1
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Han S, Chen LL. Long non-coding RNAs in the nucleolus: Biogenesis, regulation, and function. Curr Opin Struct Biol 2024; 87:102866. [PMID: 38909586 DOI: 10.1016/j.sbi.2024.102866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 04/08/2024] [Accepted: 05/27/2024] [Indexed: 06/25/2024]
Abstract
The nucleolus functions as a multi-layered regulatory hub for ribosomal RNA (rRNA) biogenesis and ribosome assembly. Long noncoding RNAs (lncRNAs) in the nucleolus, originated from transcription by different RNA polymerases, have emerged as critical players in not only fine-tuning rRNA transcription and processing, but also shaping the organization of the multi-phase nucleolar condensate. Here, we review the diverse molecular mechanisms by which functional lncRNAs operate in the nucleolus, as well as their profound implications in a variety of biological processes. We also highlight the development of emerging molecular tools for characterizing and manipulating RNA function in living cells, and how application of such tools in the nucleolus might enable the discovery of additional insights and potential therapeutic strategies.
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Affiliation(s)
- Shuo Han
- Key Laboratory of RNA Innovation, Science and Engineering, 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.
| | - Ling-Ling Chen
- Key Laboratory of RNA Innovation, Science and Engineering, 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; New Cornerstone Science Laboratory, Shenzhen, China
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2
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Xiang JS, Schafer DM, Rothamel KL, Yeo GW. Decoding protein-RNA interactions using CLIP-based methodologies. Nat Rev Genet 2024:10.1038/s41576-024-00749-3. [PMID: 38982239 DOI: 10.1038/s41576-024-00749-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2024] [Indexed: 07/11/2024]
Abstract
Protein-RNA interactions are central to all RNA processing events, with pivotal roles in the regulation of gene expression and cellular functions. Dysregulation of these interactions has been increasingly linked to the pathogenesis of human diseases. High-throughput approaches to identify RNA-binding proteins and their binding sites on RNA - in particular, ultraviolet crosslinking followed by immunoprecipitation (CLIP) - have helped to map the RNA interactome, yielding transcriptome-wide protein-RNA atlases that have contributed to key mechanistic insights into gene expression and gene-regulatory networks. Here, we review these recent advances, explore the effects of cellular context on RNA binding, and discuss how these insights are shaping our understanding of cellular biology. We also review the potential therapeutic applications arising from new knowledge of protein-RNA interactions.
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Affiliation(s)
- Joy S Xiang
- Division of Biomedical Sciences, UC Riverside, Riverside, CA, USA
| | - Danielle M Schafer
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute and Stem Cell Program, UC San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, UC San Diego, La Jolla, CA, USA
| | - Katherine L Rothamel
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute and Stem Cell Program, UC San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, UC San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA.
- Sanford Stem Cell Institute and Stem Cell Program, UC San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, UC San Diego, La Jolla, CA, USA.
- Sanford Laboratories for Innovative Medicines, La Jolla, CA, USA.
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3
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Kageler L, Perr J, Flynn RA. Tools to investigate the cell surface: Proximity as a central concept in glycoRNA biology. Cell Chem Biol 2024; 31:1132-1144. [PMID: 38772372 PMCID: PMC11193615 DOI: 10.1016/j.chembiol.2024.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/02/2024] [Accepted: 04/25/2024] [Indexed: 05/23/2024]
Abstract
Proximity is a fundamental concept in chemistry and biology, referring to the convergence of molecules to facilitate new molecular interactions or reactions. Hybrid biopolymers like glycosylphosphatidylinositol (GPI)-anchored proteins, ubiquitinated proteins, glycosylated RNAs (glycoRNAs), and RNAylated proteins exemplify this by covalent bonding of moieties that are often orthogonally active. Hybrid molecules like glycoRNAs are localized to new physical spaces, generating new interfaces for biological functions. To fully investigate the compositional and spatial features of molecules like glycoRNAs, flexible genetic and chemical tools that encompass different encoding and targeting biopolymers are required. Here we discuss concepts of molecular proximity and explore newer proximity labeling technologies that facilitate applications in RNA biology, cell surface biology, and the interface therein with a particular focus on glycoRNA biology. We review the advantages and disadvantages of methods pertaining to cell surface RNA identification and provide insights into the vast opportunities for method development in this area.
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Affiliation(s)
- Lauren Kageler
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Jonathan Perr
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Ryan A Flynn
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
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4
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Davis JA, Chakrabarti K. Molecular and Evolutionary Analysis of RNA-Protein Interactions in Telomerase Regulation. Noncoding RNA 2024; 10:36. [PMID: 38921833 PMCID: PMC11206666 DOI: 10.3390/ncrna10030036] [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: 04/08/2024] [Revised: 05/30/2024] [Accepted: 06/10/2024] [Indexed: 06/27/2024] Open
Abstract
Telomerase is an enzyme involved in the maintenance of telomeres. Telomere shortening due to the end-replication problem is a threat to the genome integrity of all eukaryotes. Telomerase inside cells depends on a myriad of protein-protein and RNA-protein interactions to properly assemble and regulate the function of the telomerase holoenzyme. These interactions are well studied in model eukaryotes, like humans, yeast, and the ciliated protozoan known as Tetrahymena thermophila. Emerging evidence also suggests that deep-branching eukaryotes, such as the parasitic protist Trypanosoma brucei require conserved and novel RNA-binding proteins for the assembly and function of their telomerase. In this review, we will discuss telomerase regulatory pathways in the context of telomerase-interacting proteins, with special attention paid to RNA-binding proteins. We will discuss these interactors on an evolutionary scale, from parasitic protists to humans, to provide a broader perspective on the extensive role that protein-protein and RNA-protein interactions play in regulating telomerase activity in eukaryotes.
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Affiliation(s)
| | - Kausik Chakrabarti
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA;
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5
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Chamrád I, Simerský R, Lenobel R, Novák O. Exploring affinity chromatography in proteomics: A comprehensive review. Anal Chim Acta 2024; 1306:342513. [PMID: 38692783 DOI: 10.1016/j.aca.2024.342513] [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: 12/12/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 05/03/2024]
Abstract
Over the past decades, the proteomics field has undergone rapid growth. Progress in mass spectrometry and bioinformatics, together with separation methods, has brought many innovative approaches to the study of the molecular biology of the cell. The potential of affinity chromatography was recognized immediately after its first application in proteomics, and since that time, it has become one of the cornerstones of many proteomic protocols. Indeed, this chromatographic technique exploiting the specific binding between two molecules has been employed for numerous purposes, from selective removal of interfering (over)abundant proteins or enrichment of scarce biomarkers in complex biological samples to mapping the post-translational modifications and protein interactions with other proteins, nucleic acids or biologically active small molecules. This review presents a comprehensive survey of this versatile analytical tool in current proteomics. To navigate the reader, the haphazard space of affinity separations is classified according to the experiment's aims and the separated molecule's nature. Different types of available ligands and experimental strategies are discussed in further detail for each of the mentioned procedures.
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Affiliation(s)
- Ivo Chamrád
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic.
| | - Radim Simerský
- Department of Chemical Biology, Faculty of Science, Palacký University, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
| | - René Lenobel
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
| | - Ondřej Novák
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
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6
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Yang H, Patel DJ. Structures, mechanisms and applications of RNA-centric CRISPR-Cas13. Nat Chem Biol 2024; 20:673-688. [PMID: 38702571 DOI: 10.1038/s41589-024-01593-6] [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: 08/15/2023] [Accepted: 02/27/2024] [Indexed: 05/06/2024]
Abstract
Prokaryotes are equipped with a variety of resistance strategies to survive frequent viral attacks or invading mobile genetic elements. Among these, CRISPR-Cas surveillance systems are abundant and have been studied extensively. This Review focuses on CRISPR-Cas type VI Cas13 systems that use single-subunit RNA-guided Cas endonucleases for targeting and subsequent degradation of foreign RNA, thereby providing adaptive immunity. Notably, distinct from single-subunit DNA-cleaving Cas9 and Cas12 systems, Cas13 exhibits target RNA-activated substrate RNase activity. This Review outlines structural, biochemical and cell biological studies toward elucidation of the unique structural and mechanistic principles underlying surveillance effector complex formation, precursor CRISPR RNA (pre-crRNA) processing, self-discrimination and RNA degradation in Cas13 systems as well as insights into suppression by bacteriophage-encoded anti-CRISPR proteins and regulation by endogenous accessory proteins. Owing to its programmable ability for RNA recognition and cleavage, Cas13 provides powerful RNA targeting, editing, detection and imaging platforms with emerging biotechnological and therapeutic applications.
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Affiliation(s)
- Hui Yang
- Key Laboratory of RNA Innovation, Science and Engineering, 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, China.
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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7
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Bae J, Kim J, Choi J, Lee H, Koh M. Split Proteins and Reassembly Modules for Biological Applications. Chembiochem 2024; 25:e202400123. [PMID: 38530024 DOI: 10.1002/cbic.202400123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/24/2024] [Accepted: 03/26/2024] [Indexed: 03/27/2024]
Abstract
Split systems, modular entities enabling controlled biological processes, have become instrumental in biological research. This review highlights their utility across applications like gene regulation, protein interaction identification, and biosensor development. Covering significant progress over the last decade, it revisits traditional split proteins such as GFP, luciferase, and inteins, and explores advancements in technologies like Cas proteins and base editors. We also examine reassembly modules and their applications in diverse fields, from gene regulation to therapeutic innovation. This review offers a comprehensive perspective on the recent evolution of split systems in biological research.
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Affiliation(s)
- Jieun Bae
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea
| | - Jonghoon Kim
- Department of Chemistry and Integrative Institute of Basic Science, Soongsil University, Seoul, 06978, Republic of Korea
| | - Jongdoo Choi
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea
| | - Hwiyeong Lee
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea
| | - Minseob Koh
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea
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8
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Recinos Y, Ustianenko D, Yeh YT, Wang X, Jacko M, Yesantharao LV, Wu Q, Zhang C. CRISPR-dCas13d-based deep screening of proximal and distal splicing-regulatory elements. Nat Commun 2024; 15:3839. [PMID: 38714659 PMCID: PMC11076525 DOI: 10.1038/s41467-024-47140-8] [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: 06/21/2023] [Accepted: 03/16/2024] [Indexed: 05/10/2024] Open
Abstract
Pre-mRNA splicing, a key process in gene expression, can be therapeutically modulated using various drug modalities, including antisense oligonucleotides (ASOs). However, determining promising targets is hampered by the challenge of systematically mapping splicing-regulatory elements (SREs) in their native sequence context. Here, we use the catalytically inactive CRISPR-RfxCas13d RNA-targeting system (dCas13d/gRNA) as a programmable platform to bind SREs and modulate splicing by competing against endogenous splicing factors. SpliceRUSH, a high-throughput screening method, was developed to map SREs in any gene of interest using a lentivirus gRNA library that tiles the genetic region, including distal intronic sequences. When applied to SMN2, a therapeutic target for spinal muscular atrophy, SpliceRUSH robustly identifies not only known SREs but also a previously unknown distal intronic SRE, which can be targeted to alter exon 7 splicing using either dCas13d/gRNA or ASOs. This technology enables a deeper understanding of splicing regulation with applications for RNA-based drug discovery.
