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Qiao Y, Yang R, Liu Y, Chen J, Zhao L, Huo P, Wang Z, Bu D, Wu Y, Zhao Y. DeepFusion: A deep bimodal information fusion network for unraveling protein-RNA interactions using in vivo RNA structures. Comput Struct Biotechnol J 2024; 23:617-625. [PMID: 38274994 PMCID: PMC10808905 DOI: 10.1016/j.csbj.2023.12.040] [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: 09/06/2023] [Revised: 12/04/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
RNA-binding proteins (RBPs) are key post-transcriptional regulators, and the malfunctions of RBP-RNA binding lead to diverse human diseases. However, prediction of RBP binding sites is largely based on RNA sequence features, whereas in vivo RNA structural features based on high-throughput sequencing are rarely incorporated. Here, we designed a deep bimodal information fusion network called DeepFusion for unraveling protein-RNA interactions by incorporating structural features derived from DMS-seq data. DeepFusion integrates two sub-models to extract local motif-like information and long-term context information. We show that DeepFusion performs best compared with other cutting-edge methods with only sequence inputs on two datasets. DeepFusion's performance is further improved with bimodal input after adding in vivo DMS-seq structural features. Furthermore, DeepFusion can be used for analyzing RNA degradation, demonstrating significantly different RBP-binding scores in genes with slow degradation rates versus those with rapid degradation rates. DeepFusion thus provides enhanced abilities for further analysis of functional RNAs. DeepFusion's code and data are available at http://bioinfo.org/deepfusion/.
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Affiliation(s)
- Yixuan Qiao
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Yang
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Liu
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiaxin Chen
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Lianhe Zhao
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Peipei Huo
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Zhihao Wang
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Dechao Bu
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Yang Wu
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Yi Zhao
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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2
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Besaratinia A, Blumenfeld H, Tommasi S. Exploring the Utility of Long Non-Coding RNAs for Assessing the Health Consequences of Vaping. Int J Mol Sci 2024; 25:8554. [PMID: 39126120 PMCID: PMC11313266 DOI: 10.3390/ijms25158554] [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: 07/04/2024] [Revised: 07/31/2024] [Accepted: 08/02/2024] [Indexed: 08/12/2024] Open
Abstract
Electronic cigarette (e-cig) use, otherwise known as "vaping", is widespread among adolescent never-smokers and adult smokers seeking a less-harmful alternative to combustible tobacco products. To date, however, the long-term health consequences of vaping are largely unknown. Many toxicants and carcinogens present in e-cig vapor and tobacco smoke exert their biological effects through epigenetic changes that can cause dysregulation of disease-related genes. Long non-coding RNAs (lncRNAs) have emerged as prime regulators of gene expression in health and disease states. A large body of research has shown that lncRNAs regulate genes involved in the pathogenesis of smoking-associated diseases; however, the utility of lncRNAs for assessing the disease-causing potential of vaping remains to be fully determined. A limited but growing number of studies has shown that lncRNAs mediate dysregulation of disease-related genes in cells and tissues of vapers as well as cells treated in vitro with e-cig aerosol extract. This review article provides an overview of the evolution of e-cig technology, trends in use, and controversies on the safety, efficacy, and health risks or potential benefits of vaping relative to smoking. While highlighting the importance of lncRNAs in cell biology and disease, it summarizes the current and ongoing research on the modulatory effects of lncRNAs on gene regulation and disease pathogenesis in e-cig users and in vitro experimental settings. The gaps in knowledge are identified, priorities for future research are highlighted, and the importance of empirical data for tobacco products regulation and public health is underscored.
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Affiliation(s)
- Ahmad Besaratinia
- Department of Population & Public Health Sciences, USC Keck School of Medicine, University of Southern California, M/C 9603, Los Angeles, CA 90033, USA; (H.B.); (S.T.)
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3
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Kristofich J, Nicchitta CV. Rapid and Efficient Isolation of Total RNA-Bound Proteomes by Liquid Emulsion-Assisted Purification of RNA-Bound Protein (LEAP-RBP). Bio Protoc 2024; 14:e5236. [PMID: 39100593 PMCID: PMC11292130 DOI: 10.21769/bioprotoc.5236] [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: 03/30/2024] [Revised: 06/19/2024] [Accepted: 06/20/2024] [Indexed: 08/06/2024] Open
Abstract
The critical roles of RNA-binding proteins (RBPs) in all aspects of RNA biology fostered the development of methods utilizing ultraviolet (UV) crosslinking and method-specific RNA enrichment steps for proteome-wide identification and assessment of RBP function. Despite the substantial contributions of these UV-based RNA-centric methods to our understanding of RNA-protein interaction networks, their utility is constrained by biases in RBP recovery and significant noise contributions, which can confound meaningful interpretation. To overcome these issues, we recently developed a method termed Liquid Emulsion-Assisted Purification of RNA-Bound Protein (LEAP-RBP) and introduced quantitative signal-to-noise (S:N)-based metrics for the proteome-wide identification of RNA interactomes and accurate assessment of global RBP occupancy dynamics. Compared to existing methodologies, LEAP-RBP provides significant advantages in speed, cost, efficiency, and selectivity for RNA-bound proteins. In this work, we provide a step-by-step guide for the successful application of the LEAP-RBP method for both small- and large-scale investigations of RNA-bound proteomes. Key features • Unbiased and efficient isolation of total RNA-bound protein, RNA, and protein from biological samples. • Cost-effective identification of proteome-wide RNA interactomes and validation of direct RNA-binding protein functionality. • Robust and accurate assessment of context- and/or condition-dependent RBP occupancy state dynamics.
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4
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Yang D, Li C, Kong Y, Pei Y, Miao B, Dai G, Ding P, Shi P, Wang Z, Pei R. Deciphering the Temporal-Spatial Interactive Heterogeneity of Long Non-Coding RNAs and RNA-Binding Proteins in Living Cells at Single-Cell Resolution. J Am Chem Soc 2024. [PMID: 39016781 DOI: 10.1021/jacs.4c05205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
The investigation of long noncoding RNAs (lncRNAs) and RNA binding proteins (RBPs) interactions in living cell holds great significance for elucidating their critical roles in a variety of biological activities, but limited techniques are available to profile the temporal-spatial dynamic heterogeneity. Here, we introduced a molecular beacon-functionalized nanoneedle array designed for spatially resolved profiling of lncRNA-RBP interactions (Nano-SpatiaLR). A nanoneedle array modified with a molecular beacon is employed to selectively isolate specific intracellular lncRNAs and their associated RBPs without affecting cell viability. The RBPs are then in situ analyzed with a fluorescent labeled antibody and colocalized with lncRNA signals to get a quantitative measurement of their dynamic interactions. Additionally, leveraging the spatial distribution and nanoscale modality of the nanoneedle array, this technique provides the spatial heterogeneity information on cellular lncRNA-RBPs interaction at single cell resolution. In this study, we tracked the temporal-spatial interactive heterogeneity dynamics of lncRNA-RBPs interaction within living cells across different biological progresses. Our findings demonstrated that the interactions between lncRNA HOTAIR and RBPs EZH2 and LSD1 undergo significant changes in response to drug treatments, particularly in tumor cells. Moreover, these interactions become more intensified as tumor cells aggregate during the proliferation process.
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Affiliation(s)
- Deyuan Yang
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory for Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Cheng Li
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory for Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Yutong Kong
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei 230026, China
- College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China
| | - Yian Pei
- CAS Key Laboratory for Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
- Duke Kunshan University Kunshan 215316, China
| | - Bing Miao
- Key Laboratory of Multifunctional Nanomaterials and Smart Systems, Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Gaole Dai
- Suzhou Institute of Systems Medicine, Suzhou 215123, China
| | - Pi Ding
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory for Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Peng Shi
- Hong Kong Centre for Cerebro-Cardiovascular Health Engineering, Hong Kong Science Park, Shatin, Hong Kong 999077, China
- Department of Biomedical Engineering, City University of Hong Kong Kowloon, Shatin, Hong Kong 999077, China
- Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518000, China
| | - Zixun Wang
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory for Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Renjun Pei
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory for Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
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5
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Ye R, Zhao H, Wang X, Xue Y. Technological advancements in deciphering RNA-RNA interactions. Mol Cell 2024:S1097-2765(24)00543-4. [PMID: 39047724 DOI: 10.1016/j.molcel.2024.06.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 06/11/2024] [Accepted: 06/28/2024] [Indexed: 07/27/2024]
Abstract
RNA-RNA interactions (RRIs) can dictate RNA molecules to form intricate higher-order structures and bind their RNA substrates in diverse biological processes. To elucidate the function, binding specificity, and regulatory mechanisms of various RNA molecules, especially the vast repertoire of non-coding RNAs, advanced technologies and methods that globally map RRIs are extremely valuable. In the past decades, many state-of-the-art technologies have been developed for this purpose. This review focuses on those high-throughput technologies for the global mapping of RRIs. We summarize the key concepts and the pros and cons of different technologies. In addition, we highlight the novel biological insights uncovered by these RRI mapping methods and discuss the future challenges for appreciating the crucial roles of RRIs in gene regulation across bacteria, viruses, archaea, and mammals.
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Affiliation(s)
- Rong Ye
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Hailian Zhao
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xi Wang
- State Key Laboratory of Female Fertility Promotion, Clinical Stem Cell Research Center, Peking University Third Hospital, Beijing 100191, China
| | - Yuanchao Xue
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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6
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Cao L, Wang L. Biospecific Chemistry for Covalent Linking of Biomacromolecules. Chem Rev 2024; 124:8516-8549. [PMID: 38913432 PMCID: PMC11240265 DOI: 10.1021/acs.chemrev.4c00066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Interactions among biomacromolecules, predominantly noncovalent, underpin biological processes. However, recent advancements in biospecific chemistry have enabled the creation of specific covalent bonds between biomolecules, both in vitro and in vivo. This Review traces the evolution of biospecific chemistry in proteins, emphasizing the role of genetically encoded latent bioreactive amino acids. These amino acids react selectively with adjacent natural groups through proximity-enabled bioreactivity, enabling targeted covalent linkages. We explore various latent bioreactive amino acids designed to target different protein residues, ribonucleic acids, and carbohydrates. We then discuss how these novel covalent linkages can drive challenging protein properties and capture transient protein-protein and protein-RNA interactions in vivo. Additionally, we examine the application of covalent peptides as potential therapeutic agents and site-specific conjugates for native antibodies, highlighting their capacity to form stable linkages with target molecules. A significant focus is placed on proximity-enabled reactive therapeutics (PERx), a pioneering technology in covalent protein therapeutics. We detail its wide-ranging applications in immunotherapy, viral neutralization, and targeted radionuclide therapy. Finally, we present a perspective on the existing challenges within biospecific chemistry and discuss the potential avenues for future exploration and advancement in this rapidly evolving field.
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Affiliation(s)
- Li Cao
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, United States
| | - Lei Wang
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, United States
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7
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Stasevich EM, Simonova AV, Bogomolova EA, Murashko MM, Uvarova AN, Zheremyan EA, Korneev KV, Schwartz AM, Kuprash DV, Demin DE. Cut from the same cloth: RNAs transcribed from regulatory elements. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195049. [PMID: 38964653 DOI: 10.1016/j.bbagrm.2024.195049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/25/2024] [Accepted: 06/28/2024] [Indexed: 07/06/2024]
Abstract
A certain degree of chromatin openness is necessary for the activity of transcription-regulating regions within the genome, facilitating accessibility to RNA polymerases and subsequent synthesis of regulatory element RNAs (regRNAs) from these regions. The rapidly increasing number of studies underscores the significance of regRNAs across diverse cellular processes and diseases, challenging the paradigm that these transcripts are non-functional transcriptional noise. This review explores the multifaceted roles of regRNAs in human cells, encompassing rather well-studied entities such as promoter RNAs and enhancer RNAs (eRNAs), while also providing insights into overshadowed silencer RNAs and insulator RNAs. Furthermore, we assess notable examples of shorter regRNAs, like miRNAs, snRNAs, and snoRNAs, playing important roles. Expanding our discourse, we deliberate on the potential usage of regRNAs as biomarkers and novel targets for cancer and other human diseases.
