51
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Esposito R, Bosch N, Lanzós A, Polidori T, Pulido-Quetglas C, Johnson R. Hacking the Cancer Genome: Profiling Therapeutically Actionable Long Non-coding RNAs Using CRISPR-Cas9 Screening. Cancer Cell 2019; 35:545-557. [PMID: 30827888 DOI: 10.1016/j.ccell.2019.01.019] [Citation(s) in RCA: 138] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/20/2018] [Accepted: 01/28/2019] [Indexed: 12/26/2022]
Abstract
Long non-coding RNAs (lncRNAs) represent a huge reservoir of potential cancer targets. Such "onco-lncRNAs" have resisted traditional RNAi methods, but CRISPR-Cas9 genome editing now promises functional screens at high throughput and low cost. The unique biology of lncRNAs demands screening strategies distinct from protein-coding genes. The first such screens have identified hundreds of onco-lncRNAs promoting cell proliferation and drug resistance. Ongoing developments will further improve screen performance and translational relevance. This Review aims to highlight the potential of CRISPR screening technology for discovering new onco-lncRNAs, and to guide molecular oncologists wishing to apply it to their cancer of interest.
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Affiliation(s)
- Roberta Esposito
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Núria Bosch
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Andrés Lanzós
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Taisia Polidori
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Carlos Pulido-Quetglas
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Rory Johnson
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland.
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52
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Turner AW, Wong D, Khan MD, Dreisbach CN, Palmore M, Miller CL. Multi-Omics Approaches to Study Long Non-coding RNA Function in Atherosclerosis. Front Cardiovasc Med 2019; 6:9. [PMID: 30838214 PMCID: PMC6389617 DOI: 10.3389/fcvm.2019.00009] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 01/30/2019] [Indexed: 12/15/2022] Open
Abstract
Atherosclerosis is a complex inflammatory disease of the vessel wall involving the interplay of multiple cell types including vascular smooth muscle cells, endothelial cells, and macrophages. Large-scale genome-wide association studies (GWAS) and the advancement of next generation sequencing technologies have rapidly expanded the number of long non-coding RNA (lncRNA) transcripts predicted to play critical roles in the pathogenesis of the disease. In this review, we highlight several lncRNAs whose functional role in atherosclerosis is well-documented through traditional biochemical approaches as well as those identified through RNA-sequencing and other high-throughput assays. We describe novel genomics approaches to study both evolutionarily conserved and divergent lncRNA functions and interactions with DNA, RNA, and proteins. We also highlight assays to resolve the complex spatial and temporal regulation of lncRNAs. Finally, we summarize the latest suite of computational tools designed to improve genomic and functional annotation of these transcripts in the human genome. Deep characterization of lncRNAs is fundamental to unravel coronary atherosclerosis and other cardiovascular diseases, as these regulatory molecules represent a new class of potential therapeutic targets and/or diagnostic markers to mitigate both genetic and environmental risk factors.
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Affiliation(s)
- Adam W. Turner
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Doris Wong
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
| | - Mohammad Daud Khan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Caitlin N. Dreisbach
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
- School of Nursing, University of Virginia, Charlottesville, VA, United States
- Data Science Institute, University of Virginia, Charlottesville, VA, United States
| | - Meredith Palmore
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Clint L. Miller
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
- Data Science Institute, University of Virginia, Charlottesville, VA, United States
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, United States
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, United States
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53
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Hansmeier NR, Widdershooven PJM, Khani S, Kornfeld JW. Rapid Generation of Long Noncoding RNA Knockout Mice Using CRISPR/Cas9 Technology. Noncoding RNA 2019; 5:ncrna5010012. [PMID: 30678101 PMCID: PMC6468733 DOI: 10.3390/ncrna5010012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 01/11/2019] [Accepted: 01/14/2019] [Indexed: 12/11/2022] Open
Abstract
In recent years, long noncoding RNAs (lncRNAs) have emerged as multifaceted regulators of gene expression, controlling key developmental and disease pathogenesis processes. However, due to the paucity of lncRNA loss-of-function mouse models, key questions regarding the involvement of lncRNAs in organism homeostasis and (patho)-physiology remain difficult to address experimentally in vivo. The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 platform provides a powerful genome-editing tool and has been successfully applied across model organisms to facilitate targeted genetic mutations, including Caenorhabditis elegans, Drosophila melanogaster, Danio rerio and Mus musculus. However, just a few lncRNA-deficient mouse lines have been created using CRISPR/Cas9-mediated genome engineering, presumably due to the need for lncRNA-specific gene targeting strategies considering the absence of open-reading frames in these loci. Here, we describe a step-wise procedure for the generation and validation of lncRNA loss-of-function mouse models using CRISPR/Cas9-mediated genome engineering. In a proof-of-principle approach, we generated mice deficient for the liver-enriched lncRNA Gm15441, which we found downregulated during development of metabolic disease and induced during the feeding/fasting transition. Further, we discuss guidelines for the selection of lncRNA targets and provide protocols for in vitro single guide RNA (sgRNA) validation, assessment of in vivo gene-targeting efficiency and knockout confirmation. The procedure from target selection to validation of lncRNA knockout mouse lines can be completed in 18–20 weeks, of which <10 days hands-on working time is required.
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Affiliation(s)
- Nils R Hansmeier
- Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany.
- Cologne Cluster of Excellence: Cellular Stress Responses in Ageing-associated Diseases, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany.
| | - Pia J M Widdershooven
- Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany.
| | - Sajjad Khani
- Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany.
- Cologne Cluster of Excellence: Cellular Stress Responses in Ageing-associated Diseases, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany.
- Institute for Prophylaxis and Epidemiology of Cardiovascular Diseases (IPEK), Ludwig Maximilian University of Munich, 80336 Munich, Germany.
| | - Jan-Wilhelm Kornfeld
- Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany.
- Cologne Cluster of Excellence: Cellular Stress Responses in Ageing-associated Diseases, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany.
- Department for Biochemistry and Molecular Biology, Functional Genomics and Metabolism Unit, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
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54
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Zhen S, Li X. Application of CRISPR-Cas9 for Long Noncoding RNA Genes in Cancer Research. Hum Gene Ther 2019; 30:3-9. [PMID: 30045635 DOI: 10.1089/hum.2018.063] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Shuai Zhen
- Center for Translational Medicine, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
- Key Laboratory for Tumor Precision Medicine of Shaanxi Province, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xu Li
- Center for Translational Medicine, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
- Key Laboratory for Tumor Precision Medicine of Shaanxi Province, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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55
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Abstract
At the beginning of this century, the Human Genome Project produced the first drafts of the human genome sequence. Following this, large-scale functional genomics studies were initiated to understand the molecular basis underlying the translation of the instructions encoded in the genome into the biological traits of organisms. Instrumental in the ensuing revolution in functional genomics were the rapid advances in massively parallel sequencing technologies as well as the development of a wide diversity of protocols that make use of these technologies to understand cellular behavior at the molecular level. Here, we review recent advances in functional genomic methods, discuss some of their current capabilities and limitations, and briefly sketch future directions within the field.