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Affiliation(s)
- Yocelyn Recinos
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Dmytro Ustianenko
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Flagship Pioneering, Cambridge, MA, 02142, USA
| | - Yow-Tyng Yeh
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Xiaojian Wang
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Martin Jacko
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Aperture Therapeutics, Inc., San Carlos, CA, 94070, USA
| | - Lekha V Yesantharao
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Qiyang Wu
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Chaolin Zhang
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.
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9
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Zhang Z, Zhang Y, Liu JL. eCRUIS captures RNA-protein interaction in vitro and in vivo. Exp Cell Res 2024; 438:114051. [PMID: 38631547 DOI: 10.1016/j.yexcr.2024.114051] [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: 01/10/2024] [Revised: 03/19/2024] [Accepted: 04/13/2024] [Indexed: 04/19/2024]
Abstract
As an information bridge between DNA and protein, RNA regulates cellular processes and gene expression in various ways. From its synthesis to degradation, RNA is associated with a range of RNA-binding proteins. Therefore, it is necessary to develop innovative methods to study the interaction between RNA and proteins. Previously, we developed an RNA-centric method, called CRISPR-based RNA-United Interacting System (CRUIS), to capture RNA-protein interaction in cells. On this basis, here we develop an enhanced CRUIS (eCRUIS) by combining the power of dCas13d and the engineered promiscuous ligase TurboID. The current version allows us to rapidly label RNA-binding proteins on the target RNA within 30 minutes, potentially for in vivo use. By introducing bait-assay with exogenous RNA, we confirm that eCRUIS can effectively label RNA-binding proteins on bait RNA in a short time. eCRUIS provides a broader range of in vitro and in vivo applications for studying RNA-protein interactions.
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Affiliation(s)
- Ziheng Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Yuanbing Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China; Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom; Shanghai Clinical Research and Trial Center, Shanghai, 201210, China.
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10
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Fan S, Zhang Y, Zhu S, Shen L. Plant RNA-binding proteins: Phase separation dynamics and functional mechanisms underlying plant development and stress responses. MOLECULAR PLANT 2024; 17:531-551. [PMID: 38419328 DOI: 10.1016/j.molp.2024.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/19/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024]
Abstract
RNA-binding proteins (RBPs) accompany RNA from synthesis to decay, mediating every aspect of RNA metabolism and impacting diverse cellular and developmental processes in eukaryotes. Many RBPs undergo phase separation along with their bound RNA to form and function in dynamic membraneless biomolecular condensates for spatiotemporal coordination or regulation of RNA metabolism. Increasing evidence suggests that phase-separating RBPs with RNA-binding domains and intrinsically disordered regions play important roles in plant development and stress adaptation. Here, we summarize the current knowledge about how dynamic partitioning of RBPs into condensates controls plant development and enables sensing of experimental changes to confer growth plasticity under stress conditions, with a focus on the dynamics and functional mechanisms of RBP-rich nuclear condensates and cytoplasmic granules in mediating RNA metabolism. We also discuss roles of multiple factors, such as environmental signals, protein modifications, and N6-methyladenosine RNA methylation, in modulating the phase separation behaviors of RBPs, and highlight the prospects and challenges for future research on phase-separating RBPs in crops.
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Affiliation(s)
- Sheng Fan
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Yu Zhang
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Shaobo Zhu
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Lisha Shen
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 1 Research Link, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore.
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11
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Eisenhut P, Marx N, Borsi G, Papež M, Ruggeri C, Baumann M, Borth N. Manipulating gene expression levels in mammalian cell factories: An outline of synthetic molecular toolboxes to achieve multiplexed control. N Biotechnol 2024; 79:1-19. [PMID: 38040288 DOI: 10.1016/j.nbt.2023.11.003] [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: 10/02/2023] [Revised: 11/06/2023] [Accepted: 11/26/2023] [Indexed: 12/03/2023]
Abstract
Mammalian cells have developed dedicated molecular mechanisms to tightly control expression levels of their genes where the specific transcriptomic signature across all genes eventually determines the cell's phenotype. Modulating cellular phenotypes is of major interest to study their role in disease or to reprogram cells for the manufacturing of recombinant products, such as biopharmaceuticals. Cells of mammalian origin, for example Chinese hamster ovary (CHO) and Human embryonic kidney 293 (HEK293) cells, are most commonly employed to produce therapeutic proteins. Early genetic engineering approaches to alter their phenotype have often been attempted by "uncontrolled" overexpression or knock-down/-out of specific genetic factors. Many studies in the past years, however, highlight that rationally regulating and fine-tuning the strength of overexpression or knock-down to an optimum level, can adjust phenotypic traits with much more precision than such "uncontrolled" approaches. To this end, synthetic biology tools have been generated that enable (fine-)tunable and/or inducible control of gene expression. In this review, we discuss various molecular tools used in mammalian cell lines and group them by their mode of action: transcriptional, post-transcriptional, translational and post-translational regulation. We discuss the advantages and disadvantages of using these tools for each cell regulatory layer and with respect to cell line engineering approaches. This review highlights the plethora of synthetic toolboxes that could be employed, alone or in combination, to optimize cellular systems and eventually gain enhanced control over the cellular phenotype to equip mammalian cell factories with the tools required for efficient production of emerging, more difficult-to-express biologics formats.
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Affiliation(s)
- Peter Eisenhut
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria
| | - Nicolas Marx
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria.
| | - Giulia Borsi
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Maja Papež
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria; BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Caterina Ruggeri
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Martina Baumann
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria
| | - Nicole Borth
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria; BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria.
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12
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Apostolopoulos A, Kawamoto N, Chow SYA, Tsuiji H, Ikeuchi Y, Shichino Y, Iwasaki S. dCas13-mediated translational repression for accurate gene silencing in mammalian cells. Nat Commun 2024; 15:2205. [PMID: 38467613 PMCID: PMC10928199 DOI: 10.1038/s41467-024-46412-7] [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: 05/19/2023] [Accepted: 02/27/2024] [Indexed: 03/13/2024] Open
Abstract
Current gene silencing tools based on RNA interference (RNAi) or, more recently, clustered regularly interspaced short palindromic repeats (CRISPR)‒Cas13 systems have critical drawbacks, such as off-target effects (RNAi) or collateral mRNA cleavage (CRISPR‒Cas13). Thus, a more specific method of gene knockdown is needed. Here, we develop CRISPRδ, an approach for translational silencing, harnessing catalytically inactive Cas13 proteins (dCas13). Owing to its tight association with mRNA, dCas13 serves as a physical roadblock for scanning ribosomes during translation initiation and does not affect mRNA stability. Guide RNAs covering the start codon lead to the highest efficacy regardless of the translation initiation mechanism: cap-dependent, internal ribosome entry site (IRES)-dependent, or repeat-associated non-AUG (RAN) translation. Strikingly, genome-wide ribosome profiling reveals the ultrahigh gene silencing specificity of CRISPRδ. Moreover, the fusion of a translational repressor to dCas13 further improves the performance. Our method provides a framework for translational repression-based gene silencing in eukaryotes.
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Grants
- JP20H05784 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP21H05278 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP21H05734 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP23H04268 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP20H05786 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP23H02415 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP20K07016 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP23K05648 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP21K15023 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP23KJ2175 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP20gm1410001 Japan Agency for Medical Research and Development (AMED)
- JP20gm1410001 Japan Agency for Medical Research and Development (AMED)
- JP23gm6910005h0001 Japan Agency for Medical Research and Development (AMED)
- JP23gm6910005 Japan Agency for Medical Research and Development (AMED)
- JP20gm1410001 Japan Agency for Medical Research and Development (AMED)
- Pioneering Projects MEXT | RIKEN
- Pioneering Projects MEXT | RIKEN
- Exploratory Research Center on Life and Living Systems (ExCELLS), 23EX601
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Affiliation(s)
- Antonios Apostolopoulos
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Naohiro Kawamoto
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Siu Yu A Chow
- Institute of Industrial Science, The University of Tokyo, Meguro-ku, Tokyo, 153-8505, Japan
| | - Hitomi Tsuiji
- Education and Research Division of Pharmacy, School of Pharmacy, Aichi Gakuin University, Nagoya, Aichi, 464-8650, Japan
| | - Yoshiho Ikeuchi
- Institute of Industrial Science, The University of Tokyo, Meguro-ku, Tokyo, 153-8505, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Institute for AI and Beyond, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yuichi Shichino
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan.
| | - Shintaro Iwasaki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan.
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan.
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13
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Dodel M, Guiducci G, Dermit M, Krishnamurthy S, Alard EL, Capraro F, Rekad Z, Stojic L, Mardakheh FK. TREX reveals proteins that bind to specific RNA regions in living cells. Nat Methods 2024; 21:423-434. [PMID: 38374261 PMCID: PMC10927567 DOI: 10.1038/s41592-024-02181-1] [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: 08/21/2023] [Accepted: 01/16/2024] [Indexed: 02/21/2024]
Abstract
Different regions of RNA molecules can often engage in specific interactions with distinct RNA-binding proteins (RBPs), giving rise to diverse modalities of RNA regulation and function. However, there are currently no methods for unbiased identification of RBPs that interact with specific RNA regions in living cells and under endogenous settings. Here we introduce TREX (targeted RNase H-mediated extraction of crosslinked RBPs)-a highly sensitive approach for identifying proteins that directly bind to specific RNA regions in living cells. We demonstrate that TREX outperforms existing methods in identifying known interactors of U1 snRNA, and reveals endogenous region-specific interactors of NORAD long noncoding RNA. Using TREX, we generated a comprehensive region-by-region interactome for 45S rRNA, uncovering both established and previously unknown interactions that regulate ribosome biogenesis. With its applicability to different cell types, TREX is an RNA-centric tool for unbiased positional mapping of endogenous RNA-protein interactions in living cells.
