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Abstract
Cardiovascular disease still remains the leading cause of morbidity and mortality worldwide. Current pharmacological or interventional treatments help to tackle symptoms and even reduce mortality, but cardiovascular disease cases continue to rise. The emergence of novel therapeutic strategies that precisely and efficiently combat cardiovascular disease is therefore deemed more essential than ever. RNA editing, the cell-intrinsic deamination of adenosine or cytidine RNA residues, changes the molecular identity of edited nucleotides, severely altering the fate of RNA molecules involved in key biological processes. The most common type of RNA editing is the deamination of adenosine residue to inosine (A-to-I), which is catalysed by adenosine deaminases acting on RNA (ADARs). Recent efforts have convincingly liaised RNA editing-based mechanisms to the pathophysiology of the cardiovascular system. In this review, we will briefly introduce the basic concepts of the RNA editing field of research. We will particularly focus our discussion on the therapeutic exploitation of RNA editing as a novel therapeutic tool as well as the future perspectives for its use in cardiovascular disease treatment.
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2
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Han W, Huang W, Wei T, Ye Y, Mao M, Wang Z. Programmable RNA base editing with a single gRNA-free enzyme. Nucleic Acids Res 2022; 50:9580-9595. [PMID: 36029126 PMCID: PMC9458445 DOI: 10.1093/nar/gkac713] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 07/02/2022] [Accepted: 08/09/2022] [Indexed: 12/24/2022] Open
Abstract
Programmable RNA editing enables rewriting gene expression without changing genome sequences. Current tools for specific RNA editing dependent on the assembly of guide RNA into an RNA/protein complex, causing delivery barrier and low editing efficiency. We report a new gRNA-free system, RNA editing with individual RNA-binding enzyme (REWIRE), to perform precise base editing with a single engineered protein. This artificial enzyme contains a human-originated programmable PUF domain to specifically recognize RNAs and different deaminase domains to achieve efficient A-to-I or C-to-U editing, which achieved 60-80% editing rate in human cells, with a few non-specific editing sites in the targeted region and a low level off-target effect globally. The RNA-binding domain in REWIREs was further optimized to improve editing efficiency and minimize off-target effects. We applied the REWIREs to correct disease-associated mutations and achieve both types of base editing in mice. As a single-component system originated from human proteins, REWIRE presents a precise and efficient RNA editing platform with broad applicability.
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Affiliation(s)
- Wenjian Han
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wendi Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tong Wei
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanwen Ye
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Miaowei Mao
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zefeng Wang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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3
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Fan X, Yang Y, Chen C, Wang Z. Pervasive translation of circular RNAs driven by short IRES-like elements. Nat Commun 2022; 13:3751. [PMID: 35768398 PMCID: PMC9242994 DOI: 10.1038/s41467-022-31327-y] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 06/09/2022] [Indexed: 12/30/2022] Open
Abstract
Some circular RNAs (circRNAs) were found to be translated through IRES-driven mechanism, however the scope and functions of circRNA translation are unclear because endogenous IRESs are rare. To determine the prevalence and mechanism of circRNA translation, we develop a cell-based system to screen random sequences and identify 97 overrepresented hexamers that drive cap-independent circRNA translation. These IRES-like short elements are significantly enriched in endogenous circRNAs and sufficient to drive circRNA translation. We further identify multiple trans-acting factors that bind these IRES-like elements to initiate translation. Using mass-spectrometry data, hundreds of circRNA-coded peptides are identified, most of which have low abundance due to rapid degradation. As judged by mass-spectrometry, 50% of translatable endogenous circRNAs undergo rolling circle translation, several of which are experimentally validated. Consistently, mutations of the IRES-like element in one circRNA reduce its translation. Collectively, our findings suggest a pervasive translation of circRNAs, providing profound implications in translation control. Unbiased screen of random sequences identified many short IRES-like elements to drive circular RNA translation and hundreds of rolling circle translation events, suggesting a pervasive cap-independent translation in human transcriptome.
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Affiliation(s)
- Xiaojuan Fan
- Bio-med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, Shanghai, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yun Yang
- Bio-med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, Shanghai, China.,CirCode BioMedicine, Pudong, Shanghai, China
| | - Chuyun Chen
- Bio-med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, Shanghai, China
| | - Zefeng Wang
- Bio-med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, Shanghai, China. .,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China.