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Affiliation(s)
- Roderic Guigo
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Michiel de Hoon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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56
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Kim J, Piao HL, Kim BJ, Yao F, Han Z, Wang Y, Xiao Z, Siverly AN, Lawhon SE, Ton BN, Lee H, Zhou Z, Gan B, Nakagawa S, Ellis MJ, Liang H, Hung MC, You MJ, Sun Y, Ma L. Long noncoding RNA MALAT1 suppresses breast cancer metastasis. Nat Genet 2018; 50:1705-1715. [PMID: 30349115 PMCID: PMC6265076 DOI: 10.1038/s41588-018-0252-3] [Citation(s) in RCA: 504] [Impact Index Per Article: 84.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 09/07/2018] [Indexed: 12/17/2022]
Abstract
MALAT1 has previously been described as a metastasis-promoting long noncoding RNA (lncRNA). We show here, however, that targeted inactivation of the Malat1 gene in a transgenic mouse model of breast cancer, without altering the expression of its adjacent genes, promotes lung metastasis, and that this phenotype can be reversed by genetic add-back of Malat1. Similarly, knockout of MALAT1 in human breast cancer cells induces their metastatic ability, which is reversed by re-expression of Malat1. Conversely, overexpression of Malat1 suppresses breast cancer metastasis in transgenic, xenograft, and syngeneic models. Mechanistically, the MALAT1 lncRNA binds and inactivates the prometastatic transcription factor TEAD, preventing TEAD from associating with its co-activator YAP and target gene promoters. Moreover, MALAT1 levels inversely correlate with breast cancer progression and metastatic ability. These findings demonstrate that MALAT1 is a metastasis-suppressing lncRNA rather than a metastasis promoter in breast cancer, calling for rectification of the model for this highly abundant and conserved lncRNA.
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Affiliation(s)
- Jongchan Kim
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hai-Long Piao
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Scientific Research Center for Translational Medicine, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Beom-Jun Kim
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Fan Yao
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhenbo Han
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yumeng Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhenna Xiao
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Ashley N Siverly
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sarah E Lawhon
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Baochau N Ton
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hyemin Lee
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhicheng Zhou
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Boyi Gan
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Matthew J Ellis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mien-Chie Hung
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Graduate Institute of Biomedical Sciences and Center for Molecular Medicine, China Medical University, Taichung, Taiwan
| | - M James You
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yutong Sun
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Li Ma
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA.
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57
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Wong NK, Huang CL, Islam R, Yip SP. Long non-coding RNAs in hematological malignancies: translating basic techniques into diagnostic and therapeutic strategies. J Hematol Oncol 2018; 11:131. [PMID: 30466456 PMCID: PMC6251105 DOI: 10.1186/s13045-018-0673-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/23/2018] [Indexed: 12/26/2022] Open
Abstract
Recent studies have revealed that non-coding regions comprise the vast majority of the human genome and long non-coding RNAs (lncRNAs) are a diverse class of non-coding RNAs that has been implicated in a variety of biological processes. Abnormal expression of lncRNAs has also been linked to different human diseases including cancers, yet the regulatory mechanisms and functional effects of lncRNAs are still ambiguous, and the molecular details also need to be confirmed. Unlike protein-coding gene, it is much more challenging to unravel the roles of lncRNAs owing to their unique and complex features such as functional diversity and low conservation among species, which greatly hamper their experimental characterization. In this review, we summarize and discuss both conventional and advanced approaches for the identification and functional characterization of lncRNAs related to hematological malignancies. In particular, the utility and advancement of clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system as gene-editing tools are envisioned to facilitate the molecular dissection of lncRNAs via different knock-in/out strategies. Besides experimental considerations specific to lncRNAs, the roles of lncRNAs in the pathogenesis and progression of leukemia are also highlighted in the review. We expect that these insights may ultimately lead to clinical applications including development of biomarkers and novel therapeutic approaches targeting lncRNAs.
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Affiliation(s)
- Nonthaphat Kent Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Y9/F, Lee Shau Kee Building, Hung Hom, Hong Kong SAR, China
| | - Chien-Ling Huang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Y9/F, Lee Shau Kee Building, Hung Hom, Hong Kong SAR, China.
| | - Rashidul Islam
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Y9/F, Lee Shau Kee Building, Hung Hom, Hong Kong SAR, China
| | - Shea Ping Yip
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Y9/F, Lee Shau Kee Building, Hung Hom, Hong Kong SAR, China.
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58
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Liu SJ, Lim DA. Modulating the expression of long non-coding RNAs for functional studies. EMBO Rep 2018; 19:embr.201846955. [PMID: 30467236 DOI: 10.15252/embr.201846955] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 10/29/2018] [Accepted: 10/30/2018] [Indexed: 01/24/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as important regulators of cell biology. The mechanisms by which lncRNAs function are likely numerous, and most are poorly understood. Currently, the mechanisms of functional lncRNAs include those that directly involve the lncRNA transcript, the process of their own transcription and splicing, and even underlying transcriptional regulatory elements within the genomic DNA that encodes the lncRNA As our understanding of lncRNA biology evolves, so have the methods that are utilized to elucidate their functions. In this review, we survey a collection of different methods used to modulate lncRNA expression levels for the assessment of biological function. From RNA-targeted strategies, genetic deletions, to engineered gene regulatory systems, the advantages and caveats of each method will be discussed. Ultimately, the selection of tools will be guided by which potential lncRNA mechanisms are being investigated, and no single method alone will likely be sufficient to reveal the function of any particular lncRNA.
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Affiliation(s)
- S John Liu
- Department of Neurological Surgery, University of California, San Francisco, CA, USA .,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA
| | - Daniel A Lim
- Department of Neurological Surgery, University of California, San Francisco, CA, USA .,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA.,San Francisco Veterans Affairs Medical Center, San Francisco, CA, USA
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59
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Pant T, Dhanasekaran A, Fang J, Bai X, Bosnjak ZJ, Liang M, Ge ZD. Current status and strategies of long noncoding RNA research for diabetic cardiomyopathy. BMC Cardiovasc Disord 2018; 18:197. [PMID: 30342478 PMCID: PMC6196023 DOI: 10.1186/s12872-018-0939-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 10/12/2018] [Indexed: 12/13/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are endogenous RNA transcripts longer than 200 nucleotides which regulate epigenetically the expression of genes but do not have protein-coding potential. They are emerging as potential key regulators of diabetes mellitus and a variety of cardiovascular diseases. Diabetic cardiomyopathy (DCM) refers to diabetes mellitus-elicited structural and functional abnormalities of the myocardium, beyond that caused by ischemia or hypertension. The purpose of this review was to summarize current status of lncRNA research for DCM and discuss the challenges and possible strategies of lncRNA research for DCM. A systemic search was performed using PubMed and Google Scholar databases. Major conference proceedings of diabetes mellitus and cardiovascular disease occurring between January, 2014 to August, 2018 were also searched to identify unpublished studies that may be potentially eligible. The pathogenesis of DCM involves elevated oxidative stress, myocardial inflammation, apoptosis, and autophagy due to metabolic disturbances. Thousands of lncRNAs are aberrantly regulated in DCM. Manipulating the expression of specific lncRNAs, such as H19, metastasis-associated lung adenocarcinoma transcript 1, and myocardial infarction-associated transcript, with genetic approaches regulates potently oxidative stress, myocardial inflammation, apoptosis, and autophagy and ameliorates DCM in experimental animals. The detail data regarding the regulation and function of individual lncRNAs in DCM are limited. However, lncRNAs have been considered as potential diagnostic and therapeutic targets for DCM. Overexpression of protective lncRNAs and knockdown of detrimental lncRNAs in the heart are crucial for defining the role and function of lncRNAs of interest in DCM, however, they are technically challenging due to the length, short life, and location of lncRNAs. Gene delivery vectors can provide exogenous sources of cardioprotective lncRNAs to ameliorate DCM, and CRISPR–Cas9 genome editing technology may be used to knockdown specific lncRNAs in DCM. In summary, current data indicate that LncRNAs are a vital regulator of DCM and act as the promising diagnostic and therapeutic targets for DCM.
