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Katsushima K, Joshi K, Yuan M, Romero B, Batish M, Stapleton S, Jallo G, Kolanthai E, Seal S, Saulnier O, Taylor MD, Wechsler-Reya RJ, Eberhart CG, Perera RJ. A therapeutically targetable positive feedback loop between lnc-HLX-2-7, HLX, and MYC that promotes group 3 medulloblastoma. Cell Rep 2024; 43:113938. [PMID: 38460130 DOI: 10.1016/j.celrep.2024.113938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/01/2024] [Accepted: 02/23/2024] [Indexed: 03/11/2024] Open
Abstract
Recent studies suggest that long non-coding RNAs (lncRNAs) contribute to medulloblastoma (MB) formation and progression. We have identified an lncRNA, lnc-HLX-2-7, as a potential therapeutic target in group 3 (G3) MBs. lnc-HLX-2-7 RNA specifically accumulates in the promoter region of HLX, a sense-overlapping gene of lnc-HLX-2-7, which activates HLX expression by recruiting multiple factors, including enhancer elements. RNA sequencing and chromatin immunoprecipitation reveal that HLX binds to and activates the promoters of several oncogenes, including TBX2, LIN9, HOXM1, and MYC. Intravenous treatment with cerium-oxide-nanoparticle-coated antisense oligonucleotides targeting lnc-HLX-2-7 (CNP-lnc-HLX-2-7) inhibits tumor growth by 40%-50% in an intracranial MB xenograft mouse model. Combining CNP-lnc-HLX-2-7 with standard-of-care cisplatin further inhibits tumor growth and significantly prolongs mouse survival compared with CNP-lnc-HLX-2-7 monotherapy. Thus, the lnc-HLX-2-7-HLX-MYC axis is important for regulating G3 MB progression, providing a strong rationale for using lnc-HLX-2-7 as a therapeutic target for G3 MBs.
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Affiliation(s)
- Keisuke Katsushima
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD 21231, USA; Johns Hopkins All Children's Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA
| | - Kandarp Joshi
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD 21231, USA; Johns Hopkins All Children's Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA
| | - Menglang Yuan
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD 21231, USA; Johns Hopkins All Children's Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA
| | - Brigette Romero
- Department of Medical and Molecular Sciences, University of Delaware, 15 Innovation Way, Newark, DE 19701, USA
| | - Mona Batish
- Department of Medical and Molecular Sciences, University of Delaware, 15 Innovation Way, Newark, DE 19701, USA
| | - Stacie Stapleton
- Johns Hopkins All Children's Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA
| | - George Jallo
- Johns Hopkins All Children's Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA
| | - Elayaraja Kolanthai
- Advanced Materials Processing and Analysis Center, Nanoscience and Technology Center, Materials Science and Engineering, College of Medicine, University of Central Florida, Orlando, FL 32816, USA
| | - Sudipta Seal
- Advanced Materials Processing and Analysis Center, Nanoscience and Technology Center, Materials Science and Engineering, College of Medicine, University of Central Florida, Orlando, FL 32816, USA
| | - Olivier Saulnier
- Genomics and Development of Childhood Cancers, Institut Curie, PSL University, 75005 Paris, France; INSERM U830, Cancer Heterogeneity Instability and Plasticity, Institut Curie, PSL University, 75005 Paris, France; SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, 75005 Paris, France
| | - Michael D Taylor
- Texas Children's Cancer Center, Hematology-Oncology Section, Houston, TX 77004, USA; Department of Pediatrics - Hematology/Oncology and Neurosurgery, Baylor College of Medicine, Houston, TX 77004, USA
| | - Robert J Wechsler-Reya
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Charles G Eberhart
- Department of Pathology, Johns Hopkins University School of Medicine, 720 Rutland Ave., Ross Bldg. 558, Baltimore, MD 21205, USA
| | - Ranjan J Perera
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD 21231, USA; Johns Hopkins All Children's Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA.
