1
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Salem AR, Bryant WB, Doja J, Griffin SH, Shi X, Han W, Su Y, Verin AD, Miano JM. Prime editing in mice with an engineered pegRNA. Vascul Pharmacol 2024; 154:107269. [PMID: 38158001 PMCID: PMC10939748 DOI: 10.1016/j.vph.2023.107269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 12/06/2023] [Accepted: 12/10/2023] [Indexed: 01/03/2024]
Abstract
CRISPR editing involves double-strand breaks in DNA with attending insertions/deletions (indels) that may result in embryonic lethality in mice. The prime editing (PE) platform uses a prime editing guide RNA (pegRNA) and a Cas9 nickase fused to a modified reverse transcriptase to precisely introduce nucleotide substitutions or small indels without the unintended editing associated with DNA double-strand breaks. Recently, engineered pegRNAs (epegRNAs), with a 3'-extension that shields the primer-binding site of the pegRNA from nucleolytic attack, demonstrated superior activity over conventional pegRNAs in cultured cells. Here, we show the inability of three-component CRISPR or conventional PE to incorporate a nonsynonymous substitution in the Capn2 gene, expected to disrupt a phosphorylation site (S50A) in CAPN2. In contrast, an epegRNA with the same protospacer correctly installed the desired edit in two founder mice, as evidenced by robust genotyping assays for the detection of subtle nucleotide substitutions. Long-read sequencing demonstrated sequence fidelity around the edited site as well as top-ranked distal off-target sites. Western blotting and histological analysis of lipopolysaccharide-treated lung tissue revealed a decrease in phosphorylation of CAPN2 and notable alleviation of inflammation, respectively. These results demonstrate the first successful use of an epegRNA for germline transmission in an animal model and provide a solution to targeting essential developmental genes that otherwise may be challenging to edit.
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Affiliation(s)
- Amr R Salem
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA 30912, United States of America.
| | - W Bart Bryant
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA 30912, United States of America
| | - Jaser Doja
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA 30912, United States of America
| | - Susan H Griffin
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA 30912, United States of America
| | - Xiaofan Shi
- Department of Pharmacology and Toxicology, Medical College of Georgia at Augusta University, Augusta, GA 30912, United States of America
| | - Weihong Han
- Department of Pharmacology and Toxicology, Medical College of Georgia at Augusta University, Augusta, GA 30912, United States of America
| | - Yunchao Su
- Department of Pharmacology and Toxicology, Medical College of Georgia at Augusta University, Augusta, GA 30912, United States of America
| | - Alexander D Verin
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA 30912, United States of America
| | - Joseph M Miano
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA 30912, United States of America
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2
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Kajuluri LP, Lyu QR, Doja J, Kumar A, Wilson MP, Sgrizzi SR, Rezaeimanesh E, Miano JM, Morgan KG. Calponin 1 inhibits agonist-induced ERK activation and decreases calcium sensitization in vascular smooth muscle. J Cell Mol Med 2024; 28:e18025. [PMID: 38147352 PMCID: PMC10805486 DOI: 10.1111/jcmm.18025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 10/07/2023] [Indexed: 12/27/2023] Open
Abstract
Smooth muscle cell (SMC) contraction and vascular tone are modulated by phosphorylation and multiple modifications of the thick filament, and thin filament regulation of SMC contraction has been reported to involve extracellular regulated kinase (ERK). Previous studies in ferrets suggest that the actin-binding protein, calponin 1 (CNN1), acts as a scaffold linking protein kinase C (PKC), Raf, MEK and ERK, promoting PKC-dependent ERK activation. To gain further insight into this function of CNN1 in ERK activation and the regulation of SMC contractility in mice, we generated a novel Calponin 1 knockout mouse (Cnn1 KO) by a single base substitution in an intronic CArG box that preferentially abolishes expression of CNN1 in vascular SMCs. Using this new Cnn1 KO mouse, we show that ablation of CNN1 has two effects, depending on the cytosolic free calcium level: (1) in the presence of elevated intracellular calcium caused by agonist stimulation, Cnn1 KO mice display a reduced amplitude of stress and stiffness but an increase in agonist-induced ERK activation; and (2) during intracellular calcium depletion, in the presence of an agonist, Cnn1 KO mice exhibit increased duration of SM tone maintenance. Together, these results suggest that CNN1 plays an important and complex modulatory role in SMC contractile tone amplitude and maintenance.
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Affiliation(s)
- Lova Prasadareddy Kajuluri
- Vascular Biology Laboratory, Department of Health SciencesBoston UniversityBostonMassachusettsUSA
- Present address:
Cardiovascular Research CenterMassachusetts General HospitalCharlestownMassachusettsUSA
| | - Qing Rex Lyu
- Vascular Biology CenterMedical College of Georgia at Augusta UniversityAugustaGeorgiaUSA
- Medical Research CenterChongqing General HospitalChongqingChina
| | - Jaser Doja
- Vascular Biology CenterMedical College of Georgia at Augusta UniversityAugustaGeorgiaUSA
| | - Ajay Kumar
- Vascular Biology CenterMedical College of Georgia at Augusta UniversityAugustaGeorgiaUSA
| | | | - Samantha R. Sgrizzi
- Vascular Biology Laboratory, Department of Health SciencesBoston UniversityBostonMassachusettsUSA
| | - Elika Rezaeimanesh
- Vascular Biology Laboratory, Department of Health SciencesBoston UniversityBostonMassachusettsUSA
| | - Joseph M. Miano
- Vascular Biology CenterMedical College of Georgia at Augusta UniversityAugustaGeorgiaUSA
| | - Kathleen G. Morgan
- Vascular Biology Laboratory, Department of Health SciencesBoston UniversityBostonMassachusettsUSA
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3
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Montoliu L. Transgenesis and Genome Engineering: A Historical Review. Methods Mol Biol 2023; 2631:1-32. [PMID: 36995662 DOI: 10.1007/978-1-0716-2990-1_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Our ability to modify DNA molecules and to introduce them into mammalian cells or embryos almost appears in parallel, starting from the 1970s of the last century. Genetic engineering techniques rapidly developed between 1970 and 1980. In contrast, robust procedures to microinject or introduce DNA constructs into individuals did not take off until 1980 and evolved during the following two decades. For some years, it was only possible to add transgenes, de novo, of different formats, including artificial chromosomes, in a variety of vertebrate species or to introduce specific mutations essentially in mice, thanks to the gene-targeting methods by homologous recombination approaches using mouse embryonic stem (ES) cells. Eventually, genome-editing tools brought the possibility to add or inactivate DNA sequences, at specific sites, at will, irrespective of the animal species involved. Together with a variety of additional techniques, this chapter will summarize the milestones in the transgenesis and genome engineering fields from the 1970s to date.