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Affiliation(s)
- Tarun Pant
- Department of Medicine, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.,Centre for Biotechnology, Anna University, Chennai, Tamil Nadu, India
| | | | - Juan Fang
- Department of Pediatrics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Xiaowen Bai
- Department of Cell Biology, Neurology & Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.,Department of Physiology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Zeljko J Bosnjak
- Department of Medicine, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.,Department of Physiology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Mingyu Liang
- Department of Physiology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Zhi-Dong Ge
- Department of Ophthalmology, Stanford School of Medicine, 1651 Page Mill Road, Stanford, CA, 94304, USA.
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60
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Guo T, Feng YL, Xiao JJ, Liu Q, Sun XN, Xiang JF, Kong N, Liu SC, Chen GQ, Wang Y, Dong MM, Cai Z, Lin H, Cai XJ, Xie AY. Harnessing accurate non-homologous end joining for efficient precise deletion in CRISPR/Cas9-mediated genome editing. Genome Biol 2018; 19:170. [PMID: 30340517 PMCID: PMC6195759 DOI: 10.1186/s13059-018-1518-x] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 08/25/2018] [Indexed: 11/25/2022] Open
Abstract
Background Many applications of CRISPR/Cas9-mediated genome editing require Cas9-induced non-homologous end joining (NHEJ), which was thought to be error prone. However, with directly ligatable ends, Cas9-induced DNA double strand breaks may be repaired preferentially by accurate NHEJ. Results In the repair of two adjacent double strand breaks induced by paired Cas9-gRNAs at 71 genome sites, accurate NHEJ accounts for about 50% of NHEJ events. This paired Cas9-gRNA approach underestimates the level of accurate NHEJ due to frequent + 1 templated insertions, which can be avoided by the predefined Watson/Crick orientation of protospacer adjacent motifs (PAMs). The paired Cas9-gRNA strategy also provides a flexible, reporter-less approach for analyzing both accurate and mutagenic NHEJ in cells and in vivo, and it has been validated in cells deficient for XRCC4 and in mouse liver. Due to high frequencies of precise deletions of defined “3n”-, “3n + 1”-, or “3n + 2”-bp length, accurate NHEJ is used to improve the efficiency and homogeneity of gene knockouts and targeted in-frame deletions. Compared to “3n + 1”-bp, “3n + 2”-bp can overcome + 1 templated insertions to increase the frequency of out-of-frame mutations. By applying paired Cas9-gRNAs to edit MDC1 and key 53BP1 domains, we are able to generate predicted, precise deletions for functional analysis. Lastly, a Plk3 inhibitor promotes NHEJ with bias towards accurate NHEJ, providing a chemical approach to improve genome editing requiring precise deletions. Conclusions NHEJ is inherently accurate in repair of Cas9-induced DNA double strand breaks and can be harnessed to improve CRISPR/Cas9 genome editing requiring precise deletion of a defined length. Electronic supplementary material The online version of this article (10.1186/s13059-018-1518-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tao Guo
- Department of General Surgery, Innovation Center for Minimally Invasive Techniques and Devices, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang, 310019, Hangzhou, China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang, 310029, Hangzhou, China
| | - Yi-Li Feng
- Department of General Surgery, Innovation Center for Minimally Invasive Techniques and Devices, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang, 310019, Hangzhou, China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang, 310029, Hangzhou, China
| | - Jing-Jing Xiao
- Department of General Surgery, Innovation Center for Minimally Invasive Techniques and Devices, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang, 310019, Hangzhou, China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang, 310029, Hangzhou, China
| | - Qian Liu
- Department of General Surgery, Innovation Center for Minimally Invasive Techniques and Devices, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang, 310019, Hangzhou, China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang, 310029, Hangzhou, China
| | - Xiu-Na Sun
- Department of General Surgery, Innovation Center for Minimally Invasive Techniques and Devices, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang, 310019, Hangzhou, China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang, 310029, Hangzhou, China
| | - Ji-Feng Xiang
- Department of General Surgery, Innovation Center for Minimally Invasive Techniques and Devices, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang, 310019, Hangzhou, China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang, 310029, Hangzhou, China.,Department of General Surgery, Chongqing General Hospital, Chongqing, 400013, China
| | - Na Kong
- Department of General Surgery, Innovation Center for Minimally Invasive Techniques and Devices, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang, 310019, Hangzhou, China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang, 310029, Hangzhou, China
| | - Si-Cheng Liu
- Department of General Surgery, Innovation Center for Minimally Invasive Techniques and Devices, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang, 310019, Hangzhou, China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang, 310029, Hangzhou, China
| | - Guo-Qiao Chen
- Department of General Surgery, Innovation Center for Minimally Invasive Techniques and Devices, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang, 310019, Hangzhou, China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang, 310029, Hangzhou, China
| | - Yue Wang
- Department of General Surgery, Innovation Center for Minimally Invasive Techniques and Devices, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang, 310019, Hangzhou, China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang, 310029, Hangzhou, China
| | - Meng-Meng Dong
- Multiple Myeloma Treatment Center & Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, 310003, Hangzhou, China
| | - Zhen Cai
- Multiple Myeloma Treatment Center & Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, 310003, Hangzhou, China
| | - Hui Lin
- Department of General Surgery, Innovation Center for Minimally Invasive Techniques and Devices, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang, 310019, Hangzhou, China
| | - Xiu-Jun Cai
- Department of General Surgery, Innovation Center for Minimally Invasive Techniques and Devices, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang, 310019, Hangzhou, China.
| | - An-Yong Xie
- Department of General Surgery, Innovation Center for Minimally Invasive Techniques and Devices, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang, 310019, Hangzhou, China. .,Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang, 310029, Hangzhou, China.
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61
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Abstract
SIGNIFICANCE To maintain homeostasis, gene expression has to be tightly regulated by complex and multiple mechanisms occurring at the epigenetic, transcriptional, and post-transcriptional levels. One crucial regulatory component is represented by long noncoding RNAs (lncRNAs), nonprotein-coding RNA species implicated in all of these levels. Thus, lncRNAs have been associated with any given process or pathway of interest in a variety of systems, including the heart. Recent Advances: Mounting evidence implicates lncRNAs in cardiovascular diseases (CVD) and progression and their presence in the blood of heart disease patients indicates that they are attractive potential biomarkers. CRITICAL ISSUES Our understanding of the regulation and molecular mechanisms of action of most lncRNAs remains rudimentary. A challenge is represented by their often low evolutionary sequence conservation that limits the use of animal models for preclinical studies. Nevertheless, a growing number of lncRNAs with an impact on heart function is rapidly accumulating. In this study, we will discuss (i) lncRNAs that control heart homeostasis and disease; (ii) concepts, approaches, and methodologies necessary to study lncRNAs in the heart; and (iii) challenges posed and opportunities presented by lncRNAs as potential therapeutic targets and biomarkers. FUTURE DIRECTIONS A deeper knowledge of the molecular mechanisms underpinning CVDs is necessary to develop more effective treatments. Further studies are needed to clarify the regulation and function of lncRNAs in the heart before they can be considered as therapeutic targets and disease biomarkers. Antioxid. Redox Signal. 29, 880-901.