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Affiliation(s)
- Martin Dodel
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Giulia Guiducci
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Maria Dermit
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Sneha Krishnamurthy
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Emilie L Alard
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Federica Capraro
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Zeinab Rekad
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Lovorka Stojic
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK.
| | - Faraz K Mardakheh
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK.
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14
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Milione RR, Schell BB, Douglas CJ, Seath CP. Creative approaches using proximity labeling to gain new biological insights. Trends Biochem Sci 2024; 49:224-235. [PMID: 38160064 PMCID: PMC10939868 DOI: 10.1016/j.tibs.2023.12.005] [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: 09/19/2023] [Revised: 12/04/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024]
Abstract
At its most fundamental level, life is a collection of synchronized cellular processes driven by interactions among biomolecules. Proximity labeling has emerged as a powerful technique to capture these interactions in native settings, revealing previously unexplored elements of biology. This review highlights recent developments in proximity labeling, focusing on methods that push the fundamental technologies beyond the classic bait-prey paradigm, such as RNA-protein interactions, ligand/small-molecule-protein interactions, cell surface protein interactions, and subcellular protein trafficking. The advancement of proximity labeling methods to address different biological problems will accelerate our understanding of the complex biological systems that make up life.
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Affiliation(s)
- Ryan R Milione
- Skaggs Graduate School of Chemical and Biological Sciences, 120 Scripps Way, Jupiter, FL 33458, USA; Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 120 Scripps Way, Jupiter, FL 33458, USA
| | - Bin-Bin Schell
- Skaggs Graduate School of Chemical and Biological Sciences, 120 Scripps Way, Jupiter, FL 33458, USA; Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 120 Scripps Way, Jupiter, FL 33458, USA
| | - Cameron J Douglas
- Skaggs Graduate School of Chemical and Biological Sciences, 120 Scripps Way, Jupiter, FL 33458, USA; Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 120 Scripps Way, Jupiter, FL 33458, USA
| | - Ciaran P Seath
- Skaggs Graduate School of Chemical and Biological Sciences, 120 Scripps Way, Jupiter, FL 33458, USA; Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 120 Scripps Way, Jupiter, FL 33458, USA.
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15
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Montagud‐Martínez R, Márquez‐Costa R, Heras‐Hernández M, Dolcemascolo R, Rodrigo G. On the ever-growing functional versatility of the CRISPR-Cas13 system. Microb Biotechnol 2024; 17:e14418. [PMID: 38381083 PMCID: PMC10880580 DOI: 10.1111/1751-7915.14418] [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: 05/11/2023] [Revised: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 02/22/2024] Open
Abstract
CRISPR-Cas systems evolved in prokaryotes to implement a powerful antiviral immune response as a result of sequence-specific targeting by ribonucleoproteins. One of such systems consists of an RNA-guided RNA endonuclease, known as CRISPR-Cas13. In very recent years, this system is being repurposed in different ways in order to decipher and engineer gene expression programmes. Here, we discuss the functional versatility of the CRISPR-Cas13 system, which includes the ability for RNA silencing, RNA editing, RNA tracking, nucleic acid detection and translation regulation. This functional palette makes the CRISPR-Cas13 system a relevant tool in the broad field of systems and synthetic biology.
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Affiliation(s)
- Roser Montagud‐Martínez
- Institute for Integrative Systems Biology (I2SysBio)CSIC – University of ValenciaPaternaSpain
| | - Rosa Márquez‐Costa
- Institute for Integrative Systems Biology (I2SysBio)CSIC – University of ValenciaPaternaSpain
| | - María Heras‐Hernández
- Institute for Integrative Systems Biology (I2SysBio)CSIC – University of ValenciaPaternaSpain
| | - Roswitha Dolcemascolo
- Institute for Integrative Systems Biology (I2SysBio)CSIC – University of ValenciaPaternaSpain
| | - Guillermo Rodrigo
- Institute for Integrative Systems Biology (I2SysBio)CSIC – University of ValenciaPaternaSpain
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16
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Shi P, Wu X. Programmable RNA targeting with CRISPR-Cas13. RNA Biol 2024; 21:1-9. [PMID: 38764173 PMCID: PMC11110701 DOI: 10.1080/15476286.2024.2351657] [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] [Accepted: 05/01/2024] [Indexed: 05/21/2024] Open
Abstract
The RNA-targeting CRISPR-Cas13 system has enabled precise engineering of endogenous RNAs, significantly advancing our understanding of RNA regulation and the development of RNA-based diagnostic and therapeutic applications. This review aims to provide a summary of Cas13-based RNA targeting tools and applications, discuss limitations and challenges of existing tools and suggest potential directions for further development of the RNA targeting system.
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Affiliation(s)
- Peiguo Shi
- Department of Medicine and Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Xuebing Wu
- Department of Medicine and Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
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17
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Wei J, Lotfy P, Faizi K, Baungaard S, Gibson E, Wang E, Slabodkin H, Kinnaman E, Chandrasekaran S, Kitano H, Durrant MG, Duffy CV, Pawluk A, Hsu PD, Konermann S. Deep learning and CRISPR-Cas13d ortholog discovery for optimized RNA targeting. Cell Syst 2023; 14:1087-1102.e13. [PMID: 38091991 DOI: 10.1016/j.cels.2023.11.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 05/03/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023]
Abstract
Effective and precise mammalian transcriptome engineering technologies are needed to accelerate biological discovery and RNA therapeutics. Despite the promise of programmable CRISPR-Cas13 ribonucleases, their utility has been hampered by an incomplete understanding of guide RNA design rules and cellular toxicity resulting from off-target or collateral RNA cleavage. Here, we quantified the performance of over 127,000 RfxCas13d (CasRx) guide RNAs and systematically evaluated seven machine learning models to build a guide efficiency prediction algorithm orthogonally validated across multiple human cell types. Deep learning model interpretation revealed preferred sequence motifs and secondary features for highly efficient guides. We next identified and screened 46 novel Cas13d orthologs, finding that DjCas13d achieves low cellular toxicity and high specificity-even when targeting abundant transcripts in sensitive cell types, including stem cells and neurons. Our Cas13d guide efficiency model was successfully generalized to DjCas13d, illustrating the power of combining machine learning with ortholog discovery to advance RNA targeting in human cells.
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Affiliation(s)
- Jingyi Wei
- Department of Bioengineering, Stanford University, Stanford, CA, USA; Department of Biochemistry, Stanford University, Stanford, CA, USA; Arc Institute, Palo Alto, CA, USA
| | - Peter Lotfy
- Laboratory of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Kian Faizi
- Laboratory of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | | | - Eleanor Wang
- Laboratory of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA, USA; Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Hannah Slabodkin
- Department of Biochemistry, Stanford University, Stanford, CA, USA; Arc Institute, Palo Alto, CA, USA
| | - Emily Kinnaman
- Department of Biochemistry, Stanford University, Stanford, CA, USA; Arc Institute, Palo Alto, CA, USA
| | - Sita Chandrasekaran
- Arc Institute, Palo Alto, CA, USA; Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Hugo Kitano
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Matthew G Durrant
- Arc Institute, Palo Alto, CA, USA; Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Connor V Duffy
- Arc Institute, Palo Alto, CA, USA; Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Patrick D Hsu
- Arc Institute, Palo Alto, CA, USA; Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
| | - Silvana Konermann
- Department of Biochemistry, Stanford University, Stanford, CA, USA; Arc Institute, Palo Alto, CA, USA.
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18
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Yin P, Ge M, Xie S, Zhang L, Kuang S, Nie Z. A universal orthogonal imaging platform for living-cell RNA detection using fluorogenic RNA aptamers. Chem Sci 2023; 14:14131-14139. [PMID: 38098702 PMCID: PMC10717586 DOI: 10.1039/d3sc04957d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023] Open
Abstract
MicroRNAs (miRNAs) are crucial regulators of gene expression at the post-transcriptional level, offering valuable insights into disease mechanisms and prospects for targeted therapeutic interventions. Herein, we present a class of miRNA-induced light-up RNA sensors (miLS) that are founded on the toehold mediated principle and employ the fluorogenic RNA aptamers Pepper and Squash as imaging modules. By incorporating a sensor switch to disrupt the stabilizing stem of these aptamers, our design offers enhanced flexibility and convertibility for different target miRNAs and aptamers. These sensors detect multiple miRNA targets (miR-21 and miR-122) with detection limits of 0.48 and 0.2 nM, respectively, while achieving a robust signal-to-noise ratio of up to 44 times. Capitalizing on the distinct fluorescence imaging channels afforded by Pepper-HBC620 (red) and Squash-DFHBI-1T (green), we establish an orthogonal miRNA activation imaging platform, enabling the simultaneous visualization of different intracellular miRNAs in living cells. Our dual-color orthogonal miLS imaging platform provides a powerful tool for sequence-specific miRNA imaging in different cells, opening up new avenues for studying the intricate functions of RNA in living cells.
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Affiliation(s)
- Peng Yin
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University Changsha 410082 China
| | - Mingmin Ge
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University Changsha 410082 China
| | - Shiyi Xie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University Changsha 410082 China
| | - Li Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University Changsha 410082 China
| | - Shi Kuang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University Changsha 410082 China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University Changsha 410082 China
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19
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Blank HM, Griffith WP, Polymenis M. Targeting APEX2 to the mRNA encoding fatty acid synthase β in yeast identifies interacting proteins that control its abundance in the cell cycle. Mol Biol Cell 2023; 34:br20. [PMID: 37792491 PMCID: PMC10848943 DOI: 10.1091/mbc.e23-05-0166] [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: 05/12/2023] [Revised: 09/25/2023] [Accepted: 09/29/2023] [Indexed: 10/06/2023] Open
Abstract
Profiling the repertoire of proteins associated with a given mRNA during the cell cycle is unstudied. Furthermore, it is easier to ask and answer what mRNAs a specific protein might bind to than the other way around. Here, we implemented an RNA-centric proximity labeling technology at different points in the cell cycle in highly synchronous yeast cultures. To understand how the abundance of FAS1, encoding fatty acid synthase, peaks late in the cell cycle, we identified proteins that interact with the FAS1 transcript in a cell cycle-dependent manner. We used dCas13d-APEX2 fusions to target FAS1 and label nearby proteins, which were then identified by mass spectrometry. The glycolytic enzyme Tdh3p, a known RNA-binding protein, interacted with the FAS1 mRNA, and it was necessary for the periodic abundance of Fas1p in the cell cycle. These results point to unexpected connections between major metabolic pathways. They also underscore the role of mRNA-protein interactions for gene expression during cell division.
