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Lyu QR, Zhang S, Zhang Z, Tang Z. Functional knockout of long non-coding RNAs with genome editing. Front Genet 2023; 14:1242129. [PMID: 37705609 PMCID: PMC10495571 DOI: 10.3389/fgene.2023.1242129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 08/16/2023] [Indexed: 09/15/2023] Open
Abstract
An effective loss-of-function study is necessary to investigate the biological function of long non-coding RNA (lncRNA). Various approaches are available, including RNA silencing, antisense oligos, and CRISPR-based genome editing. CRISPR-based genome editing is the most widely used for inactivating lncRNA function at the genomic level. Knocking out the lncRNA function can be achieved by removing the promoter and the first exon (PE1), introducing pre-termination poly(A) signals, or deleting the entire locus, unlike frameshift strategies used for messenger RNA (mRNA). However, the intricate genomic interplay between lncRNA and neighbor genes makes it challenging to interpret lncRNA function accurately. This article discusses the advantages and disadvantages of each lncRNA knockout method and envisions the potential future directions to facilitate lncRNA functional study.
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Affiliation(s)
- Qing Rex Lyu
- Medical Research Center, Chongqing General Hospital, Chongqing, China
- Chongqing Academy of Medical Sciences, Chongqing, China
| | - Shikuan Zhang
- Key Lab in Healthy Science and Technology of Shenzhen, Tsinghua Shenzhen International Graduate School, Shenzhen, China
| | - Zhe Zhang
- Department of Chinese Medical Gastrointestinal of China-Japan Friendship Hospital, Beijing, China
| | - Zhiyu Tang
- Medical Research Center, Chongqing General Hospital, Chongqing, China
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Abstract
The number of human LncRNAs has now exceeded all known protein-coding genes. Most studies of human LncRNAs have been conducted in cell culture systems where various mechanisms of action have been worked out. On the other hand, efforts to elucidate the function of human LncRNAs in an in vivo setting have been limited. In this brief review, we highlight some strengths and weaknesses of studying human LncRNAs in the mouse. Special consideration is given to bacterial artificial chromosome transgenesis and genome editing. The integration of these technical innovations offers an unprecedented opportunity to complement and extend the expansive literature of cell culture models for the study of human LncRNAs. Two different examples of how BAC transgenesis and genome editing can be leveraged to gain insight into human LncRNA regulation and function in mice are presented: the random integration of a vascular cell-enriched LncRNA and a targeted approach for a new LncRNA immediately upstream of the ACE2 gene, which encodes the receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiologic agent underlying the coronavirus disease-19 (COVID-19) pandemic.
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Affiliation(s)
- Amr R Ghanam
- Vascular Biology Center, Department of Medicine, Medical College of Georgia at Augusta University, 1460 Laney Walker Blvd, CL-3060, Augusta, GA, 30912, USA
| | - William B Bryant
- Vascular Biology Center, Department of Medicine, Medical College of Georgia at Augusta University, 1460 Laney Walker Blvd, CL-3060, Augusta, GA, 30912, USA
| | - Joseph M Miano
- Vascular Biology Center, Department of Medicine, Medical College of Georgia at Augusta University, 1460 Laney Walker Blvd, CL-3060, Augusta, GA, 30912, USA.
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Vitiello M, Poliseno L, Pandolfi PP. In Vivo Silencing/Overexpression of lncRNAs by CRISPR/Cas System. Methods Mol Biol 2021; 2348:205-20. [PMID: 34160809 DOI: 10.1007/978-1-0716-1581-2_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Long noncoding RNAs (lncRNAs) are implicated in several biological processes and it has been observed that their expression is altered in several diseases. The generation of animal models where selective silencing or overexpression of lncRNAs can be attained is crucial for their biological characterization, since it offers the opportunity to analyze their function at the tissue specific or organismal level. CRISPR/Cas technology is a newly developed tool that allows to easily manipulate the mouse genome, in turn allowing to discover lncRNAs functions in an in vivo context. Here, we provide an overview of how CRISPR/Cas technology can be used to generate transgenic mouse models in which lncRNAs can be studied.
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Abstract
Genetically engineered mouse (GEM) models are commonly used in biomedical research. Generating GEMs involve complex set of experimental procedures requiring sophisticated equipment and highly skilled technical staff. Because of these reasons, most research institutes set up centralized core facilities where custom GEMs are created for research groups. Researchers, on the other hand, when they begin thinking about generating GEMs for their research, several questions arise in their minds. For example, what type of model(s) would be best useful for my research, how do I design them, what are the latest technologies and tools available for developing my model(s), and finally how to breed GEMs in my research. As there are several considerations and options in mouse designs, and as it is an expensive and time-consuming endeavor, careful planning upfront can ensure the highest chance of success. In this article, we provide brief answers to several frequently asked questions that arise when researchers begin thinking about generating mouse model(s) for their work.