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Affiliation(s)
- Simona Greco
- 1 Molecular Cardiology Laboratory, IRCCS Policlinico San Donato , Milan, Italy
| | - Antonio Salgado Somoza
- 2 Cardiovascular Research Unit, Luxembourg Institute of Health (LIH) , Luxembourg, Luxembourg
| | - Yvan Devaux
- 2 Cardiovascular Research Unit, Luxembourg Institute of Health (LIH) , Luxembourg, Luxembourg
| | - Fabio Martelli
- 1 Molecular Cardiology Laboratory, IRCCS Policlinico San Donato , Milan, Italy
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62
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Gao D, Smith S, Spagnuolo M, Rodriguez G, Blenner M. Dual CRISPR-Cas9 Cleavage Mediated Gene Excision and Targeted Integration in Yarrowia lipolytica. Biotechnol J 2018; 13:e1700590. [PMID: 29809313 DOI: 10.1002/biot.201700590] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 05/23/2018] [Indexed: 12/12/2022]
Abstract
CRISPR-Cas9 technology has been successfully applied in Yarrowia lipolytica for targeted genomic editing including gene disruption and integration; however, disruptions by existing methods typically result from small frameshift mutations caused by indels within the coding region, which usually resulted in unnatural protein. In this study, a dual cleavage strategy directed by paired sgRNAs is developed for gene knockout. This method allows fast and robust gene excision, demonstrated on six genes of interest. The targeted regions for excision vary in length from 0.3 kb up to 3.5 kb and contain both non-coding and coding regions. The majority of the gene excisions are repaired by perfect nonhomologous end-joining without indel. Based on this dual cleavage system, two targeted markerless integration methods are developed by providing repair templates. While both strategies are effective, homology mediated end joining (HMEJ) based method are twice as efficient as homology recombination (HR) based method. In both cases, dual cleavage leads to similar or improved gene integration efficiencies compared to gene excision without integration. This dual cleavage strategy will be useful for not only generating more predictable and robust gene knockout, but also for efficient targeted markerless integration, and simultaneous knockout and integration in Y. lipolytica.
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Affiliation(s)
- Difeng Gao
- Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina, USA
| | - Spencer Smith
- Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina, USA
| | - Michael Spagnuolo
- Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina, USA
| | - Gabriel Rodriguez
- Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina, USA
| | - Mark Blenner
- Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina, USA
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63
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Parker S, Fraczek MG, Wu J, Shamsah S, Manousaki A, Dungrattanalert K, de Almeida RA, Invernizzi E, Burgis T, Omara W, Griffiths-Jones S, Delneri D, O’Keefe RT. Large-scale profiling of noncoding RNA function in yeast. PLoS Genet 2018; 14:e1007253. [PMID: 29529031 PMCID: PMC5864082 DOI: 10.1371/journal.pgen.1007253] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 03/22/2018] [Accepted: 02/13/2018] [Indexed: 11/19/2022] Open
Abstract
Noncoding RNAs (ncRNAs) are emerging as key regulators of cellular function. We have exploited the recently developed barcoded ncRNA gene deletion strain collections in the yeast Saccharomyces cerevisiae to investigate the numerous ncRNAs in yeast with no known function. The ncRNA deletion collection contains deletions of tRNAs, snoRNAs, snRNAs, stable unannotated transcripts (SUTs), cryptic unstable transcripts (CUTs) and other annotated ncRNAs encompassing 532 different individual ncRNA deletions. We have profiled the fitness of the diploid heterozygous ncRNA deletion strain collection in six conditions using batch and continuous liquid culture, as well as the haploid ncRNA deletion strain collections arrayed individually onto solid rich media. These analyses revealed many novel environmental-specific haplo-insufficient and haplo-proficient phenotypes providing key information on the importance of each specific ncRNA in every condition. Co-fitness analysis using fitness data from the heterozygous ncRNA deletion strain collection identified two ncRNA groups required for growth during heat stress and nutrient deprivation. The extensive fitness data for each ncRNA deletion strain has been compiled into an easy to navigate database called Yeast ncRNA Analysis (YNCA). By expanding the original ncRNA deletion strain collection we identified four novel essential ncRNAs; SUT527, SUT075, SUT367 and SUT259/691. We defined the effects of each new essential ncRNA on adjacent gene expression in the heterozygote background identifying both repression and induction of nearby genes. Additionally, we discovered a function for SUT527 in the expression, 3' end formation and localization of SEC4, an essential protein coding mRNA. Finally, using plasmid complementation we rescued the SUT075 lethal phenotype revealing that this ncRNA acts in trans. Overall, our findings provide important new insights into the function of ncRNAs.
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Affiliation(s)
- Steven Parker
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Marcin G. Fraczek
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Jian Wu
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Sara Shamsah
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Alkisti Manousaki
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Kobchai Dungrattanalert
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Rogerio Alves de Almeida
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Edith Invernizzi
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Tim Burgis
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Walid Omara
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Sam Griffiths-Jones
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Daniela Delneri
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Raymond T. O’Keefe
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
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64
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Janga H, Aznaourova M, Boldt F, Damm K, Grünweller A, Schulte LN. Cas9-mediated excision of proximal DNaseI/H3K4me3 signatures confers robust silencing of microRNA and long non-coding RNA genes. PLoS One 2018; 13:e0193066. [PMID: 29451908 PMCID: PMC5815609 DOI: 10.1371/journal.pone.0193066] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 02/02/2018] [Indexed: 01/01/2023] Open
Abstract
CRISPR/Cas9-based approaches have greatly facilitated targeted genomic deletions. Contrary to coding genes however, which can be functionally knocked out by frame-shift mutagenesis, non-coding RNA (ncRNA) gene knockouts have remained challenging. Here we present a universal ncRNA knockout approach guided by epigenetic hallmarks, which enables robust gene silencing even in provisionally annotated gene loci. We build on previous work reporting the presence of overlapping histone H3 lysine 4 tri-methylation (H3K4me3) and DNaseI hypersensitivity sites around the transcriptional start sites of most genes. We demonstrate that excision of this gene-proximal signature leads to loss of microRNA and lincRNA transcription and reveals ncRNA phenotypes. Exemplarily we demonstrate silencing of the constitutively transcribed MALAT1 lincRNA gene as well as of the inducible miR-146a and miR-155 genes in human monocytes. Our results validate a role of miR-146a and miR-155 in negative feedback control of the activity of inflammation master-regulator NFκB and suggest that cell-cycle control is a unique feature of miR-155. We suggest that our epigenetically guided CRISPR approach may improve existing ncRNA knockout strategies and contribute to the development of high-confidence ncRNA phenotyping applications.
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Affiliation(s)
| | | | - Fabian Boldt
- Institute for Lung Research, Philipps University, Marburg, Germany
| | - Katrin Damm
- Institute for Pharmaceutical Chemistry, Philipps University, Marburg, Germany
| | - Arnold Grünweller
- Institute for Pharmaceutical Chemistry, Philipps University, Marburg, Germany
| | - Leon N. Schulte
- Institute for Lung Research, Philipps University, Marburg, Germany
- * E-mail:
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65
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Klein JC, Chen W, Gasperini M, Shendure J. Identifying Novel Enhancer Elements with CRISPR-Based Screens. ACS Chem Biol 2018; 13:326-332. [PMID: 29300083 PMCID: PMC6218247 DOI: 10.1021/acschembio.7b00778] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Enhancers control the spatiotemporal expression of genes and are essential for encoding differentiation and development. Since their discovery more than three decades ago, researchers have largely studied enhancers removed from their genomic context. The recent adaptation of CRISPR/Cas9 to genome editing in higher organisms now allows researchers to perturb and test these elements in their genomic context, through both mutation and epigenetic modulation. In this Perspective, we discuss recent advances in scanning noncoding regions of the genome for enhancer activity using CRISPR-based tools.