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Affiliation(s)
- Heidi M. Blank
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
| | - Wendell P. Griffith
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, TX 78249
| | - Michael Polymenis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
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20
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Wang B, Yang H. Progress of CRISPR-based programmable RNA manipulation and detection. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1804. [PMID: 37282821 DOI: 10.1002/wrna.1804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 05/09/2023] [Accepted: 05/12/2023] [Indexed: 06/08/2023]
Abstract
Prokaryotic clustered regularly interspaced short palindromic repeats and CRISPR associated (CRISPR-Cas) systems provide adaptive immunity by using RNA-guided endonucleases to recognize and eliminate invading foreign nucleic acids. Type II Cas9, type V Cas12, type VI Cas13, and type III Csm/Cmr complexes have been well characterized and developed as programmable platforms for selectively targeting and manipulating RNA molecules of interest in prokaryotic and eukaryotic cells. These Cas effectors exhibit remarkable diversity of ribonucleoprotein (RNP) composition, target recognition and cleavage mechanisms, and self discrimination mechanisms, which are leveraged for various RNA targeting applications. Here, we summarize the current understanding of mechanistic and functional characteristics of these Cas effectors, give an overview on RNA detection and manipulation toolbox established so far including knockdown, editing, imaging, modification, and mapping RNA-protein interactions, and discuss the future directions for CRISPR-based RNA targeting tools. This article is categorized under: RNA Methods > RNA Analyses in Cells RNA Processing > RNA Editing and Modification RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Beibei Wang
- State Key Laboratory of Molecular Biology, 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, China
| | - Hui Yang
- State Key Laboratory of Molecular Biology, 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, China
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21
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Guo J, Guo S, Lu S, Gong J, Wang L, Ding L, Chen Q, Liu W. The development of proximity labeling technology and its applications in mammals, plants, and microorganisms. Cell Commun Signal 2023; 21:269. [PMID: 37777761 PMCID: PMC10544124 DOI: 10.1186/s12964-023-01310-1] [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: 07/31/2023] [Accepted: 09/07/2023] [Indexed: 10/02/2023] Open
Abstract
Protein‒protein, protein‒RNA, and protein‒DNA interaction networks form the basis of cellular regulation and signal transduction, making it crucial to explore these interaction networks to understand complex biological processes. Traditional methods such as affinity purification and yeast two-hybrid assays have been shown to have limitations, as they can only isolate high-affinity molecular interactions under nonphysiological conditions or in vitro. Moreover, these methods have shortcomings for organelle isolation and protein subcellular localization. To address these issues, proximity labeling techniques have been developed. This technology not only overcomes the limitations of traditional methods but also offers unique advantages in studying protein spatial characteristics and molecular interactions within living cells. Currently, this technique not only is indispensable in research on mammalian nucleoprotein interactions but also provides a reliable approach for studying nonmammalian cells, such as plants, parasites and viruses. Given these advantages, this article provides a detailed introduction to the principles of proximity labeling techniques and the development of labeling enzymes. The focus is on summarizing the recent applications of TurboID and miniTurbo in mammals, plants, and microorganisms. Video Abstract.
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Affiliation(s)
- Jieyu Guo
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Shuang Guo
- Medicine Research Institute, Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Siao Lu
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Jun Gong
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Long Wang
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Liqiong Ding
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Qingjie Chen
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China.
| | - Wu Liu
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China.
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22
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Huang S, Dai R, Zhang Z, Zhang H, Zhang M, Li Z, Zhao K, Xiong W, Cheng S, Wang B, Wan Y. CRISPR/Cas-Based Techniques for Live-Cell Imaging and Bioanalysis. Int J Mol Sci 2023; 24:13447. [PMID: 37686249 PMCID: PMC10487896 DOI: 10.3390/ijms241713447] [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: 07/21/2023] [Revised: 08/09/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
CRISPR/Cas systems have found widespread applications in gene editing due to their high accuracy, high programmability, ease of use, and affordability. Benefiting from the cleavage properties (trans- or cis-) of Cas enzymes, the scope of CRISPR/Cas systems has expanded beyond gene editing and they have been utilized in various fields, particularly in live-cell imaging and bioanalysis. In this review, we summarize some fundamental working mechanisms and concepts of the CRISPR/Cas systems, describe the recent advances and design principles of CRISPR/Cas mediated techniques employed in live-cell imaging and bioanalysis, highlight the main applications in the imaging and biosensing of a wide range of molecular targets, and discuss the challenges and prospects of CRISPR/Cas systems in live-cell imaging and biosensing. By illustrating the imaging and bio-sensing processes, we hope this review will guide the best use of the CRISPR/Cas in imaging and quantifying biological and clinical elements and inspire new ideas for better tool design in live-cell imaging and bioanalysis.
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Affiliation(s)
- Shuo Huang
- College of Life Sciences, Hainan University, Haikou 570228, China; (S.H.); (Z.Z.); (H.Z.); (M.Z.); (Z.L.); (K.Z.); (W.X.)
| | - Rui Dai
- Institute of Oceanography, Hainan University, Haikou 570228, China;
| | - Zhiqi Zhang
- College of Life Sciences, Hainan University, Haikou 570228, China; (S.H.); (Z.Z.); (H.Z.); (M.Z.); (Z.L.); (K.Z.); (W.X.)
| | - Han Zhang
- College of Life Sciences, Hainan University, Haikou 570228, China; (S.H.); (Z.Z.); (H.Z.); (M.Z.); (Z.L.); (K.Z.); (W.X.)
| | - Meng Zhang
- College of Life Sciences, Hainan University, Haikou 570228, China; (S.H.); (Z.Z.); (H.Z.); (M.Z.); (Z.L.); (K.Z.); (W.X.)
| | - Zhangjun Li
- College of Life Sciences, Hainan University, Haikou 570228, China; (S.H.); (Z.Z.); (H.Z.); (M.Z.); (Z.L.); (K.Z.); (W.X.)
| | - Kangrui Zhao
- College of Life Sciences, Hainan University, Haikou 570228, China; (S.H.); (Z.Z.); (H.Z.); (M.Z.); (Z.L.); (K.Z.); (W.X.)
| | - Wenjun Xiong
- College of Life Sciences, Hainan University, Haikou 570228, China; (S.H.); (Z.Z.); (H.Z.); (M.Z.); (Z.L.); (K.Z.); (W.X.)
| | - Siyu Cheng
- College of Art and Design, Hainan University, Haikou 570228, China;
| | - Buhua Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
| | - Yi Wan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
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23
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Recinos Y, Ustianenko D, Yeh YT, Wang X, Jacko M, Yesantharao LV, Wu Q, Zhang C. Deep screening of proximal and distal splicing-regulatory elements in a native sequence context. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.21.554109. [PMID: 37662340 PMCID: PMC10473672 DOI: 10.1101/2023.08.21.554109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Pre-mRNA splicing, a key process in gene expression, can be therapeutically modulated using various drug modalities, including antisense oligonucleotides (ASOs). However, determining promising targets is impeded by the challenge of systematically mapping splicing-regulatory elements (SREs) in their native sequence context. Here, we use the catalytically dead CRISPR-RfxCas13d RNA-targeting system (dCas13d/gRNA) as a programmable platform to bind SREs and modulate splicing by competing against endogenous splicing factors. SpliceRUSH, a high-throughput screening method, was developed to map SREs in any gene of interest using a lentivirus gRNA library that tiles the genetic region, including distal intronic sequences. When applied to SMN2, a therapeutic target for spinal muscular atrophy, SpliceRUSH robustly identified not only known SREs, but also a novel distal intronic splicing enhancer, which can be targeted to alter exon 7 splicing using either dCas13d/gRNA or ASOs. This technology enables a deeper understanding of splicing regulation with applications for RNA-based drug discovery.
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Affiliation(s)
- Yocelyn Recinos
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | - Dmytro Ustianenko
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
- Present address: Flagship Pioneering, Cambridge, MA 02142, USA
| | - Yow-Tyng Yeh
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | - Xiaojian Wang
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | - Martin Jacko
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
- Present address: Aperture Therapeutics, Inc., San Carlos, CA 94070, USA
| | - Lekha V. Yesantharao
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
- Present address: Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Qiyang Wu
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | - Chaolin Zhang
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
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24
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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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Liu Z, Jillette N, Robson P, Cheng AW. Simultaneous multifunctional transcriptome engineering by CRISPR RNA scaffold. Nucleic Acids Res 2023; 51:e77. [PMID: 37395412 PMCID: PMC10415119 DOI: 10.1093/nar/gkad547] [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: 06/23/2022] [Revised: 06/06/2023] [Accepted: 06/15/2023] [Indexed: 07/04/2023] Open
Abstract
RNA processing and metabolism are subjected to precise regulation in the cell to ensure integrity and functions of RNA. Though targeted RNA engineering has become feasible with the discovery and engineering of the CRISPR-Cas13 system, simultaneous modulation of different RNA processing steps remains unavailable. In addition, off-target events resulting from effectors fused with dCas13 limit its application. Here we developed a novel platform, Combinatorial RNA Engineering via Scaffold Tagged gRNA (CREST), which can simultaneously execute multiple RNA modulation functions on different RNA targets. In CREST, RNA scaffolds are appended to the 3' end of Cas13 gRNA and their cognate RNA binding proteins are fused with enzymatic domains for manipulation. Taking RNA alternative splicing, A-to-G and C-to-U base editing as examples, we developed bifunctional and tri-functional CREST systems for simultaneously RNA manipulation. Furthermore, by fusing two split fragments of the deaminase domain of ADAR2 to dCas13 and/or PUFc respectively, we reconstituted its enzyme activity at target sites. This split design can reduce nearly 99% of off-target events otherwise induced by a full-length effector. The flexibility of the CREST framework will enrich the transcriptome engineering toolbox for the study of RNA biology.