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Lee JH, Perez-Flores MC, Park S, Kim HJ, Chen Y, Kang M, Kersigo J, Choi J, Thai PN, Woltz RL, Perez-Flores DC, Perkins G, Sihn CR, Trinh P, Zhang XD, Sirish P, Dong Y, Feng WW, Pessah IN, Dixon RE, Sokolowski B, Fritzsch B, Chiamvimonvat N, Yamoah EN. The Piezo channel is a mechano-sensitive complex component in the mammalian inner ear hair cell. Nat Commun 2024; 15:526. [PMID: 38228630 PMCID: PMC10791687 DOI: 10.1038/s41467-023-44230-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 12/04/2023] [Indexed: 01/18/2024] Open
Abstract
The inner ear is the hub where hair cells (HCs) transduce sound, gravity, and head acceleration stimuli to the brain. Hearing and balance rely on mechanosensation, the fastest sensory signals transmitted to the brain. The mechanoelectrical transducer (MET) channel is the entryway for the sound-balance-brain interface, but the channel-complex composition is not entirely known. Here, we report that the mouse utilizes Piezo1 (Pz1) and Piezo2 (Pz2) isoforms as MET-complex components. The Pz channels, expressed in HC stereocilia, and cell lines are co-localized and co-assembled with MET complex partners. Mice expressing non-functional Pz1 and Pz2 at the ROSA26 locus have impaired auditory and vestibular traits that can only be explained if the Pzs are integral to the MET complex. We suggest that Pz subunits constitute part of the MET complex and that interactions with other MET complex components yield functional MET units to generate HC MET currents.
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Affiliation(s)
- Jeong Han Lee
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV, 89557, USA
| | - Maria C Perez-Flores
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV, 89557, USA
| | - Seojin Park
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV, 89557, USA
- Prestige Biopharma, 11-12F, 44, Myongjigukje7-ro, Gangseo-gu, Busan, 67264, South Korea
| | - Hyo Jeong Kim
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV, 89557, USA
| | - Yingying Chen
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV, 89557, USA
| | - Mincheol Kang
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV, 89557, USA
- Prestige Biopharma, 11-12F, 44, Myongjigukje7-ro, Gangseo-gu, Busan, 67264, South Korea
| | | | - Jinsil Choi
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV, 89557, USA
| | - Phung N Thai
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of California, Davis, CA, 95616, USA
| | - Ryan L Woltz
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of California, Davis, CA, 95616, USA
| | | | - Guy Perkins
- National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla, CA, 92093, USA
| | - Choong-Ryoul Sihn
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV, 89557, USA
| | - Pauline Trinh
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of California, Davis, CA, 95616, USA
| | - Xiao-Dong Zhang
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of California, Davis, CA, 95616, USA
| | - Padmini Sirish
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of California, Davis, CA, 95616, USA
| | - Yao Dong
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, 1089 VM3B, Davis, CA, 95616, USA
| | - Wayne Wei Feng
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, 1089 VM3B, Davis, CA, 95616, USA
| | - Isaac N Pessah
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, 1089 VM3B, Davis, CA, 95616, USA
| | - Rose E Dixon
- Department of Physiology & Membrane Biology, Tupper Hall, One Shields Avenue, Davis, CA, 95616, USA
| | - Bernd Sokolowski
- Department of Otolaryngology-Head and Neck Surgery, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Bernd Fritzsch
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Nipavan Chiamvimonvat
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of California, Davis, CA, 95616, USA
- VA Northern California Healthcare System, Sacramento, USA
| | - Ebenezer N Yamoah
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV, 89557, USA.