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Affiliation(s)
- Jason C. Klein
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Wei Chen
- Molecular Engineering & Science Institute, University of Washington, Seattle, Washington 98195, United States
| | - Molly Gasperini
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, United States
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66
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When Long Noncoding RNAs Meet Genome Editing in Pluripotent Stem Cells. Stem Cells Int 2017; 2017:3250624. [PMID: 29333164 PMCID: PMC5733163 DOI: 10.1155/2017/3250624] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 10/25/2017] [Indexed: 11/18/2022] Open
Abstract
Most of the human genome can be transcribed into RNAs, but only a minority of these regions produce protein-coding mRNAs whereas the remaining regions are transcribed into noncoding RNAs. Long noncoding RNAs (lncRNAs) were known for their influential regulatory roles in multiple biological processes such as imprinting, dosage compensation, transcriptional regulation, and splicing. The physiological functions of protein-coding genes have been extensively characterized through genome editing in pluripotent stem cells (PSCs) in the past 30 years; however, the study of lncRNAs with genome editing technologies only came into attentions in recent years. Here, we summarize recent advancements in dissecting the roles of lncRNAs with genome editing technologies in PSCs and highlight potential genome editing tools useful for examining the functions of lncRNAs in PSCs.
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67
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Chen Q, Cai J, Wang Q, Wang Y, Liu M, Yang J, Zhou J, Kang C, Li M, Jiang C. Long Noncoding RNA NEAT1, Regulated by the EGFR Pathway, Contributes to Glioblastoma Progression Through the WNT/β-Catenin Pathway by Scaffolding EZH2. Clin Cancer Res 2017; 24:684-695. [PMID: 29138341 DOI: 10.1158/1078-0432.ccr-17-0605] [Citation(s) in RCA: 235] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 06/04/2017] [Accepted: 11/08/2017] [Indexed: 11/16/2022]
Affiliation(s)
- Qun Chen
- Department of Neurosurgery, the Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Neuroscience Institute, Heilongjiang Academy of Medical Sciences, Harbin, China
- Glioma Cooperative Group (CGCG), Beijing, China
| | - Jinquan Cai
- Department of Neurosurgery, the Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Neuroscience Institute, Heilongjiang Academy of Medical Sciences, Harbin, China
- Glioma Cooperative Group (CGCG), Beijing, China
| | - Qixue Wang
- Glioma Cooperative Group (CGCG), Beijing, China
- Department of Neurosurgery, Laboratory of Neuro-oncology, Tianjin Neurological Institute, Key Laboratory of Post-Neuro Injury Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin Medical University General Hospital, Tianjin, China
| | - Yunfei Wang
- Glioma Cooperative Group (CGCG), Beijing, China
- Department of Neurosurgery, Laboratory of Neuro-oncology, Tianjin Neurological Institute, Key Laboratory of Post-Neuro Injury Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin Medical University General Hospital, Tianjin, China
| | - Mingyang Liu
- Department of Medicine, Department of Surgery, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Jingxuan Yang
- Department of Medicine, Department of Surgery, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Junhu Zhou
- Glioma Cooperative Group (CGCG), Beijing, China
- Department of Neurosurgery, Laboratory of Neuro-oncology, Tianjin Neurological Institute, Key Laboratory of Post-Neuro Injury Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin Medical University General Hospital, Tianjin, China
| | - Chunsheng Kang
- Glioma Cooperative Group (CGCG), Beijing, China.
- Department of Neurosurgery, Laboratory of Neuro-oncology, Tianjin Neurological Institute, Key Laboratory of Post-Neuro Injury Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin Medical University General Hospital, Tianjin, China
| | - Min Li
- Department of Medicine, Department of Surgery, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma.
| | - Chuanlu Jiang
- Department of Neurosurgery, the Second Affiliated Hospital of Harbin Medical University, Harbin, China.
- Neuroscience Institute, Heilongjiang Academy of Medical Sciences, Harbin, China
- Glioma Cooperative Group (CGCG), Beijing, China
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68
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Goyal A, Myacheva K, Groß M, Klingenberg M, Duran Arqué B, Diederichs S. Challenges of CRISPR/Cas9 applications for long non-coding RNA genes. Nucleic Acids Res 2017; 45:e12. [PMID: 28180319 PMCID: PMC5388423 DOI: 10.1093/nar/gkw883] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 09/01/2016] [Accepted: 09/23/2016] [Indexed: 12/14/2022] Open
Abstract
The CRISPR/Cas9 system provides a revolutionary genome editing tool for all areas of molecular biology. In long non-coding RNA (lncRNA) research, the Cas9 nuclease can delete lncRNA genes or introduce RNA-destabilizing elements into their locus. The nuclease-deficient dCas9 mutant retains its RNA-dependent DNA-binding activity and can modulate gene expression when fused to transcriptional repressor or activator domains. Here, we systematically analyze whether CRISPR approaches are suitable to target lncRNAs. Many lncRNAs are derived from bidirectional promoters or overlap with promoters or bodies of sense or antisense genes. In a genome-wide analysis, we find only 38% of 15929 lncRNA loci are safely amenable to CRISPR applications while almost two-thirds of lncRNA loci are at risk to inadvertently deregulate neighboring genes. CRISPR- but not siPOOL or Antisense Oligo (ASO)-mediated targeting of lncRNAs NOP14-AS1, LOC389641, MNX1-AS1 or HOTAIR also affects their respective neighboring genes. Frequently overlooked, the same restrictions may apply to mRNAs. For example, the tumor suppressor TP53 and its head-to-head neighbor WRAP53 are jointly affected by the same sgRNAs but not siPOOLs. Hence, despite the advantages of CRISPR/Cas9 to modulate expression bidirectionally and in cis, approaches based on ASOs or siPOOLs may be the better choice to target specifically the transcript from complex loci.
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Affiliation(s)
- Ashish Goyal
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Ksenia Myacheva
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Division of Cancer Research, Dept. of Thoracic Surgery, Medical Center - University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK), Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Matthias Groß
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Marcel Klingenberg
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology (HBIGS), University of Heidelberg, Heidelberg, Germany
| | - Berta Duran Arqué
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sven Diederichs
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Division of Cancer Research, Dept. of Thoracic Surgery, Medical Center - University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK), Freiburg, Germany.,Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology (HBIGS), University of Heidelberg, Heidelberg, Germany
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69
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Arslan S, Berkan Ö, Lalem T, Özbilüm N, Göksel S, Korkmaz Ö, Çetin N, Devaux Y. Long non-coding RNAs in the atherosclerotic plaque. Atherosclerosis 2017; 266:176-181. [PMID: 29035780 DOI: 10.1016/j.atherosclerosis.2017.10.012] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 09/28/2017] [Accepted: 10/06/2017] [Indexed: 01/05/2023]
Abstract
BACKGROUND AND AIMS Genetic and environmental factors are important components of the development of atherosclerosis. Long non-coding RNA (lncRNAs) have emerged as regulators of multiple pathophysiological pathways in the cardiovascular system. Here, we investigated potential associations between lncRNAs and atherosclerosis. METHODS Tissue samples from atherosclerotic coronary artery plaques and non-atherosclerotic internal mammary artery were obtained from 20 patients during coronary artery bypass surgery. Expression levels of five lncRNAs known to be associated with coronary artery disease were measured using quantitative PCR. RESULTS Cyclin-dependent kinase inhibitor 2B antisense RNA 1 (ANRIL) and myocardial infarction-associated transcript (MIAT) were more expressed in the atherosclerotic arteries compared to the non-atherosclerotic arteries. Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) was less expressed in the atherosclerotic plaques. Expression levels of potassium voltage-gated channel, KQT-like subfamily, member 1 opposite strand/antisense transcript 1 (KCNQ1OT1) and hypoxia inducible factor 1A antisense RNA 2 (aHIF) were comparable between atherosclerotic and non-atherosclerotic arteries. In the atherosclerotic plaque, expression levels of MALAT1, MIAT, KCNQ1OT1 and aHIF were inversely correlated with age. CONCLUSIONS We report significant associations between lncRNAs and atherosclerosis. These findings support a role for lncRNAs in coronary artery disease development.
