metabolism3, but its function and mechanism of action are unknown. Here we report an approach to site-specifically detect N1-methyladenosine (m1A), N3-methylcytidine (m3C), N1-methylguanosine (m1G) and N2,N2-dimethylguanosine (m22G) modifications simultaneously within all cellular RNAs, and discovered that human ALKBH7 demethylates m22G and m1A within mitochondrial Ile and Leu1 pre-tRNA regions, respectively, in nascent polycistronic mitochondrial RNA4-6. We further show that ALKBH7 regulates the processing and structural dynamics of polycistronic mitochondrial RNAs. Depletion of ALKBH7 leads to increased polycistronic mitochondrial RNA processing, reduced steady-state mitochondria-encoded tRNA levels and protein translation, and notably decreased mitochondrial activity. Thus, we identify ALKBH7 as an RNA demethylase that controls nascent mitochondrial RNA processing and mitochondrial activity.
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Affiliation(s)
- Li-Sheng Zhang
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Qing-Ping Xiong
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, PR China
| | - Sonia Peña Perez
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway.,Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Chang Liu
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Jiangbo Wei
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Cassy Le
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Linda Zhang
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Bryan T. Harada
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Qing Dai
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Xinran Feng
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Ziyang Hao
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Yuru Wang
- Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Xueyang Dong
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Lulu Hu
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - En-Duo Wang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, PR China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, PR China
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Arne Klungland
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway.,Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Ru-Juan Liu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, PR China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, PR China
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.,Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
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43
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Abstract
The majority of the mammalian genome is transcribed into non-coding RNAs, many of which co-evolve with RNA-binding proteins (RBPs) to function as biochemically defined and tractable ribonucleoproteins (RNPs). Here, we applied icSHAPE- a robust and versatile RNA structural probing pipeline- to endogenous RNPs purified from nuclei, providing base-resolution structural rationale for RNP activity and subcellular localization. Combining with genetic and biochemical reconstitutions, structural and functional alternations can be directly attributed to a given RBP without ambiguity. For complete details on the use and execution of this protocol, please refer to Chen et al. (2018).
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Affiliation(s)
- Lu Chen
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Howard Y. Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Steven E. Artandi
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
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44
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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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45
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Zhu J, Li C, Peng X, Zhang X. RNA architecture influences plant biology. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4144-4160. [PMID: 33484251 PMCID: PMC8130982 DOI: 10.1093/jxb/erab030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 01/18/2021] [Indexed: 05/13/2023]
Abstract
The majority of the genome is transcribed to RNA in living organisms. RNA transcripts can form astonishing arrays of secondary and tertiary structures via Watson-Crick, Hoogsteen, or wobble base pairing. In vivo, RNA folding is not a simple thermodynamic event of minimizing free energy. Instead, the process is constrained by transcription, RNA-binding proteins, steric factors, and the microenvironment. RNA secondary structure (RSS) plays myriad roles in numerous biological processes, such as RNA processing, stability, transportation, and translation in prokaryotes and eukaryotes. Emerging evidence has also implicated RSS in RNA trafficking, liquid-liquid phase separation, and plant responses to environmental variations such as temperature and salinity. At molecular level, RSS is correlated with splicing, polyadenylation, protein synthesis, and miRNA biogenesis and functions. In this review, we summarize newly reported methods for probing RSS in vivo and functions and mechanisms of RSS in plant physiology.
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Affiliation(s)
- Jiaying Zhu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Changhao Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Xu Peng
- Department of Medical Physiology, College of Medicine, Texas A&M University, College Station, TX 77843, USA
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Correspondence:
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46
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Flynn RA, Pedram K, Malaker SA, Batista PJ, Smith BAH, Johnson AG, George BM, Majzoub K, Villalta PW, Carette JE, Bertozzi CR. Small RNAs are modified with N-glycans and displayed on the surface of living cells. Cell 2021; 184:3109-3124.e22. [PMID: 34004145 DOI: 10.1016/j.cell.2021.04.023] [Citation(s) in RCA: 234] [Impact Index Per Article: 78.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/18/2020] [Accepted: 04/14/2021] [Indexed: 12/20/2022]
Abstract
Glycans modify lipids and proteins to mediate inter- and intramolecular interactions across all domains of life. RNA is not thought to be a major target of glycosylation. Here, we challenge this view with evidence that mammals use RNA as a third scaffold for glycosylation. Using a battery of chemical and biochemical approaches, we found that conserved small noncoding RNAs bear sialylated glycans. These "glycoRNAs" were present in multiple cell types and mammalian species, in cultured cells, and in vivo. GlycoRNA assembly depends on canonical N-glycan biosynthetic machinery and results in structures enriched in sialic acid and fucose. Analysis of living cells revealed that the majority of glycoRNAs were present on the cell surface and can interact with anti-dsRNA antibodies and members of the Siglec receptor family. Collectively, these findings suggest the existence of a direct interface between RNA biology and glycobiology, and an expanded role for RNA in extracellular biology.