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Affiliation(s)
- Lluis Montoliu
- National Centre for Biotechnology (CNB-CSIC) and Center for Biomedical Network Research on Rare Diseases (CIBERER-ISCIII), Madrid, Spain.
- National Centre for Biotechnology (CNB-CSIC), Madrid, Spain.
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4
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Lim CK, McCallister TX, Saporito-Magriña C, McPheron GD, Krishnan R, Zeballos C MA, Powell JE, Clark LV, Perez-Pinera P, Gaj T. CRISPR base editing of cis-regulatory elements enables the perturbation of neurodegeneration-linked genes. Mol Ther 2022; 30:3619-3631. [PMID: 35965414 PMCID: PMC9734028 DOI: 10.1016/j.ymthe.2022.08.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/25/2022] [Accepted: 08/09/2022] [Indexed: 12/15/2022] Open
Abstract
CRISPR technology has demonstrated broad utility for controlling target gene expression; however, there remains a need for strategies capable of modulating expression via the precise editing of non-coding regulatory elements. Here, we demonstrate that CRISPR base editors, a class of gene-modifying proteins capable of creating single-base substitutions in DNA, can be used to perturb gene expression via their targeted mutagenesis of cis-acting sequences. Using the promoter region of the human huntingtin (HTT) gene as an initial target, we show that editing of the binding site for the transcription factor NF-κB led to a marked reduction in HTT gene expression in base-edited cell populations. We found that these gene perturbations were persistent and specific, as a transcriptome-wide RNA analysis revealed minimal off-target effects resulting from the action of the base editor protein. We further demonstrate that this base-editing platform could influence gene expression in vivo as its delivery to a mouse model of Huntington's disease led to a potent decrease in HTT mRNA in striatal neurons. Finally, to illustrate the applicability of this concept, we target the amyloid precursor protein, showing that multiplex editing of its promoter region significantly perturbed its expression. These findings demonstrate the potential for base editors to regulate target gene expression.
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Affiliation(s)
- Colin K.W. Lim
- Department of Bioengineering, University of Illinois, Urbana, IL 61801, USA
| | | | | | | | - Ramya Krishnan
- Department of Bioengineering, University of Illinois, Urbana, IL 61801, USA
| | | | - Jackson E. Powell
- Department of Bioengineering, University of Illinois, Urbana, IL 61801, USA
| | - Lindsay V. Clark
- Roy J. Carver Biotechnology Center, University of Illinois, Urbana, IL 61801, USA
| | - Pablo Perez-Pinera
- Department of Bioengineering, University of Illinois, Urbana, IL 61801, USA,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA,Department of Biomedical and Translational Sciences, Carle-Illinois College of Medicine, University of Illinois, Urbana, IL 61801, USA,Cancer Center at Illinois, University of Illinois, Urbana, IL 61801, USA,Corresponding author: Pablo Perez-Pinera, Department of Bioengineering, University of Illinois, Urbana, IL 61801, USA.
| | - Thomas Gaj
- Department of Bioengineering, University of Illinois, Urbana, IL 61801, USA,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA,Corresponding author: Thomas Gaj, Department of Bioengineering, University of Illinois, Urbana, IL 61801, USA.
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5
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Hazra R, Brine L, Garcia L, Benz B, Chirathivat N, Shen MM, Wilkinson JE, Lyons SK, Spector DL. Platr4 is an early embryonic lncRNA that exerts its function downstream on cardiogenic mesodermal lineage commitment. Dev Cell 2022; 57:2450-2468.e7. [PMID: 36347239 PMCID: PMC9680017 DOI: 10.1016/j.devcel.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 08/22/2022] [Accepted: 10/07/2022] [Indexed: 11/09/2022]
Abstract
The mammalian genome encodes thousands of long non-coding RNAs (lncRNAs), many of which are developmentally regulated and differentially expressed across tissues, suggesting their potential roles in cellular differentiation. Despite this expression pattern, little is known about how lncRNAs influence lineage commitment at the molecular level. Here, we demonstrate that perturbation of an embryonic stem cell/early embryonic lncRNA, pluripotency-associated transcript 4 (Platr4), directly influences the specification of cardiac-mesoderm-lineage differentiation. We show that Platr4 acts as a molecular scaffold or chaperone interacting with the Hippo-signaling pathway molecules Yap and Tead4 to regulate the expression of a downstream target gene, Ctgf, which is crucial to the cardiac-lineage program. Importantly, Platr4 knockout mice exhibit myocardial atrophy and valve mucinous degeneration, which are both associated with reduced cardiac output and sudden heart failure. Together, our findings provide evidence that Platr4 is required in cardiac-lineage specification and adult heart function in mice.