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Affiliation(s)
- Zukai Liu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06030, USA
| | | | - Paul Robson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06030, USA
- The Jackson Laboratory Cancer Center, Bar Harbor, ME 04609, USA
- Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Albert Wu Cheng
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06030, USA
- The Jackson Laboratory Cancer Center, Bar Harbor, ME 04609, USA
- Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT 06030, USA
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85281, USA
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Yi M, Wang M, Xu Y, Cao Z, Ling Y, Zhang Z, Cao H. CRISPR-based m 6A modification and its potential applications in telomerase regulation. Front Cell Dev Biol 2023; 11:1200734. [PMID: 37519297 PMCID: PMC10382234 DOI: 10.3389/fcell.2023.1200734] [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: 04/05/2023] [Accepted: 06/27/2023] [Indexed: 08/01/2023] Open
Abstract
Telomerase determines cell lifespan by controlling chromosome stability and cell viability, m6A epigenetic modification plays an important role in the regulation of telomerase activity. Using CRISPR epigenome editing to analyze specific m6A modification sites in telomerase will provide an important tool for analyzing the molecular mechanism of m6A modification regulating telomerase activity. In this review, we clarified the relevant applications of CRISPR system, paid special attention to the regulation of m6A modification in stem cells and cancer cells based on CRISPR system, emphasized the regulation of m6A modification on telomerase activity, pointed out that m6A modification sites regulate telomerase activity, and discussed strategies based on telomerase activity and disease treatment, which are helpful to promote the research of anti-aging and tumor related diseases.
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Affiliation(s)
- Mingliang Yi
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, China
| | - Mingyue Wang
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, China
| | - Yongjie Xu
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, China
| | - Zhikun Cao
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, China
| | - Yinghui Ling
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, China
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Zijun Zhang
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, China
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Hongguo Cao
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, China
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
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27
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Gao P, Yao F, Pang J, Yin K, Zhu X. m 6A methylation in cellular senescence of age-associated diseases. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1168-1183. [PMID: 37394885 PMCID: PMC10449638 DOI: 10.3724/abbs.2023107] [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: 01/27/2023] [Accepted: 04/14/2023] [Indexed: 07/04/2023] Open
Abstract
Cellular senescence is a state of irreversible cellular growth arrest that occurs in response to various stresses. In addition to exiting the cell cycle, senescent cells undergo many phenotypic alterations, including metabolic reprogramming, chromatin rearrangement, and senescence-associated secretory phenotype (SASP) development. Furthermore, senescent cells can affect most physiological and pathological processes, such as physiological development; tissue homeostasis; tumour regression; and age-associated disease progression, including diabetes, atherosclerosis, Alzheimer's disease, and hypertension. Although corresponding anti-senescence therapies are actively being explored for the treatment of age-associated diseases, the specific regulatory mechanisms of senescence remain unclear. N 6-methyladenosine (m 6A), a chemical modification commonly distributed in eukaryotic RNA, plays an important role in biological processes such as translation, shearing, and RNA transcription. Numerous studies have shown that m 6A plays an important regulatory role in cellular senescence and aging-related disease. In this review, we systematically summarize the role of m 6A modifications in cellular senescence with regard to oxidative stress, DNA damage, telomere alterations, and SASP development. Additionally, diabetes, atherosclerosis, and Alzheimer's disease regulation via m 6A-mediated cellular senescence is discussed. We further discuss the challenges and prospects of m 6A in cellular senescence and age-associated diseases with the aim of providing rational strategies for the treatment of these age-associated diseases.
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Affiliation(s)
- Pan Gao
- Guangxi Key Laboratory of Diabetic Systems MedicineGuilin Medical UniversityGuilin541100China
| | - Feng Yao
- Guangxi Key Laboratory of Diabetic Systems MedicineGuilin Medical UniversityGuilin541100China
| | - Jin Pang
- Guangxi Key Laboratory of Diabetic Systems MedicineGuilin Medical UniversityGuilin541100China
| | - Kai Yin
- The Fifth Affiliated Hospital of Southern Medical UniversityGuangzhou510900China
| | - Xiao Zhu
- Guangxi Key Laboratory of Diabetic Systems MedicineGuilin Medical UniversityGuilin541100China
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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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Becker JT, Auerbach AA, Harris RS. APEX3 - an optimized tool for rapid and unbiased proximity labeling. J Mol Biol 2023; 435:168145. [PMID: 37182813 DOI: 10.1016/j.jmb.2023.168145] [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: 02/15/2023] [Revised: 05/03/2023] [Accepted: 05/09/2023] [Indexed: 05/16/2023]
Abstract
Macromolecular interactions regulate all aspects of biology. The identification of interacting partners and complexes is important for understanding cellular processes, host-pathogen conflicts, and organismal development. Multiple methods exist to label and enrich interacting proteins in living cells. Notably, the soybean ascorbate peroxidase, APEX2, rapidly biotinylates adjacent biomolecules in the presence of biotin-phenol and hydrogen peroxide. However, during initial experiments with this system, we found that APEX2 exhibits a cytoplasmic-biased localization and is sensitive to the nuclear export inhibitor leptomycin B (LMB). This led us to identify a putative nuclear export signal (NES) at the carboxy-terminus of APEX2 (NESAPEX2), structurally adjacent to the conserved heme binding site. This putative NES is functional as evidenced by cytoplasmic localization and LMB sensitivity of a mCherry-NESAPEX2 chimeric construct. Single amino acid substitutions of multiple hydrophobic residues within NESAPEX2 eliminate cytoplasm-biased localization of both mCherry-NESAPEX2 as well as full-length APEX2. However, all but one of these NES substitutions also compromises peroxide-dependent labeling. This unique separation-of-function mutant, APEX2-L242A, is termed APEX3. Localization and functionality of APEX3 are confirmed by fusion to the nucleocytoplasmic shuttling transcriptional factor, RELA. APEX3 is therefore an optimized tool for unbiased proximity labeling of cellular proteins and interacting factors.
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Affiliation(s)
- Jordan T Becker
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN, USA 55455; Department of Microbiology and Immunology, University of Minnesota Twin Cities, Minneapolis, MN, USA 55455; Institute for Molecular Virology, University of Minnesota Twin Cities, Minneapolis, MN, USA 55455.
| | - Ashley A Auerbach
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA 78229
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN, USA 55455; Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA 78229; Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX, USA 78229.
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30
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Zhang F, Neik TX, Thomas WJW, Batley J. CRISPR-Based Genome Editing Tools: An Accelerator in Crop Breeding for a Changing Future. Int J Mol Sci 2023; 24:ijms24108623. [PMID: 37239967 DOI: 10.3390/ijms24108623] [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: 02/03/2023] [Revised: 05/03/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
Genome editing is an important strategy to maintain global food security and achieve sustainable agricultural development. Among all genome editing tools, CRISPR-Cas is currently the most prevalent and offers the most promise. In this review, we summarize the development of CRISPR-Cas systems, outline their classification and distinctive features, delineate their natural mechanisms in plant genome editing and exemplify the applications in plant research. Both classical and recently discovered CRISPR-Cas systems are included, detailing the class, type, structures and functions of each. We conclude by highlighting the challenges that come with CRISPR-Cas and offer suggestions on how to tackle them. We believe the gene editing toolbox will be greatly enriched, providing new avenues for a more efficient and precise breeding of climate-resilient crops.
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Affiliation(s)
- Fangning Zhang
- College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Ting Xiang Neik
- School of Biosciences, University of Nottingham Malaysia, Semenyih 43500, Malaysia
| | - William J W Thomas
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - Jacqueline Batley
- School of Biological Sciences, Institute of Agriculture, University of Western Australia, Perth, WA 6009, Australia
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31
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Gunitseva N, Evteeva M, Borisova A, Patrushev M, Subach F. RNA-Dependent RNA Targeting by CRISPR-Cas Systems: Characterizations and Applications. Int J Mol Sci 2023; 24:ijms24086894. [PMID: 37108063 PMCID: PMC10138764 DOI: 10.3390/ijms24086894] [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: 03/06/2023] [Revised: 04/01/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
Genome editing technologies that are currently available and described have a fundamental impact on the development of molecular biology and medicine, industrial and agricultural biotechnology and other fields. However, genome editing based on detection and manipulation of the targeted RNA is a promising alternative to control the gene expression at the spatiotemporal transcriptomic level without complete elimination. The innovative CRISPR-Cas RNA-targeting systems changed the conception of biosensing systems and also allowed the RNA effectors to be used in various applications; for example, genomic editing, effective virus diagnostic tools, biomarkers, transcription regulations. In this review, we discussed the current state-of-the-art of specific CRISPR-Cas systems known to bind and cleave RNA substrates and summarized potential applications of the versatile RNA-targeting systems.
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Affiliation(s)
- Natalia Gunitseva
- Complex of NBICS Technologies, National Research Center "Kurchatov Institute", 123182 Moscow, Russia
| | - Marta Evteeva
- Complex of NBICS Technologies, National Research Center "Kurchatov Institute", 123182 Moscow, Russia
| | - Anna Borisova
- Complex of NBICS Technologies, National Research Center "Kurchatov Institute", 123182 Moscow, Russia
| | - Maxim Patrushev
- Complex of NBICS Technologies, National Research Center "Kurchatov Institute", 123182 Moscow, Russia
| | - Fedor Subach
- Complex of NBICS Technologies, National Research Center "Kurchatov Institute", 123182 Moscow, Russia
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Davis JA, Reyes AV, Nitika, Saha A, Wolfgeher DJ, Xu SL, Truman AW, Li B, Chakrabarti K. Proteomic analysis defines the interactome of telomerase in the protozoan parasite, Trypanosoma brucei. Front Cell Dev Biol 2023; 11:1110423. [PMID: 37009488 PMCID: PMC10061497 DOI: 10.3389/fcell.2023.1110423] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/03/2023] [Indexed: 03/17/2023] Open
Abstract
Telomerase is a ribonucleoprotein enzyme responsible for maintaining the telomeric end of the chromosome. The telomerase enzyme requires two main components to function: the telomerase reverse transcriptase (TERT) and the telomerase RNA (TR), which provides the template for telomeric DNA synthesis. TR is a long non-coding RNA, which forms the basis of a large structural scaffold upon which many accessory proteins can bind and form the complete telomerase holoenzyme. These accessory protein interactions are required for telomerase activity and regulation inside cells. The interacting partners of TERT have been well studied in yeast, human, and Tetrahymena models, but not in parasitic protozoa, including clinically relevant human parasites. Here, using the protozoan parasite, Trypanosoma brucei (T. brucei) as a model, we have identified the interactome of T. brucei TERT (TbTERT) using a mass spectrometry-based approach. We identified previously known and unknown interacting factors of TbTERT, highlighting unique features of T. brucei telomerase biology. These unique interactions with TbTERT, suggest mechanistic differences in telomere maintenance between T. brucei and other eukaryotes.