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Affiliation(s)
- Serdal Arslan
- Department of Medical Biology, Faculty of Medicine, Sivas, Turkey
| | - Öcal Berkan
- Department of Cardiovascular Surgery, Faculty of Medicine, Cumhuriyet University, Sivas, Turkey
| | - Torkia Lalem
- Cardiovascular Research Unit, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Nil Özbilüm
- Department of Molecular Biology and Genetics, Faculty of Science, Cumhuriyet University, Sivas, Turkey
| | - Sabahattin Göksel
- Department of Cardiovascular Surgery, Faculty of Medicine, Cumhuriyet University, Sivas, Turkey
| | - Özge Korkmaz
- Department of Cardiovascular Surgery, Faculty of Medicine, Cumhuriyet University, Sivas, Turkey
| | - Nilgün Çetin
- Department of Medical Biology, Faculty of Medicine, Sivas, Turkey
| | - Yvan Devaux
- Cardiovascular Research Unit, Luxembourg Institute of Health, Luxembourg, Luxembourg.
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70
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Chaterji S, Ahn EH, Kim DH. CRISPR Genome Engineering for Human Pluripotent Stem Cell Research. Theranostics 2017; 7:4445-4469. [PMID: 29158838 PMCID: PMC5695142 DOI: 10.7150/thno.18456] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 08/24/2017] [Indexed: 12/13/2022] Open
Abstract
The emergence of targeted and efficient genome editing technologies, such as repurposed bacterial programmable nucleases (e.g., CRISPR-Cas systems), has abetted the development of cell engineering approaches. Lessons learned from the development of RNA-interference (RNA-i) therapies can spur the translation of genome editing, such as those enabling the translation of human pluripotent stem cell engineering. In this review, we discuss the opportunities and the challenges of repurposing bacterial nucleases for genome editing, while appreciating their roles, primarily at the epigenomic granularity. First, we discuss the evolution of high-precision, genome editing technologies, highlighting CRISPR-Cas9. They exist in the form of programmable nucleases, engineered with sequence-specific localizing domains, and with the ability to revolutionize human stem cell technologies through precision targeting with greater on-target activities. Next, we highlight the major challenges that need to be met prior to bench-to-bedside translation, often learning from the path-to-clinic of complementary technologies, such as RNA-i. Finally, we suggest potential bioinformatics developments and CRISPR delivery vehicles that can be deployed to circumvent some of the challenges confronting genome editing technologies en route to the clinic.
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71
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Fok ET, Scholefield J, Fanucchi S, Mhlanga MM. The emerging molecular biology toolbox for the study of long noncoding RNA biology. Epigenomics 2017; 9:1317-1327. [PMID: 28875715 DOI: 10.2217/epi-2017-0062] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) have been implicated in many biological processes. However, due to the unique nature of lncRNAs and the consequential difficulties associated with their characterization, there is a growing disparity between the rate at which lncRNAs are being discovered and the assignment of biological function to these transcripts. Here we present a molecular biology toolbox equipped to help dissect aspects of lncRNA biology and reveal functionality. We outline an approach that begins with a broad survey of genome-wide, high-throughput datasets to identify potential lncRNA candidates and then narrow the focus on specific methods that are well suited to interrogate the transcripts of interest more closely. This involves the use of imaging-based strategies to validate these candidates and observe the behaviors of these transcripts at single molecule resolution in individual cells. We also describe the use of gene editing tools and interactome capture techniques to interrogate functionality and infer mechanism, respectively. With the emergence of lncRNAs as important molecules in healthy and diseased cellular function, it remains crucial to deepen our understanding of their biology.
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Affiliation(s)
- Ezio T Fok
- Gene Expression & Biophysics Group, Biosciences, CSIR, Pretoria, Gauteng, South Africa.,Division of Chemical, Systems & Synthetic Biology, Institute for Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Janine Scholefield
- Gene Expression & Biophysics Group, Biosciences, CSIR, Pretoria, Gauteng, South Africa.,Division of Chemical, Systems & Synthetic Biology, Institute for Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Stephanie Fanucchi
- Gene Expression & Biophysics Group, Biosciences, CSIR, Pretoria, Gauteng, South Africa.,Division of Chemical, Systems & Synthetic Biology, Institute for Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Musa M Mhlanga
- Gene Expression & Biophysics Group, Biosciences, CSIR, Pretoria, Gauteng, South Africa.,Division of Chemical, Systems & Synthetic Biology, Institute for Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, Western Cape, South Africa.,Instituto de Medicina Molecular, Faculdade de Medicina Universidade de Lisboa, Lisbon, Portugal
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72
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Gasperini M, Findlay GM, McKenna A, Milbank JH, Lee C, Zhang MD, Cusanovich DA, Shendure J. CRISPR/Cas9-Mediated Scanning for Regulatory Elements Required for HPRT1 Expression via Thousands of Large, Programmed Genomic Deletions. Am J Hum Genet 2017; 101:192-205. [PMID: 28712454 PMCID: PMC5544381 DOI: 10.1016/j.ajhg.2017.06.010] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 06/16/2017] [Indexed: 11/22/2022] Open
Abstract
The extent to which non-coding mutations contribute to Mendelian disease is a major unknown in human genetics. Relatedly, the vast majority of candidate regulatory elements have yet to be functionally validated. Here, we describe a CRISPR-based system that uses pairs of guide RNAs (gRNAs) to program thousands of kilobase-scale deletions that deeply scan across a targeted region in a tiling fashion ("ScanDel"). We applied ScanDel to HPRT1, the housekeeping gene underlying Lesch-Nyhan syndrome, an X-linked recessive disorder. Altogether, we programmed 4,342 overlapping 1 and 2 kb deletions that tiled 206 kb centered on HPRT1 (including 87 kb upstream and 79 kb downstream) with median 27-fold redundancy per base. We functionally assayed programmed deletions in parallel by selecting for loss of HPRT function with 6-thioguanine. As expected, sequencing gRNA pairs before and after selection confirmed that all HPRT1 exons are needed. However, HPRT1 function was robust to deletion of any intergenic or deeply intronic non-coding region, indicating that proximal regulatory sequences are sufficient for HPRT1 expression. Although our screen did identify the disruption of exon-proximal non-coding sequences (e.g., the promoter) as functionally consequential, long-read sequencing revealed that this signal was driven by rare, imprecise deletions that extended into exons. Our results suggest that no singular distal regulatory element is required for HPRT1 expression and that distal mutations are unlikely to contribute substantially to Lesch-Nyhan syndrome burden. Further application of ScanDel could shed light on the role of regulatory mutations in disease at other loci while also facilitating a deeper understanding of endogenous gene regulation.
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Affiliation(s)
- Molly Gasperini
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
| | - Gregory M Findlay
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Aaron McKenna
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Jennifer H Milbank
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Choli Lee
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Melissa D Zhang
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Darren A Cusanovich
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA.
