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Peixoto ML, Madan E. Unraveling the complexity: Advanced methods in analyzing DNA, RNA, and protein interactions. Adv Cancer Res 2024; 163:251-302. [PMID: 39271265 DOI: 10.1016/bs.acr.2024.06.010] [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: 09/15/2024]
Abstract
Exploring the intricate interplay within and between nucleic acids, as well as their interactions with proteins, holds pivotal significance in unraveling the molecular complexities steering cancer initiation and progression. To investigate these interactions, a diverse array of highly specific and sensitive molecular techniques has been developed. The selection of a particular technique depends on the specific nature of the interactions. Typically, researchers employ an amalgamation of these different techniques to obtain a comprehensive and holistic understanding of inter- and intramolecular interactions involving DNA-DNA, RNA-RNA, DNA-RNA, or protein-DNA/RNA. Examining nucleic acid conformation reveals alternative secondary structures beyond conventional ones that have implications for cancer pathways. Mutational hotspots in cancer often lie within sequences prone to adopting these alternative structures, highlighting the importance of investigating intra-genomic and intra-transcriptomic interactions, especially in the context of mutations, to deepen our understanding of oncology. Beyond these intramolecular interactions, the interplay between DNA and RNA leads to formations like DNA:RNA hybrids (known as R-loops) or even DNA:DNA:RNA triplex structures, both influencing biological processes that ultimately impact cancer. Protein-nucleic acid interactions are intrinsic cellular phenomena crucial in both normal and pathological conditions. In particular, genetic mutations or single amino acid variations can alter a protein's structure, function, and binding affinity, thus influencing cancer progression. It is thus, imperative to understand the differences between wild-type (WT) and mutated (MT) genes, transcripts, and proteins. The review aims to summarize the frequently employed methods and techniques for investigating interactions involving nucleic acids and proteins, highlighting recent advancements and diverse adaptations of each technique.
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Affiliation(s)
- Maria Leonor Peixoto
- Champalimaud Center for the Unknown, Lisbon, Portugal; Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Esha Madan
- Department of Surgery, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; Massey Comprehensive Cancer Center, Virginia Commonwealth University, Richmond, VA, United States; VCU Institute of Molecular Medicine, Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States.
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Deng J, Fang X, Huang L, Li S, Xu L, Ye K, Zhang J, Zhang K, Zhang QC. RNA structure determination: From 2D to 3D. FUNDAMENTAL RESEARCH 2023; 3:727-737. [PMID: 38933295 PMCID: PMC11197651 DOI: 10.1016/j.fmre.2023.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 06/04/2023] [Accepted: 06/05/2023] [Indexed: 06/28/2024] Open
Abstract
RNA molecules serve a wide range of functions that are closely linked to their structures. The basic structural units of RNA consist of single- and double-stranded regions. In order to carry out advanced functions such as catalysis and ligand binding, certain types of RNAs can adopt higher-order structures. The analysis of RNA structures has progressed alongside advancements in structural biology techniques, but it comes with its own set of challenges and corresponding solutions. In this review, we will discuss recent advances in RNA structure analysis techniques, including structural probing methods, X-ray crystallography, nuclear magnetic resonance, cryo-electron microscopy, and small-angle X-ray scattering. Often, a combination of multiple techniques is employed for the integrated analysis of RNA structures. We also survey important RNA structures that have been recently determined using various techniques.
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Affiliation(s)
- Jie Deng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Xianyang Fang
- Beijing Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Lin Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Shanshan Li
- MOE Key Laboratory for Cellular Dynamics and Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Lilei Xu
- Beijing Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Keqiong Ye
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinsong Zhang
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Kaiming Zhang
- MOE Key Laboratory for Cellular Dynamics and Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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Twittenhoff C, Brandenburg VB, Righetti F, Nuss AM, Mosig A, Dersch P, Narberhaus F. Lead-seq: transcriptome-wide structure probing in vivo using lead(II) ions. Nucleic Acids Res 2020; 48:e71. [PMID: 32463449 PMCID: PMC7337928 DOI: 10.1093/nar/gkaa404] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 04/08/2020] [Accepted: 05/06/2020] [Indexed: 12/24/2022] Open
Abstract
The dynamic conformation of RNA molecules within living cells is key to their function. Recent advances in probing the RNA structurome in vivo, including the use of SHAPE (Selective 2'-Hydroxyl Acylation analyzed by Primer Extension) or kethoxal reagents or DMS (dimethyl sulfate), provided unprecedented insights into the architecture of RNA molecules in the living cell. Here, we report the establishment of lead probing in a global RNA structuromics approach. In order to elucidate the transcriptome-wide RNA landscape in the enteric pathogen Yersinia pseudotuberculosis, we combined lead(II) acetate-mediated cleavage of single-stranded RNA regions with high-throughput sequencing. This new approach, termed 'Lead-seq', provides structural information independent of base identity. We show that the method recapitulates secondary structures of tRNAs, RNase P RNA, tmRNA, 16S rRNA and the rpsT 5'-untranslated region, and that it reveals global structural features of mRNAs. The application of Lead-seq to Y. pseudotuberculosis cells grown at two different temperatures unveiled the first temperature-responsive in vivo RNA structurome of a bacterial pathogen. The translation of candidate genes derived from this approach was confirmed to be temperature regulated. Overall, this study establishes Lead-seq as complementary approach to interrogate intracellular RNA structures on a global scale.
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Affiliation(s)
| | | | | | - Aaron M Nuss
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, 381214 Braunschweig, Germany
| | - Axel Mosig
- Department of Biophysics, Ruhr University Bochum, 44780 Bochum, Germany
| | - Petra Dersch
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, 381214 Braunschweig, Germany
- Institute of Infectiology, Center for Molecular Biology of Inflammation, University of Münster, 48149 Münster, Germany
| | - Franz Narberhaus
- Microbial Biology, Ruhr University Bochum, 44780 Bochum, Germany
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Hill AC, Schroeder SJ. Thermodynamic stabilities of three-way junction nanomotifs in prohead RNA. RNA (NEW YORK, N.Y.) 2017; 23:521-529. [PMID: 28069889 PMCID: PMC5340915 DOI: 10.1261/rna.059220.116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 12/24/2016] [Indexed: 06/06/2023]
Abstract
The thermodynamic stabilities of four natural prohead or packaging RNA (pRNA) three-way junction (3WJ) nanomotifs and seven phi29 pRNA 3WJ deletion mutant nanomotifs were investigated using UV optical melting on a three-component RNA system. Our data reveal that some pRNA 3WJs are more stable than the phi29 pRNA 3WJ. The stability of the 3WJ contributes to the unique self-assembly properties of pRNA. Thus, ultrastable pRNA 3WJ motifs suggest new scaffolds for pRNA-based nanotechnology. We present data demonstrating that pRNA 3WJs differentially respond to the presence of metal ions. A comparison of our data with free energies predicted by currently available RNA secondary structure prediction programs shows that these programs do not accurately predict multibranch loop stabilities. These results will expand the existing parameters used for RNA secondary structure prediction from sequence in order to better inform RNA structure-function hypotheses and guide the rational design of functional RNA supramolecular assemblies.
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Affiliation(s)
| | - Susan J Schroeder
- Department of Microbiology and Plant Biology
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, USA
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