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Affiliation(s)
- Rasmani Hazra
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Lily Brine
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Libia Garcia
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Brian Benz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Napon Chirathivat
- Departments of Medicine, Genetics and Development, Urology, and Systems Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Michael M Shen
- Departments of Medicine, Genetics and Development, Urology, and Systems Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | | | - Scott K Lyons
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - David L Spector
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
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6
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Khachigian LM, Black BL, Ferdinandy P, De Caterina R, Madonna R, Geng YJ. Transcriptional regulation of vascular smooth muscle cell proliferation, differentiation and senescence: Novel targets for therapy. Vascul Pharmacol 2022; 146:107091. [PMID: 35896140 DOI: 10.1016/j.vph.2022.107091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/21/2022] [Accepted: 07/21/2022] [Indexed: 10/16/2022]
Abstract
Vascular smooth muscle cells (SMC) possess a unique cytoplasticity, regulated by transcriptional, translational and phenotypic transformation in response to a diverse range of extrinsic and intrinsic pathogenic factors. The mature, differentiated SMC phenotype is physiologically typified transcriptionally by expression of genes encoding "contractile" proteins, such as SMα-actin (ACTA2), SM-MHC (myosin-11) and SM22α (transgelin). When exposed to various pathological conditions (e.g., pro-atherogenic risk factors, hypertension), SMC undergo phenotypic modulation, a bioprocess enabling SMC to de-differentiate in immature stages or trans-differentiate into other cell phenotypes. As recent studies suggest, the process of SMC phenotypic transformation involves five distinct states characterized by different patterns of cell growth, differentiation, migration, matrix protein expression and declined contractility. These changes are mediated via the action of several transcriptional regulators, including myocardin and serum response factor. Conversely, other factors, including Kruppel-like factor 4 and nuclear factor-κB, can inhibit SMC differentiation and growth arrest, while factors such as yin yang-1, can promote SMC differentiation whilst inhibiting proliferation. This article reviews recent advances in our understanding of regulatory mechanisms governing SMC phenotypic modulation. We propose the concept that transcription factors mediating this switching are important biomarkers and potential pharmacological targets for therapeutic intervention in cardiovascular disease.
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Affiliation(s)
- Levon M Khachigian
- Vascular Biology and Translational Research, Department of Pathology, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Brian L Black
- Cardiovascular Research Institute, University of California, San Francisco, CA, United States of America
| | - Péter Ferdinandy
- Cardiovascular and Metabolic Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1089 Budapest, Hungary; Pharmahungary Group, 6722 Szeged, Hungary
| | - Raffaele De Caterina
- Cardiovascular Division, Pisa University Hospital & University of Pisa, Via Paradisa, 2, Pisa 56124, Italy
| | - Rosalinda Madonna
- Cardiovascular Division, Pisa University Hospital & University of Pisa, Via Paradisa, 2, Pisa 56124, Italy; Division of Cardiovascular Medicine, Department of Internal Medicine, The Center for Cardiovascular Biology and Atherosclerosis Research, McGovern School of Medicine, University of Texas Health Science Center at Houston, Houston, TX, United States of America
| | - Yong-Jian Geng
- Division of Cardiovascular Medicine, Department of Internal Medicine, The Center for Cardiovascular Biology and Atherosclerosis Research, McGovern School of Medicine, University of Texas Health Science Center at Houston, Houston, TX, United States of America
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7
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Gao P, Lyu Q, Ghanam AR, Lazzarotto CR, Newby GA, Zhang W, Choi M, Slivano OJ, Holden K, Walker JA, Kadina AP, Munroe RJ, Abratte CM, Schimenti JC, Liu DR, Tsai SQ, Long X, Miano JM. Prime editing in mice reveals the essentiality of a single base in driving tissue-specific gene expression. Genome Biol 2021; 22:83. [PMID: 33722289 PMCID: PMC7962346 DOI: 10.1186/s13059-021-02304-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 02/24/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Most single nucleotide variants (SNVs) occur in noncoding sequence where millions of transcription factor binding sites (TFBS) reside. Here, a comparative analysis of CRISPR-mediated homology-directed repair (HDR) versus the recently reported prime editing 2 (PE2) system was carried out in mice over a TFBS called a CArG box in the Tspan2 promoter. RESULTS Quantitative RT-PCR showed loss of Tspan2 mRNA in aorta and bladder, but not heart or brain, of mice homozygous for an HDR-mediated three base pair substitution in the Tspan2 CArG box. Using the same protospacer, mice homozygous for a PE2-mediated single-base substitution in the Tspan2 CArG box displayed similar cell-specific loss of Tspan2 mRNA; expression of an overlapping long noncoding RNA was also nearly abolished in aorta and bladder. Immuno-RNA fluorescence in situ hybridization validated loss of Tspan2 in vascular smooth muscle cells of HDR and PE2 CArG box mutant mice. Targeted sequencing demonstrated variable frequencies of on-target editing in all PE2 and HDR founders. However, whereas no on-target indels were detected in any of the PE2 founders, all HDR founders showed varying levels of on-target indels. Off-target analysis by targeted sequencing revealed mutations in many HDR founders, but none in PE2 founders. CONCLUSIONS PE2 directs high-fidelity editing of a single base in a TFBS leading to cell-specific loss in expression of an mRNA/long noncoding RNA gene pair. The PE2 platform expands the genome editing toolbox for modeling and correcting relevant noncoding SNVs in the mouse.
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Affiliation(s)
- Pan Gao
- Department of Medicine, Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA 30912 USA
| | - Qing Lyu
- Department of Medicine, Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA 30912 USA
| | - Amr R. Ghanam
- Department of Medicine, Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA 30912 USA
| | - Cicera R. Lazzarotto
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN 38195 USA
| | - Gregory A. Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138 USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138 USA
| | - Wei Zhang
- Department of Medicine, Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA 30912 USA
| | - Mihyun Choi
- Department of Physiology, Albany Medical College, Albany, NY 12208 USA
| | - Orazio J. Slivano
- Department of Medicine, Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA 30912 USA
| | - Kevin Holden
- Synthego Corporation, Redwood City, CA 94025 USA
| | | | | | - Rob J. Munroe
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853 USA
| | | | - John C. Schimenti
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853 USA
| | - David R. Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138 USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138 USA
| | - Shengdar Q. Tsai
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN 38195 USA
| | - Xiaochun Long
- Department of Medicine, Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA 30912 USA
| | - Joseph M. Miano
- Department of Medicine, Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA 30912 USA
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8
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Bae B, Gruner HN, Lynch M, Feng T, So K, Oliver D, Mastick GS, Yan W, Pieraut S, Miura P. Elimination of Calm1 long 3'-UTR mRNA isoform by CRISPR-Cas9 gene editing impairs dorsal root ganglion development and hippocampal neuron activation in mice. RNA 2020; 26:1414-1430. [PMID: 32522888 PMCID: PMC7491327 DOI: 10.1261/rna.076430.120] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 06/06/2020] [Indexed: 05/04/2023]
Abstract
The majority of mouse and human genes are subject to alternative cleavage and polyadenylation (APA), which most often leads to the expression of two or more alternative length 3' untranslated region (3'-UTR) mRNA isoforms. In neural tissues, there is enhanced expression of APA isoforms with longer 3'-UTRs on a global scale, but the physiological relevance of these alternative 3'-UTR isoforms is poorly understood. Calmodulin 1 (Calm1) is a key integrator of calcium signaling that generates short (Calm1-S) and long (Calm1-L) 3'-UTR mRNA isoforms via APA. We found Calm1-L expression to be largely restricted to neural tissues in mice including the dorsal root ganglion (DRG) and hippocampus, whereas Calm1-S was more broadly expressed. smFISH revealed that both Calm1-S and Calm1-L were subcellularly localized to neural processes of primary hippocampal neurons. In contrast, cultured DRG showed restriction of Calm1-L to soma. To investigate the in vivo functions of Calm1-L, we implemented a CRISPR-Cas9 gene editing strategy to delete a small region encompassing the Calm1 distal poly(A) site. This eliminated Calm1-L expression while maintaining expression of Calm1-S Mice lacking Calm1-L (Calm1ΔL/ΔL ) exhibited disorganized DRG migration in embryos, and reduced experience-induced neuronal activation in the adult hippocampus. These data indicate that Calm1-L plays functional roles in the central and peripheral nervous systems.