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Chang MW, Yang JH, Tsitsipatis D, Yang X, Martindale J, Munk R, Pandey P, Banskota N, Romero B, Batish M, Piao Y, Mazan-Mamczarz K, De S, Abdelmohsen K, Wilson G, Gorospe M. Enhanced myogenesis through lncFAM-mediated recruitment of HNRNPL to the MYBPC2 promoter. Nucleic Acids Res 2022; 50:13026-13044. [PMID: 36533518 PMCID: PMC9825165 DOI: 10.1093/nar/gkac1174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 11/16/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022] Open
Abstract
The mammalian transcriptome comprises a vast family of long noncoding (lnc)RNAs implicated in physiologic processes such as myogenesis, through which muscle forms during embryonic development and regenerates in the adult. However, the specific molecular mechanisms by which lncRNAs regulate human myogenesis are poorly understood. Here, we identified a novel muscle-specific lncRNA, lncFAM71E1-2:2 (lncFAM), which increased robustly during early human myogenesis. Overexpression of lncFAM promoted differentiation of human myoblasts into myotubes, while silencing lncFAM suppressed this process. As lncFAM resides in the nucleus, chromatin isolation by RNA purification followed by mass spectrometry (ChIRP-MS) analysis was employed to identify the molecular mechanisms whereby it might promote myogenesis. Analysis of lncFAM-interacting proteins revealed that lncFAM recruited the RNA-binding protein HNRNPL to the promoter of MYBPC2, in turn increasing MYBPC2 mRNA transcription and enhancing production of the myogenic protein MYBPC2. These results highlight a mechanism whereby a novel ribonucleoprotein complex, lncFAM-HNRNPL, elevates MYBPC2 expression transcriptionally to promote myogenesis.
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Affiliation(s)
| | - Jen-Hao Yang
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Dimitrios Tsitsipatis
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Xiaoling Yang
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Jennifer L Martindale
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Rachel Munk
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Poonam R Pandey
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Nirad Banskota
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Brigette Romero
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA
| | - Mona Batish
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA
| | - Yulan Piao
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Krystyna Mazan-Mamczarz
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Gerald M Wilson
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Myriam Gorospe
- To whom correspondence should be addressed. Tel: +1 410 454 8412;
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Xia P, Dutta A, Gupta K, Batish M, Parashar V. Structural basis of cyclic oligoadenylate binding to the transcription factor Csa3 outlines cross talk between type III and type I CRISPR systems. J Biol Chem 2022; 298:101591. [PMID: 35038453 PMCID: PMC8844856 DOI: 10.1016/j.jbc.2022.101591] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 01/28/2023] Open
Abstract
RNA interference by type III CRISPR systems results in the synthesis of cyclic oligoadenylate (cOA) second messengers, which are known to bind and regulate various CARF domain-containing nuclease receptors. The CARF domain-containing Csa3 family of transcriptional factors associated with the DNA-targeting type I CRISPR systems regulate expression of various CRISPR and DNA repair genes in many prokaryotes. In this study, we extend the known receptor repertoire of cOA messengers to include transcriptional factors by demonstrating specific binding of cyclic tetra-adenylate (cA4) to Saccharolobus solfataricus Csa3 (Csa3Sso). Our 2.0-Å resolution X-ray crystal structure of cA4-bound full-length Csa3Sso reveals the binding of its CARF domain to an elongated conformation of cA4. Using cA4 binding affinity analyses of Csa3Sso mutants targeting the observed Csa3Sso•cA4 structural interface, we identified a Csa3-specific cA4 binding motif distinct from a more widely conserved cOA-binding CARF motif. Using a rational surface engineering approach, we increased the cA4 binding affinity of Csa3Sso up to ∼145-fold over the wildtype, which has potential applications for future second messenger-driven CRISPR gene expression and editing systems. Our in-solution Csa3Sso structural analysis identified cA4-induced allosteric and asymmetric conformational rearrangement of its C-terminal winged helix-turn-helix effector domains, which could potentially be incompatible to DNA binding. However, specific in vitro binding of the purified Csa3Sso to its putative promoter (PCas4a) was found to be cA4 independent, suggesting a complex mode of Csa3Sso regulation. Overall, our results support cA4-and Csa3-mediated cross talk between type III and type I CRISPR systems.
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Affiliation(s)
- Pengjun Xia
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - Anirudha Dutta
- Department of Medical and Molecular Sciences, University of Delaware, Newark, Delaware, USA
| | - Kushol Gupta
- The Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Mona Batish
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA; Department of Medical and Molecular Sciences, University of Delaware, Newark, Delaware, USA
| | - Vijay Parashar
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA; Department of Medical and Molecular Sciences, University of Delaware, Newark, Delaware, USA.