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Liu R, Yang J, Yao J, Zhao Z, He W, Su N, Zhang Z, Zhang C, Zhang Z, Cai H, Zhu L, Zhao Y, Quan S, Chen X, Yang Y. Optogenetic control of RNA function and metabolism using engineered light-switchable RNA-binding proteins. Nat Biotechnol 2022; 40:779-786. [PMID: 34980910 DOI: 10.1038/s41587-021-01112-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 10/01/2021] [Indexed: 12/13/2022]
Abstract
RNA-binding proteins (RBPs) play an essential role in regulating the function of RNAs in a cellular context, but our ability to control RBP activity in time and space is limited. Here, we describe the engineering of LicV, a photoswitchable RBP that binds to a specific RNA sequence in response to blue light irradiation. When fused to various RNA effectors, LicV allows for optogenetic control of RNA localization, splicing, translation and stability in cell culture. Furthermore, LicV-assisted CRISPR-Cas systems allow for efficient and tunable photoswitchable regulation of transcription and genomic locus labeling. These data demonstrate that the photoswitchable RBP LicV can serve as a programmable scaffold for the spatiotemporal control of synthetic RNA effectors.
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Affiliation(s)
- Renmei Liu
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Jing Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Jing Yao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Zhou Zhao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Wei He
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Ni Su
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Zeyi Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Chenxia Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Zhuo Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Haibo Cai
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Linyong Zhu
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Yuzheng Zhao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Shu Quan
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Xianjun Chen
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- School of Pharmacy, East China University of Science and Technology, Shanghai, China.
- CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
| | - Yi Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- School of Pharmacy, East China University of Science and Technology, Shanghai, China.
- CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
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5
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Manavski N, Mathieu S, Rojas M, Méteignier LV, Brachmann A, Barkan A, Hammani K. In vivo stabilization of endogenous chloroplast RNAs by customized artificial pentatricopeptide repeat proteins. Nucleic Acids Res 2021; 49:5985-5997. [PMID: 34037778 PMCID: PMC8191804 DOI: 10.1093/nar/gkab390] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 04/05/2021] [Accepted: 04/28/2021] [Indexed: 12/17/2022] Open
Abstract
Pentatricopeptide repeat (PPR) proteins are helical repeat-proteins that bind RNA in a modular fashion with a sequence-specificity that can be manipulated by the use of an amino acid code. As such, PPR repeats are promising scaffolds for the design of RNA binding proteins for synthetic biology applications. However, the in vivo functional capabilities of artificial PPR proteins built from consensus PPR motifs are just starting to be explored. Here, we report in vivo functions of an artificial PPR protein, dPPRrbcL, made of consensus PPR motifs that were designed to bind a sequence near the 5′ end of rbcL transcripts in Arabidopsis chloroplasts. We used a functional complementation assay to demonstrate that this protein bound its intended RNA target with specificity in vivo and that it substituted for a natural PPR protein by stabilizing processed rbcL mRNA. We targeted a second protein of analogous design to the petL 5′ UTR, where it substituted for the native stabilizing PPR protein PGR3, albeit inefficiently. These results showed that artificial PPR proteins can be engineered to functionally mimic the class of native PPR proteins that serve as physical barriers against exoribonucleases.
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Affiliation(s)
- Nikolay Manavski
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - Sébastien Mathieu
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - Margarita Rojas
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403 USA
| | - Louis-Valentin Méteignier
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - Andreas Brachmann
- Genetics, Faculty of Biology, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried Germany
| | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403 USA
| | - Kamel Hammani
- To whom correspondence should be addressed. Tel: +33 367155281; Fax: +33 367155300;
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6
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Toudji-Zouaz A, Bertrand V, Barrière A. Imaging of native transcription and transcriptional dynamics in vivo using a tagged Argonaute protein. Nucleic Acids Res 2021; 49:e86. [PMID: 34107044 PMCID: PMC8421136 DOI: 10.1093/nar/gkab469] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 04/16/2021] [Accepted: 05/18/2021] [Indexed: 12/26/2022] Open
Abstract
A flexible method to image unmodified transcripts and transcription in vivo would be a valuable tool to understand the regulation and dynamics of transcription. Here, we present a novel approach to follow native transcription, with fluorescence microscopy, in live C. elegans. By using the fluorescently tagged Argonaute protein NRDE-3, programmed by exposure to defined dsRNA to bind to nascent transcripts of the gene of interest, we demonstrate transcript labelling of multiple genes, at the transcription site and in the cytoplasm. This flexible approach does not require genetic manipulation, and can be easily scaled up by relying on whole-genome dsRNA libraries. We apply this method to image the transcriptional dynamics of the heat-shock inducible gene hsp-4 (a member of the hsp70 family), as well as two transcription factors: ttx-3 (a LHX2/9 orthologue) in embryos, and hlh-1 (a MyoD orthologue) in larvae, respectively involved in neuronal and muscle development.