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73
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Gomes CPC, Spencer H, Ford KL, Michel LYM, Baker AH, Emanueli C, Balligand JL, Devaux Y. The Function and Therapeutic Potential of Long Non-coding RNAs in Cardiovascular Development and Disease. MOLECULAR THERAPY-NUCLEIC ACIDS 2017; 8:494-507. [PMID: 28918050 PMCID: PMC5565632 DOI: 10.1016/j.omtn.2017.07.014] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 07/25/2017] [Indexed: 02/09/2023]
Abstract
The popularization of genome-wide analyses and RNA sequencing led to the discovery that a large part of the human genome, while effectively transcribed, does not encode proteins. Long non-coding RNAs have emerged as critical regulators of gene expression in both normal and disease states. Studies of long non-coding RNAs expressed in the heart, in combination with gene association studies, revealed that these molecules are regulated during cardiovascular development and disease. Some long non-coding RNAs have been functionally implicated in cardiac pathophysiology and constitute potential therapeutic targets. Here, we review the current knowledge of the function of long non-coding RNAs in the cardiovascular system, with an emphasis on cardiovascular development and biology, focusing on hypertension, coronary artery disease, myocardial infarction, ischemia, and heart failure. We discuss potential therapeutic implications and the challenges of long non-coding RNA research, with directions for future research and translational focus.
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Affiliation(s)
- Clarissa P C Gomes
- Cardiovascular Research Unit, Luxembourg Institute of Health, 1526 Luxembourg, Luxembourg
| | - Helen Spencer
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh EH8 9YL, UK
| | - Kerrie L Ford
- Bristol Heart Institute, University of Bristol, Bristol BS8 1TH, UK
| | - Lauriane Y M Michel
- Unité de Pharmacologie et de Thérapeutique, Institut de Recherche Experimentale et Clinique, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Andrew H Baker
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh EH8 9YL, UK
| | - Costanza Emanueli
- Bristol Heart Institute, University of Bristol, Bristol BS8 1TH, UK; National Heart and Lung Institute, Imperial College London, London SW7 2AZ, UK
| | - Jean-Luc Balligand
- Unité de Pharmacologie et de Thérapeutique, Institut de Recherche Experimentale et Clinique, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Yvan Devaux
- Cardiovascular Research Unit, Luxembourg Institute of Health, 1526 Luxembourg, Luxembourg.
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74
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Salehi S, Taheri MN, Azarpira N, Zare A, Behzad-Behbahani A. State of the art technologies to explore long non-coding RNAs in cancer. J Cell Mol Med 2017. [PMID: 28631377 PMCID: PMC5706582 DOI: 10.1111/jcmm.13238] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Long non‐coding RNAs (lncRNAs) comprise a vast repertoire of RNAs playing a wide variety of crucial roles in tissue physiology in a cell‐specific manner. Despite being engaged in myriads of regulatory mechanisms, many lncRNAs have still remained to be assigned any functions. A constellation of experimental techniques including single‐molecule RNA in situ hybridization (sm‐RNA FISH), cross‐linking and immunoprecipitation (CLIP), RNA interference (RNAi), Clustered regularly interspaced short palindromic repeats (CRISPR) and so forth has been employed to shed light on lncRNA cellular localization, structure, interaction networks and functions. Here, we review these and other experimental approaches in common use for identification and characterization of lncRNAs, particularly those involved in different types of cancer, with focus on merits and demerits of each technique.
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Affiliation(s)
- Saeede Salehi
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Medical Biotechnology, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran.,Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Naser Taheri
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Medical Biotechnology, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran.,Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Negar Azarpira
- Transplant Research Center, Namazi Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abdolhossein Zare
- Transplant Research Center, Namazi Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abbas Behzad-Behbahani
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Medical Biotechnology, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
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75
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Canver MC, Bauer DE, Orkin SH. Functional interrogation of non-coding DNA through CRISPR genome editing. Methods 2017; 121-122:118-129. [PMID: 28288828 PMCID: PMC5483188 DOI: 10.1016/j.ymeth.2017.03.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 02/18/2017] [Accepted: 03/03/2017] [Indexed: 12/26/2022] Open
Abstract
Methodologies to interrogate non-coding regions have lagged behind coding regions despite comprising the vast majority of the genome. However, the rapid evolution of clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing has provided a multitude of novel techniques for laboratory investigation including significant contributions to the toolbox for studying non-coding DNA. CRISPR-mediated loss-of-function strategies rely on direct disruption of the underlying sequence or repression of transcription without modifying the targeted DNA sequence. CRISPR-mediated gain-of-function approaches similarly benefit from methods to alter the targeted sequence through integration of customized sequence into the genome as well as methods to activate transcription. Here we review CRISPR-based loss- and gain-of-function techniques for the interrogation of non-coding DNA.
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Affiliation(s)
| | - Daniel E Bauer
- Harvard Medical School, Boston, MA 02115, United States; Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, United States; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, United States.
| | - Stuart H Orkin
- Harvard Medical School, Boston, MA 02115, United States; Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, United States; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, United States; Howard Hughes Medical Institute, Boston, MA 02115, United States.
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76
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Pulido-Quetglas C, Aparicio-Prat E, Arnan C, Polidori T, Hermoso T, Palumbo E, Ponomarenko J, Guigo R, Johnson R. Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion. PLoS Comput Biol 2017; 13:e1005341. [PMID: 28253259 PMCID: PMC5333799 DOI: 10.1371/journal.pcbi.1005341] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 12/30/2016] [Indexed: 11/23/2022] Open
Abstract
CRISPR-Cas9 technology can be used to engineer precise genomic deletions with pairs of single guide RNAs (sgRNAs). This approach has been widely adopted for diverse applications, from disease modelling of individual loci, to parallelized loss-of-function screens of thousands of regulatory elements. However, no solution has been presented for the unique bioinformatic design requirements of CRISPR deletion. We here present CRISPETa, a pipeline for flexible and scalable paired sgRNA design based on an empirical scoring model. Multiple sgRNA pairs are returned for each target, and any number of targets can be analyzed in parallel, making CRISPETa equally useful for focussed or high-throughput studies. Fast run-times are achieved using a pre-computed off-target database. sgRNA pair designs are output in a convenient format for visualisation and oligonucleotide ordering. We present pre-designed, high-coverage library designs for entire classes of protein-coding and non-coding elements in human, mouse, zebrafish, Drosophila melanogaster and Caenorhabditis elegans. In human cells, we reproducibly observe deletion efficiencies of ≥50% for CRISPETa designs targeting an enhancer and exonic fragment of the MALAT1 oncogene. In the latter case, deletion results in production of desired, truncated RNA. CRISPETa will be useful for researchers seeking to harness CRISPR for targeted genomic deletion, in a variety of model organisms, from single-target to high-throughput scales.