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Affiliation(s)
- Justin A. Davis
- Department of Biological Sciences, University of North Carolina, Charlotte, NC, United States
| | - Andres V. Reyes
- Department of Plant Biology and Carnegie Mass Spectrometry Facility, Carnegie Institution for Science, Stanford, CA, United States
| | - Nitika
- Department of Biological Sciences, University of North Carolina, Charlotte, NC, United States
| | - Arpita Saha
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Arts and Sciences, Cleveland State University, Cleveland, OH, United States
| | - Donald J. Wolfgeher
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, United States
| | - Shou-Ling Xu
- Department of Plant Biology and Carnegie Mass Spectrometry Facility, Carnegie Institution for Science, Stanford, CA, United States
| | - Andrew W. Truman
- Department of Biological Sciences, University of North Carolina, Charlotte, NC, United States
| | - Bibo Li
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Arts and Sciences, Cleveland State University, Cleveland, OH, United States
| | - Kausik Chakrabarti
- Department of Biological Sciences, University of North Carolina, Charlotte, NC, United States
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Fu H, Zhu X, Di Q, Sun J, Jiang Q, Xu Q. m6A contributes to a pro-survival state in GC-2 cells by facilitating DNA damage repair: Novel perspectives on the mechanism underlying DEHP genotoxicity in male germ cells. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160432. [PMID: 36423848 DOI: 10.1016/j.scitotenv.2022.160432] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/18/2022] [Accepted: 11/19/2022] [Indexed: 06/16/2023]
Abstract
Di(2-ethyl-hexyl) phthalate (DEHP), an environmental endocrine disruptor, can destroy the sperm genomic integrity and impairs spermatogenesis. N6-methyladenosine (m6A) is involved in the cellular effects of DEHP. However, the genotoxic effect of DEHP on spermatocytes and the possible role of m6A in this process remain unclear. This study demonstrated that m6A alleviates DEHP genotoxicity in GC-2 cells. In DEHP-treated mice, DNA double-strand breaks (DSBs) were induced in the testis and spermatocytes. To further explore the molecular mechanism of DEHP genotoxicity on spermatocytes, GC-2 cells were exposed to DEHP. DEHP produced distinct genotoxicity and caused DSBs, which led to the inhibition of DNA synthesis and cell cycle arrest. The DNA damage response (DDR) was initiated to repair the DSBs induced by environmentally relevant levels of DEHP (100 μM and 200 μM). During this process, METTL3 upregulated m6A, which facilitated the DDR via stabilizing the DNA damage repair factors (Rad51 and Xrcc5) mRNA to maintain the pro-survival state. Moreover, Mettl3 knockdown partially inhibited DDR. Interestingly, high-dose DEHP (400 μM and 600 μM) directly induced apoptosis rather than the pro-survival state. Altogether: METTL3-mediated m6A participates in maintaining the pro-survival state by upregulating DDR, providing guidance for mitigating the genotoxicity of environment-related level DEHP exposure.
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Affiliation(s)
- Haowei Fu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Xiaofang Zhu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Qiannan Di
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Jiahui Sun
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Qianqian Jiang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Qian Xu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China.
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Shi X, Won M, Tang C, Ding Q, Sharma A, Wang F, Kim JS. RNA splicing based on reporter genes system: Detection, imaging and applications. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2022.214929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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35
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Tsue AF, Kania EE, Lei DQ, Fields R, McGann CD, Hershberg E, Deng X, Kihiu M, Ong SE, Disteche CM, Kugel S, Beliveau BJ, Schweppe DK, Shechner DM. Oligonucleotide-directed proximity-interactome mapping (O-MAP): A unified method for discovering RNA-interacting proteins, transcripts and genomic loci in situ. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.19.524825. [PMID: 36711823 PMCID: PMC9882335 DOI: 10.1101/2023.01.19.524825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Throughout biology, RNA molecules form complex networks of molecular interactions that are central to their function, but remain challenging to investigate. Here, we introduce Oligonucleotide-mediated proximity-interactome MAPping (O-MAP), a straightforward method for elucidating the biomolecules near an RNA of interest, within its native cellular context. O-MAP uses programmable oligonucleotide probes to deliver proximity-biotinylating enzymes to a target RNA, enabling nearby molecules to be enriched by streptavidin pulldown. O-MAP induces exceptionally precise RNA-localized in situ biotinylation, and unlike alternative methods it enables straightforward optimization of its targeting accuracy. Using the 47S pre-ribosomal RNA and long noncoding RNA Xist as models, we develop O-MAP workflows for unbiased discovery of RNA-proximal proteins, transcripts, and genomic loci. This revealed unexpected co-compartmentalization of Xist and other chromatin-regulatory RNAs and enabled systematic characterization of nucleolar-chromatin interactions across multiple cell lines. O-MAP is portable to cultured cells, organoids, and tissues, and to RNAs of various lengths, abundances, and sequence composition. And, O-MAP requires no genetic manipulation and uses exclusively off-the-shelf parts. We therefore anticipate its application to a broad array of RNA phenomena.
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37
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Furtado CLM, da Silva Santos R, Sales SLA, Teixeira LPR, Pessoa CDÓ. Long Non-coding RNAs and CRISPR-Cas Edition in Tumorigenesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1429:41-58. [PMID: 37486515 DOI: 10.1007/978-3-031-33325-5_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Long non-coding RNAs (lncRNAs) are one of the most abundant and heterogeneous transcripts with key roles in chromatin remodeling and gene regulation at the transcriptional and post-transcriptional levels. Due to their role in cell growth and differentiation, lncRNAs have emerged as an important biomarker in cancer diagnosis, prognosis, and targeted treatment. Recent studies have focused on elucidating lncRNA function during malignant transformation, tumor progression and drug resistance. The advent of the CRISPR system has made it possible to precisely edit complex genomic loci such as lncRNAs. Thus, we summarized the advances in CRISPR-Cas approaches for functional studies of lncRNAs including gene knockout, knockdown, overexpression and RNA targeting in tumorigenesis and drug resistance. Additionally, we highlighted the perspectives and potential applications of CRISPR approaches to treat cancer, as an emerging and promising target therapy.
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Affiliation(s)
- Cristiana Libardi Miranda Furtado
- University of Fortaleza, Experimental Biology Center, Fortaleza, Ceara, Brazil.
- Drug Research and Development Center, Postgraduate Program in Translational Medicine, Federal University of Ceara, Fortaleza, Brazil.
| | - Renan da Silva Santos
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceara, Fortaleza, Brazil
| | - Sarah Leyenne Alves Sales
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceara, Fortaleza, Brazil
| | | | - Claudia do Ó Pessoa
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceara, Fortaleza, Brazil
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38
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Yang J, Song Y, Deng X, Vanegas JA, You Z, Zhang Y, Weng Z, Avery L, Dieckhaus KD, Peddi A, Gao Y, Zhang Y, Gao X. Engineered LwaCas13a with enhanced collateral activity for nucleic acid detection. Nat Chem Biol 2023; 19:45-54. [PMID: 36138140 DOI: 10.1038/s41589-022-01135-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 08/08/2022] [Indexed: 12/31/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 13 (Cas13) has been rapidly developed for nucleic-acid-based diagnostics by using its characteristic collateral activity. Despite the recent progress in optimizing the Cas13 system for the detection of nucleic acids, engineering Cas13 protein with enhanced collateral activity has been challenging, mostly because of its complex structural dynamics. Here we successfully employed a novel strategy to engineer the Leptotrichia wadei (Lwa)Cas13a by inserting different RNA-binding domains into a unique active-site-proximal loop within its higher eukaryotes and prokaryotes nucleotide-binding domain. Two LwaCas13a variants showed enhanced collateral activity and improved sensitivity over the wild type in various buffer conditions. By combining with an electrochemical method, our variants detected the SARS-CoV-2 genome at attomolar concentrations from both inactive viral and unextracted clinical samples, without target preamplification. Our engineered LwaCas13a enzymes with enhanced collateral activity are ready to be integrated into other Cas13a-based platforms for ultrasensitive detection of nucleic acids.
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Affiliation(s)
- Jie Yang
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Yang Song
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, USA.,Institute of Materials Science, University of Connecticut, Storrs, CT, USA
| | - Xiangyu Deng
- Department of Biosciences, Rice University, Houston, TX, USA
| | - Jeffrey A Vanegas
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Zheng You
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Yuxuan Zhang
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, USA.,Institute of Materials Science, University of Connecticut, Storrs, CT, USA
| | - Zhengyan Weng
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, USA.,Institute of Materials Science, University of Connecticut, Storrs, CT, USA
| | - Lori Avery
- Department of Pathology and Laboratory Medicine, UConn Health, Farmington, CT, USA
| | - Kevin D Dieckhaus
- Division of Infectious Diseases, Department of Medicine, UConn Health, Farmington, CT, USA
| | - Advaith Peddi
- Department of Biosciences, Rice University, Houston, TX, USA
| | - Yang Gao
- Department of Biosciences, Rice University, Houston, TX, USA.
| | - Yi Zhang
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, USA. .,Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, CT, USA.
| | - Xue Gao
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA. .,Department of Bioengineering, Rice University, Houston, TX, USA. .,Department of Chemistry, Rice University, Houston, TX, USA.
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Li J, Zhang J, Bui S, Ahat E, Kolli D, Reid W, Xing L, Wang Y. Common Assays in Mammalian Golgi Studies. Methods Mol Biol 2022; 2557:303-332. [PMID: 36512224 DOI: 10.1007/978-1-0716-2639-9_20] [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] [Indexed: 12/15/2022]
Abstract
The Golgi is a complex structure characterized by stacks of tightly aligned flat cisternae. In mammalian cells, Golgi stacks often concentrate in the perinuclear region and link together to form a ribbon. This structure is dynamic to accommodate continuous cargo flow in and out of the Golgi in both directions and undergoes morphological changes under physiological and pathological conditions. The fine, stacked Golgi structure makes it difficult to study by conventional light or even super-resolution microscopy. Furthermore, efforts to understand how Golgi structural dynamics impact cellular processes have been slow because of the knowledge gap in the protein machinery that maintains the complex and dynamic Golgi structure. In this method article, we list the common assays used in our research to help new and established researchers select the most appropriate method to properly address their questions.
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Affiliation(s)
- Jie Li
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Jianchao Zhang
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Sarah Bui
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Erpan Ahat
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Divya Kolli
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Whitney Reid
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Lijuan Xing
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Yanzhuang Wang
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
- Department of Neurology, University of Michigan School of Medicine, Ann Arbor, MI, USA.