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Affiliation(s)
- Bongmin Bae
- Department of Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Hannah N Gruner
- Department of Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Maebh Lynch
- Department of Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Ting Feng
- Department of Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Kevin So
- Department of Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Daniel Oliver
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada 89557, USA
| | - Grant S Mastick
- Department of Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Wei Yan
- Department of Biology, University of Nevada, Reno, Nevada 89557, USA
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada 89557, USA
| | - Simon Pieraut
- Department of Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Pedro Miura
- Department of Biology, University of Nevada, Reno, Nevada 89557, USA
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9
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Nagao M, Lyu Q, Zhao Q, Wirka RC, Bagga J, Nguyen T, Cheng P, Kim JB, Pjanic M, Miano JM, Quertermous T. Coronary Disease-Associated Gene TCF21 Inhibits Smooth Muscle Cell Differentiation by Blocking the Myocardin-Serum Response Factor Pathway. Circ Res 2020; 126:517-529. [PMID: 31815603 PMCID: PMC7274203 DOI: 10.1161/circresaha.119.315968] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
RATIONALE The gene encoding TCF21 (transcription factor 21) has been linked to coronary artery disease risk by human genome-wide association studies in multiple racial ethnic groups. In murine models, Tcf21 is required for phenotypic modulation of smooth muscle cells (SMCs) in atherosclerotic tissues and promotes a fibroblast phenotype in these cells. In humans, TCF21 expression inhibits risk for coronary artery disease. The molecular mechanism by which TCF21 regulates SMC phenotype is not known. OBJECTIVE To better understand how TCF21 affects the SMC phenotype, we sought to investigate the possible mechanisms by which it regulates the lineage determining MYOCD (myocardin)-SRF (serum response factor) pathway. METHODS AND RESULTS Modulation of TCF21 expression in human coronary artery SMC revealed that TCF21 suppresses a broad range of SMC markers, as well as key SMC transcription factors MYOCD and SRF, at the RNA and protein level. We conducted chromatin immunoprecipitation-sequencing to map SRF-binding sites in human coronary artery SMC, showing that binding is colocalized in the genome with TCF21, including at a novel enhancer in the SRF gene, and at the MYOCD gene promoter. In vitro genome editing indicated that the SRF enhancer CArG box regulates transcription of the SRF gene, and mutation of this conserved motif in the orthologous mouse SRF enhancer revealed decreased SRF expression in aorta and heart tissues. Direct TCF21 binding and transcriptional inhibition at colocalized sites were established by reporter gene transfection assays. Chromatin immunoprecipitation and protein coimmunoprecipitation studies provided evidence that TCF21 blocks MYOCD and SRF association by direct TCF21-MYOCD interaction. CONCLUSIONS These data indicate that TCF21 antagonizes the MYOCD-SRF pathway through multiple mechanisms, further establishing a role for this coronary artery disease-associated gene in fundamental SMC processes and indicating the importance of smooth muscle response to vascular stress and phenotypic modulation of this cell type in coronary artery disease risk.
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Affiliation(s)
- Manabu Nagao
- Division of Cardiovascular Medicine and Cardiovascular Institute, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305
| | - Qing Lyu
- Aab Cardiovascular Research Institute, University of Rochester School of Medicine & Dentistry, 601 Elmwood Ave, Rochester, NY 14624
| | - Quanyi Zhao
- Division of Cardiovascular Medicine and Cardiovascular Institute, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305
| | - Robert C Wirka
- Division of Cardiovascular Medicine and Cardiovascular Institute, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305
| | - Joetsaroop Bagga
- Division of Cardiovascular Medicine and Cardiovascular Institute, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305
| | - Trieu Nguyen
- Division of Cardiovascular Medicine and Cardiovascular Institute, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305
| | - Paul Cheng
- Division of Cardiovascular Medicine and Cardiovascular Institute, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305
| | - Juyong Brian Kim
- Division of Cardiovascular Medicine and Cardiovascular Institute, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305
| | - Milos Pjanic
- Division of Cardiovascular Medicine and Cardiovascular Institute, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305
| | - Joseph M. Miano
- Aab Cardiovascular Research Institute, University of Rochester School of Medicine & Dentistry, 601 Elmwood Ave, Rochester, NY 14624
| | - Thomas Quertermous
- Division of Cardiovascular Medicine and Cardiovascular Institute, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305
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10
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Abstract
Coronary artery disease is a complex cardiovascular disease involving an interplay of genetic and environmental influences over a lifetime. Although considerable progress has been made in understanding lifestyle risk factors, genetic factors identified from genome-wide association studies may capture additional hidden risk undetected by traditional clinical tests. These genetic discoveries have highlighted many candidate genes and pathways dysregulated in the vessel wall, including those involving smooth muscle cell phenotypic modulation and injury responses. Here, we summarize experimental evidence for a few genome-wide significant loci supporting their roles in smooth muscle cell biology and disease. We also discuss molecular quantitative trait locus mapping as a powerful discovery and fine-mapping approach applied to smooth muscle cell and coronary artery disease-relevant tissues. We emphasize the critical need for alternative genetic strategies, including cis/trans-regulatory network analysis, genome editing, and perturbations, as well as single-cell sequencing in smooth muscle cell tissues and model organisms, under both normal and disease states. By integrating multiple experimental and analytical modalities, these multidimensional datasets should improve the interpretation of coronary artery disease genome-wide association studies and molecular quantitative trait locus signals and inform candidate targets for therapeutic intervention or risk prediction.