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Affiliation(s)
- Amel Toudji-Zouaz
- Aix Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
| | - Vincent Bertrand
- Aix Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
| | - Antoine Barrière
- Aix Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
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7
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Pei Y, Lu M. Programmable RNA manipulation in living cells. Cell Mol Life Sci 2019; 76:4861-4867. [PMID: 31367845 PMCID: PMC11105762 DOI: 10.1007/s00018-019-03252-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/23/2019] [Accepted: 07/24/2019] [Indexed: 02/07/2023]
Abstract
RNAs are responsible for mediating genetic information flow within the cell. RNA splicing, modification, trafficking, translation, and stability are all controlled at the transcript level. However, biological tools to study and manipulate them in a programmable fashion are currently limited. In this review, we summarize recent advances regarding available RNA-targeting systems discovered so far, including CRISPR-based technologies-Cas9 and Cas13, and programmable RNA-binding proteins-PUF and PPR. These tools allow transcript-specific manipulation in gene expression.
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Affiliation(s)
- Yu Pei
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Mingxing Lu
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong, Hong Kong.
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8
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Shotwell CR, Cleary JD, Berglund JA. The potential of engineered eukaryotic RNA-binding proteins as molecular tools and therapeutics. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1573. [PMID: 31680457 DOI: 10.1002/wrna.1573] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/21/2019] [Accepted: 10/08/2019] [Indexed: 02/06/2023]
Abstract
Eukaroytic RNA-binding proteins (RBPs) recognize and process RNAs through recognition of their sequence motifs via RNA-binding domains (RBDs). RBPs usually consist of one or more RBDs and can include additional functional domains that modify or cleave RNA. Engineered RBPs have been used to answer basic biology questions, control gene expression, locate viral RNA in vivo, as well as many other tasks. Given the growing number of diseases associated with RNA and RBPs, engineered RBPs also have the potential to serve as therapeutics. This review provides an in depth description of recent advances in engineered RBPs and discusses opportunities and challenges in the field. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Methods > RNA Nanotechnology RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Carl R Shotwell
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida
| | - John D Cleary
- RNA Institute, University at Albany, Albany, New York
| | - J Andrew Berglund
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, New York
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Yan J, Yao Y, Hong S, Yang Y, Shen C, Zhang Q, Zhang D, Zou T, Yin P. Delineation of pentatricopeptide repeat codes for target RNA prediction. Nucleic Acids Res 2019; 47:3728-3738. [PMID: 30753696 PMCID: PMC6468296 DOI: 10.1093/nar/gkz075] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 01/23/2019] [Accepted: 01/31/2019] [Indexed: 12/18/2022] Open
Abstract
Members of the pentatricopeptide repeat (PPR) protein family are sequence-specific RNA-binding proteins that play crucial roles in organelle RNA metabolism. Each PPR protein consists of a tandem array of PPR motifs, each of which aligns to one nucleotide of the RNA target. The di-residues in the PPR motif, which are referred to as the PPR codes, determine nucleotide specificity. Numerous PPR codes are distributed among the vast number of PPR motifs, but the correlation between PPR codes and RNA bases is poorly understood, which hinders target RNA prediction and functional investigation of PPR proteins. To address this issue, we developed a modular assembly method for high-throughput construction of designer PPRs, and by using this method, 62 designer PPR proteins containing various PPR codes were assembled. Then, the correlation between these PPR codes and RNA bases was systematically explored and delineated. Based on this correlation, the web server PPRCODE (http://yinlab.hzau.edu.cn/pprcode) was developed. Our study will not only serve as a platform for facilitating target RNA prediction and functional investigation of the large number of PPR family proteins but also provide an alternative strategy for the assembly of custom PPRs that can potentially be used for plant organelle RNA manipulation.