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Affiliation(s)
- E M Stasevich
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - A V Simonova
- Laboratory of Intracellular Signaling in Health and Disease, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - E A Bogomolova
- Laboratory of Intracellular Signaling in Health and Disease, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia; Moscow Center for Advanced Studies, Moscow, Russia
| | - M M Murashko
- Laboratory of Intracellular Signaling in Health and Disease, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia; Moscow Center for Advanced Studies, Moscow, Russia
| | - A N Uvarova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - E A Zheremyan
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - K V Korneev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - A M Schwartz
- Department of Human Biology, University of Haifa, Haifa, Israel
| | - D V Kuprash
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - D E Demin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
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8
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Wang C, Qiu J, Liu M, Wang Y, Yu Y, Liu H, Zhang Y, Han L. Microfluidic Biochips for Single-Cell Isolation and Single-Cell Analysis of Multiomics and Exosomes. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401263. [PMID: 38767182 PMCID: PMC11267386 DOI: 10.1002/advs.202401263] [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: 02/02/2024] [Revised: 04/26/2024] [Indexed: 05/22/2024]
Abstract
Single-cell multiomic and exosome analyses are potent tools in various fields, such as cancer research, immunology, neuroscience, microbiology, and drug development. They facilitate the in-depth exploration of biological systems, providing insights into disease mechanisms and aiding in treatment. Single-cell isolation, which is crucial for single-cell analysis, ensures reliable cell isolation and quality control for further downstream analyses. Microfluidic chips are small lightweight systems that facilitate efficient and high-throughput single-cell isolation and real-time single-cell analysis on- or off-chip. Therefore, most current single-cell isolation and analysis technologies are based on the single-cell microfluidic technology. This review offers comprehensive guidance to researchers across different fields on the selection of appropriate microfluidic chip technologies for single-cell isolation and analysis. This review describes the design principles, separation mechanisms, chip characteristics, and cellular effects of various microfluidic chips available for single-cell isolation. Moreover, this review highlights the implications of using this technology for subsequent analyses, including single-cell multiomic and exosome analyses. Finally, the current challenges and future prospects of microfluidic chip technology are outlined for multiplex single-cell isolation and multiomic and exosome analyses.
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Affiliation(s)
- Chao Wang
- Institute of Marine Science and TechnologyShandong UniversityQingdao266237China
| | - Jiaoyan Qiu
- Institute of Marine Science and TechnologyShandong UniversityQingdao266237China
| | - Mengqi Liu
- Institute of Marine Science and TechnologyShandong UniversityQingdao266237China
| | - Yihe Wang
- Institute of Marine Science and TechnologyShandong UniversityQingdao266237China
| | - Yang Yu
- Department of PeriodontologySchool and Hospital of StomatologyCheeloo College of MedicineShandong UniversityJinan250100China
| | - Hong Liu
- State Key Laboratory of Crystal MaterialsShandong UniversityJinan250100China
| | - Yu Zhang
- Institute of Marine Science and TechnologyShandong UniversityQingdao266237China
| | - Lin Han
- Institute of Marine Science and TechnologyShandong UniversityQingdao266237China
- Shandong Engineering Research Center of Biomarker and Artificial Intelligence ApplicationJinan250100China
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9
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Si Y, Zou J, Gao Y, Chuai G, Liu Q, Chen L. Foundation models in molecular biology. BIOPHYSICS REPORTS 2024; 10:135-151. [PMID: 39027316 PMCID: PMC11252241 DOI: 10.52601/bpr.2024.240006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/04/2024] [Indexed: 07/20/2024] Open
Abstract
Determining correlations between molecules at various levels is an important topic in molecular biology. Large language models have demonstrated a remarkable ability to capture correlations from large amounts of data in the field of natural language processing as well as image generation, and correlations captured from data using large language models can also be applicable to solving a wide range of specific tasks, hence large language models are also referred to as foundation models. The massive amount of data that exists in the field of molecular biology provides an excellent basis for the development of foundation models, and the recent emergence of foundation models in the field of molecular biology has really pushed the entire field forward. We summarize the foundation models developed based on RNA sequence data, DNA sequence data, protein sequence data, single-cell transcriptome data, and spatial transcriptome data respectively, and further discuss the research directions for the development of foundation models in molecular biology.
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Affiliation(s)
- Yunda Si
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310024, China
| | - Jiawei Zou
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Yicheng Gao
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai 201804, China
| | - Guohui Chuai
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai 201804, China
| | - Qi Liu
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai 201804, China
| | - Luonan Chen
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310024, China
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
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10
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Zeng X, Wei Z, Du Q, Li J, Xie Z, Wang X. Unveil cis-acting combinatorial mRNA motifs by interpreting deep neural network. Bioinformatics 2024; 40:i381-i389. [PMID: 38940172 PMCID: PMC11211823 DOI: 10.1093/bioinformatics/btae262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024] Open
Abstract
SUMMARY Cis-acting mRNA elements play a key role in the regulation of mRNA stability and translation efficiency. Revealing the interactions of these elements and their impact plays a crucial role in understanding the regulation of the mRNA translation process, which supports the development of mRNA-based medicine or vaccines. Deep neural networks (DNN) can learn complex cis-regulatory codes from RNA sequences. However, extracting these cis-regulatory codes efficiently from DNN remains a significant challenge. Here, we propose a method based on our toolkit NeuronMotif and motif mutagenesis, which not only enables the discovery of diverse and high-quality motifs but also efficiently reveals motif interactions. By interpreting deep-learning models, we have discovered several crucial motifs that impact mRNA translation efficiency and stability, as well as some unknown motifs or motif syntax, offering novel insights for biologists. Furthermore, we note that it is challenging to enrich motif syntax in datasets composed of randomly generated sequences, and they may not contain sufficient biological signals. AVAILABILITY AND IMPLEMENTATION The source code and data used to produce the results and analyses presented in this manuscript are available from GitHub (https://github.com/WangLabTHU/combmotif).
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Affiliation(s)
- Xiaocheng Zeng
- Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Zheng Wei
- Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Qixiu Du
- Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Jiaqi Li
- Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Zhen Xie
- Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Xiaowo Wang
- Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing, 100084, China
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11
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Völkers M, Preiss T, Hentze MW. RNA-binding proteins in cardiovascular biology and disease: the beat goes on. Nat Rev Cardiol 2024; 21:361-378. [PMID: 38163813 DOI: 10.1038/s41569-023-00958-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/06/2023] [Indexed: 01/03/2024]
Abstract
Cardiac development and function are becoming increasingly well understood from different angles, including signalling, transcriptional and epigenetic mechanisms. By contrast, the importance of the post-transcriptional landscape of cardiac biology largely remains to be uncovered, building on the foundation of a few existing paradigms. The discovery during the past decade of hundreds of additional RNA-binding proteins in mammalian cells and organs, including the heart, is expected to accelerate progress and has raised intriguing possibilities for better understanding the intricacies of cardiac development, metabolism and adaptive alterations. In this Review, we discuss the progress and new concepts on RNA-binding proteins and RNA biology and appraise them in the context of common cardiovascular clinical conditions, from cell and organ-wide perspectives. We also discuss how a better understanding of cardiac RNA-binding proteins can fill crucial knowledge gaps in cardiology and might pave the way to developing better treatments to reduce cardiovascular morbidity and mortality.
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Affiliation(s)
- Mirko Völkers
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg and Mannheim, Germany
| | - Thomas Preiss
- Shine-Dalgarno Centre for RNA Innovation, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
- Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
| | - Matthias W Hentze
- European Molecular Biology Laboratory, Heidelberg, Germany.
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany.
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12
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Kristofich J, Nicchitta CV. High-throughput quantitation of protein-RNA UV-crosslinking efficiencies as a predictive tool for high-confidence identification of RNA-binding proteins. RNA (NEW YORK, N.Y.) 2024; 30:644-661. [PMID: 38423626 PMCID: PMC11098464 DOI: 10.1261/rna.079848.123] [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: 09/21/2023] [Accepted: 02/12/2024] [Indexed: 03/02/2024]
Abstract
UV-crosslinking has proven to be an invaluable tool for the identification of RNA-protein interactomes. The paucity of methods for distinguishing background from bona fide RNA-protein interactions, however, makes attribution of RNA-binding function on UV-crosslinking alone challenging. To address this need, we previously reported an RNA-binding protein (RBP) confidence scoring metric (RCS), incorporating both signal-to-noise (S:N) and protein abundance determinations to distinguish high- and low-confidence candidate RBPs. Although RCS has utility, we sought a direct metric for quantification and comparative evaluation of protein-RNA interactions. Here we propose the use of protein-specific UV-crosslinking efficiency (%CL), representing the molar fraction of a protein that is crosslinked to RNA, for functional evaluation of candidate RBPs. Application to the HeLa RNA interactome yielded %CL values for 1097 proteins. Remarkably, %CL values span over five orders of magnitude. For the HeLa RNA interactome, %CL values comprise a range from high efficiency, high specificity interactions, e.g., the Elav protein HuR and the Pumilio homolog Pum2, with %CL values of 45.9 and 24.2, respectively, to very low efficiency and specificity interactions, for example, the metabolic enzymes glyceraldehyde-3-phosphate dehydrogenase, fructose-bisphosphate aldolase, and alpha-enolase, with %CL values of 0.0016, 0.006, and 0.008, respectively. We further extend the utility of %CL through prediction of protein domains and classes with known RNA-binding functions, thus establishing it as a useful metric for RNA interactome analysis. We anticipate that this approach will benefit efforts to establish functional RNA interactomes and support the development of more predictive computational approaches for RBP identification.
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Affiliation(s)
- JohnCarlo Kristofich
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Christopher V Nicchitta
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
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13
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Shen Z, Naveed M, Bao J. Untacking small RNA profiling and RNA fragment footprinting: Approaches and challenges in library construction. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1852. [PMID: 38715192 DOI: 10.1002/wrna.1852] [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: 02/21/2024] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 06/06/2024]
Abstract
Small RNAs (sRNAs) with sizes ranging from 15 to 50 nucleotides (nt) are critical regulators of gene expression control. Prior studies have shown that sRNAs are involved in a broad range of biological processes, such as organ development, tumorigenesis, and epigenomic regulation; however, emerging evidence unveils a hidden layer of diversity and complexity of endogenously encoded sRNAs profile in eukaryotic organisms, including novel types of sRNAs and the previously unknown post-transcriptional RNA modifications. This underscores the importance for accurate, unbiased detection of sRNAs in various cellular contexts. A multitude of high-throughput methods based on next-generation sequencing (NGS) are developed to decipher the sRNA expression and their modifications. Nonetheless, distinct from mRNA sequencing, the data from sRNA sequencing suffer frequent inconsistencies and high variations emanating from the adapter contaminations and RNA modifications, which overall skew the sRNA libraries. Here, we summarize the sRNA-sequencing approaches, and discuss the considerations and challenges for the strategies and methods of sRNA library construction. The pros and cons of sRNA sequencing have significant implications for implementing RNA fragment footprinting approaches, including CLIP-seq and Ribo-seq. We envision that this review can inspire novel improvements in small RNA sequencing and RNA fragment footprinting in future. This article is categorized under: RNA Evolution and Genomics > Computational Analyses of RNA RNA Processing > Processing of Small RNAs Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs.
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Affiliation(s)
- Zhaokang Shen
- Department of Obstetrics and Gynecology, Center for Reproduction and Genetics, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Hefei, Anhui, China
| | - Muhammad Naveed
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Hefei, Anhui, China
- Department of Obstetrics and Gynecology, Center for Reproduction and Genetics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Jianqiang Bao
- Department of Obstetrics and Gynecology, Center for Reproduction and Genetics, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Hefei, Anhui, China
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14
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Zacco E, Broglia L, Kurihara M, Monti M, Gustincich S, Pastore A, Plath K, Nagakawa S, Cerase A, Sanchez de Groot N, Tartaglia GG. RNA: The Unsuspected Conductor in the Orchestra of Macromolecular Crowding. Chem Rev 2024; 124:4734-4777. [PMID: 38579177 PMCID: PMC11046439 DOI: 10.1021/acs.chemrev.3c00575] [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: 08/14/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 04/07/2024]
Abstract
This comprehensive Review delves into the chemical principles governing RNA-mediated crowding events, commonly referred to as granules or biological condensates. We explore the pivotal role played by RNA sequence, structure, and chemical modifications in these processes, uncovering their correlation with crowding phenomena under physiological conditions. Additionally, we investigate instances where crowding deviates from its intended function, leading to pathological consequences. By deepening our understanding of the delicate balance that governs molecular crowding driven by RNA and its implications for cellular homeostasis, we aim to shed light on this intriguing area of research. Our exploration extends to the methodologies employed to decipher the composition and structural intricacies of RNA granules, offering a comprehensive overview of the techniques used to characterize them, including relevant computational approaches. Through two detailed examples highlighting the significance of noncoding RNAs, NEAT1 and XIST, in the formation of phase-separated assemblies and their influence on the cellular landscape, we emphasize their crucial role in cellular organization and function. By elucidating the chemical underpinnings of RNA-mediated molecular crowding, investigating the role of modifications, structures, and composition of RNA granules, and exploring both physiological and aberrant phase separation phenomena, this Review provides a multifaceted understanding of the intriguing world of RNA-mediated biological condensates.