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Affiliation(s)
- Doris Wong
- From the Center for Public Health Genomics (D.W., A.W.T., C.L.M.), University of Virginia, Charlottesville.,Department of Biochemistry and Molecular Genetics (D.W., C.L.M.), University of Virginia, Charlottesville
| | - Adam W Turner
- From the Center for Public Health Genomics (D.W., A.W.T., C.L.M.), University of Virginia, Charlottesville
| | - Clint L Miller
- From the Center for Public Health Genomics (D.W., A.W.T., C.L.M.), University of Virginia, Charlottesville.,Department of Biochemistry and Molecular Genetics (D.W., C.L.M.), University of Virginia, Charlottesville.,Department of Biomedical Engineering (C.L.M.), University of Virginia, Charlottesville.,Department of Public Health Sciences (C.L.M.), University of Virginia, Charlottesville
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11
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Choi M, Lu YW, Zhao J, Wu M, Zhang W, Long X. Transcriptional control of a novel long noncoding RNA Mymsl in smooth muscle cells by a single Cis-element and its initial functional characterization in vessels. J Mol Cell Cardiol 2020; 138:147-57. [PMID: 31751568 DOI: 10.1016/j.yjmcc.2019.11.148] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/10/2019] [Accepted: 11/05/2019] [Indexed: 02/08/2023]
Abstract
Differentiated vascular smooth muscle cells (VSMCs) are crucial in maintaining vascular homeostasis. While the coding transcriptome of the differentiated VSMC phenotype has been defined, we know little about its noncoding signature. Herein, we identified a Myocardin-induced muscle specific long noncoding RNA (lncRNA) (Mymsl) downregulated upon VSMC phenotypic modulation. We demonstrated an essential role of a proximal consensus CArG element in response to MYOCD/SRF in vitro. To validate the in vivo role of this CArG element, we generated CArG mutant mice via CRISPR-Cas9 genome editing. While the CArG mutation had no impact on the expression of surrounding genes, it abolished Mymsl expression in SMCs, but not skeletal and cardiac muscle. Chromatin immunoprecipitation assays (ChIPs) showed decreased SRF binding to CArG region in mutants whereas the enrichment of H3K79Me2 remained the same. RNA-seq analysis showed a downregulation of matrix genes in aortas from Mymsl knockout mice, which was further validated in injured carotid arteries. Our study defined the transcriptional control of a novel lncRNA in SMCs via a single transcription factor binding site, which may offer a new strategy for generating SMC-specific knockout mouse models. We also provided in vivo evidence supporting the potential importance of Mymsl in vascular pathophysiology.
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12
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Abstract
Variants within non-coding genomic regions can greatly affect disease. In recent years, increasing focus has been given to these variants, and how they can alter regulatory elements, such as enhancers, transcription factor binding sites and DNA methylation regions. Such variants can be considered regulatory variants. Concurrently, much effort has been put into establishing international consortia to undertake large projects aimed at discovering regulatory elements in different tissues, cell lines and organisms, and probing the effects of genetic variants on regulation by measuring gene expression. Here, we describe methods and techniques for discovering disease-associated non-coding variants using sequencing technologies. We then explain the computational procedures that can be used for annotating these variants using the information from the aforementioned projects, and prediction of their putative effects, including potential pathogenicity, based on rule-based and machine learning approaches. We provide the details of techniques to validate these predictions, by mapping chromatin-chromatin and chromatin-protein interactions, and introduce Clustered Regularly Interspaced Short Palindromic Repeats-Associated Protein 9 (CRISPR-Cas9) technology, which has already been used in this field and is likely to have a big impact on its future evolution. We also give examples of regulatory variants associated with multiple complex diseases. This review is aimed at bioinformaticians interested in the characterization of regulatory variants, molecular biologists and geneticists interested in understanding more about the nature and potential role of such variants from a functional point of views, and clinicians who may wish to learn about variants in non-coding genomic regions associated with a given disease and find out what to do next to uncover how they impact on the underlying mechanisms.
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Affiliation(s)
- Elena Rojano
- Department of Molecular Biology and Biochemistry, University of Malaga (UMA), 29010 Malaga, Spain
| | - Pedro Seoane
- Department of Molecular Biology and Biochemistry, University of Malaga (UMA), 29010 Malaga, Spain
| | - Juan A G Ranea
- CIBER de Enfermedades Raras, ISCIII, Madrid, Spain and Department of Molecular Biology and Biochemistry, University of Malaga (UMA), 29010 Malaga, Spain
| | - James R Perkins
- Research laboratory, IBIMA-Regional University Hospital of Malaga, UMA, Malaga 29009, Spain
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13
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Babaei M, Liu Y, Wuerzberger-Davis SM, McCaslin EZ, DiRusso CJ, Yeo AT, Kagermazova L, Miyamoto S, Gilmore TD. CRISPR/Cas9-based editing of a sensitive transcriptional regulatory element to achieve cell type-specific knockdown of the NEMO scaffold protein. PLoS One 2019; 14:e0222588. [PMID: 31553754 PMCID: PMC6760803 DOI: 10.1371/journal.pone.0222588] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 09/02/2019] [Indexed: 11/25/2022] Open
Abstract
The use of alternative promoters for the cell type-specific expression of a given mRNA/protein is a common cell strategy. NEMO is a scaffold protein required for canonical NF-κB signaling. Transcription of the NEMO gene is primarily controlled by two promoters: one (promoter B) drives NEMO transcription in most cell types and the second (promoter D) is largely responsible for NEMO transcription in liver cells. Herein, we have used a CRISPR/Cas9-based approach to disrupt a core sequence element of promoter B, and this genetic editing essentially eliminates expression of NEMO mRNA and protein in 293T human kidney cells. By cell subcloning, we have isolated targeted 293T cell lines that express no detectable NEMO protein, have defined genomic alterations at promoter B, and do not support activation of canonical NF-κB signaling in response to treatment with tumor necrosis factor. Nevertheless, non-canonical NF-κB signaling is intact in these NEMO-deficient cells. Expression of ectopic wild-type NEMO, but not certain human NEMO disease mutants, in the edited cells restores downstream NF-κB signaling in response to tumor necrosis factor. Targeting of the promoter B element does not substantially reduce NEMO expression (from promoter D) in the human SNU-423 liver cancer cell line. Thus, we have created a strategy for selectively eliminating cell type-specific expression from an alternative promoter and have generated 293T cell lines with a functional knockout of NEMO. The implications of these findings for further studies and for therapeutic approaches to target canonical NF-κB signaling are discussed.