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Affiliation(s)
- Junjie Yan
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Yinying Yao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Sixing Hong
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Yan Yang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Cuicui Shen
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Qunxia Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Delin Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Tingting Zou
- College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
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Rau K, Rösner L, Rentmeister A. Sequence-specific m 6A demethylation in RNA by FTO fused to RCas9. RNA (NEW YORK, N.Y.) 2019; 25:1311-1323. [PMID: 31263003 PMCID: PMC6800472 DOI: 10.1261/rna.070706.119] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/18/2019] [Indexed: 05/21/2023]
Abstract
N6-methyladenosine (m6A) is the most common internal modification in eukaryotic mRNA and associated with numerous cellular processes in health and disease. Up- and down-regulation of its "writer" or "eraser" proteins alter the global m6A level; however, modifying distinct m6A sites has remained elusive. We genetically fused the dioxygenase FTO responsible for m6A demethylation to RCas9 as an RNA-targeting module. The resulting RCas9-FTO retained demethylation activity and bound to RNA in a sequence-specific manner depending on the sgRNA and PAMmer. Using SCARLET analysis, we quantified the m6A level at a specific site and analyzed the effect of the PAM-to-m6A distance on activity. Sequence-specific demethylation by RCas9-FTO was tested on different RNA combinations and showed up to 15-fold sequence preference for target RNA compared to off-target RNA. Taken together, RCas9-FTO represents a new tool for sequence-specific demethylation of m6A in RNA that can be readily adapted to any given RNA sequence and opens the door to studying the function of distinct m6A sites.
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Affiliation(s)
- Kristina Rau
- Institute of Biochemistry, Department of Chemistry, University of Münster, 48149 Münster, Germany
| | - Lukas Rösner
- Institute of Biochemistry, Department of Chemistry, University of Münster, 48149 Münster, Germany
| | - Andrea Rentmeister
- Institute of Biochemistry, Department of Chemistry, University of Münster, 48149 Münster, Germany
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11
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Zhang Y, Lu C. The Enigmatic Roles of PPR-SMR Proteins in Plants. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1900361. [PMID: 31380188 PMCID: PMC6662315 DOI: 10.1002/advs.201900361] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 04/03/2019] [Indexed: 05/21/2023]
Abstract
The pentatricopeptide repeat (PPR) protein family, with more than 400 members, is one of the largest and most diverse protein families in land plants. A small subset of PPR proteins contain a C-terminal small MutS-related (SMR) domain. Although there are relatively few PPR-SMR proteins, they play essential roles in embryo development, chloroplast biogenesis and gene expression, and plastid-to-nucleus retrograde signaling. Here, recent advances in understanding the roles of PPR-SMR proteins and the SMR domain based on a combination of genetic, biochemical, and physiological analyses are described. In addition, the potential of the PPR-SMR protein SOT1 to serve as a tool for RNA manipulation is highlighted.
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Affiliation(s)
- Yi Zhang
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTaianShandong271018P. R. China
| | - Congming Lu
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTaianShandong271018P. R. China
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12
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Bhushan K. CRISPR/Cas13a targeting of RNA virus in plants. PLANT CELL REPORTS 2018; 37:1707-1712. [PMID: 29779095 DOI: 10.1007/s00299-018-2297-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 05/11/2018] [Indexed: 06/08/2023]
Abstract
KEY MESSAGE This approach is quite promising to control plant viral diseases and create synthetic networks to better understand the structure/function relationship in RNA and proteins. Plant viruses are obligate intracellular parasites which causes enormous losses in crop yield worldwide. These viruses replicate into infected cells by highjacking host cellular machinery. Over the last two decades, diverse approaches such as conventional breeding, transgenic approach and gene silencing strategies have been used to control RNA viruses, but escaped due to high rate of mutation. Recently, a novel CRISPR enzyme, called Cas13a, has been used engineered to confer RNA viruses resistance in plants. Here, we summarize the recent breakthrough of CRISPR/Cas13a and its applications in RNA biology.