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Affiliation(s)
- Elsa Zacco
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Laura Broglia
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Misuzu Kurihara
- RNA
Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Michele Monti
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Stefano Gustincich
- Central
RNA Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Annalisa Pastore
- UK
Dementia Research Institute at the Maurice Wohl Institute of King’s
College London, London SE5 9RT, U.K.
| | - Kathrin Plath
- Department
of Biological Chemistry, David Geffen School
of Medicine at the University of California Los Angeles, Los Angeles, California 90095, United States
| | - Shinichi Nagakawa
- RNA
Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Andrea Cerase
- Blizard
Institute,
Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 4NS, U.K.
- Unit
of Cell and developmental Biology, Department of Biology, Università di Pisa, 56123 Pisa, Italy
| | - Natalia Sanchez de Groot
- Unitat
de Bioquímica, Departament de Bioquímica i Biologia
Molecular, Universitat Autònoma de
Barcelona, 08193 Barcelona, Spain
| | - Gian Gaetano Tartaglia
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
- Catalan
Institution for Research and Advanced Studies, ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
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15
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Li X, Qu W, Yan J, Tan J. RPI-EDLCN: An Ensemble Deep Learning Framework Based on Capsule Network for ncRNA-Protein Interaction Prediction. J Chem Inf Model 2024; 64:2221-2235. [PMID: 37158609 DOI: 10.1021/acs.jcim.3c00377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Noncoding RNAs (ncRNAs) play crucial roles in many cellular life activities by interacting with proteins. Identification of ncRNA-protein interactions (ncRPIs) is key to understanding the function of ncRNAs. Although a number of computational methods for predicting ncRPIs have been developed, the problem of predicting ncRPIs remains challenging. It has always been the focus of ncRPIs research to select suitable feature extraction methods and develop a deep learning architecture with better recognition performance. In this work, we proposed an ensemble deep learning framework, RPI-EDLCN, based on a capsule network (CapsuleNet) to predict ncRPIs. In terms of feature input, we extracted the sequence features, secondary structure sequence features, motif information, and physicochemical properties of ncRNA/protein. The sequence and secondary structure sequence features of ncRNA/protein are encoded by the conjoint k-mer method and then input into an ensemble deep learning model based on CapsuleNet by combining the motif information and physicochemical properties. In this model, the encoding features are processed by convolution neural network (CNN), deep neural network (DNN), and stacked autoencoder (SAE). Then the advanced features obtained from the processing are input into the CapsuleNet for further feature learning. Compared with other state-of-the-art methods under 5-fold cross-validation, the performance of RPI-EDLCN is the best, and the accuracy of RPI-EDLCN on RPI1807, RPI2241, and NPInter v2.0 data sets was 93.8%, 88.2%, and 91.9%, respectively. The results of the independent test indicated that RPI-EDLCN can effectively predict potential ncRPIs in different organisms. In addition, RPI-EDLCN successfully predicted hub ncRNAs and proteins in Mus musculus ncRNA-protein networks. Overall, our model can be used as an effective tool to predict ncRPIs and provides some useful guidance for future biological studies.
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Affiliation(s)
- Xiaoyi Li
- Department of Biomedical Engineering, Faculty of Environment and Life, Beijing University of Technology, Beijing International Science and Technology Cooperation Base for Intelligent Physiological Measurement and Clinical Transformation, Beijing 100124, China
| | - Wenyan Qu
- Department of Biomedical Engineering, Faculty of Environment and Life, Beijing University of Technology, Beijing International Science and Technology Cooperation Base for Intelligent Physiological Measurement and Clinical Transformation, Beijing 100124, China
| | - Jing Yan
- Department of Biomedical Engineering, Faculty of Environment and Life, Beijing University of Technology, Beijing International Science and Technology Cooperation Base for Intelligent Physiological Measurement and Clinical Transformation, Beijing 100124, China
| | - Jianjun Tan
- Department of Biomedical Engineering, Faculty of Environment and Life, Beijing University of Technology, Beijing International Science and Technology Cooperation Base for Intelligent Physiological Measurement and Clinical Transformation, Beijing 100124, China
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16
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Siraj A, Bouwmeester R, Declercq A, Welp L, Chernev A, Wulf A, Urlaub H, Martens L, Degroeve S, Kohlbacher O, Sachsenberg T. Intensity and retention time prediction improves the rescoring of protein-nucleic acid cross-links. Proteomics 2024; 24:e2300144. [PMID: 38629965 DOI: 10.1002/pmic.202300144] [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: 05/27/2023] [Revised: 12/29/2023] [Accepted: 01/05/2024] [Indexed: 04/19/2024]
Abstract
In protein-RNA cross-linking mass spectrometry, UV or chemical cross-linking introduces stable bonds between amino acids and nucleic acids in protein-RNA complexes that are then analyzed and detected in mass spectra. This analytical tool delivers valuable information about RNA-protein interactions and RNA docking sites in proteins, both in vitro and in vivo. The identification of cross-linked peptides with oligonucleotides of different length leads to a combinatorial increase in search space. We demonstrate that the peptide retention time prediction tasks can be transferred to the task of cross-linked peptide retention time prediction using a simple amino acid composition encoding, yielding improved identification rates when the prediction error is included in rescoring. For the more challenging task of including fragment intensity prediction of cross-linked peptides in the rescoring, we obtain, on average, a similar improvement. Further improvement in the encoding and fine-tuning of retention time and intensity prediction models might lead to further gains, and merit further research.
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Affiliation(s)
- Arslan Siraj
- Department of Computer Science, Applied Bioinformatics, University of Tübingen, Tübingen, Germany
- Institute for Biological and Medical Informatics, University of Tübingen, Tübingen, Germany
| | - Robbin Bouwmeester
- Department of Biomolecular Medicine, Ghent University, Gent, Belgium
- VIB-UGent Center for Medical Biotechnology, VIB, Gent, Belgium
| | - Arthur Declercq
- Department of Biomolecular Medicine, Ghent University, Gent, Belgium
- VIB-UGent Center for Medical Biotechnology, VIB, Gent, Belgium
| | - Luisa Welp
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Bioanalytics, Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Aleksandar Chernev
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Alexander Wulf
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Bioanalytics, Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Lennart Martens
- Department of Biomolecular Medicine, Ghent University, Gent, Belgium
- VIB-UGent Center for Medical Biotechnology, VIB, Gent, Belgium
| | - Sven Degroeve
- Department of Biomolecular Medicine, Ghent University, Gent, Belgium
- VIB-UGent Center for Medical Biotechnology, VIB, Gent, Belgium
| | - Oliver Kohlbacher
- Department of Computer Science, Applied Bioinformatics, University of Tübingen, Tübingen, Germany
- Institute for Biological and Medical Informatics, University of Tübingen, Tübingen, Germany
| | - Timo Sachsenberg
- Department of Computer Science, Applied Bioinformatics, University of Tübingen, Tübingen, Germany
- Institute for Biological and Medical Informatics, University of Tübingen, Tübingen, Germany
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17
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Yuan S, Zhou G, Xu G. Translation machinery: the basis of translational control. J Genet Genomics 2024; 51:367-378. [PMID: 37536497 DOI: 10.1016/j.jgg.2023.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/23/2023] [Accepted: 07/23/2023] [Indexed: 08/05/2023]
Abstract
Messenger RNA (mRNA) translation consists of initiation, elongation, termination, and ribosome recycling, carried out by the translation machinery, primarily including tRNAs, ribosomes, and translation factors (TrFs). Translational regulators transduce signals of growth and development, as well as biotic and abiotic stresses, to the translation machinery, where global or selective translational control occurs to modulate mRNA translation efficiency (TrE). As the basis of translational control, the translation machinery directly determines the quality and quantity of newly synthesized peptides and, ultimately, the cellular adaption. Thus, regulating the availability of diverse machinery components is reviewed as the central strategy of translational control. We provide classical signaling pathways (e.g., integrated stress responses) and cellular behaviors (e.g., liquid-liquid phase separation) to exemplify this strategy within different physiological contexts, particularly during host-microbe interactions. With new technologies developed, further understanding this strategy will speed up translational medicine and translational agriculture.
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Affiliation(s)
- Shu Yuan
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China
| | - Guilong Zhou
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China
| | - Guoyong Xu
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China.
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18
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Aydin J, Gabel A, Zielinski S, Ganskih S, Schmidt N, Hartigan C, Schenone M, Carr S, Munschauer M. SHIFTR enables the unbiased identification of proteins bound to specific RNA regions in live cells. Nucleic Acids Res 2024; 52:e26. [PMID: 38281241 PMCID: PMC10954451 DOI: 10.1093/nar/gkae038] [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: 10/01/2023] [Revised: 11/29/2023] [Accepted: 01/10/2024] [Indexed: 01/30/2024] Open
Abstract
RNA-protein interactions determine the cellular fate of RNA and are central to regulating gene expression outcomes in health and disease. To date, no method exists that is able to identify proteins that interact with specific regions within endogenous RNAs in live cells. Here, we develop SHIFTR (Selective RNase H-mediated interactome framing for target RNA regions), an efficient and scalable approach to identify proteins bound to selected regions within endogenous RNAs using mass spectrometry. Compared to state-of-the-art techniques, SHIFTR is superior in accuracy, captures minimal background interactions and requires orders of magnitude lower input material. We establish SHIFTR workflows for targeting RNA classes of different length and abundance, including short and long non-coding RNAs, as well as mRNAs and demonstrate that SHIFTR is compatible with sequentially mapping interactomes for multiple target RNAs in a single experiment. Using SHIFTR, we comprehensively identify interactions of cis-regulatory elements located at the 5' and 3'-terminal regions of authentic SARS-CoV-2 RNAs in infected cells and accurately recover known and novel interactions linked to the function of these viral RNA elements. SHIFTR enables the systematic mapping of region-resolved RNA interactomes for any RNA in any cell type and has the potential to revolutionize our understanding of transcriptomes and their regulation.
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Affiliation(s)
- Jens Aydin
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
| | - Alexander Gabel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
| | - Sebastian Zielinski
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
| | - Sabina Ganskih
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
| | - Nora Schmidt
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
| | | | - Monica Schenone
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Mathias Munschauer
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
- Faculty of Medicine, University of Würzburg, Würzburg, Germany
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19
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TREX identifies region-specific protein interactors of RNA molecules. Nat Methods 2024; 21:381-382. [PMID: 38374268 DOI: 10.1038/s41592-024-02182-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
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20
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Wang S, Sun H, Chen G, Wu C, Sun B, Lin J, Lin D, Zeng D, Lin B, Huang G, Lu X, Lin H, Liang Y. RNA-binding proteins in breast cancer: Biological implications and therapeutic opportunities. Crit Rev Oncol Hematol 2024; 195:104271. [PMID: 38272151 DOI: 10.1016/j.critrevonc.2024.104271] [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: 06/27/2023] [Revised: 01/05/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
RNA-binding proteins (RBPs) refer to a class of proteins that participate in alternative splicing, RNA stability, polyadenylation, localization and translation of RNAs, thus regulating gene expression in post-transcriptional manner. Dysregulation of RNA-RBP interaction contributes to various diseases, including cancer. In breast cancer, disorders in RBP expression and function influence the biological characteristics of tumor cells. Targeting RBPs has fostered the development of innovative therapies for breast cancer. However, the RBP-related mechanisms in breast cancer are not completely clear. In this review, we summarize the regulatory mechanisms of RBPs and their signaling crosstalk in breast cancer. Specifically, we emphasize the potential of certain RBPs as prognostic factors due to their effects on proliferation, invasion, apoptosis, and therapy resistance of breast cancer cells. Most importantly, we present a comprehensive overview of the latest RBP-related therapeutic strategies and novel therapeutic targets that have proven to be useful in the treatment of breast cancer.
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Affiliation(s)
- Shimeng Wang
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Hexing Sun
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Guanyuan Chen
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Chengyu Wu
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Bingmei Sun
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Jiajia Lin
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Danping Lin
- Department of Medical Oncology, Cancer Hospital of SUMC, Shantou 515000, China
| | - De Zeng
- Department of Medical Oncology, Cancer Hospital of SUMC, Shantou 515000, China
| | - Baohang Lin
- Department of Thyroid, Breast and Vascular Surgery, Longgang District Central Hospital of Shenzhen, Shenzhen 518116, China
| | - Guan Huang
- Department of Pathology, Longgang District Central Hospital of Shenzhen, Shenzhen 518116, China
| | - Xiaofeng Lu
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Haoyu Lin
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China.
| | - Yuanke Liang
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China.