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Affiliation(s)
- Ryan A Flynn
- Department of Chemistry, Stanford University, Stanford, CA, USA.
| | - Kayvon Pedram
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Stacy A Malaker
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Pedro J Batista
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Benjamin A H Smith
- Department of Chemical and Systems Biology and ChEM-H, Stanford University, Stanford, CA, USA
| | - Alex G Johnson
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Benson M George
- Department of Cancer Biology, Stanford University, Stanford, CA, USA
| | - Karim Majzoub
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA; IGMM, CNRS, University of Montpellier, Montpellier, France
| | - Peter W Villalta
- Masonic Cancer Center and Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
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47
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Qi Y, Zhang Y, Zheng G, Chen B, Zhang M, Li J, Peng T, Huang J, Wang X. In Vivo and In Vitro Genome-Wide Profiling of RNA Secondary Structures Reveals Key Regulatory Features in Plasmodium falciparum. Front Cell Infect Microbiol 2021; 11:673966. [PMID: 34079769 PMCID: PMC8166286 DOI: 10.3389/fcimb.2021.673966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/26/2021] [Indexed: 11/13/2022] Open
Abstract
It is widely accepted that the structure of RNA plays important roles in a number of biological processes, such as polyadenylation, splicing, and catalytic functions. Dynamic changes in RNA structure are able to regulate the gene expression programme and can be used as a highly specific and subtle mechanism for governing cellular processes. However, the nature of most RNA secondary structures in Plasmodium falciparum has not been determined. To investigate the genome-wide RNA secondary structural features at single-nucleotide resolution in P. falciparum, we applied a novel high-throughput method utilizing the chemical modification of RNA structures to characterize these structures. Structural data from parasites are in close agreement with the known 18S ribosomal RNA secondary structures of P. falciparum and can help to predict the in vivo RNA secondary structure of a total of 3,396 transcripts in the ring-stage and trophozoite-stage developmental cycles. By parallel analysis of RNA structures in vivo and in vitro during the Plasmodium parasite ring-stage and trophozoite-stage intraerythrocytic developmental cycles, we identified some key regulatory features. Recent studies have established that the RNA structure is a ubiquitous and fundamental regulator of gene expression. Our study indicate that there is a critical connection between RNA secondary structure and mRNA abundance during the complex biological programme of P. falciparum. This work presents a useful framework and important results, which may facilitate further research investigating the interactions between RNA secondary structure and the complex biological programme in P. falciparum. The RNA secondary structure characterized in this study has potential applications and important implications regarding the identification of RNA structural elements, which are important for parasite infection and elucidating host-parasite interactions and parasites in the environment.
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Affiliation(s)
- Yanwei Qi
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Yuhong Zhang
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Guixing Zheng
- Department of Blood Transfusion, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Bingxia Chen
- The Third Clinical School, Guangzhou Medical University, Guangzhou, China
| | - Mengxin Zhang
- The Third Clinical School, Guangzhou Medical University, Guangzhou, China
| | - Jian Li
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China
| | - Tao Peng
- Sino-French Hoffmann Institute, State Key Laboratory of Respiratory Disease, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Jun Huang
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Xinhua Wang
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
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48
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Sun L, Xu K, Huang W, Yang YT, Li P, Tang L, Xiong T, Zhang QC. Predicting dynamic cellular protein-RNA interactions by deep learning using in vivo RNA structures. Cell Res 2021; 31:495-516. [PMID: 33623109 PMCID: PMC7900654 DOI: 10.1038/s41422-021-00476-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 01/19/2021] [Indexed: 01/31/2023] Open
Abstract
Interactions with RNA-binding proteins (RBPs) are integral to RNA function and cellular regulation, and dynamically reflect specific cellular conditions. However, presently available tools for predicting RBP-RNA interactions employ RNA sequence and/or predicted RNA structures, and therefore do not capture their condition-dependent nature. Here, after profiling transcriptome-wide in vivo RNA secondary structures in seven cell types, we developed PrismNet, a deep learning tool that integrates experimental in vivo RNA structure data and RBP binding data for matched cells to accurately predict dynamic RBP binding in various cellular conditions. PrismNet results for 168 RBPs support its utility for both understanding CLIP-seq results and largely extending such interaction data to accurately analyze additional cell types. Further, PrismNet employs an "attention" strategy to computationally identify exact RBP-binding nucleotides, and we discovered enrichment among dynamic RBP-binding sites for structure-changing variants (riboSNitches), which can link genetic diseases with dysregulated RBP bindings. Our rich profiling data and deep learning-based prediction tool provide access to a previously inaccessible layer of cell-type-specific RBP-RNA interactions, with clear utility for understanding and treating human diseases.