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Affiliation(s)
- Milad Babaei
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Yuekun Liu
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Shelly M. Wuerzberger-Davis
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Ethan Z. McCaslin
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Christopher J. DiRusso
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Alan T. Yeo
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Larisa Kagermazova
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Shigeki Miyamoto
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Thomas D. Gilmore
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
- * E-mail:
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14
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Lyu Q, Dhagia V, Han Y, Guo B, Wines-Samuelson ME, Christie CK, Yin Q, Slivano OJ, Herring P, Long X, Gupte SA, Miano JM. CRISPR-Cas9-Mediated Epitope Tagging Provides Accurate and Versatile Assessment of Myocardin-Brief Report. Arterioscler Thromb Vasc Biol 2019; 38:2184-2190. [PMID: 29976770 DOI: 10.1161/atvbaha.118.311171] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Objective- Unreliable antibodies often hinder the accurate detection of an endogenous protein, and this is particularly true for the cardiac and smooth muscle cofactor, MYOCD (myocardin). Accordingly, the mouse Myocd locus was targeted with 2 independent epitope tags for the unambiguous expression, localization, and activity of MYOCD protein. Approach and Results- 3cCRISPR (3-component clustered regularly interspaced short palindromic repeat) was used to engineer a carboxyl-terminal 3×FLAG or 3×HA epitope tag in mouse embryos. Western blotting with antibodies to each tag revealed a MYOCD protein product of ≈150 kDa, a size considerably larger than that reported in virtually all publications. MYOCD protein was most abundant in some adult smooth muscle-containing tissues with surprisingly low-level expression in the heart. Both alleles of Myocd are active in aorta because a 2-fold increase in protein was seen in mice homozygous versus heterozygous for FLAG-tagged Myocd. ChIP (chromatin immunoprecipitation)-quantitative polymerase chain reaction studies provide proof-of-principle data demonstrating the utility of this mouse line in conducting genome-wide ChIP-seq studies to ascertain the full complement of MYOCD-dependent target genes in vivo. Although FLAG-tagged MYOCD protein was undetectable in sections of adult mouse tissues, low-passaged vascular smooth muscle cells exhibited expected nuclear localization. Conclusions- This report validates new mouse models for analyzing MYOCD protein expression, localization, and binding activity in vivo and highlights the need for rigorous authentication of antibodies in biomedical research.
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Affiliation(s)
- Qing Lyu
- From the Aab Cardiovascular Research Institute, University of Rochester Medical Center, Rochester, NY (Q.L., Y.H., B.G., M.E.W.-S., C.K.C., Q.Y., O.J.S., J.M.M.)
| | - Vidhi Dhagia
- Department of Pharmacology, New York Medical College, Valhalla (V.D., S.A.G.)
| | - Yu Han
- From the Aab Cardiovascular Research Institute, University of Rochester Medical Center, Rochester, NY (Q.L., Y.H., B.G., M.E.W.-S., C.K.C., Q.Y., O.J.S., J.M.M.)
| | - Bing Guo
- From the Aab Cardiovascular Research Institute, University of Rochester Medical Center, Rochester, NY (Q.L., Y.H., B.G., M.E.W.-S., C.K.C., Q.Y., O.J.S., J.M.M.)
| | - Mary E Wines-Samuelson
- From the Aab Cardiovascular Research Institute, University of Rochester Medical Center, Rochester, NY (Q.L., Y.H., B.G., M.E.W.-S., C.K.C., Q.Y., O.J.S., J.M.M.)
| | - Christine K Christie
- From the Aab Cardiovascular Research Institute, University of Rochester Medical Center, Rochester, NY (Q.L., Y.H., B.G., M.E.W.-S., C.K.C., Q.Y., O.J.S., J.M.M.)
| | - Qiangzong Yin
- From the Aab Cardiovascular Research Institute, University of Rochester Medical Center, Rochester, NY (Q.L., Y.H., B.G., M.E.W.-S., C.K.C., Q.Y., O.J.S., J.M.M.)
| | - Orazio J Slivano
- From the Aab Cardiovascular Research Institute, University of Rochester Medical Center, Rochester, NY (Q.L., Y.H., B.G., M.E.W.-S., C.K.C., Q.Y., O.J.S., J.M.M.)
| | - Paul Herring
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis (P.H.)
| | - Xiaochun Long
- Department of Molecular and Cellular Physiology, Albany Medical College, NY (X.L.)
| | - Sachin A Gupte
- Department of Pharmacology, New York Medical College, Valhalla (V.D., S.A.G.)
| | - Joseph M Miano
- From the Aab Cardiovascular Research Institute, University of Rochester Medical Center, Rochester, NY (Q.L., Y.H., B.G., M.E.W.-S., C.K.C., Q.Y., O.J.S., J.M.M.)
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15
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Abstract
Next generation sequencing has uncovered a trove of short noncoding RNAs (e.g., microRNAs) and long noncoding RNAs (lncRNAs) that act as molecular rheostats in the control of diverse homeostatic processes. Meanwhile, the tsunamic emergence of clustered regularly interspaced short palindromic repeats (CRISPR) editing has transformed our influence over all DNA-carrying entities, heralding global CRISPRization. This is evident in biomedical research where the ease and low-cost of CRISPR editing has made it the preferred method of manipulating the mouse genome, facilitating rapid discovery of genome function in an in vivo context. Here, CRISPR genome editing components are updated for elucidating lncRNA function in mice. Various strategies are highlighted for understanding the function of lncRNAs residing in intergenic sequence space, as host genes that harbor microRNAs or other genes, and as natural antisense, overlapping or intronic genes. Also discussed is CRISPR editing of mice carrying human lncRNAs as well as the editing of competing endogenous RNAs. The information described herein should assist labs in the rigorous design of experiments that interrogate lncRNA function in mice where complex disease processes can be modeled thus accelerating translational discovery.