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21
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Xia Y, Pei T, Zhao J, Wang Z, Shen Y, Yang Y, Liang J. Long noncoding RNA H19: functions and mechanisms in regulating programmed cell death in cancer. Cell Death Discov 2024; 10:76. [PMID: 38355574 PMCID: PMC10866971 DOI: 10.1038/s41420-024-01832-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/16/2024] [Accepted: 01/25/2024] [Indexed: 02/16/2024] Open
Abstract
Long noncoding RNAs (lncRNAs) are a group of noncoding RNAs with transcript lengths of >200 nucleotides. Mounting evidence suggests that lncRNAs are closely associated with tumorigenesis. LncRNA H19 (H19) was the first lncRNA to function as an oncogene in many malignant tumors. Apart from the established role of H19 in promoting cell growth, proliferation, invasion, migration, epithelial-mesenchymal transition (EMT), and metastasis, it has been recently discovered that H19 also inhibits programmed cell death (PCD) of cancer cells. In this review, we summarize the mechanisms by which H19 regulates PCD in cancer cells through various signaling pathways, molecular mechanisms, and epigenetic modifications. H19 regulates PCD through the Wnt/β-catenin pathway and the PI3K-Akt-mTOR pathway. It also acts as a competitive endogenous RNA (ceRNA) in PCD regulation. The interaction between H19 and RNA-binding proteins (RBP) regulates apoptosis in cancer. Moreover, epigenetic modifications, including DNA and RNA methylation and histone modifications, are also involved in H19-associated PCD regulation. In conclusion, we summarize the role of H19 signaling via PCD in cancer chemoresistance, highlighting the promising research significance of H19 as a therapeutic target. We hope that our study will contribute to a broader understanding of H19 in cancer development and treatment.
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Affiliation(s)
- Yuyang Xia
- Department of Urology, Institute of Urology, West China Hospital, West China School of Medicine, Sichuan University, 610041, Chengdu, China
| | - Tianjiao Pei
- Department of Reproductive Medicine, West China Second University Hospital of Sichuan University, Chengdu, China.
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital of Sichuan University, Chengdu, China.
| | - Junjie Zhao
- Department of Urology, Institute of Urology, West China Hospital, West China School of Medicine, Sichuan University, 610041, Chengdu, China
| | - Zilin Wang
- Department of Urology, Institute of Urology, West China Hospital, West China School of Medicine, Sichuan University, 610041, Chengdu, China
| | - Yu Shen
- Department of Urology, Institute of Urology, West China Hospital, West China School of Medicine, Sichuan University, 610041, Chengdu, China
| | - Yang Yang
- Department of Urology, Institute of Urology, West China Hospital, West China School of Medicine, Sichuan University, 610041, Chengdu, China
| | - Jiayu Liang
- Department of Urology, Institute of Urology, West China Hospital, West China School of Medicine, Sichuan University, 610041, Chengdu, China.
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22
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Bailey MA, Martyr JG, Hargrove AE, Fitzgerald MC. Stability-Based Proteomics for Investigation of Structured RNA-Protein Interactions. Anal Chem 2024:10.1021/acs.analchem.3c04978. [PMID: 38341805 PMCID: PMC11316846 DOI: 10.1021/acs.analchem.3c04978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2024]
Abstract
RNA-protein interactions are essential to RNA function throughout biology. Identifying the protein interactions associated with a specific RNA, however, is currently hindered by the need for RNA labeling or costly tiling-based approaches. Conventional strategies, which commonly rely on affinity pull-down approaches, are also skewed to the detection of high affinity interactions and frequently miss weaker interactions that may be biologically important. Reported here is the first adaptation of stability-based mass spectrometry methods for the global analysis of RNA-protein interactions. The stability of proteins from rates of oxidation (SPROX) and thermal protein profiling (TPP) methods are used to identify the protein targets of three RNA ligands, the MALAT1 triple helix (TH), a viral stem loop (SL), and an unstructured RNA (PolyU), in LNCaP nuclear lysate. The 315 protein hits with RNA-induced conformational and stability changes detected by TPP and/or SPROX were enriched in previously annotated RNA-binding proteins and included new proteins for hypothesis generation. Also demonstrated are the orthogonality of the SPROX and TPP approaches and the utility of the domain-specific information available with SPROX. This work establishes a novel platform for the global discovery and interrogation of RNA-protein interactions that is generalizable to numerous biological contexts and RNA targets.
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Affiliation(s)
- Morgan A Bailey
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Justin G Martyr
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Amanda E Hargrove
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Michael C Fitzgerald
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States
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23
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Shamustakimova AO. Halo-RPD: searching for RNA-binding protein targets in plants. Vavilovskii Zhurnal Genet Selektsii 2024; 28:74-79. [PMID: 38465250 PMCID: PMC10917663 DOI: 10.18699/vjgb-24-09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 03/12/2024] Open
Abstract
Study of RNA-protein interactions and identification of RNA targets are among the key aspects of understanding RNA biology. Currently, various methods are available to investigate these interactions with, RNA immunoprecipitation (RIP) being the most common. The search for RNA targets has largely been conducted using antibodies to an endogenous protein or to GFP-tag directly. Having to be dependent on the expression level of the target protein and having to spend time selecting highly specific antibodies make immunoprecipitation complicated. Expression of the GFP-fused protein can lead to cytotoxicity and, consequently, to improper recognition or degradation of the chimeric protein. Over the past few years, multifunctional tags have been developed. SNAP-tag and HaloTag allow the target protein to be studied from different perspectives. Labeling of the fusion protein with custom-made fluorescent dyes makes it possible to study protein expression and to localize it in the cell or the whole organism. A high-affinity substrate has been created to allow covalent binding by chimeric proteins, minimizing protein loss during protein isolation. In this paper, a HaloTag-based method, which we called Halo-RPD (HaloTag RNA PullDown), is presented. The proposed protocol uses plants with stable fusion protein expression and Magne® HaloTag® magnetic beads to capture RNA-protein complexes directly from the cytoplasmic lysate of transgenic Arabidopsis thaliana plants. The key stages described in the paper are as follows: (1) preparation of the magnetic beads; (2) tissue homogenization and collection of control samples; (3) precipitation and wash of RNA-protein complexes; (4) evaluation of protein binding efficiency; (5) RNA isolation; (6) analysis of the RNA obtained. Recommendations for better NGS assay designs are provided.
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Affiliation(s)
- A O Shamustakimova
- All-Russian Research Institute of Agricultural Biotechnology, Moscow, Russia
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24
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Adibi JJ, Zhao Y, Koistinen H, Mitchell RT, Barrett ES, Miller R, O'Connor TG, Xun X, Liang HW, Birru R, Smith M, Moog NK. Molecular pathways in placental-fetal development and disruption. Mol Cell Endocrinol 2024; 581:112075. [PMID: 37852527 PMCID: PMC10958409 DOI: 10.1016/j.mce.2023.112075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/11/2023] [Accepted: 09/24/2023] [Indexed: 10/20/2023]
Abstract
The first trimester of pregnancy ranks high in priority when minimizing harmful exposures, given the wide-ranging types of organogenesis occurring between 4- and 12-weeks' gestation. One way to quantify potential harm to the fetus in the first trimester is to measure a corollary effect on the placenta. Placental biomarkers are widely present in maternal circulation, cord blood, and placental tissue biopsied at birth or at the time of pregnancy termination. Here we evaluate ten diverse pathways involving molecules expressed in the first trimester human placenta based on their relevance to normal fetal development and to the hypothesis of placental-fetal endocrine disruption (perturbation in development that results in abnormal endocrine function in the offspring), namely: human chorionic gonadotropin (hCG), thyroid hormone regulation, peroxisome proliferator activated receptor protein gamma (PPARγ), leptin, transforming growth factor beta, epiregulin, growth differentiation factor 15, small nucleolar RNAs, serotonin, and vitamin D. Some of these are well-established as biomarkers of placental-fetal endocrine disruption, while others are not well studied and were selected based on discovery analyses of the placental transcriptome. A literature search on these biomarkers summarizes evidence of placenta-specific production and regulation of each biomarker, and their role in fetal reproductive tract, brain, and other specific domains of fetal development. In this review, we extend the theory of fetal programming to placental-fetal programming.
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Affiliation(s)
- Jennifer J Adibi
- Department of Epidemiology, University of Pittsburgh School of Public Health, USA; Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Yaqi Zhao
- St. Jude's Research Hospital, Memphis, TN, USA
| | - Hannu Koistinen
- Department of Clinical Chemistry, University of Helsinki, Helsinki, Finland
| | - Rod T Mitchell
- Department of Paediatric Endocrinology, Royal Hospital for Children and Young People, Edinburgh BioQuarter, Edinburgh, UK
| | - Emily S Barrett
- Environmental and Population Health Bio-Sciences, Rutgers University School of Public Health, Piscataway, NJ, USA
| | - Richard Miller
- Department of Obstetrics and Gynecology, University of Rochester Medical Center, Rochester, NY, USA
| | - Thomas G O'Connor
- Department of Psychiatry, University of Rochester Medical Center, Rochester, NY, USA
| | - Xiaoshuang Xun
- Department of Epidemiology, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
| | - Hai-Wei Liang
- Department of Epidemiology, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
| | - Rahel Birru
- Department of Epidemiology, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
| | - Megan Smith
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nora K Moog
- Department of Medical Psychology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
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25
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Jablunovsky A, Jose J. The Dynamic Landscape of Capsid Proteins and Viral RNA Interactions in Flavivirus Genome Packaging and Virus Assembly. Pathogens 2024; 13:120. [PMID: 38392858 PMCID: PMC10893219 DOI: 10.3390/pathogens13020120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
The Flavivirus genus of the Flaviviridae family of enveloped single-stranded RNA viruses encompasses more than 70 members, many of which cause significant disease in humans and livestock. Packaging and assembly of the flavivirus RNA genome is essential for the formation of virions, which requires intricate coordination of genomic RNA, viral structural, and nonstructural proteins in association with virus-induced, modified endoplasmic reticulum (ER) membrane structures. The capsid (C) protein, a small but versatile RNA-binding protein, and the positive single-stranded RNA genome are at the heart of the elusive flavivirus assembly process. The nucleocapsid core, consisting of the genomic RNA encapsidated by C proteins, buds through the ER membrane, which contains viral glycoproteins prM and E organized as trimeric spikes into the lumen, forming an immature virus. During the maturation process, which involves the low pH-mediated structural rearrangement of prM and E and furin cleavage of prM in the secretory pathway, the spiky immature virus with a partially ordered nucleocapsid core becomes a smooth, mature virus with no discernible nucleocapsid. This review focuses on the mechanisms of genome packaging and assembly by examining the structural and functional aspects of C protein and viral RNA. We review the current lexicon of critical C protein features and evaluate interactions between C and genomic RNA in the context of assembly and throughout the life cycle.
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Affiliation(s)
- Anastazia Jablunovsky
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA;
| | - Joyce Jose
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA;
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
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26
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Jiang XM, Xin QL, Liu K, Peng XF, Han S, Zhang LY, Liu W, Xiao GF, Li H, Zhang LK. Regulation of the WNT-CTNNB1 signaling pathway by severe fever with thrombocytopenia syndrome virus in a cap-snatching manner. mBio 2023; 14:e0168823. [PMID: 37882780 PMCID: PMC10746258 DOI: 10.1128/mbio.01688-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/14/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE One of the conserved mechanisms at the stage of genome transcription of segmented negative-strand RNA viruses (sNSVs) is the cap-snatching process, which is vital for sNSVs transcription and provides drugable targets for the development of antivirals. However, the specificity of RNAs snatched by sNSV is still unclear. By transcriptomics analysis of whole blood samples from SFTS patients, we found WNT-CTNNB1 signaling pathway was regulated according to the course of the disease. We then demonstrated that L protein of severe fever with thrombocytopenia syndrome virus (SFTSV) could interact with mRNAs of WNT-CTNNB1 signaling pathway-related gene, thus affecting WNT-CTNNB1 signaling pathway through its cap-snatching activity. Activation of WNT-CTNNB1 signaling pathway enhanced SFTSV replication, while inhibition of this pathway decreased SFTSV replication in vitro and in vivo. These findings suggest that WNT-associated genes may be the substrate for SFTSV "cap-snatching", and indicate a conserved sNSVs replication mechanism involving WNT-CTNNB1 signaling.