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Affiliation(s)
- Kul Bhushan
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
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13
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Mao M, Hu Y, Yang Y, Qian Y, Wei H, Fan W, Yang Y, Li X, Wang Z. Modeling and Predicting the Activities of Trans-Acting Splicing Factors with Machine Learning. Cell Syst 2018; 7:510-520.e4. [PMID: 30414922 DOI: 10.1016/j.cels.2018.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 05/10/2018] [Accepted: 09/19/2018] [Indexed: 02/06/2023]
Abstract
Alternative splicing (AS) is generally regulated by trans-splicing factors that specifically bind to cis-elements in pre-mRNAs. The human genome encodes ∼1,500 RNA binding proteins (RBPs) that potentially regulate AS, yet their functions remain largely unknown. To explore their potential activities, we fused the putative functional domains of RBPs to a sequence-specific RNA-binding domain and systemically analyzed how these engineered factors affect splicing. We discovered that ∼80% of low-complexity domains in endogenous RBPs displayed distinct context-dependent activities in regulating splicing, indicating that AS is under more extensive regulation than previously expected. We developed a machine learning approach to classify and predict the activities of RBPs based on their sequence compositions and further validated this model using endogenous RBPs and synthetic polypeptides. These results represent a systematic inspection, modeling, prediction, and validation of how RBP sequences affect their activities in controlling splicing, paving the way for de novo engineering of artificial splicing factors.
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Affiliation(s)
- Miaowei Mao
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China; Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Yue Hu
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yun Yang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yajie Qian
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Huanhuan Wei
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Wei Fan
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Yi Yang
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xiaoling Li
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Zefeng Wang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.
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14
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Zhao YY, Mao MW, Zhang WJ, Wang J, Li HT, Yang Y, Wang Z, Wu JW. Expanding RNA binding specificity and affinity of engineered PUF domains. Nucleic Acids Res 2018; 46:4771-4782. [PMID: 29490074 PMCID: PMC5961129 DOI: 10.1093/nar/gky134] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 02/08/2018] [Accepted: 02/16/2018] [Indexed: 12/26/2022] Open
Abstract
Specific manipulation of RNA is necessary for the research in biotechnology and medicine. The RNA-binding domains of Pumilio/fem-3 mRNA binding factors (PUF domains) are programmable RNA binding scaffolds used to engineer artificial proteins that specifically modulate RNAs. However, the native PUF domains generally recognize 8-nt RNAs, limiting their applications. Here, we modify the PUF domain of human Pumilio1 to engineer PUFs that recognize RNA targets of different length. The engineered PUFs bind to their RNA targets specifically and PUFs with more repeats have higher binding affinity than the canonical eight-repeat domains; however, the binding affinity reaches the peak at those with 9 and 10 repeats. Structural analysis on PUF with nine repeats reveals a higher degree of curvature, and the RNA binding unexpectedly and dramatically opens the curved structure. Investigation of the residues positioned in between two RNA bases demonstrates that tyrosine and arginine have favored stacking interactions. Further tests on the availability of the engineered PUFs in vitro and in splicing function assays indicate that our engineered PUFs bind RNA targets with high affinity in a programmable way.