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CircFISH: A Novel Method for the Simultaneous Imaging of Linear and Circular RNAs. Cancers (Basel) 2022; 14:cancers14020428. [PMID: 35053590 PMCID: PMC8773908 DOI: 10.3390/cancers14020428] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/09/2022] [Accepted: 01/12/2022] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Circular RNAs are a recently appreciated class of regulatory non-coding RNAs. Although a number of high-resolution methods have been developed for the imaging of RNAs in cells and tissues, there is no reliable method for the simultaneous imaging of circular RNAs distinctly from their linear counterparts. Here, we report circFISH as a simple and single-molecule resolution method that will simultaneously image linear and circular RNAs in fixed cells and tissues. We demonstrate that multiple circular RNAs can be imaged using circFISH. We also show the ability of circFISH to work seamlessly with protein and other organelle imaging. We optimized the method to work across sample types, making it a versatile tool for the functional characterization of circular RNAs. Abstract Circular RNAs (circRNAs) are regulatory RNAs which have recently been shown to have clinical significance in several diseases, including, but not limited to, various cancers, neurological diseases and cardiovascular diseases. The function of such regulatory RNAs is largely dependent on their subcellular localization. Several circRNAs have been shown to conduct antagonistic roles compared to the products of the linear isoforms, and thus need to be characterized distinctly from the linear RNAs. However, conventional fluorescent in situ hybridization (FISH) techniques cannot be employed directly to distinguish the signals from linear and circular isoforms because most circRNAs share the same sequence with the linear RNAs. In order to address this unmet need, we adapted the well-established method of single-molecule FISH by designing two sets of probes to differentiate the linear and circular RNA isoforms by virtue of signal colocalization. We call this method ‘circular fluorescent in situ hybridization’ (circFISH). Linear and circular RNAs were successfully visualized and quantified at a single-molecule resolution in fixed cells. RNase R treatment during the circFISH reduced the levels of linear RNAs while the circRNA levels remain unaltered. Furthermore, cells with shRNAs specific to circRNA showed the loss of circRNA levels, whereas the linear RNA levels were unaffected. The optimization of the in-situ RNase R treatment allowed the multiplexing of circFISH to combine it with organelle staining. CircFISH was found to be compatible with multiple sample types, including cultured cells and fresh-frozen and formalin-fixed tissue sections. Thus, we present circFISH as a versatile method for the simultaneous visualization and quantification of the distribution and localization of linear and circular RNA in fixed cells and tissue samples.
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Stress granule formation, disassembly, and composition are regulated by alphavirus ADP-ribosylhydrolase activity. Proc Natl Acad Sci U S A 2021; 118:2021719118. [PMID: 33547245 DOI: 10.1073/pnas.2021719118] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
While biomolecular condensates have emerged as an important biological phenomenon, mechanisms regulating their composition and the ways that viruses hijack these mechanisms remain unclear. The mosquito-borne alphaviruses cause a range of diseases from rashes and arthritis to encephalitis, and no licensed drugs are available for treatment or vaccines for prevention. The alphavirus virulence factor nonstructural protein 3 (nsP3) suppresses the formation of stress granules (SGs)-a class of cytoplasmic condensates enriched with translation initiation factors and formed during the early stage of infection. nsP3 has a conserved N-terminal macrodomain that hydrolyzes ADP-ribose from ADP-ribosylated proteins and a C-terminal hypervariable domain that binds the essential SG component G3BP1. Here, we show that macrodomain hydrolase activity reduces the ADP-ribosylation of G3BP1, disassembles virus-induced SGs, and suppresses SG formation. Expression of nsP3 results in the formation of a distinct class of condensates that lack translation initiation factors but contain G3BP1 and other SG-associated RNA-binding proteins. Expression of ADP-ribosylhydrolase-deficient nsP3 results in condensates that retain translation initiation factors as well as RNA-binding proteins, similar to SGs. Therefore, our data reveal that ADP-ribosylation controls the composition of biomolecular condensates, specifically the localization of translation initiation factors, during alphavirus infection.