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Affiliation(s)
- Xia-Ming Jiang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qi-Lin Xin
- University of Lyon, INRAE, EPHE, IVPC, Lyon, France
| | - Kai Liu
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, China
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Xue-Fang Peng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Shuo Han
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ling-Yu Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Wei Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Geng-Fu Xiao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hao Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lei-Ke Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
- Hubei Jiangxia Laboratory, Wuhan, China
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27
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Li X, Liu Q, Liu J. Long Non-Coding RNAs: Discoveries, Mechanisms, and Research Strategies in Seeds. Genes (Basel) 2023; 14:2214. [PMID: 38137035 PMCID: PMC10742540 DOI: 10.3390/genes14122214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/11/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
Seeds provide nutrients for the embryo and allow for dormancy in stressed environments to better adapt the plant to its environment. In addition, seeds are an essential source of food for human survival and are the basis for the formation of food production and quality. Therefore, the research on the genetic mechanism of seed development and germination will provide a theoretical basis and technical support for the improvement of crop yield and quality. Recent studies have shown that long non-coding RNAs (lncRNAs) occupy a pivotal position in seed development and germination. In this review, we describe the key processes in seed biology and examine discoveries and insights made in seed lncRNA, with emphasis on lncRNAs that regulate seed biology through multiple mechanisms. Given that thousands of lncRNAs are present in the seed transcriptome, characterization has lagged far behind identification. We provide an overview of research strategies and approaches including some exciting new techniques that may uncover the function of lncRNAs in seed. Finally, we discuss the challenges facing the field and the opening questions. All in all, we hope to provide a clear perspective on discoveries of seed lncRNA by linking discoveries, mechanisms, and technologies.
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Affiliation(s)
| | | | - Jun Liu
- Guangdong Provincial Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (X.L.); (Q.L.)
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28
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Yang J, Liu X, Zhao Y, Dong W, Xue Y, Ruan X, Wang P, Liu L, E T, Song J, Cui Z, Liu Y. Mechanism of Dcp2/RNCR3/Dkc1/Snora62 axis regulating neuronal apoptosis in chronic cerebral ischemia. Cell Biol Toxicol 2023; 39:2881-2898. [PMID: 37097350 DOI: 10.1007/s10565-023-09807-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 04/08/2023] [Indexed: 04/26/2023]
Abstract
RNA-binding proteins (RBPs), long non-coding RNAs (lncRNAs), and small nucleolar RNAs (snoRNAs) were found to play crucial regulatory roles in ischemic injury. Based on GEO databases and our experimental results, we selected Dcp2, lncRNA-RNCR3, Dkc1, and Snora62 and Foxh1 as research candidates. We found that expression levels of Dcp2, RNCR3, Dkc1, Snora62, and Foxh1 were upregulated in oxygen glucose deprivation-treated HT22 cells and hippocampal tissues subject to chronic cerebral ischemia (CCI). Silencing of Dcp2, RNCR3, Dkc1, Snora62, and Foxh1 all inhibited apoptosis of oxygen glucose deprivation-treated HT22 cells. Moreover, Dcp2 promoted RNCR3 expression by increasing its stability. Importantly, RNCR3 may act as a molecular skeleton to bind to Dkc1 and recruit Dck1 to promote snoRNP assembly. Snora62 was responsible for pseudouridylation at 28S rRNA U3507 and U3509 sites. Pseudouridylation levels of 28S rRNA were reduced after knockdown of Snora62. Decreased pseudouridylation levels inhibited the translational activity of its downstream target, Foxh1. Our study further confirmed that Foxh1 transcriptionally promoted the expression of Bax and Fam162a. Notably, experiments in vivo showed that Dcp2 knockdown combined with RNCR3 knockdown and Snora62 knockdown resulted in an anti-apoptosis effect. In conclusion, this study suggests that the axis Dcp2/RNCR3/Dkc1/Snora621 is important for the regulation of neuronal apoptosis induced by CCI.
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Affiliation(s)
- Jin Yang
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China
- Key Laboratory of Neuro-Oncology in Liaoning Province, Shenyang, 110004, China
- Liaoning Medical Surgery and Rehabilitation Robot Technology Engineering Research Center, Shenyang, 110004, China
| | - Xiaobai Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China
- Key Laboratory of Neuro-Oncology in Liaoning Province, Shenyang, 110004, China
- Liaoning Medical Surgery and Rehabilitation Robot Technology Engineering Research Center, Shenyang, 110004, China
| | - Yubo Zhao
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China
- Key Laboratory of Neuro-Oncology in Liaoning Province, Shenyang, 110004, China
- Liaoning Medical Surgery and Rehabilitation Robot Technology Engineering Research Center, Shenyang, 110004, China
| | - Weiwei Dong
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China
- Key Laboratory of Neuro-Oncology in Liaoning Province, Shenyang, 110004, China
- Liaoning Medical Surgery and Rehabilitation Robot Technology Engineering Research Center, Shenyang, 110004, China
| | - Yixue Xue
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, China
| | - Xuelei Ruan
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, China
| | - Ping Wang
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, China
| | - Libo Liu
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, China
| | - Tiange E
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China
- Key Laboratory of Neuro-Oncology in Liaoning Province, Shenyang, 110004, China
- Liaoning Medical Surgery and Rehabilitation Robot Technology Engineering Research Center, Shenyang, 110004, China
| | - Jian Song
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China
- Key Laboratory of Neuro-Oncology in Liaoning Province, Shenyang, 110004, China
- Liaoning Medical Surgery and Rehabilitation Robot Technology Engineering Research Center, Shenyang, 110004, China
| | - Zheng Cui
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China
- Key Laboratory of Neuro-Oncology in Liaoning Province, Shenyang, 110004, China
- Liaoning Medical Surgery and Rehabilitation Robot Technology Engineering Research Center, Shenyang, 110004, China
| | - Yunhui Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China.
- Key Laboratory of Neuro-Oncology in Liaoning Province, Shenyang, 110004, China.
- Liaoning Medical Surgery and Rehabilitation Robot Technology Engineering Research Center, Shenyang, 110004, China.
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29
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Wang Y, Pan Z, Mou M, Xia W, Zhang H, Zhang H, Liu J, Zheng L, Luo Y, Zheng H, Yu X, Lian X, Zeng Z, Li Z, Zhang B, Zheng M, Li H, Hou T, Zhu F. A task-specific encoding algorithm for RNAs and RNA-associated interactions based on convolutional autoencoder. Nucleic Acids Res 2023; 51:e110. [PMID: 37889083 PMCID: PMC10682500 DOI: 10.1093/nar/gkad929] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 08/01/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023] Open
Abstract
RNAs play essential roles in diverse physiological and pathological processes by interacting with other molecules (RNA/protein/compound), and various computational methods are available for identifying these interactions. However, the encoding features provided by existing methods are limited and the existing tools does not offer an effective way to integrate the interacting partners. In this study, a task-specific encoding algorithm for RNAs and RNA-associated interactions was therefore developed. This new algorithm was unique in (a) realizing comprehensive RNA feature encoding by introducing a great many of novel features and (b) enabling task-specific integration of interacting partners using convolutional autoencoder-directed feature embedding. Compared with existing methods/tools, this novel algorithm demonstrated superior performances in diverse benchmark testing studies. This algorithm together with its source code could be readily accessed by all user at: https://idrblab.org/corain/ and https://github.com/idrblab/corain/.
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Affiliation(s)
- Yunxia Wang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Ziqi Pan
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Minjie Mou
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Weiqi Xia
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Hongning Zhang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Hanyu Zhang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Jin Liu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Lingyan Zheng
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-ZJU Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Yongchao Luo
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Hanqi Zheng
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Xinyuan Yu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Xichen Lian
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Zhenyu Zeng
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-ZJU Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Zhaorong Li
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-ZJU Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Bing Zhang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-ZJU Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Mingyue Zheng
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Honglin Li
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
- School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-ZJU Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
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30
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Zhu J, Liu S, Fang J, Cui Z, Wang B, Wang Y, Liu L, Wang Q, Cao X. Enzymolysis-based RNA pull-down identifies YTHDC2 as an inhibitor of antiviral innate response. Cell Rep 2023; 42:113192. [PMID: 37776518 DOI: 10.1016/j.celrep.2023.113192] [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: 11/11/2022] [Revised: 06/06/2023] [Accepted: 09/15/2023] [Indexed: 10/02/2023] Open
Abstract
The innate immune response must be terminated in a timely manner at the late stage of infection to prevent unwanted inflammation. The role of m6A-modified RNAs and their binding partners in this process is not well known. Here, we develop an enzymolysis-based RNA pull-down (eRP) method that utilizes the immunoglobulin G-degrading enzyme of Streptococcus pyogenes (IdeS) to fish out m6A-modified RNA-associated proteins. We apply eRP to capture the methylated single-stranded RNA (ssRNA) probe-associated proteins and identify YT521-B homology domain-containing 2 (YTHDC2) as the m6A-modified interferon β (IFN-β) mRNA-binding protein. YTHDC2, induced in macrophages at the late stage of virus infection, recruits IFN-stimulated exonuclease ISG20 (IFN-stimulated exonuclease gene 20) to degrade IFN-β mRNA, consequently inhibiting antiviral innate immune response. In vitro and in vivo deficiency of YTHDC2 increases IFN-β production at the late stage of viral infection. Our findings establish an eRP method to effectively identify RNA-protein interactions and add mechanistic insight to the termination of innate response for maintaining homeostasis.
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Affiliation(s)
- Jun Zhu
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China; Frontier Research Center for Cell Response, Institute of Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Shuo Liu
- Department of Immunology, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Jiali Fang
- Frontier Research Center for Cell Response, Institute of Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Zenghui Cui
- Frontier Research Center for Cell Response, Institute of Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Bingjing Wang
- Department of Immunology, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Yuzhou Wang
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Lin Liu
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Qingqing Wang
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xuetao Cao
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China; Frontier Research Center for Cell Response, Institute of Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China; Department of Immunology, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China; Chinese Academy of Medical Sciences Oxford Institute, Chinese Academy of Medical Sciences, Beijing 100005, China.
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31
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Buonaiuto G, Taliani V, Nicoletti C, Desideri F, Ballarino M. Preparation of Cardiac Extracts from Embryonal Hearts to Capture RNA-protein Interactions by CLIP. Bio Protoc 2023; 13:e4857. [PMID: 37900102 PMCID: PMC10603259 DOI: 10.21769/bioprotoc.4857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/28/2023] [Accepted: 08/28/2023] [Indexed: 10/31/2023] Open
Abstract
The interaction of RNA with specific RNA-binding proteins (RBP) leads to the establishment of complex regulatory networks through which gene expression is controlled. Careful consideration should be given to the exact environment where a given RNA/RBP interplay occurs, as the functional responses might depend on the type of organism as well as the specific cellular or subcellular contexts. This requisite becomes particularly crucial for the study of long non-coding RNAs (lncRNA), as a consequence of their peculiar tissue-specificity and timely regulated expression. The functional characterization of lncRNAs has traditionally relied on the use of established cell lines that, although useful, are unable to fully recapitulate the complexity of a tissue or organ. Here, we detail an optimized protocol, with comments and tips, to identify the RNA interactome of given RBPs by performing cross-linking immunoprecipitation (CLIP) from mouse embryonal hearts. We tested the efficiency of this protocol on the murine pCharme, a muscle-specific lncRNA interacting with Matrin3 (MATR3) and forming RNA-enriched condensates of biological significance in the nucleus. Key features • The protocol refines previous methods of cardiac extracts preparation to use for CLIP assays. • The protocol allows the quantitative RNA-seq analysis of transcripts interacting with selected proteins. • Depending on the embryonal stage, a high number of hearts can be required as starting material. • The steps are adaptable to other tissues and biochemical assays.
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Affiliation(s)
- Giulia Buonaiuto
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Rome, Italy
| | | | - Carmine Nicoletti
- DAHFMO-Unit of Histology and Medical Embryology, Sapienza University of Rome, Rome, Italy
| | - Fabio Desideri
- Center for Life Nano- and Neuro-Science, Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Monica Ballarino
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Rome, Italy
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32
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Heindel AJ, Brulet JW, Wang X, Founds MW, Libby AH, Bai DL, Lemke MC, Leace DM, Harris TE, Hafner M, Hsu KL. Chemoproteomic capture of RNA binding activity in living cells. Nat Commun 2023; 14:6282. [PMID: 37805600 PMCID: PMC10560261 DOI: 10.1038/s41467-023-41844-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 09/20/2023] [Indexed: 10/09/2023] Open
Abstract
Proteomic methods for RNA interactome capture (RIC) rely principally on crosslinking native or labeled cellular RNA to enrich and investigate RNA-binding protein (RBP) composition and function in cells. The ability to measure RBP activity at individual binding sites by RIC, however, has been more challenging due to the heterogenous nature of peptide adducts derived from the RNA-protein crosslinked site. Here, we present an orthogonal strategy that utilizes clickable electrophilic purines to directly quantify protein-RNA interactions on proteins through photoaffinity competition with 4-thiouridine (4SU)-labeled RNA in cells. Our photo-activatable-competition and chemoproteomic enrichment (PACCE) method facilitated detection of >5500 cysteine sites across ~3000 proteins displaying RNA-sensitive alterations in probe binding. Importantly, PACCE enabled functional profiling of canonical RNA-binding domains as well as discovery of moonlighting RNA binding activity in the human proteome. Collectively, we present a chemoproteomic platform for global quantification of protein-RNA binding activity in living cells.