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Affiliation(s)
- Channabasavaiah B Gurumurthy
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68106-5915, USA.,Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68106-5915, USA
| | - Thomas L Saunders
- Department of Internal Medicine, Division of Genetic Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Transgenic Animal Model Core, University of Michigan, Ann Arbor, MI 48109, USA
| | - Masato Ohtsuka
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan.,The Institute of Medical Sciences, Tokai University, Isehara, Kanagawa 259-1193, Japan
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Gu YY, Lu FH, Huang XR, Zhang L, Mao W, Yu XQ, Liu XS, Lan HY. Non-Coding RNAs as Biomarkers and Therapeutic Targets for Diabetic Kidney Disease. Front Pharmacol 2021; 11:583528. [PMID: 33574750 PMCID: PMC7870688 DOI: 10.3389/fphar.2020.583528] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 12/14/2020] [Indexed: 12/20/2022] Open
Abstract
Diabetic kidney disease (DKD) is the most common diabetic complication and is a leading cause of end-stage kidney disease. Increasing evidence shows that DKD is regulated not only by many classical signaling pathways but also by epigenetic mechanisms involving chromatin histone modifications, DNA methylation, and non-coding RNA (ncRNAs). In this review, we focus on our current understanding of the role and mechanisms of ncRNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) in the pathogenesis of DKD. Of them, the regulatory role of TGF-β/Smad3-dependent miRNAs and lncRNAs in DKD is highlighted. Importantly, miRNAs and lncRNAs as biomarkers and therapeutic targets for DKD are also described, and the perspective of ncRNAs as a novel therapeutic approach for combating diabetic nephropathy is also discussed.
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Affiliation(s)
- Yue-Yu Gu
- Department of Nephrology and State Key Laboratory of Dampness Syndrome of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Fu-Hua Lu
- Department of Nephrology and State Key Laboratory of Dampness Syndrome of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiao-Ru Huang
- Department of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Guangdong-Hong Kong Joint Laboratory for Immunological and Genetic Kidney Diseases, Guangdong Academy of Medical Sciences, Guangdong Provincial People's Hospital, Guangzhou, China.,Guangdong-Hong Kong Joint Laboratory for Immunological and Genetic Kidney Diseases, The Chinese University of Hong Kong, Hong Kong, China
| | - Lei Zhang
- Department of Nephrology and State Key Laboratory of Dampness Syndrome of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Wei Mao
- Department of Nephrology and State Key Laboratory of Dampness Syndrome of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xue-Qing Yu
- Guangdong-Hong Kong Joint Laboratory for Immunological and Genetic Kidney Diseases, Guangdong Academy of Medical Sciences, Guangdong Provincial People's Hospital, Guangzhou, China
| | - Xu-Sheng Liu
- Department of Nephrology and State Key Laboratory of Dampness Syndrome of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Hui-Yao Lan
- Department of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Guangdong-Hong Kong Joint Laboratory for Immunological and Genetic Kidney Diseases, Guangdong Academy of Medical Sciences, Guangdong Provincial People's Hospital, Guangzhou, China.,Guangdong-Hong Kong Joint Laboratory for Immunological and Genetic Kidney Diseases, The Chinese University of Hong Kong, Hong Kong, China
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Gao P, Gao P, Choi M, Chegireddy K, Slivano OJ, Zhao J, Zhang W, Long X. Transcriptome analysis of mouse aortae reveals multiple novel pathways regulated by aging. Aging (Albany NY) 2020; 12:15603-15623. [PMID: 32805724 PMCID: PMC7467355 DOI: 10.18632/aging.103652] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 06/22/2020] [Indexed: 01/10/2023]
Abstract
Vascular aging has been documented as a vital process leading to arterial dysfunction and age-related cardiovascular and cerebrovascular diseases. However, our understanding of the molecular underpinnings of age-related phenotypes in the vascular system is incomplete. Here we performed bulk RNA sequencing in young and old mouse aortae to elucidate age-associated changes in the transcriptome. Results showed that the majority of upregulated pathways in aged aortae relate to immune response, including inflammation activation, apoptotic clearance, and phagocytosis. The top downregulated pathway in aged aortae was extracellular matrix organization. Additionally, protein folding control and stress response pathways were downregulated in the aged vessels, with an array of downregulated genes encoding heat shock proteins (HSPs). We also found that circadian core clock genes were differentially expressed in young versus old aortae. Finally, transcriptome analysis combined with protein expression examination and smooth muscle cell (SMC) lineage tracing revealed that SMCs in aged aortae retained the differentiated phenotype, with an insignificant decrease in SMC marker gene expression. Our results therefore unveiled critical pathways regulated by arterial aging in mice, which will provide important insight into strategies to defy vascular aging and age-associated vascular diseases.