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Affiliation(s)
- Yang-Yang Zhao
- Center for Life Sciences, Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Miao-Wei Mao
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biological Science, Shanghai 200031, China
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Wen-Jing Zhang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning 116044, China
| | - Jue Wang
- Institute of Molecular Enzymology, Soochow University, Suzhou, Jiangsu 215123, China
| | - Hai-Tao Li
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yi Yang
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zefeng Wang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biological Science, Shanghai 200031, China
- Enzerna Biosciences, Inc., 125 South Road, 925B Kenan Labs, CB#3266, Chapel Hill, NC 27599, USA
| | - Jia-Wei Wu
- Center for Life Sciences, Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Institute of Molecular Enzymology, Soochow University, Suzhou, Jiangsu 215123, China
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15
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Mahas A, Neal Stewart C, Mahfouz MM. Harnessing CRISPR/Cas systems for programmable transcriptional and post-transcriptional regulation. Biotechnol Adv 2018; 36:295-310. [DOI: 10.1016/j.biotechadv.2017.11.008] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/03/2017] [Accepted: 11/27/2017] [Indexed: 12/26/2022]
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16
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Song X, Zeng Z, Wei H, Wang Z. Alternative splicing in cancers: From aberrant regulation to new therapeutics. Semin Cell Dev Biol 2017; 75:13-22. [PMID: 28919308 DOI: 10.1016/j.semcdb.2017.09.018] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 09/09/2017] [Accepted: 09/11/2017] [Indexed: 12/18/2022]
Abstract
Alternative splicing is one of the most common mechanisms for gene regulation in humans, and plays a vital role to increase the complexity of functional proteins. In this article, we seek to provide a general review on the relationships between alternative splicing and tumorigenesis. We briefly introduce the basic rules for regulation of alternative splicing, and discuss recent advances on dynamic regulation of alternative splicing in cancers by highlighting the roles of a variety of RNA splicing factors in tumorigenesis. We further discuss several important questions regarding the splicing of long noncoding RNAs and back-splicing of circular RNAs in cancers. Finally, we discuss the current technologies that can be used to manipulate alternative splicing and serve as potential cancer treatment.
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Affiliation(s)
- Xiaowei Song
- CAS Key Lab for Computational Biology, CAS Center for Excellence in Molecular Cell Science, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Department of Cardiology, Changhai Hospital, 168 Changhai Road, Shanghai 200433, China.
| | - Zhenyu Zeng
- Department of Cardiology, Changhai Hospital, 168 Changhai Road, Shanghai 200433, China
| | - Huanhuan Wei
- CAS Key Lab for Computational Biology, CAS Center for Excellence in Molecular Cell Science, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zefeng Wang
- CAS Key Lab for Computational Biology, CAS Center for Excellence in Molecular Cell Science, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
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17
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Wang B, Ye K. Nop9 binds the central pseudoknot region of 18S rRNA. Nucleic Acids Res 2017; 45:3559-3567. [PMID: 28053123 PMCID: PMC5389560 DOI: 10.1093/nar/gkw1323] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 12/19/2016] [Indexed: 01/21/2023] Open
Abstract
The assembly of eukaryotic ribosomes requires numerous factors that transiently associate with evolving pre-ribosomal particles. The Pumilio repeat-containing protein Nop9 briefly associates with the 90S pre-ribosome during its co-transcriptional assembly. Here, we show that Nop9 specifically binds an 11-nucleotide sequence of 18S rRNA that forms the 3΄ side of the central pseudoknot and helix 28 in the mature subunit. Crystal structures of Nop9 in the free and RNA-bound states reveal a new type of Pumilio repeat protein with a distinct structure, target sequence and RNA-binding mode. Nop9 contains 10 Pumilio repeats arranged into a U-shaped scaffold. The target RNA is recognized by two stretches of repeats in a bipartite manner, and three central bases are unrecognized as a result of the degeneracy of repeats 6 and 7. Our data suggest that Nop9 regulates the folding of 18S rRNA at early assembly stages of 90S.
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Affiliation(s)
- Bing Wang
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing 100875, China.,National Institute of Biological Sciences, Beijing 102206, China.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Keqiong Ye
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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18
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Bach-Pages M, Castello A, Preston GM. Plant RNA Interactome Capture: Revealing the Plant RBPome. TRENDS IN PLANT SCIENCE 2017; 22:449-451. [PMID: 28478905 DOI: 10.1016/j.tplants.2017.04.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 04/07/2017] [Accepted: 04/07/2017] [Indexed: 06/07/2023]
Abstract
The application of RNA interactome capture to plants has enabled comprehensive determination of the plant RNA-binding proteome and the identification of novel families of RNA-binding proteins (RBPs). The technique is providing insight into the evolution of the eukaryotic repertoire of RBPs and will enhance prospects for engineering RBPs to improve crop traits.