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Affiliation(s)
- Andrew J Heindel
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Jeffrey W Brulet
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA
| | - Xiantao Wang
- RNA Molecular Biology Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD, 20892, USA
| | - Michael W Founds
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA
| | - Adam H Libby
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA
- University of Virginia Cancer Center, University of Virginia, Charlottesville, VA, 22903, USA
| | - Dina L Bai
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA
| | - Michael C Lemke
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - David M Leace
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Thurl E Harris
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Markus Hafner
- RNA Molecular Biology Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD, 20892, USA
| | - Ku-Lung Hsu
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA.
- University of Virginia Cancer Center, University of Virginia, Charlottesville, VA, 22903, USA.
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, 22908, USA.
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA.
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33
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Esteban‐Serna S, McCaughan H, Granneman S. Advantages and limitations of UV cross-linking analysis of protein-RNA interactomes in microbes. Mol Microbiol 2023; 120:477-489. [PMID: 37165708 PMCID: PMC10952675 DOI: 10.1111/mmi.15073] [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: 01/30/2023] [Revised: 04/28/2023] [Accepted: 04/30/2023] [Indexed: 05/12/2023]
Abstract
RNA-binding proteins (RBPs) govern the lifespan of nearly all transcripts and play key roles in adaptive responses in microbes. A robust approach to examine protein-RNA interactions involves irradiating cells with UV light to form covalent adducts between RBPs and their cognate RNAs. Combined with RNA or protein purification, these procedures can provide global RBP censuses or transcriptomic maps for all target sequences of a single protein in living cells. The recent development of novel methods has quickly populated the RBP landscape in microorganisms. Here, we provide an overview of prominent UV cross-linking techniques which have been applied to investigate RNA interactomes in microbes. By assessing their advantages and caveats, this technical evaluation intends to guide the selection of appropriate methods and experimental design as well as to encourage the use of complementary UV-dependent techniques to inspect RNA-binding activity.
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Affiliation(s)
- Sofia Esteban‐Serna
- Centre for Engineering Biology, School of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Hugh McCaughan
- Centre for Engineering Biology, School of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Sander Granneman
- Centre for Engineering Biology, School of Biological SciencesUniversity of EdinburghEdinburghUK
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Vaculík O, Chalupová E, Grešová K, Majtner T, Alexiou P. Transfer Learning Allows Accurate RBP Target Site Prediction with Limited Sample Sizes. BIOLOGY 2023; 12:1276. [PMID: 37886986 PMCID: PMC10604046 DOI: 10.3390/biology12101276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 10/28/2023]
Abstract
RNA-binding proteins are vital regulators in numerous biological processes. Their disfunction can result in diverse diseases, such as cancer or neurodegenerative disorders, making the prediction of their binding sites of high importance. Deep learning (DL) has brought about a revolution in various biological domains, including the field of protein-RNA interactions. Nonetheless, several challenges persist, such as the limited availability of experimentally validated binding sites to train well-performing DL models for the majority of proteins. Here, we present a novel training approach based on transfer learning (TL) to address the issue of limited data. Employing a sophisticated and interpretable architecture, we compare the performance of our method trained using two distinct approaches: training from scratch (SCR) and utilizing TL. Additionally, we benchmark our results against the current state-of-the-art methods. Furthermore, we tackle the challenges associated with selecting appropriate input features and determining optimal interval sizes. Our results show that TL enhances model performance, particularly in datasets with minimal training data, where satisfactory results can be achieved with just a few hundred RNA binding sites. Moreover, we demonstrate that integrating both sequence and evolutionary conservation information leads to superior performance. Additionally, we showcase how incorporating an attention layer into the model facilitates the interpretation of predictions within a biologically relevant context.
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Affiliation(s)
- Ondřej Vaculík
- Central European Institute of Technology (CEITEC), Masaryk University, 625 00 Brno, Czech Republic
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, 625 00 Brno, Czech Republic
| | - Eliška Chalupová
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, 625 00 Brno, Czech Republic
| | - Katarína Grešová
- Central European Institute of Technology (CEITEC), Masaryk University, 625 00 Brno, Czech Republic
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, 625 00 Brno, Czech Republic
| | - Tomáš Majtner
- Central European Institute of Technology (CEITEC), Masaryk University, 625 00 Brno, Czech Republic
- Department of Molecular Sociology, Max Planck Institute of Biophysics, 60439 Frankfurt am Main, Germany
| | - Panagiotis Alexiou
- Central European Institute of Technology (CEITEC), Masaryk University, 625 00 Brno, Czech Republic
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, MSD 2080 Msida, Malta
- Centre for Molecular Medicine & Biobanking, University of Malta, MSD 2080 Msida, Malta
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35
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Kristofich J, Nicchitta CV. Signal-noise metrics for RNA binding protein identification reveal broad spectrum protein-RNA interaction frequencies and dynamics. Nat Commun 2023; 14:5868. [PMID: 37735163 PMCID: PMC10514315 DOI: 10.1038/s41467-023-41284-9] [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: 08/05/2022] [Accepted: 08/30/2023] [Indexed: 09/23/2023] Open
Abstract
Recent efforts towards the comprehensive identification of RNA-bound proteomes have revealed a large, surprisingly diverse family of candidate RNA-binding proteins (RBPs). Quantitative metrics for characterization and validation of protein-RNA interactions and their dynamic interactions have, however, proven analytically challenging and prone to error. Here we report a method termed LEAP-RBP (Liquid-Emulsion-Assisted-Purification of RNA-Bound Protein) for the selective, quantitative recovery of UV-crosslinked RNA-protein complexes. By virtue of its high specificity and yield, LEAP-RBP distinguishes RNA-bound and RNA-free protein levels and reveals common sources of experimental noise in RNA-centric RBP enrichment methods. We introduce strategies for accurate RBP identification and signal-based metrics for quantifying protein-RNA complex enrichment, relative RNA occupancy, and method specificity. In this work, the utility of our approach is validated by comprehensive identification of RBPs whose association with mRNA is modulated in response to global mRNA translation state changes and through in-depth benchmark comparisons with current methodologies.
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Affiliation(s)
- JohnCarlo Kristofich
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, 27710, USA
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36
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Broglia L, Le Rhun A, Charpentier E. Methodologies for bacterial ribonuclease characterization using RNA-seq. FEMS Microbiol Rev 2023; 47:fuad049. [PMID: 37656885 PMCID: PMC10503654 DOI: 10.1093/femsre/fuad049] [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: 03/23/2023] [Revised: 08/06/2023] [Accepted: 08/23/2023] [Indexed: 09/03/2023] Open
Abstract
Bacteria adjust gene expression at the post-transcriptional level through an intricate network of small regulatory RNAs and RNA-binding proteins, including ribonucleases (RNases). RNases play an essential role in RNA metabolism, regulating RNA stability, decay, and activation. These enzymes exhibit species-specific effects on gene expression, bacterial physiology, and different strategies of target recognition. Recent advances in high-throughput RNA sequencing (RNA-seq) approaches have provided a better understanding of the roles and modes of action of bacterial RNases. Global studies aiming to identify direct targets of RNases have highlighted the diversity of RNase activity and RNA-based mechanisms of gene expression regulation. Here, we review recent RNA-seq approaches used to study bacterial RNases, with a focus on the methods for identifying direct RNase targets.
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Affiliation(s)
- Laura Broglia
- Max Planck Unit for the Science of Pathogens, D-10117 Berlin, Germany
- Center for Human Technologies, Istituto Italiano di Tecnologia, 16152 Genova, Italy
| | - Anaïs Le Rhun
- Max Planck Unit for the Science of Pathogens, D-10117 Berlin, Germany
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Emmanuelle Charpentier
- Max Planck Unit for the Science of Pathogens, D-10117 Berlin, Germany
- Institute for Biology, Humboldt University, D-10115 Berlin, Germany
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37
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Hommen P, Hwang J, Huang F, Borgelt L, Hohnen L, Wu P. Chromenopyrazole-Peptide Conjugates as Small-Molecule Based Inhibitors Disrupting the Protein-RNA Interaction of LIN28-let-7. Chembiochem 2023; 24:e202300376. [PMID: 37224100 DOI: 10.1002/cbic.202300376] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 05/24/2023] [Indexed: 05/26/2023]
Abstract
Targeting the protein-RNA interaction of LIN28 and let-7 is a promising strategy for the development of novel anticancer therapeutics. However, a limited number of small-molecule inhibitors disrupting the LIN28-let-7 interaction with potent efficacy are available. Herein, we developed a novel LIN28-inhibiting strategy by targeting selective hotspot amino acids at the LIN28-let-7 binding interface with small-molecule-based bifunctional conjugates. Starting from reported small-molecule LIN28 inhibitors, we identified a feasible linker-attachment position after performing a structure-activity relationship exploration based on the LIN28-targeting chromenopyrazoles. In parallel, a virtual alanine scan identified hotspot residues at the protein-RNA binding interface, based on which we designed a set of peptides to enhance the interaction with the identified hotspot residues. Conjugation of the tailor-designed peptides with linker-attached chromenopyrazoles yielded a series of bifunctional small-molecule-peptide conjugates, represented by compound 83 (PH-223), as a new LIN28-targeting chemical modality. Our result demonstrated an unexplored rational design approach using bifunctional conjugates to target protein-RNA interactions.
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Affiliation(s)
- Pascal Hommen
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Str. 6, Dortmund, 44227, Germany
| | - Jimin Hwang
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Str. 6, Dortmund, 44227, Germany
| | - Fubao Huang
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
| | - Lydia Borgelt
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Str. 6, Dortmund, 44227, Germany
| | - Lisa Hohnen
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, Universitätsstr. 150, Bochum, 44780, Germany
| | - Peng Wu
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
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38
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Hamilton DJ, Hein AE, Wuttke DS, Batey RT. The DNA binding high mobility group box protein family functionally binds RNA. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1778. [PMID: 36646476 PMCID: PMC10349909 DOI: 10.1002/wrna.1778] [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: 10/26/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 01/18/2023]
Abstract
Nucleic acid binding proteins regulate transcription, splicing, RNA stability, RNA localization, and translation, together tailoring gene expression in response to stimuli. Upon discovery, these proteins are typically classified as either DNA or RNA binding as defined by their in vivo functions; however, recent evidence suggests dual DNA and RNA binding by many of these proteins. High mobility group box (HMGB) proteins have a DNA binding HMGB domain, act as transcription factors and chromatin remodeling proteins, and are increasingly understood to interact with RNA as means to regulate gene expression. Herein, multiple layers of evidence that the HMGB family are dual DNA and RNA binding proteins is comprehensively reviewed. For example, HMGB proteins directly interact with RNA in vitro and in vivo, are localized to RNP granules involved in RNA processing, and their protein interactors are enriched in RNA binding proteins involved in RNA metabolism. Importantly, in cell-based systems, HMGB-RNA interactions facilitate protein-protein interactions, impact splicing outcomes, and modify HMGB protein genomic or cellular localization. Misregulation of these HMGB-RNA interactions are also likely involved in human disease. This review brings to light that as a family, HMGB proteins are likely to bind RNA which is essential to HMGB protein biology. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Lyu QR, Zhang S, Zhang Z, Tang Z. Functional knockout of long non-coding RNAs with genome editing. Front Genet 2023; 14:1242129. [PMID: 37705609 PMCID: PMC10495571 DOI: 10.3389/fgene.2023.1242129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 08/16/2023] [Indexed: 09/15/2023] Open
Abstract
An effective loss-of-function study is necessary to investigate the biological function of long non-coding RNA (lncRNA). Various approaches are available, including RNA silencing, antisense oligos, and CRISPR-based genome editing. CRISPR-based genome editing is the most widely used for inactivating lncRNA function at the genomic level. Knocking out the lncRNA function can be achieved by removing the promoter and the first exon (PE1), introducing pre-termination poly(A) signals, or deleting the entire locus, unlike frameshift strategies used for messenger RNA (mRNA). However, the intricate genomic interplay between lncRNA and neighbor genes makes it challenging to interpret lncRNA function accurately. This article discusses the advantages and disadvantages of each lncRNA knockout method and envisions the potential future directions to facilitate lncRNA functional study.