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40
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Wu S, Tian P, Tan T. CRISPR-Cas13 technology portfolio and alliance with other genetic tools. Biotechnol Adv 2022; 61:108047. [DOI: 10.1016/j.biotechadv.2022.108047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/03/2022] [Accepted: 09/29/2022] [Indexed: 11/02/2022]
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41
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Liang Y, Xu H, Cheng T, Fu Y, Huang H, Qian W, Wang J, Zhou Y, Qian P, Yin Y, Xu P, Zou W, Chen B. Gene activation guided by nascent RNA-bound transcription factors. Nat Commun 2022; 13:7329. [PMID: 36443367 PMCID: PMC9705438 DOI: 10.1038/s41467-022-35041-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/16/2022] [Indexed: 11/29/2022] Open
Abstract
Technologies for gene activation are valuable tools for the study of gene functions and have a wide range of potential applications in bioengineering and medicine. In contrast to existing methods based on recruiting transcriptional modulators via DNA-binding proteins, we developed a strategy termed Narta (nascent RNA-guided transcriptional activation) to achieve gene activation by recruiting artificial transcription factors (aTFs) to transcription sites through nascent RNAs of the target gene. Using Narta, we demonstrate robust activation of a broad range of exogenous and endogenous genes in various cell types, including zebrafish embryos, mouse and human cells. Importantly, the activation is reversible, tunable and specific. Moreover, Narta provides better activation potency of some expressed genes than CRISPRa and, when used in combination with CRISPRa, has an enhancing effect on gene activation. Quantitative imaging illustrated that nascent RNA-directed aTFs could induce the high-density assembly of coactivators at transcription sites, which may explain the larger transcriptional burst size induced by Narta. Overall, our work expands the gene activation toolbox for biomedical research.
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Affiliation(s)
- Ying Liang
- grid.13402.340000 0004 1759 700XDepartment of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China ,grid.13402.340000 0004 1759 700XLiangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Haiyue Xu
- grid.13402.340000 0004 1759 700XDepartment of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China ,grid.13402.340000 0004 1759 700XLiangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Tao Cheng
- grid.13402.340000 0004 1759 700XWomen’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yujuan Fu
- grid.13402.340000 0004 1759 700XDepartment of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hanwei Huang
- grid.13402.340000 0004 1759 700XDepartment of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wenchang Qian
- grid.13402.340000 0004 1759 700XCenter of Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Junyan Wang
- grid.13402.340000 0004 1759 700XDepartment of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuenan Zhou
- grid.13402.340000 0004 1759 700XDepartment of Cell Biology, Zhejiang University School of Medicine, Hangzhou, China
| | - Pengxu Qian
- grid.13402.340000 0004 1759 700XCenter of Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Yafei Yin
- grid.13402.340000 0004 1759 700XDepartment of Cell Biology, Zhejiang University School of Medicine, Hangzhou, China
| | - Pengfei Xu
- grid.13402.340000 0004 1759 700XWomen’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wei Zou
- grid.13402.340000 0004 1759 700XThe Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China ,grid.13402.340000 0004 1759 700XInsititute of Translational Medicine, Zhejiang University, Hangzhou, China
| | - Baohui Chen
- grid.13402.340000 0004 1759 700XDepartment of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China ,grid.13402.340000 0004 1759 700XLiangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China ,grid.13402.340000 0004 1759 700XInstitute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China ,grid.13402.340000 0004 1759 700XZhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Hangzhou, China
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Mei R, Wan Z, Li Z, Wei M, Qin W, Yuan L, Liu L, Yang G. "All-in-One" Exosome Engineering Strategy for Effective Therapy of Familial Hypercholesterolemia. ACS APPLIED MATERIALS & INTERFACES 2022; 14:50626-50636. [PMID: 36342824 DOI: 10.1021/acsami.2c15785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Exosomes serve as a promising therapeutic nanoplatform. However, the exosomes produced by donor cells are a heterogeneous group, with only a small portion having high therapeutic efficacy. Specific isolation of the subpopulation with high efficacy is important for lowering the dose and minimizing toxicity. In this study, we loaded target mRNA and displayed specific Flag in engineered exosomes simultaneously. Briefly, the donor cells were transfected with plasmid expressing a fusion protein Flag-TCS-PTGFRN-CTSL-MCP, namely, exosome sorter. During biogenesis, the RNA-binding motif MCP can specifically bind with MS2-containing RNA and sort the target RNA into the lumen of exosomes. Anti-Flag magnetic beads can capture and thus purify the engineered exosomes via recognition of the Flag on the surface of exosomes. After purification, the Flag could be cleaved by thrombin treatment while MCP can be separated from the fusion protein by CTSL autocleavage upon exosome acidification, minimizing the side effects and augmenting the therapeutic effects. By the proof-of-concept experiment, the exosome sorter-based "all-in-one" strategy was confirmed effective in both the encapsulation of therapeutic mRNA (Ldlr-MS2) into exosomes and the subsequent purification. The purified Ldlr-MS2-containing exosomes had much higher efficacy in alleviating atherosclerosis, in comparison with the bulk exosomes, confirming the advantage of the proposed "all-in-one" strategy.
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Affiliation(s)
- Ruiyan Mei
- Department of Hematology, Tangdu Hospital, Fourth Military Medical University, Xi'an 710032, Shaanxi, China
- Shaanxi Department of National Clinical Research Center for Hematological Diseases, Xi'an 710032, China
- Clinical Medical Research Center for Hematological Diseases of Shaanxi Province, Xi'an 710032, China
| | - Zhuo Wan
- Department of Hematology, Tangdu Hospital, Fourth Military Medical University, Xi'an 710032, Shaanxi, China
- Shaanxi Department of National Clinical Research Center for Hematological Diseases, Xi'an 710032, China
- Clinical Medical Research Center for Hematological Diseases of Shaanxi Province, Xi'an 710032, China
| | - Zhelong Li
- Department of Ultrasound Diagnostics, Tangdu Hospital, Fourth Military Medical University, Xi'an 710032, Shaanxi, China
| | - Mengying Wei
- The State Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an 710032, Shaanxi, China
| | - Weiwei Qin
- Department of Hematology, Tangdu Hospital, Fourth Military Medical University, Xi'an 710032, Shaanxi, China
- Shaanxi Department of National Clinical Research Center for Hematological Diseases, Xi'an 710032, China
- Clinical Medical Research Center for Hematological Diseases of Shaanxi Province, Xi'an 710032, China
| | - Lijun Yuan
- Department of Ultrasound Diagnostics, Tangdu Hospital, Fourth Military Medical University, Xi'an 710032, Shaanxi, China
| | - Li Liu
- Department of Hematology, Tangdu Hospital, Fourth Military Medical University, Xi'an 710032, Shaanxi, China
- Shaanxi Department of National Clinical Research Center for Hematological Diseases, Xi'an 710032, China
- Clinical Medical Research Center for Hematological Diseases of Shaanxi Province, Xi'an 710032, China
| | - Guodong Yang
- The State Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an 710032, Shaanxi, China
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Giambruno R, Nicassio F. Proximity-dependent biotinylation technologies for mapping RNA-protein interactions in live cells. Front Mol Biosci 2022; 9:1062448. [PMID: 36452457 PMCID: PMC9702341 DOI: 10.3389/fmolb.2022.1062448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 10/25/2022] [Indexed: 12/01/2023] Open
Abstract
Proximity ligation technologies are extremely powerful tools for unveiling RNA-protein interactions occurring at different stages in living cells. These approaches mainly rely on the inducible activity of enzymes (biotin ligases or peroxidases) that promiscuously biotinylate macromolecules within a 20 nm range. These enzymes can be either fused to an RNA binding protein or tethered to any RNA of interest and expressed in living cells to biotinylate the amino acids and nucleic acids of binding partners in proximity. The biotinylated molecules can then be easily affinity purified under denaturing conditions and analyzed by mass spectrometry or next generation sequencing. These approaches have been widely used in recent years, providing a potent instrument to map the molecular interactions of specific RNA-binding proteins as well as RNA transcripts occurring in mammalian cells. In addition, they permit the identification of transient interactions as well as interactions among low expressed molecules that are often missed by standard affinity purification strategies. This review will provide a brief overview of the currently available proximity ligation methods, highlighting both their strengths and shortcomings. Furthermore, it will bring further insights to the way these technologies could be further used to characterize post-transcriptional modifications that are known to regulate RNA-protein interactions.
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Affiliation(s)
- Roberto Giambruno
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Milano, Italy
- Institute of Biomedical Technologies, National Research Council, Segrate, Italy
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Milano, Italy
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44
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Liu L, Pei DS. Insights Gained from RNA Editing Targeted by the CRISPR-Cas13 Family. Int J Mol Sci 2022; 23:11400. [PMID: 36232699 PMCID: PMC9569848 DOI: 10.3390/ijms231911400] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 11/17/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) systems, especially type II (Cas9) systems, have been widely developed for DNA targeting and formed a set of mature precision gene-editing systems. However, the basic research and application of the CRISPR-Cas system in RNA is still in its early stages. Recently, the discovery of the CRISPR-Cas13 type VI system has provided the possibility for the expansion of RNA targeting technology, which has broad application prospects. Most type VI Cas13 effectors have dinuclease activity that catalyzes pre-crRNA into mature crRNA and produces strong RNA cleavage activity. Cas13 can specifically recognize targeted RNA fragments to activate the Cas13/crRNA complex for collateral cleavage activity. To date, the Cas13X protein is the smallest effector of the Cas13 family, with 775 amino acids, which is a promising platform for RNA targeting due to its lack of protospacer flanking sequence (PFS) restrictions, ease of packaging, and absence of permanent damage. This study highlighted the latest progress in RNA editing targeted by the CRISPR-Cas13 family, and discussed the application of Cas13 in basic research, nucleic acid diagnosis, nucleic acid tracking, and genetic disease treatment. Furthermore, we clarified the structure of the Cas13 protein family and their molecular mechanism, and proposed a future vision of RNA editing targeted by the CRISPR-Cas13 family.