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Affiliation(s)
- Marcel Bach-Pages
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Alfredo Castello
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Gail M Preston
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
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19
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Wei HH, Liu Y, Wang Y, Lu Q, Yang X, Li J, Wang Z. Engineering Artificial Factors to Specifically Manipulate Alternative Splicing in Human Cells. J Vis Exp 2017. [PMID: 28518098 DOI: 10.3791/54967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The processing of most eukaryotic RNAs is mediated by RNA Binding Proteins (RBPs) with modular configurations, including an RNA recognition module, which specifically binds the pre-mRNA target and an effector domain. Previously, we have taken advantage of the unique RNA binding mode of the PUF domain in human Pumilio 1 to generate a programmable RNA binding scaffold, which was used to engineer various artificial RBPs to manipulate RNA metabolism. Here, a detailed protocol is described to construct Engineered Splicing Factors (ESFs) that are specifically designed to modulate the alternative splicing of target genes. The protocol includes how to design and construct a customized PUF scaffold for a specific RNA target, how to construct an ESF expression plasmid by fusing a designer PUF domain and an effector domain, and how to use ESFs to manipulate the splicing of target genes. In the representative results of this method, we have also described the common assays of ESF activities using splicing reporters, the application of ESF in cultured human cells, and the subsequent effect of splicing changes. By following the detailed protocols in this report, it is possible to design and generate ESFs for the regulation of different types of Alternative Splicing (AS), providing a new strategy to study splicing regulation and the function of different splicing isoforms. Moreover, by fusing different functional domains with a designed PUF domain, researchers can engineer artificial factors that target specific RNAs to manipulate various steps of RNA processing.
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Affiliation(s)
- Huan-Huan Wei
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences (SIBS)
| | - Yuanlong Liu
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences (SIBS)
| | - Yang Wang
- Institute of Cancer Stem Cell, Second Affiliated Hospital, Cancer Center, Dalian Medical University
| | - Qianyun Lu
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences (SIBS)
| | - Xuerong Yang
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences (SIBS)
| | - Jiefu Li
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences (SIBS)
| | - Zefeng Wang
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences (SIBS);
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20
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Walia RR, El-Manzalawy Y, Honavar VG, Dobbs D. Sequence-Based Prediction of RNA-Binding Residues in Proteins. Methods Mol Biol 2017; 1484:205-235. [PMID: 27787829 PMCID: PMC5796408 DOI: 10.1007/978-1-4939-6406-2_15] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Identifying individual residues in the interfaces of protein-RNA complexes is important for understanding the molecular determinants of protein-RNA recognition and has many potential applications. Recent technical advances have led to several high-throughput experimental methods for identifying partners in protein-RNA complexes, but determining RNA-binding residues in proteins is still expensive and time-consuming. This chapter focuses on available computational methods for identifying which amino acids in an RNA-binding protein participate directly in contacting RNA. Step-by-step protocols for using three different web-based servers to predict RNA-binding residues are described. In addition, currently available web servers and software tools for predicting RNA-binding sites, as well as databases that contain valuable information about known protein-RNA complexes, RNA-binding motifs in proteins, and protein-binding recognition sites in RNA are provided. We emphasize sequence-based methods that can reliably identify interfacial residues without the requirement for structural information regarding either the RNA-binding protein or its RNA partner.
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Affiliation(s)
| | - Yasser El-Manzalawy
- College of Information Sciences and Technology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Vasant G Honavar
- College of Information Sciences and Technology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Drena Dobbs
- Genetics, Development and Cell Biology Department, Iowa State University, 3112 Molecular Biology Building, Ames, IA, 50011-3650, USA.
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21
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Melonek J, Stone JD, Small I. Evolutionary plasticity of restorer-of-fertility-like proteins in rice. Sci Rep 2016; 6:35152. [PMID: 27775031 PMCID: PMC5075784 DOI: 10.1038/srep35152] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 09/26/2016] [Indexed: 11/09/2022] Open
Abstract
Hybrid seed production in rice relies on cytoplasmic male sterility (CMS) induced by specific mitochondrial proteins, whose deleterious effects are suppressed by nuclear Restorer of Fertility (RF) genes. The majority of RF proteins belong to a specific clade of the RNA-binding pentatricopeptide repeat protein family. We have characterised 'restorer-of-fertility-like' (RFL) sequences from 13 Oryza genomes and the Brachypodium distachyon genome. The majority of the RFL sequences are found in genomic clusters located at two or three chromosomal loci with only a minor proportion being present as isolated genes. The RFL genomic cluster located on Oryza chromosome 10, the location of almost all known active rice RF genes, shows extreme variation in structure and gene content between species. We show evidence for homologous recombination events as an efficient mechanism for generating the huge repertoire of RNA sequence recognition motifs within RFL proteins and a major driver of RFL sequence evolution. The RFL sequences identified here will improve our understanding of the molecular basis of CMS and fertility restoration in plants and will accelerate the development of new breeding strategies.