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Affiliation(s)
- Ping Gao
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA
| | - Pan Gao
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA
| | - Mihyun Choi
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA
| | - Kavya Chegireddy
- School of Public Health, University at Albany, Albany, NY 12222, USA
| | - Orazio J Slivano
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA
| | - Jinjing Zhao
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA
| | - Wei Zhang
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA
| | - Xiaochun Long
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA.,Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA
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Das S, Shah R, Dimmeler S, Freedman JE, Holley C, Lee JM, Moore K, Musunuru K, Wang DZ, Xiao J, Yin KJ. Noncoding RNAs in Cardiovascular Disease: Current Knowledge, Tools and Technologies for Investigation, and Future Directions: A Scientific Statement From the American Heart Association. Circ: Genomic and Precision Medicine 2020; 13:e000062. [DOI: 10.1161/hcg.0000000000000062] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Background:
The discovery that much of the non–protein-coding genome is transcribed and plays a diverse functional role in fundamental cellular processes has led to an explosion in the development of tools and technologies to investigate the role of these noncoding RNAs in cardiovascular health. Furthermore, identifying noncoding RNAs for targeted therapeutics to treat cardiovascular disease is an emerging area of research. The purpose of this statement is to review existing literature, offer guidance on tools and technologies currently available to study noncoding RNAs, and identify areas of unmet need.
Methods:
The writing group used systematic literature reviews (including MEDLINE, Web of Science through 2018), expert opinion/statements, analyses of databases and computational tools/algorithms, and review of current clinical trials to provide a broad consensus on the current state of the art in noncoding RNA in cardiovascular disease.
Results:
Significant progress has been made since the initial studies focusing on the role of miRNAs (microRNAs) in cardiovascular development and disease. Notably, recent progress on understanding the role of novel types of noncoding small RNAs such as snoRNAs (small nucleolar RNAs), tRNA (transfer RNA) fragments, and Y-RNAs in cellular processes has revealed a noncanonical function for many of these molecules. Similarly, the identification of long noncoding RNAs that appear to play an important role in cardiovascular disease processes, coupled with the development of tools to characterize their interacting partners, has led to significant mechanistic insight. Finally, recent work has characterized the unique role of extracellular RNAs in mediating intercellular communication and their potential role as biomarkers.
Conclusions:
The rapid expansion of tools and pipelines for isolating, measuring, and annotating these entities suggests that caution in interpreting results is warranted until these methodologies are rigorously validated. Most investigators have focused on investigating the functional role of single RNA entities, but studies suggest complex interaction between different RNA molecules. The use of network approaches and advanced computational tools to understand the interaction of different noncoding RNA species to mediate a particular phenotype may be required to fully comprehend the function of noncoding RNAs in mediating disease phenotypes.
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Choi M, Lu YW, Zhao J, Wu M, Zhang W, Long X. Transcriptional control of a novel long noncoding RNA Mymsl in smooth muscle cells by a single Cis-element and its initial functional characterization in vessels. J Mol Cell Cardiol 2020; 138:147-57. [PMID: 31751568 DOI: 10.1016/j.yjmcc.2019.11.148] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/10/2019] [Accepted: 11/05/2019] [Indexed: 02/08/2023]
Abstract
Differentiated vascular smooth muscle cells (VSMCs) are crucial in maintaining vascular homeostasis. While the coding transcriptome of the differentiated VSMC phenotype has been defined, we know little about its noncoding signature. Herein, we identified a Myocardin-induced muscle specific long noncoding RNA (lncRNA) (Mymsl) downregulated upon VSMC phenotypic modulation. We demonstrated an essential role of a proximal consensus CArG element in response to MYOCD/SRF in vitro. To validate the in vivo role of this CArG element, we generated CArG mutant mice via CRISPR-Cas9 genome editing. While the CArG mutation had no impact on the expression of surrounding genes, it abolished Mymsl expression in SMCs, but not skeletal and cardiac muscle. Chromatin immunoprecipitation assays (ChIPs) showed decreased SRF binding to CArG region in mutants whereas the enrichment of H3K79Me2 remained the same. RNA-seq analysis showed a downregulation of matrix genes in aortas from Mymsl knockout mice, which was further validated in injured carotid arteries. Our study defined the transcriptional control of a novel lncRNA in SMCs via a single transcription factor binding site, which may offer a new strategy for generating SMC-specific knockout mouse models. We also provided in vivo evidence supporting the potential importance of Mymsl in vascular pathophysiology.
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