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Affiliation(s)
- Joseph M Miano
- Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, NY, United States of America.
| | - Xiaochun Long
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, United States of America
| | - Qing Lyu
- Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, NY, United States of America
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16
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Abstract
Though making up nearly half of the known CRISPR-Cas9 family of enzymes, the Type II-C CRISPR-Cas9 has been underexplored for their molecular mechanisms and potential in safe gene editing applications. In comparison with the more popular Type II-A CRISPR-Cas9, the Type II-C enzymes are generally smaller in size and utilize longer base pairing in identification of their DNA substrates. These characteristics suggest easier portability and potentially less off-targets for Type II-C in gene editing applications. We describe identification and biochemical characterization of a thermophilic Type II-C CRISPR-Cas from Acidothermus cellulolyticus (AceCas9). We describe several library-based methods that enabled us to identify the PAM sequence and elements critical to protospacer mismatch surveillance of AceCas9.
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17
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Hand TH, Das A, Roth MO, Smith CL, Jean-Baptiste UL, Li H. Phosphate Lock Residues of Acidothermus cellulolyticus Cas9 Are Critical to Its Substrate Specificity. ACS Synth Biol 2018; 7:2908-2917. [PMID: 30458109 PMCID: PMC6525624 DOI: 10.1021/acssynbio.8b00455] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Despite being utilized widely in genome sciences, CRISPR-Cas9 remains limited in achieving high fidelity in cleaving DNA. A better understanding of the molecular basis of Cas9 holds the key to improve Cas9-based tools. We employed direct evolution and in vitro characterizations to explore structural parameters that impact the specificity of the thermophilic Cas9 from Acidothermus cellulolyticus (AceCas9). By identifying variants that are able to cleave mismatched protospacers within the seed region, we found a critical role of the phosphate lock residues in substrate specificity in a manner that depends on their sizes and charges. Removal of the negative charge from the phosphate lock residues significantly decreases sensitivity to the guide-DNA mismatches. An increase in size of the substituted residues further reduces the sensitivity to mismatches at the first position of the protospacer. Our findings identify the phosphate lock residues as an important site for tuning the specificity and catalytic efficiency of Cas9.
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Affiliation(s)
- Travis H. Hand
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Anuska Das
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Mitchell O. Roth
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Chardasia L. Smith
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Uriel L. Jean-Baptiste
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Hong Li
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
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18
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Suzuki M, Hayashi T, Inoue T, Agata K, Hirayama M, Suzuki M, Shigenobu S, Takeuchi T, Yamamoto T, Suzuki KIT. Cas9 ribonucleoprotein complex allows direct and rapid analysis of coding and noncoding regions of target genes in Pleurodeles waltl development and regeneration. Dev Biol 2018; 443:127-136. [DOI: 10.1016/j.ydbio.2018.09.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 09/07/2018] [Accepted: 09/07/2018] [Indexed: 12/14/2022]
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19
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Zhu B, Rippe C, Holmberg J, Zeng S, Perisic L, Albinsson S, Hedin U, Uvelius B, Swärd K. Nexilin/NEXN controls actin polymerization in smooth muscle and is regulated by myocardin family coactivators and YAP. Sci Rep 2018; 8:13025. [PMID: 30158653 PMCID: PMC6115340 DOI: 10.1038/s41598-018-31328-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 08/17/2018] [Indexed: 01/03/2023] Open
Abstract
Nexilin, encoded by the NEXN gene, is expressed in striated muscle and localizes to Z-discs, influencing mechanical stability. We examined Nexilin/NEXN in smooth muscle cells (SMCs), and addressed if Nexilin localizes to dense bodies and dense bands and whether it is regulated by actin-controlled coactivators from the MRTF (MYOCD, MKL1, MKL2) and YAP/TAZ (YAP1 and WWTR1) families. NEXN expression in SMCs was comparable to that in striated muscles. Immunofluorescence and immunoelectron microscopy suggested that Nexilin localizes to dense bodies and dense bands. Correlations at the mRNA level suggested that NEXN expression might be controlled by actin polymerization. Depolymerization of actin using Latrunculin B repressed the NEXN mRNA and protein in bladder and coronary artery SMCs. Overexpression and knockdown supported involvement of both YAP/TAZ and MRTFs in the transcriptional control of NEXN. YAP/TAZ and MRTFs appeared equally important in bladder SMCs, whereas MRTFs dominated in vascular SMCs. Expression of NEXN was moreover reduced in situations of SMC phenotypic modulation in vivo. The proximal promoter of NEXN conferred control by MRTF-A/MKL1 and MYOCD. NEXN silencing reduced actin polymerization and cell migration, as well as SMC marker expression. NEXN targeting by actin-controlled coactivators thus amplifies SMC differentiation through the actin cytoskeleton, probably via dense bodies and dense bands.
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Affiliation(s)
- Baoyi Zhu
- Department of Experimental Medical Science, Lund University, SE-221 84, Lund, Sweden. .,Department of Urology, the Sixth Affiliated Hospital of Guangzhou Medical University (Qingyuan People's Hospital), 511518, Guangdong, China.