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Affiliation(s)
- Joanna Melonek
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 6009 Crawley, Western Australia
| | - James D Stone
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 6009 Crawley, Western Australia.,Institute of Botany, Czech Academy of Sciences, Zámek 1, Průhonice, 25243 Czech Republic
| | - Ian Small
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 6009 Crawley, Western Australia
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22
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A splicing isoform of TEAD4 attenuates the Hippo-YAP signalling to inhibit tumour proliferation. Nat Commun 2016; 7:ncomms11840. [PMID: 27291620 PMCID: PMC4909989 DOI: 10.1038/ncomms11840] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 05/05/2016] [Indexed: 02/07/2023] Open
Abstract
Aberrant splicing is frequently found in cancer, yet the biological consequences of such alterations are mostly undefined. Here we report that the Hippo–YAP signalling, a key pathway that regulates cell proliferation and organ size, is under control of a splicing switch. We show that TEAD4, the transcription factor that mediates Hippo–YAP signalling, undergoes alternative splicing facilitated by the tumour suppressor RBM4, producing a truncated isoform, TEAD4-S, which lacks an N-terminal DNA-binding domain, but maintains YAP interaction domain. TEAD4-S is located in both the nucleus and cytoplasm, acting as a dominant negative isoform to YAP activity. Consistently, TEAD4-S is reduced in cancer cells, and its re-expression suppresses cancer cell proliferation and migration, inhibiting tumour growth in xenograft mouse models. Furthermore, TEAD4-S is reduced in human cancers, and patients with elevated TEAD4-S levels have improved survival. Altogether, these data reveal a splicing switch that serves to fine tune the Hippo–YAP pathway. The Hippo/Yap signalling pathway is found deregulated in several cancers. Here, the authors uncover an additional mechanism of YAP regulation that occurs via alternately spliced isoform of TEAD4, which acts as a dominant negative regulator of YAP-TEAD signalling.
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23
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De-coding and re-coding RNA recognition by PUF and PPR repeat proteins. Curr Opin Struct Biol 2016; 36:116-21. [PMID: 26874972 DOI: 10.1016/j.sbi.2016.01.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 01/14/2016] [Accepted: 01/15/2016] [Indexed: 11/22/2022]
Abstract
PUF and PPR proteins are two families of α-helical repeat proteins that recognize single-stranded RNA sequences. Both protein families hold promise as scaffolds for designed RNA-binding domains. A modular protein RNA recognition code was apparent from the first crystal structures of a PUF protein in complex with RNA, and recent studies continue to advance our understanding of natural PUF protein recognition (de-coding) and our ability to engineer specificity (re-coding). Degenerate recognition motifs make de-coding specificity of individual PPR proteins challenging. Nevertheless, re-coding PPR protein specificity using a consensus recognition code has been successful.
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24
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Wang Y, Wang Z. Design of RNA-Binding Proteins: Manipulate Alternative Splicing in Human Cells with Artificial Splicing Factors. Methods Mol Biol 2016; 1421:227-41. [PMID: 26965269 DOI: 10.1007/978-1-4939-3591-8_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The majority of human genes undergo alternative splicing to produce multiple isoforms with distinct functions. The dysregulations of alternative splicing have been found to be closely associated with various human diseases; thus new approaches to modulate disease-associated splicing events will provide great therapeutic potentials. Here we report protocols for constructing novel artificial splicing factors that can be designed to specifically modulate alternative splicing of target genes. By following the method outlined in this protocol, it is possible to design and generate artificial splicing factors with diverse activities in regulating different types of alternative splicing. The artificial splicing factors can be used to change splicing of either minigenes or endogenous genes in cultured human cells, providing a new strategy to study the regulation of alternative splicing and function of alternatively spliced products.
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Affiliation(s)
- Yang Wang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, China
| | - Zefeng Wang
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, CB # 7365, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA.
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