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Affiliation(s)
- Qing Rex Lyu
- Medical Research Center, Chongqing General Hospital, Chongqing, China
- Chongqing Academy of Medical Sciences, Chongqing, China
| | - Shikuan Zhang
- Key Lab in Healthy Science and Technology of Shenzhen, Tsinghua Shenzhen International Graduate School, Shenzhen, China
| | - Zhe Zhang
- Department of Chinese Medical Gastrointestinal of China-Japan Friendship Hospital, Beijing, China
| | - Zhiyu Tang
- Medical Research Center, Chongqing General Hospital, Chongqing, China
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40
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Hao L, Zhang J, Liu Z, Zhang Z, Mao T, Guo J. Role of the RNA-binding protein family in gynecologic cancers. Am J Cancer Res 2023; 13:3799-3821. [PMID: 37693158 PMCID: PMC10492115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 08/15/2023] [Indexed: 09/12/2023] Open
Abstract
Gynecological cancers pose a threat to women's health. Although early-stage gynecological cancers show good outcomes after standardized treatment, the prognosis of patients with advanced, met-astatic, and recurrent cancers is poor. RNA-binding proteins (RBPs) are important cellular proteins that interact with RNA through RNA-binding domains and participate extensively in post-transcriptional regulatory processes, such as mRNA alternative splicing, polyadenylation, intracellular localization and stability, and translation. Abnormal RBP expression affects the normal function of oncogenes and tumor suppressor genes in many malignancies, thus leading to the occurrence or progression of cancers. Similarly, RBPs play crucial roles in gynecological carcinogenesis. We summarize the role of RBPs in gynecological malignancies and explore their potential in the diagnosis and treatment of cancers. The findings summarized in this review may provide a guide for future research on the functions of RBPs.
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Affiliation(s)
- Linlin Hao
- Department of Tumor Radiotherapy, The Second Hospital of Jilin UniversityChangchun 130041, Jilin, China
| | - Jian Zhang
- School of Life Sciences, Department of Biology, Southern University of Science and TechnologyShenzhen 518055, Guangdong, China
| | - Zhongshan Liu
- Department of Tumor Radiotherapy, The Second Hospital of Jilin UniversityChangchun 130041, Jilin, China
| | - Zhiliang Zhang
- Department of Tumor Radiotherapy, The Second Hospital of Jilin UniversityChangchun 130041, Jilin, China
| | - Tiezhu Mao
- Department of Tumor Radiotherapy, The Second Hospital of Jilin UniversityChangchun 130041, Jilin, China
| | - Jie Guo
- Department of Tumor Radiotherapy, The Second Hospital of Jilin UniversityChangchun 130041, Jilin, China
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41
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Trendel J, Boileau E, Jochem M, Dieterich C, Krijgsveld J. PEPseq quantifies transcriptome-wide changes in protein occupancy and reveals selective translational repression after translational stress. Nucleic Acids Res 2023; 51:e79. [PMID: 37395449 PMCID: PMC10415142 DOI: 10.1093/nar/gkad557] [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: 12/29/2022] [Revised: 05/24/2023] [Accepted: 06/30/2023] [Indexed: 07/04/2023] Open
Abstract
Post-transcriptional gene regulation is accomplished by the interplay of the transcriptome with RNA-binding proteins, which occurs in a dynamic manner in response to altered cellular conditions. Recording the combined occupancy of all proteins binding to the transcriptome offers the opportunity to interrogate if a particular treatment leads to any interaction changes, pointing to sites in RNA that undergo post-transcriptional regulation. Here, we establish a method to monitor protein occupancy in a transcriptome-wide fashion by RNA sequencing. To this end, peptide-enhanced pull-down for RNA sequencing (or PEPseq) uses metabolic RNA labelling with 4-thiouridine (4SU) for light-induced protein-RNA crosslinking, and N-hydroxysuccinimide (NHS) chemistry to isolate protein-crosslinked RNA fragments across all long RNA biotypes. We use PEPseq to investigate changes in protein occupancy during the onset of arsenite-induced translational stress in human cells and reveal an increase of protein interactions in the coding region of a distinct set of mRNAs, including mRNAs coding for the majority of cytosolic ribosomal proteins. We use quantitative proteomics to demonstrate that translation of these mRNAs remains repressed during the initial hours of recovery after arsenite stress. Thus, we present PEPseq as a discovery platform for the unbiased investigation of post-transcriptional regulation.
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Affiliation(s)
- Jakob Trendel
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Etienne Boileau
- Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research) Partner Site Heidelberg/Mannheim, Germany
| | - Marco Jochem
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christoph Dieterich
- Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research) Partner Site Heidelberg/Mannheim, Germany
| | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty, Heidelberg, Germany
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42
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Zhai B, Xie SC, Zhang J, He JJ, Zhu XQ. Dynamic RNA profiles in the small intestinal epithelia of cats after Toxoplasma gondii infection. Infect Dis Poverty 2023; 12:68. [PMID: 37491273 PMCID: PMC10367386 DOI: 10.1186/s40249-023-01121-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/14/2023] [Indexed: 07/27/2023] Open
Abstract
BACKGROUND Felids are the only definitive hosts of Toxoplasma gondii. However, the biological features of the feline small intestine following T. gondii infection are poorly understood. We investigated the changes in the expression of RNAs (including mRNAs, long non-coding RNAs and circular RNAs) in the small intestinal epithelia of cats following T. gondii infection to improve our understanding of the life cycle of T. gondii and cat responses to T. gondii infection. METHODS Fifteen cats were randomly assigned to five groups, and the infection groups were inoculated with 600 tissue cysts of the T. gondii Pru strain by gavage. The small intestinal epithelia of cats were collected at 6, 10, 14, and 30 days post infection (DPI). Using high-throughput RNA sequencing (RNA-seq), we investigated the changes in RNA expression. The expression levels of differentially expressed (DE) genes and non-coding RNAs (ncRNAs) identified by RNA-seq were validated by quantitative reverse transcription PCR (qRT-PCR). Differential expression was determined using the DESeq R package. RESULTS In total, 207 annotated lncRNAs, 20,552 novel lncRNAs, 3342 novel circRNAs and 19,409 mRNAs were identified. Among these, 70 to 344 DE mRNAs, lncRNAs and circRNAs were detected, and the post-cleavage binding sites between 725 ncRNAs and 2082 miRNAs were predicted. Using the co-location method, we predicted that a total of 235 lncRNAs target 1044 protein-coding genes, while the results of co-expression analysis revealed that 174 lncRNAs target 2097 mRNAs. Pathway enrichment analyses of the genes targeted by ncRNAs suggested that most ncRNAs were significantly enriched in immune or diseases-related pathways. NcRNA regulatory networks revealed that a single ncRNA could be directly or indirectly regulated by multiple genes or ncRNAs that could influence the immune response of cats. Co-expression analysis showed that 242 circRNAs, mainly involved in immune responses, were significantly associated with T. gondii infection. In contrast, 1352 protein coding RNAs, mainly involved in nucleic acid process/repair pathways or oocyte development pathways, were negatively associated with T. gondii infection. CONCLUSIONS This study is the first to reveal the expression profiles of circRNAs, lncRNAs and mRNAs in the cat small intestine following T. gondii infection and will facilitate the elucidation of the role of ncRNAs in the pathogenesis of T. gondii infection in its definitive host, thereby facilitating the development of novel intervention strategies against T. gondii infection in humans and animals.
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Affiliation(s)
- Bintao Zhai
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, Gansu, People's Republic of China
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, People's Republic of China
| | - Shi-Chen Xie
- Laboratory of Parasitic Diseases, College of Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, Shanxi, People's Republic of China
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, People's Republic of China
| | - Jiyu Zhang
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, Gansu, People's Republic of China
| | - Jun-Jun He
- Key Laboratory of Veterinary Public Health of Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China.
| | - Xing-Quan Zhu
- Laboratory of Parasitic Diseases, College of Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, Shanxi, People's Republic of China.
- Key Laboratory of Veterinary Public Health of Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China.
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43
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DeSouza NR, Quaranto D, Carnazza M, Jarboe T, Tiwari RK, Geliebter J. Interactome of Long Non-Coding RNAs: Transcriptomic Expression Patterns and Shaping Cancer Cell Phenotypes. Int J Mol Sci 2023; 24:9914. [PMID: 37373059 DOI: 10.3390/ijms24129914] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
RNA biology has gained extensive recognition in the last two decades due to the identification of novel transcriptomic elements and molecular functions. Cancer arises, in part, due to the accumulation of mutations that greatly contribute to genomic instability. However, the identification of differential gene expression patterns of wild-type loci has exceeded the boundaries of mutational study and has significantly contributed to the identification of molecular mechanisms that drive carcinogenic transformation. Non-coding RNA molecules have provided a novel avenue of exploration, providing additional routes for evaluating genomic and epigenomic regulation. Of particular focus, long non-coding RNA molecule expression has been demonstrated to govern and direct cellular activity, thus evidencing a correlation between aberrant long non-coding RNA expression and the pathological transformation of cells. lncRNA classification, structure, function, and therapeutic utilization have expanded cancer studies and molecular targeting, and understanding the lncRNA interactome aids in defining the unique transcriptomic signatures of cancer cell phenotypes.
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Affiliation(s)
- Nicole R DeSouza
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
| | - Danielle Quaranto
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
| | - Michelle Carnazza
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
| | - Tara Jarboe
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
| | - Raj K Tiwari
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
- Department of Otolaryngology, New York Medical College, Valhalla, NY 10591, USA
| | - Jan Geliebter
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
- Department of Otolaryngology, New York Medical College, Valhalla, NY 10591, USA
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44
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Wolin E, Guo JK, Blanco MR, Perez AA, Goronzy IN, Abdou AA, Gorhe D, Guttman M, Jovanovic M. SPIDR: a highly multiplexed method for mapping RNA-protein interactions uncovers a potential mechanism for selective translational suppression upon cellular stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.05.543769. [PMID: 37333139 PMCID: PMC10274648 DOI: 10.1101/2023.06.05.543769] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
RNA binding proteins (RBPs) play crucial roles in regulating every stage of the mRNA life cycle and mediating non-coding RNA functions. Despite their importance, the specific roles of most RBPs remain unexplored because we do not know what specific RNAs most RBPs bind. Current methods, such as crosslinking and immunoprecipitation followed by sequencing (CLIP-seq), have expanded our knowledge of RBP-RNA interactions but are generally limited by their ability to map only one RBP at a time. To address this limitation, we developed SPIDR (Split and Pool Identification of RBP targets), a massively multiplexed method to simultaneously profile global RNA binding sites of dozens to hundreds of RBPs in a single experiment. SPIDR employs split-pool barcoding coupled with antibody-bead barcoding to increase the throughput of current CLIP methods by two orders of magnitude. SPIDR reliably identifies precise, single-nucleotide RNA binding sites for diverse classes of RBPs simultaneously. Using SPIDR, we explored changes in RBP binding upon mTOR inhibition and identified that 4EBP1 acts as a dynamic RBP that selectively binds to 5'-untranslated regions of specific translationally repressed mRNAs only upon mTOR inhibition. This observation provides a potential mechanism to explain the specificity of translational regulation controlled by mTOR signaling. SPIDR has the potential to revolutionize our understanding of RNA biology and both transcriptional and post-transcriptional gene regulation by enabling rapid, de novo discovery of RNA-protein interactions at an unprecedented scale.