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Markey FB, Romero B, Parashar V, Batish M. Identification of a New Transcriptional Co-Regulator of STEAP1 in Ewing's Sarcoma. Cells 2021; 10:cells10061300. [PMID: 34073779 PMCID: PMC8225120 DOI: 10.3390/cells10061300] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/18/2021] [Accepted: 05/21/2021] [Indexed: 12/28/2022] Open
Abstract
Ewing’s sarcoma (ES) is caused by a chromosomal translocation leading to the formation of the fused EWSFLI1 gene, which codes for an aberrant transcription factor EWSFLI1. The transcriptional targets of EWSFLI1 have been viewed as promising and novel drug targets in the treatment of ES. One such target is six transmembrane epithelial antigen of the prostate 1 (STEAP1), a transmembrane protein that is upregulated by EWSFLI1 in ES. STEAP1 is a hallmark of tumor invasiveness and an indicator of tumor responsiveness to therapy. EWSFLI1 binds to the STEAP1 promoter region, but the mechanism of action by which it upregulates STEAP1 expression in ES is not entirely understood. Upon analysis of the STEAP1 promoter, we predicted two binding sites for NKX2.2, another crucial transcription factor involved in ES pathogenesis. We confirmed the interaction of NKX2.2 with the STEAP1 promoter using chromatin immunoprecipitation (ChIP) analysis. We used single-molecule RNA imaging, biochemical, and genetic studies to identify the novel role of NKX2.2 in regulating STEAP1 expression in ES. Our results show that NKX2.2 is a co-regulator of STEAP1 expression and functions by interacting with the STEAP1 promoter at sites proximal to the reported EWSFLI1 sites. The co-operative interaction of NKX2.2 with EWSFLI1 in regulating STEAP1 holds potential as a new target for therapeutic interventions for ES.
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Affiliation(s)
- Fatu Badiane Markey
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers Biomedical and Health Sciences, Rutgers University, Newark, NJ 07103, USA;
| | - Brigette Romero
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19713, USA; (B.R.); (V.P.)
| | - Vijay Parashar
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19713, USA; (B.R.); (V.P.)
| | - Mona Batish
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers Biomedical and Health Sciences, Rutgers University, Newark, NJ 07103, USA;
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19713, USA; (B.R.); (V.P.)
- Correspondence: ; Tel.: +1-302-831-8591
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Markey FB, Parashar V, Batish M. Methods for spatial and temporal imaging of the different steps involved in RNA processing at single-molecule resolution. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1608. [PMID: 32543077 DOI: 10.1002/wrna.1608] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 05/06/2020] [Accepted: 05/07/2020] [Indexed: 12/26/2022]
Abstract
RNA plays a quintessential role as a messenger of information from genotype (DNA) to phenotype (proteins), as well as acts as a regulatory molecule (noncoding RNAs). All steps in the journey of RNA from synthesis (transcription), splicing, transport, localization, translation, to its eventual degradation, comprise important steps in gene expression, thereby controlling the fate of the cell. This lifecycle refers to the majority of RNAs (primarily mRNAs), but not other RNAs such as tRNAs. Imaging these processes in fixed cells and in live cells has been an important tool in developing an understanding of the regulatory steps in RNAs journey. Single-cell and single-molecule imaging techniques enable a much deeper understanding of cellular biology, which is not possible with bulk studies involving RNA isolated from a large pool of cells. Classic techniques, such as fluorescence in situ hybridization (FISH), as well as more recent aptamer-based approaches, have provided detailed insights into RNA localization, and have helped to predict the functions carried out by many RNA species. However, there are still certain processing steps that await high-resolution imaging, which is an exciting and upcoming area of research. In this review, we will discuss the methods that have revolutionized single-molecule resolution imaging in general, the steps of RNA processing in which these methods have been used, and new emerging technologies. This article is categorized under: RNA Export and Localization > RNA Localization RNA Methods > RNA Analyses in Cells RNA Interactions with Proteins and Other Molecules > Small Molecule-RNA Interactions.
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Affiliation(s)
- Fatu Badiane Markey
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Vijay Parashar
- Department of Medical and Molecular Sciences, University of Delaware, Newark, Delaware, USA
| | - Mona Batish
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA.,Department of Medical and Molecular Sciences, University of Delaware, Newark, Delaware, USA
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