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Affiliation(s)
- Li Liu
- Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing 400714, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Public Health and Management, Chongqing Medical University, Chongqing 400016, China
| | - De-Sheng Pei
- School of Public Health and Management, Chongqing Medical University, Chongqing 400016, China
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Zhu X, Fu H, Sun J, Di Q, Xu Q. N6-methyladenosine modification on Hmbox1 is related to telomere dysfunction in DEHP-induced male reproductive injury. Life Sci 2022; 309:121005. [PMID: 36174712 DOI: 10.1016/j.lfs.2022.121005] [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: 07/14/2022] [Revised: 09/12/2022] [Accepted: 09/23/2022] [Indexed: 11/19/2022]
Abstract
AIMS Di (2-ethylhexyl) phthalate (DEHP), as an environmental endocrine-disrupting chemical (EDC), can induce male reproductive injury. N6-methyladenosine (m6A) plays a vital role in environmental exposure-induced diseases by regulating gene expression. Therefore, we aim to investigate the role of m6A in DEHP-induced reproductive injury. MAIN METHODS We established an in vivo model of mice exposed to DEHP to explore the effect of DEHP on reproductive injury and m6A. To further explore the molecular mechanism of DEHP toxicity, we built a model of GC-2 cells exposed to mono-(2-ethylhexyl) phthalate (MEHP) in vitro and further silenced Mettl3 in GC-2cells. Besides, we also conducted MeRIP-qPCR and RIP assays to identify the target genes for m6A modification. KEY FINDINGS DEHP induced testicular injury and senescence. And telomeres shortening, reduced levels of telomere repeat-binding factor 1 (TRF1), TRF2, protection of telomeres 1 (POT1), and telomerase reverse transcriptase (TERT) can be observed in DEHP-treated testes. MEHP also induced GC-2 cellular senescence and telomere dysfunction. Besides, increased m6A mediated by METTL3 stabilized homeobox containing 1 (Hmbox1) in an m6A-dependent manner in MEHP-exposed GC-2 cells. Mettl3 knockdown led to lower m6A modification and reduced Hmbox1 stability, resulting in further shortening of telomere length. SIGNIFICANCE our work uncovered that DEHP led to male reproductive injury by telomere dysfunction and m6A modified Hmbox1 contributed to maintaining telomere homeostasis in this process, suggesting that accurate regulation of m6A modification level by drugs has potential value in the treatment of DEHP-induced male reproductive injury.
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Affiliation(s)
- Xiaofang Zhu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Haowei Fu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Jiahui Sun
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Qiannan Di
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Qian Xu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China.
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Lv S, Zhao X, Ma X, Zou Q, Li N, Yan Y, Sun L, Song T. Efficient and reversible Cas13d-mediated knockdown with an all-in-one lentivirus-vector. Front Bioeng Biotechnol 2022; 10:960192. [PMID: 36185457 PMCID: PMC9521038 DOI: 10.3389/fbioe.2022.960192] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/22/2022] [Indexed: 11/25/2022] Open
Abstract
Type VI CRISPR effector Cas13d from Ruminococcus flavefaciens XPD3002 (RfxCas13d) is an RNA-guided RNA endonuclease. RfxCas13d has been harnessed to knockdown gene expression with high specificity in various systems including mammalian cells. While inducible knockdown is advantageous over constitutive knockdown in many scenarios, current inducible systems of RfxCas13d express CRISPR RNA and Cas13d separately. Such systems could be cumbersome to handle and may hamper the application of RfxCas13d in some scenarios. Here, we design an all-in-one Cas13d lentivirus vector which renders efficient and inducible knockdown in a doxycycline dosage-dependent manner. Furthermore, we find that Cas13d has a short half-life in mammalian cells. As a result, knockdown can be promptly reversed after doxycycline withdrawal. This vector is particularly useful for applications involving indispensable genes and/or in cells hard to transduce.
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Affiliation(s)
- Suli Lv
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xuefeng Zhao
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xianyun Ma
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qingli Zou
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Neng Li
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yingying Yan
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lidong Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Cell Architecture Research Institute, Huazhong University of Science and Technology, Wuhan, Hubei, China
- *Correspondence: Tanjing Song, ; Lidong Sun,
| | - Tanjing Song
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Cell Architecture Research Institute, Huazhong University of Science and Technology, Wuhan, Hubei, China
- *Correspondence: Tanjing Song, ; Lidong Sun,
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Peng KL, Vasudevan HN, Lockney DT, Baum R, Hendrickson RC, Raleigh DR, Schmitt AM. Miat and interacting protein Metadherin maintain a stem-like niche to promote medulloblastoma tumorigenesis and treatment resistance. Proc Natl Acad Sci U S A 2022; 119:e2203738119. [PMID: 36067288 PMCID: PMC9478675 DOI: 10.1073/pnas.2203738119] [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: 03/04/2022] [Accepted: 08/09/2022] [Indexed: 11/18/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) play essential roles in the development and progression of many cancers. However, the contributions of lncRNAs to medulloblastoma (MB) remain poorly understood. Here, we identify Miat as an lncRNA enriched in the sonic hedgehog group of MB that is required for maintenance of a treatment-resistant stem-like phenotype in the disease. Loss of Miat results in the differentiation of tumor-initiating, stem-like MB cells and enforces the differentiation of tumorigenic stem-like MB cells into a nontumorigenic state. Miat expression in stem-like MB cells also facilitates treatment resistance by down-regulating p53 signaling and impairing radiation-induced cell death, which can be reversed by therapeutic inhibition of Miat using antisense oligonucleotides. Mechanistically, the RNA binding protein Metadherin (Mtdh), previously linked to resistance to cytotoxic therapy in cancer, binds to Miat in stem-like MB cells. Like the loss of Miat, the loss of Mtdh reduces tumorigenicity and increases sensitivity to radiation-induced death in stem-like MB cells. Moreover, Miat and Mtdh function to regulate the biogenesis of several microRNAs and facilitate tumorigenesis and treatment resistance. Taken together, these data reveal an essential role for the lncRNA Miat in sustaining a treatment-resistant pool of tumorigenic stem-like MB cells.
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Affiliation(s)
- Kai-Lin Peng
- Division of Translational Oncology, Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065
| | - Harish N. Vasudevan
- Division of Translational Oncology, Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065
- Department of Radiation Oncology, University of California San Francisco, CA, 94143
| | - Dennis T. Lockney
- Division of Translational Oncology, Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065
| | - Rachel Baum
- Division of Translational Oncology, Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065
| | - Ronald C. Hendrickson
- Microchemistry and Proteomics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065
| | - David R. Raleigh
- Department of Radiation Oncology, University of California San Francisco, CA, 94143
- Department of Neurological Surgery, University of California San Francisco, CA, 94143
| | - Adam M. Schmitt
- Division of Translational Oncology, Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065
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The landscape of aging. SCIENCE CHINA LIFE SCIENCES 2022; 65:2354-2454. [PMID: 36066811 PMCID: PMC9446657 DOI: 10.1007/s11427-022-2161-3] [Citation(s) in RCA: 101] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/05/2022] [Indexed: 02/07/2023]
Abstract
Aging is characterized by a progressive deterioration of physiological integrity, leading to impaired functional ability and ultimately increased susceptibility to death. It is a major risk factor for chronic human diseases, including cardiovascular disease, diabetes, neurological degeneration, and cancer. Therefore, the growing emphasis on “healthy aging” raises a series of important questions in life and social sciences. In recent years, there has been unprecedented progress in aging research, particularly the discovery that the rate of aging is at least partly controlled by evolutionarily conserved genetic pathways and biological processes. In an attempt to bring full-fledged understanding to both the aging process and age-associated diseases, we review the descriptive, conceptual, and interventive aspects of the landscape of aging composed of a number of layers at the cellular, tissue, organ, organ system, and organismal levels.
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CRISPR-Guided Proximity Labeling of RNA–Protein Interactions. Genes (Basel) 2022; 13:genes13091549. [PMID: 36140717 PMCID: PMC9498842 DOI: 10.3390/genes13091549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 12/02/2022] Open
Abstract
Proximity labeling employs modified biotin ligases or peroxidases that produce reactive radicals to covalently label proximate proteins with biotin in living cells. The resulting biotinylated proteins can then be isolated and identified. A combination of programmable DNA targeting and proximity labeling that maps proteomic landscape at DNA elements with dCas9-APEX2 has been established in living cells. However, defining interactome at RNA elements has lagged behind. In combination with RNA-targeting CRISPR-Cas13, proximity labeling can also be used to identify proteins that interact with specific RNA elements in living cells. From this viewpoint, we briefly summarize the latest advances in CRISPR-guided proximity labeling in studying RNA–protein interactions, and we propose applying the most recent engineered proximity-labeling enzymes to study RNA-centric interactions in the future.
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Kelley CP, Haerle MC, Wang ET. Negative autoregulation mitigates collateral RNase activity of repeat-targeting CRISPR-Cas13d in mammalian cells. Cell Rep 2022; 40:111226. [PMID: 35977479 PMCID: PMC9809062 DOI: 10.1016/j.celrep.2022.111226] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/29/2022] [Accepted: 07/26/2022] [Indexed: 01/05/2023] Open
Abstract
CRISPR-Cas13 RNA endonucleases show promise for programmable RNA knockdown. However, sequence-specific binding of Cas13 unleashes non-specific bystander RNA cleavage, or collateral activity, raising concerns for experiments and therapeutic applications. Although robust in cell-free and bacterial environments, collateral activity in mammalian cells remains disputed. We investigate Cas13d collateral activity in a therapeutic context for myotonic dystrophy type 1, caused by a transcribed CTG repeat expansion. We find that, when targeting CUGn RNA in mammalian cells, Cas13d depletes endogenous and transgenic RNAs, interferes with critical cellular processes, and activates stress response and apoptosis. Collateral effects also occur when targeting abundant endogenous transcripts. To minimize collateral activity for repeat-targeting approaches, we introduce GENO, an adeno-associated virus-compatible strategy that leverages guide RNA processing to control Cas13d expression. We argue that thorough assessment of collateral activity is necessary when applying Cas13 in mammalian cells and that GENO illustrates advantages of compact regulatory systems for Cas-based gene therapies.
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Affiliation(s)
- Chase P Kelley
- Department of Molecular Genetics & Microbiology, Center for NeuroGenetics, Genetics Institute, University of Florida, Gainesville, FL 32608, USA; Genetics and Genomics Graduate Program, University of Florida, Gainesville, FL 32608, USA
| | - Maja C Haerle
- Department of Molecular Genetics & Microbiology, Center for NeuroGenetics, Genetics Institute, University of Florida, Gainesville, FL 32608, USA
| | - Eric T Wang
- Department of Molecular Genetics & Microbiology, Center for NeuroGenetics, Genetics Institute, University of Florida, Gainesville, FL 32608, USA; Myology Institute, University of Florida, Gainesville, FL 32608, USA.
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