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Affiliation(s)
- Lei Sun
- 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
| | - Kui Xu
- 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
| | - Wenze Huang
- 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
| | - Yucheng T Yang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Pan Li
- 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
| | - Lei Tang
- 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
| | - Tuanlin Xiong
- 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
| | - 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.
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49
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Zhang M, Li K, Bai J, Velema WA, Yu C, van Damme R, Lee WH, Corpuz ML, Chen JF, Lu Z. Optimized photochemistry enables efficient analysis of dynamic RNA structuromes and interactomes in genetic and infectious diseases. Nat Commun 2021; 12:2344. [PMID: 33879794 PMCID: PMC8058046 DOI: 10.1038/s41467-021-22552-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 03/18/2021] [Indexed: 02/02/2023] Open
Abstract
Direct determination of RNA structures and interactions in living cells is critical for understanding their functions in normal physiology and disease states. Here, we present PARIS2, a dramatically improved method for RNA duplex determination in vivo with >4000-fold higher efficiency than previous methods. PARIS2 captures ribosome binding sites on mRNAs, reporting translation status on a transcriptome scale. Applying PARIS2 to the U8 snoRNA mutated in the neurological disorder LCC, we discover a network of dynamic RNA structures and interactions which are destabilized by patient mutations. We report the first whole genome structure of enterovirus D68, an RNA virus that causes polio-like symptoms, revealing highly dynamic conformations altered by antiviral drugs and different pathogenic strains. We also discover a replication-associated asymmetry on the (+) and (-) strands of the viral genome. This study establishes a powerful technology for efficient interrogation of the RNA structurome and interactome in human diseases.
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MESH Headings
- Calcinosis/genetics
- Calcinosis/metabolism
- Central Nervous System Cysts/genetics
- Central Nervous System Cysts/metabolism
- Communicable Diseases/genetics
- Communicable Diseases/metabolism
- Cross-Linking Reagents
- Enterovirus D, Human/genetics
- Furocoumarins
- Genetic Diseases, Inborn/genetics
- Genetic Diseases, Inborn/metabolism
- Genome, Viral
- Humans
- Leukoencephalopathies/genetics
- Leukoencephalopathies/metabolism
- Models, Molecular
- Mutation
- Nucleic Acid Conformation
- Photochemical Processes
- Photochemistry/methods
- RNA/chemistry
- RNA/genetics
- RNA/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- RNA, Viral/chemistry
- RNA, Viral/genetics
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Affiliation(s)
- Minjie Zhang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Kongpan Li
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Jianhui Bai
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Willem A Velema
- Institute for Molecules and Materials, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Chengqing Yu
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Ryan van Damme
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Wilson H Lee
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Maia L Corpuz
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Jian-Fu Chen
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA, USA
| | - Zhipeng Lu
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA.
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50
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Conserved long-range base pairings are associated with pre-mRNA processing of human genes. Nat Commun 2021; 12:2300. [PMID: 33863890 PMCID: PMC8052449 DOI: 10.1038/s41467-021-22549-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 03/20/2021] [Indexed: 02/07/2023] Open
Abstract
The ability of nucleic acids to form double-stranded structures is essential for all living systems on Earth. Current knowledge on functional RNA structures is focused on locally-occurring base pairs. However, crosslinking and proximity ligation experiments demonstrated that long-range RNA structures are highly abundant. Here, we present the most complete to-date catalog of conserved complementary regions (PCCRs) in human protein-coding genes. PCCRs tend to occur within introns, suppress intervening exons, and obstruct cryptic and inactive splice sites. Double-stranded structure of PCCRs is supported by decreased icSHAPE nucleotide accessibility, high abundance of RNA editing sites, and frequent occurrence of forked eCLIP peaks. Introns with PCCRs show a distinct splicing pattern in response to RNAPII slowdown suggesting that splicing is widely affected by co-transcriptional RNA folding. The enrichment of 3'-ends within PCCRs raises the intriguing hypothesis that coupling between RNA folding and splicing could mediate co-transcriptional suppression of premature pre-mRNA cleavage and polyadenylation.
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