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Affiliation(s)
- Carlos Pulido-Quetglas
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institut Hospital del Mar d’Investigacions Mediques (IMIM), Barcelona, Spain
| | - Estel Aparicio-Prat
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institut Hospital del Mar d’Investigacions Mediques (IMIM), Barcelona, Spain
| | - Carme Arnan
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institut Hospital del Mar d’Investigacions Mediques (IMIM), Barcelona, Spain
| | - Taisia Polidori
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institut Hospital del Mar d’Investigacions Mediques (IMIM), Barcelona, Spain
| | - Toni Hermoso
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Emilio Palumbo
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institut Hospital del Mar d’Investigacions Mediques (IMIM), Barcelona, Spain
| | - Julia Ponomarenko
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Roderic Guigo
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institut Hospital del Mar d’Investigacions Mediques (IMIM), Barcelona, Spain
| | - Rory Johnson
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institut Hospital del Mar d’Investigacions Mediques (IMIM), Barcelona, Spain
- Department of Clinical Research, University of Bern, Bern, Switzerland
- Department of Medical Oncology, Inselspital, University Hospital and University of Bern, Bern, Switzerland
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77
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Zhuo C, Hou W, Hu L, Lin C, Chen C, Lin X. Genomic Editing of Non-Coding RNA Genes with CRISPR/Cas9 Ushers in a Potential Novel Approach to Study and Treat Schizophrenia. Front Mol Neurosci 2017; 10:28. [PMID: 28217082 PMCID: PMC5289958 DOI: 10.3389/fnmol.2017.00028] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 01/23/2017] [Indexed: 12/13/2022] Open
Abstract
Schizophrenia is a genetically related mental illness, in which the majority of genetic alterations occur in the non-coding regions of the human genome. In the past decade, a growing number of regulatory non-coding RNAs (ncRNAs) including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) have been identified to be strongly associated with schizophrenia. However, the studies of these ncRNAs in the pathophysiology of schizophrenia and the reverting of their genetic defects in restoration of the normal phenotype have been hampered by insufficient technology to manipulate these ncRNA genes effectively as well as a lack of appropriate animal models. Most recently, a revolutionary gene editing technology known as Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated nuclease 9 (Cas9; CRISPR/Cas9) has been developed that enable researchers to overcome these challenges. In this review article, we mainly focus on the schizophrenia-related ncRNAs and the use of CRISPR/Cas9-mediated editing on the non-coding regions of the genomic DNA in proving causal relationship between the genetic defects and the pathophysiology of schizophrenia. We subsequently discuss the potential of translating this advanced technology into a clinical therapy for schizophrenia, although the CRISPR/Cas9 technology is currently still in its infancy and immature to put into use in the treatment of diseases. Furthermore, we suggest strategies to accelerate the pace from the bench to the bedside. This review describes the application of the powerful and feasible CRISPR/Cas9 technology to manipulate schizophrenia-associated ncRNA genes. This technology could help researchers tackle this complex health problem and perhaps other genetically related mental disorders due to the overlapping genetic alterations of schizophrenia with other mental illnesses.
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Affiliation(s)
- Chuanjun Zhuo
- Department of Psychiatry, Wenzhou Seventh People's HospitalWenzhou, China; Department of Psychiatry, Tianjin Mental Health Center, Tianjin Anding HospitalTianjin, China; Department of Psychiatry, Tianjin Anning HospitalTianjin, China
| | - Weihong Hou
- Department of Biology, University of North Carolina at Charlotte Charlotte, NC, USA
| | - Lirong Hu
- Department of Psychiatry, Wenzhou Seventh People's Hospital Wenzhou, China
| | - Chongguang Lin
- Department of Psychiatry, Wenzhou Seventh People's Hospital Wenzhou, China
| | - Ce Chen
- Department of Psychiatry, Wenzhou Seventh People's Hospital Wenzhou, China
| | - Xiaodong Lin
- Department of Psychiatry, Wenzhou Seventh People's Hospital Wenzhou, China
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78
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Liu SJ, Horlbeck MA, Cho SW, Birk HS, Malatesta M, He D, Attenello FJ, Villalta JE, Cho MY, Chen Y, Mandegar MA, Olvera MP, Gilbert LA, Conklin BR, Chang HY, Weissman JS, Lim DA. CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells. Science 2016; 355:science.aah7111. [PMID: 27980086 DOI: 10.1126/science.aah7111] [Citation(s) in RCA: 473] [Impact Index Per Article: 59.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 11/30/2016] [Indexed: 12/29/2022]
Abstract
The human genome produces thousands of long noncoding RNAs (lncRNAs)-transcripts >200 nucleotides long that do not encode proteins. Although critical roles in normal biology and disease have been revealed for a subset of lncRNAs, the function of the vast majority remains untested. We developed a CRISPR interference (CRISPRi) platform targeting 16,401 lncRNA loci in seven diverse cell lines, including six transformed cell lines and human induced pluripotent stem cells (iPSCs). Large-scale screening identified 499 lncRNA loci required for robust cellular growth, of which 89% showed growth-modifying function exclusively in one cell type. We further found that lncRNA knockdown can perturb complex transcriptional networks in a cell type-specific manner. These data underscore the functional importance and cell type specificity of many lncRNAs.
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Affiliation(s)
- S John Liu
- Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
| | - Max A Horlbeck
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143, USA.,Howard Hughes Medical Institute, University of California, San Francisco, CA 94143, USA.,California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94143, USA.,Center for RNA Systems Biology, University of California, San Francisco, CA 94143, USA
| | - Seung Woo Cho
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Harjus S Birk
- Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
| | - Martina Malatesta
- Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
| | - Daniel He
- Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
| | - Frank J Attenello
- Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
| | - Jacqueline E Villalta
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143, USA.,Howard Hughes Medical Institute, University of California, San Francisco, CA 94143, USA.,California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94143, USA.,Center for RNA Systems Biology, University of California, San Francisco, CA 94143, USA
| | - Min Y Cho
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143, USA.,Howard Hughes Medical Institute, University of California, San Francisco, CA 94143, USA.,California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94143, USA.,Center for RNA Systems Biology, University of California, San Francisco, CA 94143, USA
| | - Yuwen Chen
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143, USA.,Howard Hughes Medical Institute, University of California, San Francisco, CA 94143, USA.,California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94143, USA.,Center for RNA Systems Biology, University of California, San Francisco, CA 94143, USA
| | - Mohammad A Mandegar
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143, USA
| | - Michael P Olvera
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143, USA
| | - Luke A Gilbert
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143, USA.,Howard Hughes Medical Institute, University of California, San Francisco, CA 94143, USA.,California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94143, USA.,Center for RNA Systems Biology, University of California, San Francisco, CA 94143, USA
| | - Bruce R Conklin
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143, USA.,Deparment of Medicine, University of California, San Francisco, CA 94143, USA.,Gladstone Institute of Cardiovascular Disease, San Francisco, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143, USA. .,Howard Hughes Medical Institute, University of California, San Francisco, CA 94143, USA.,California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94143, USA.,Center for RNA Systems Biology, University of California, San Francisco, CA 94143, USA
| | - Daniel A Lim
- Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA. .,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA.,San Francisco Veterans Affairs Medical Center, San Francisco, CA, USA
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79
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Aparicio-Prat E, Arnan C, Sala I, Bosch N, Guigó R, Johnson R. Erratum to: 'DECKO: Single-oligo, dual-CRISPR deletion of genomic elements including long non-coding RNAs'. BMC Genomics 2016; 17:215. [PMID: 26960900 PMCID: PMC4784307 DOI: 10.1186/s12864-016-2544-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Estel Aparicio-Prat
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.,Institut Hospital del Mar d' Investigacions Mèdiques (IMIM), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Carme Arnan
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.,Institut Hospital del Mar d' Investigacions Mèdiques (IMIM), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Ilaria Sala
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.,Institut Hospital del Mar d' Investigacions Mèdiques (IMIM), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Núria Bosch
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.,Institut Hospital del Mar d' Investigacions Mèdiques (IMIM), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.,Institut Hospital del Mar d' Investigacions Mèdiques (IMIM), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Rory Johnson
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain. .,Institut Hospital del Mar d' Investigacions Mèdiques (IMIM), Dr. Aiguader 88, 08003, Barcelona, Spain.
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