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Affiliation(s)
- Erica Wolin
- Department of Biological Sciences, Columbia University, New York City, New York 10027, USA
| | - Jimmy K. Guo
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena CA 91125, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Mario R. Blanco
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena CA 91125, USA
| | - Andrew A. Perez
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena CA 91125, USA
| | - Isabel N. Goronzy
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena CA 91125, USA
| | - Ahmed A. Abdou
- Department of Biological Sciences, Columbia University, New York City, New York 10027, USA
| | - Darvesh Gorhe
- Department of Biological Sciences, Columbia University, New York City, New York 10027, USA
| | - Mitchell Guttman
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena CA 91125, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York City, New York 10027, USA
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45
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Ruan X, Hu K, Zhang X. PIE-seq: identifying RNA-binding protein targets by dual RNA-deaminase editing and sequencing. Nat Commun 2023; 14:3275. [PMID: 37280234 DOI: 10.1038/s41467-023-39054-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 05/26/2023] [Indexed: 06/08/2023] Open
Abstract
RNA-binding proteins (RBPs) are essential for gene regulation, but it remains a challenge to identify their RNA targets across cell types. Here we present PIE-Seq to investigate Protein-RNA Interaction with dual-deaminase Editing and Sequencing by conjugating C-to-U and A-to-I base editors to RBPs. We benchmark PIE-Seq and demonstrate its sensitivity in single cells, its application in the developing brain, and its scalability with 25 human RBPs. Bulk PIE-Seq identifies canonical binding features for RBPs such as PUM2 and NOVA1, and nominates additional target genes for most tested RBPs such as SRSF1 and TDP-43/TARDBP. Homologous RBPs frequently edit similar sequences and gene sets in PIE-Seq while different RBP families show distinct targets. Single-cell PIE-PUM2 uncovers comparable targets to bulk samples and applying PIE-PUM2 to the developing mouse neocortex identifies neural-progenitor- and neuron-specific target genes such as App. In summary, PIE-Seq provides an orthogonal approach and resource to uncover RBP targets in mice and human cells.
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Affiliation(s)
- Xiangbin Ruan
- Department of Human Genetics and The Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - Kaining Hu
- Department of Human Genetics and The Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - Xiaochang Zhang
- Department of Human Genetics and The Neuroscience Institute, University of Chicago, Chicago, IL, USA.
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46
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Das R, Dey A, Uppal S. A method for in situ visualization of Protein-Nascent RNA interactions in single cell using Proximity Ligation Assay (IPNR-PLA) in mammalian cells. Transcription 2023; 14:146-157. [PMID: 36927323 PMCID: PMC10807467 DOI: 10.1080/21541264.2023.2190296] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 03/18/2023] Open
Abstract
Proximity ligation assay (PLA) is an immunofluorescence assay, which determines in situ interaction of two biomolecules present within 40 nm close proximity. Here, we describe a modification of PLA for visual detection of in situ protein interactions with nascent RNA in a single cell (IPNR-PLA). In IPNR-PLA, nascent RNA is labeled by incorporating 5-fluorouridine (FU), a uridine nucleotide analogue, followed by covalent cross-linking of the interacting partners in proximity to newly synthesized RNA. By using combination of anti-BrdU antibody, which specifically binds to FU, and primary antibody against a protein of interest, the IPNR reaction results in fluorescent puncta as a positive signal, only if the candidate proteins are in proximity to nascent RNA. We have validated this method by demonstrating known CDK9 and elongating RNA pol II interaction with nascent RNA. Finally, we used this method to test for the presence of DNA double strand breaks as well as Poly (ADP-ribose) polymerase 1 (PARP1), an RNA binding protein, in the vicinity of nascent RNA in cancer cells. The capability of performing parallel IF labeling and quantifiable multiparameter measurements within heterogeneous cell populations makes IPNR-PLA very attractive for use in biological studies. Overall, we have developed the IPNR-PLA method for analysis of protein association with nascent RNA with single-cell resolution, which is highly sensitive, quantitative, efficient, and requires little starting experimental material.
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Affiliation(s)
- Rituparna Das
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay,Mumbai, India
- Life Sciences, Homi Bhabha National Institute, Anushakti Nagar, Mumbai, India
| | - Anusree Dey
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay,Mumbai, India
- Life Sciences, Homi Bhabha National Institute, Anushakti Nagar, Mumbai, India
| | - Sheetal Uppal
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay,Mumbai, India
- Life Sciences, Homi Bhabha National Institute, Anushakti Nagar, Mumbai, India
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47
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Sharma H, Yadav V, D'Souza-Schorey C, Go DB, Senapati S, Chang HC. A Scalable High-Throughput Isoelectric Fractionation Platform for Extracellular Nanocarriers: Comprehensive and Bias-Free Isolation of Ribonucleoproteins from Plasma, Urine, and Saliva. ACS NANO 2023; 17:9388-9404. [PMID: 37071723 PMCID: PMC10756736 DOI: 10.1021/acsnano.3c01340] [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] [Indexed: 05/24/2023]
Abstract
Extracellular nanocarriers (extracellular vesicles (EVs), lipoproteins, and ribonucleoproteins) of protein and nucleic acids mediate intercellular communication and are clinically adaptable as distinct circulating biomarkers. However, the overlapping size and density of the nanocarriers have so far prevented their efficient physical fractionation, thus impeding independent downstream molecular assays. Here, we report a bias-free high-throughput and high-yield continuous isoelectric fractionation nanocarrier fractionation technique based on their distinct isoelectric points. This nanocarrier fractionation platform is enabled by a robust and tunable linear pH profile provided by water-splitting at a bipolar membrane and stabilized by flow without ampholytes. The linear pH profile that allows easy tuning is a result of rapid equilibration of the water dissociation reaction and stabilization by flow. The platform is automated with a machine learning procedure to allow recalibration for different physiological fluids and nanocarriers. The optimized technique has a resolution of 0.3 ΔpI, sufficient to separate all nanocarriers and even subclasses of nanocarriers. Its performance is then evaluated with several biofluids, including plasma, urine, and saliva samples. Comprehensive, high-purity (plasma: >93%, urine: >95% and saliva: >97%), high-yield (plasma: >78%, urine: >87% and saliva: >96%), and probe-free isolation of ribonucleoproteins in 0.75 mL samples of various biofluids in 30 min is demonstrated, significantly outperforming affinity-based and highly biased gold standards having low yield and day-long protocols. Binary fractionation of EVs and different lipoproteins is also achieved with similar performance.
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Affiliation(s)
- Himani Sharma
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Vivek Yadav
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Crislyn D'Souza-Schorey
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana 46556, United States
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - David B Go
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Satyajyoti Senapati
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Hsueh-Chia Chang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana 46556, United States
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48
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Piao W, Li C, Sun P, Yang M, Ding Y, Song W, Jia Y, Yu L, Lu Y, Jin H. Identification of RNA-Binding Protein Targets with HyperTRIBE in Saccharomyces cerevisiae. Int J Mol Sci 2023; 24:ijms24109033. [PMID: 37240377 DOI: 10.3390/ijms24109033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
As a master regulator in cells, RNA-binding protein (RBP) plays critical roles in organismal development, metabolism and various diseases. It regulates gene expression at various levels mostly by specific recognition of target RNA. The traditional CLIP-seq method to detect transcriptome-wide RNA targets of RBP is less efficient in yeast due to the low UV transmissivity of their cell walls. Here, we established an efficient HyperTRIBE (Targets of RNA-binding proteins Identified By Editing) in yeast, by fusing an RBP to the hyper-active catalytic domain of human RNA editing enzyme ADAR2 and expressing the fusion protein in yeast cells. The target transcripts of RBP were marked with new RNA editing events and identified by high-throughput sequencing. We successfully applied HyperTRIBE to identifying the RNA targets of two yeast RBPs, KHD1 and BFR1. The antibody-free HyperTRIBE has competitive advantages including a low background, high sensitivity and reproducibility, as well as a simple library preparation procedure, providing a reliable strategy for RBP target identification in Saccharomyces cerevisiae.
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Affiliation(s)
- Weilan Piao
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing 100081, China
| | - Chong Li
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing 100081, China
| | - Pengkun Sun
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing 100081, China
| | - Miaomiao Yang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing 100081, China
| | - Yansong Ding
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing 100081, China
| | - Wei Song
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing 100081, China
| | - Yunxiao Jia
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing 100081, China
| | - Liqun Yu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing 100081, China
| | - Yanming Lu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing 100081, China
| | - Hua Jin
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing 100081, China
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49
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Wang X, Jing S, Wang W, Wang J. Direct and noninvasive fluorescence analysis of an RNA-protein interaction based on a CRISPR/Cas12a-powered assay. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 299:122884. [PMID: 37210856 DOI: 10.1016/j.saa.2023.122884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/25/2023] [Accepted: 05/12/2023] [Indexed: 05/23/2023]
Abstract
RNA-protein interactions (RPIs) play critical roles in gene transcription and protein expression, but current analytical methods for RPIs are mainly performed in an invasive manner, involving special RNA/protein labeling, hampering access to intact and precise information on RPIs. In this work, we present the first CRISPR/Cas12a-based fluorescence assay for the direct analysis of RPIs without RNA/protein labeling steps. Select vascular endothelial growth factor 165 (VEGF165)/its RNA aptamer interaction as a model, the RNA sequence simultaneously serves as both the aptamer of VEGF165 and crRNA of CRISPR/Cas12a system, and the presence of VEGF165 facilitates VEGF165/its RNA aptamer interaction, thus prohibiting the formation of Cas12a-crRNA-DNA ternary complex along with low fluorescence signal. The assay showed a detection limit of 0.23 pg mL-1, and good performance in serum-spiked samples with an RSD of 0.4 %-13.1 %. This simple and selective strategy opens the door for establishing CRISPR/Cas-based biosensors for gaining intact information on RPIs, and shows widespread potential for other RPIs analysis.
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Affiliation(s)
- Xueliang Wang
- Xi'an Key Laboratory of Stem Cell and Regenerative Medicine, Institute of Medical Research, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi 710072, China; Collaborative Innovation Center of NPU, Shanghai 201100, P.R. China; Research & Development Institute of Northwestern Polytechnical University in Shenzhen, 45 South Gaoxin Road, Shenzhen 518057, China; Northwestern Polytechnical University Chongqing Technology Innovation Center, Chongqing 400000, PR China
| | - Shaozhen Jing
- Xi'an Key Laboratory of Stem Cell and Regenerative Medicine, Institute of Medical Research, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi 710072, China; Collaborative Innovation Center of NPU, Shanghai 201100, P.R. China; Research & Development Institute of Northwestern Polytechnical University in Shenzhen, 45 South Gaoxin Road, Shenzhen 518057, China; Northwestern Polytechnical University Chongqing Technology Innovation Center, Chongqing 400000, PR China
| | - Wanhe Wang
- Xi'an Key Laboratory of Stem Cell and Regenerative Medicine, Institute of Medical Research, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi 710072, China; Collaborative Innovation Center of NPU, Shanghai 201100, P.R. China; Research & Development Institute of Northwestern Polytechnical University in Shenzhen, 45 South Gaoxin Road, Shenzhen 518057, China; Northwestern Polytechnical University Chongqing Technology Innovation Center, Chongqing 400000, PR China.
| | - Jing Wang
- Xi'an Key Laboratory of Stem Cell and Regenerative Medicine, Institute of Medical Research, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi 710072, China; Collaborative Innovation Center of NPU, Shanghai 201100, P.R. China; Research & Development Institute of Northwestern Polytechnical University in Shenzhen, 45 South Gaoxin Road, Shenzhen 518057, China; Northwestern Polytechnical University Chongqing Technology Innovation Center, Chongqing 400000, PR China.
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50
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He S, Valkov E, Cheloufi S, Murn J. The nexus between RNA-binding proteins and their effectors. Nat Rev Genet 2023; 24:276-294. [PMID: 36418462 DOI: 10.1038/s41576-022-00550-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2022] [Indexed: 11/25/2022]
Abstract
RNA-binding proteins (RBPs) regulate essentially every event in the lifetime of an RNA molecule, from its production to its destruction. Whereas much has been learned about RNA sequence specificity and general functions of individual RBPs, the ways in which numerous RBPs instruct a much smaller number of effector molecules, that is, the core engines of RNA processing, as to where, when and how to act remain largely speculative. Here, we survey the known modes of communication between RBPs and their effectors with a particular focus on converging RBP-effector interactions and their roles in reducing the complexity of RNA networks. We discern the emerging unifying principles and discuss their utility in our understanding of RBP function, regulation of biological processes and contribution to human disease.
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Affiliation(s)
- Shiyang He
- Department of Biochemistry, University of California, Riverside, CA, USA
- Center for RNA Biology and Medicine, Riverside, CA, USA
| | - Eugene Valkov
- RNA Biology Laboratory & Center for Structural Biology, Center for Cancer Research, National Cancer Institute (NCI), Frederick, MD, USA
| | - Sihem Cheloufi
- Department of Biochemistry, University of California, Riverside, CA, USA.
- Center for RNA Biology and Medicine, Riverside, CA, USA.
- Stem Cell Center, University of California, Riverside, CA, USA.
| | - Jernej Murn
- Department of Biochemistry, University of California, Riverside, CA, USA.
- Center for RNA Biology and Medicine, Riverside, CA, USA.
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