| | - Catarina Rippe
- Department of Experimental Medical Science, Lund University, SE-221 84, Lund, Sweden
| | - Johan Holmberg
- Department of Experimental Medical Science, Lund University, SE-221 84, Lund, Sweden
| | - Shaohua Zeng
- Department of Experimental Medical Science, Lund University, SE-221 84, Lund, Sweden.,Department of Urology, the Sixth Affiliated Hospital of Guangzhou Medical University (Qingyuan People's Hospital), 511518, Guangdong, China
| | - Ljubica Perisic
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Sebastian Albinsson
- Department of Experimental Medical Science, Lund University, SE-221 84, Lund, Sweden
| | - Ulf Hedin
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Bengt Uvelius
- Department of Clinical Science, Section of Urology, Lund University, SE-221 84, Lund, Sweden
| | - Karl Swärd
- Department of Experimental Medical Science, Lund University, SE-221 84, Lund, Sweden
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20
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Abstract
Prokaryotic type II adaptive immune systems have been developed into the versatile CRISPR technology, which has been widely applied in site-specific genome editing and has revolutionized biomedical research due to its superior efficiency and flexibility. Recent studies have greatly diversified CRISPR technologies by coupling it with various DNA repair mechanisms and targeting strategies. These new advances have significantly expanded the generation of genetically modified animal models, either by including species in which targeted genetic modification could not be achieved previously, or through introducing complex genetic modifications that take multiple steps and cost years to achieve using traditional methods. Herein, we review the recent developments and applications of CRISPR-based technology in generating various animal models, and discuss the everlasting impact of this new progress on biomedical research.
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Affiliation(s)
- Xun Ma
- Key Laboratory for Regenerative Medicine in Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Avery Sum-Yu Wong
- Key Laboratory for Regenerative Medicine in Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Hei-Yin Tam
- Key Laboratory for Regenerative Medicine in Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Samuel Yung-Kin Tsui
- Key Laboratory for Regenerative Medicine in Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Dittman Lai-Shun Chung
- Key Laboratory for Regenerative Medicine in Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Bo Feng
- Key Laboratory for Regenerative Medicine in Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China. .,Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Guangdong 510530, China.,SBS Core Laboratory, CUHK Shenzhen Research Institute, Shenzhen Guangdong 518057, China
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21
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Musunuru K. Genome Editing: The Recent History and Perspective in Cardiovascular Diseases. J Am Coll Cardiol 2017; 70:2808-2821. [PMID: 29191331 DOI: 10.1016/j.jacc.2017.10.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Revised: 10/02/2017] [Accepted: 10/03/2017] [Indexed: 02/07/2023]
Abstract
The genome-editing field has advanced to a remarkable degree in the last 5 years, culminating in the successful correction of a cardiomyopathy gene mutation in viable human embryos. In this review, the author discusses the basic principles of genome editing, recent advances in clustered regularly interspaced short palindromic repeats and clustered regularly interspaced short palindromic repeats-associated 9 technology, the impact on cardiovascular basic science research, possible therapeutic applications in patients with cardiovascular diseases, and finally the implications of potential clinical uses of human germline genome editing.
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Affiliation(s)
- Kiran Musunuru
- Cardiovascular Institute, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania; and the Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.
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22
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Aschrafi A, Gioio AE, Dong L, Kaplan BB. Disruption of the Axonal Trafficking of Tyrosine Hydroxylase mRNA Impairs Catecholamine Biosynthesis in the Axons of Sympathetic Neurons. eNeuro 2017; 4:ENEURO. [PMID: 28630892 DOI: 10.1523/ENEURO.0385-16.2017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Tyrosine hydroxylase (TH) is the enzyme that catalyzes the rate-limiting step in the biosynthesis of the catecholamine neurotransmitters. In a previous communication, evidence was provided that TH mRNA is trafficked to the axon, where it is locally translated. In addition, a 50-bp sequence element in the 3'untranslated region (3'UTR) of TH mRNA was identified that directs TH mRNA to distal axons (i.e., zip-code). In the present study, the hypothesis was tested that local translation of TH plays an important role in the biosynthesis of the catecholamine neurotransmitters in the axon and/or presynaptic nerve terminal. Toward this end, a targeted deletion of the axonal transport sequence element was developed, using the lentiviral delivery of the CRISPR/Cas9 system, and two guide RNA (gRNA) sequences flanking the 50-bp cis-acting regulatory element in rat superior cervical ganglion (SCG) neurons. Deletion of the axonal transport element reduced TH mRNA levels in the distal axons and reduced the axonal protein levels of TH and TH activity as measured by phosphorylation of SER40 in SCG neurons. Moreover, deletion of the zip-code diminished the axonal levels of dopamine (DA) and norepinephrine (NE). Conversely, the local translation of exogenous TH mRNA in the distal axon enhanced TH levels and activity, and elevated axonal NE levels. Taken together, these results provide direct evidence to support the hypothesis that TH mRNA trafficking and local synthesis of TH play an important role in the synthesis of catecholamines in the axon and presynaptic terminal.
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23
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24
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Shin HY, Wang C, Lee HK, Yoo KH, Zeng X, Kuhns T, Yang CM, Mohr T, Liu C, Hennighausen L. CRISPR/Cas9 targeting events cause complex deletions and insertions at 17 sites in the mouse genome. Nat Commun 2017; 8:15464. [PMID: 28561021 PMCID: PMC5460021 DOI: 10.1038/ncomms15464] [Citation(s) in RCA: 207] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Accepted: 03/31/2017] [Indexed: 12/29/2022] Open
Abstract
Although CRISPR/Cas9 genome editing has provided numerous opportunities to interrogate the functional significance of any given genomic site, there is a paucity of data on the extent of molecular scars inflicted on the mouse genome. Here we interrogate the molecular consequences of CRISPR/Cas9-mediated deletions at 17 sites in four loci of the mouse genome. We sequence targeted sites in 632 founder mice and analyse 54 established lines. While the median deletion size using single sgRNAs is 9 bp, we also obtain large deletions of up to 600 bp. Furthermore, we show unreported asymmetric deletions and large insertions of middle repetitive sequences. Simultaneous targeting of distant loci results in the removal of the intervening sequences. Reliable deletion of juxtaposed sites is only achieved through two-step targeting. Our findings also demonstrate that an extended analysis of F1 genotypes is required to obtain conclusive information on the exact molecular consequences of targeting events.
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Affiliation(s)
- Ha Youn Shin
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland 20892, USA
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Chaochen Wang
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Hye Kyung Lee
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland 20892, USA
- Department of Cell and Developmental Biology & Dental Research Institute, Seoul National University, Seoul 110-749, Republic of Korea
| | - Kyung Hyun Yoo
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland 20892, USA
- Department of Life Systems, Sookmyung Women's University, Seoul 140-742, Republic of Korea
| | - Xianke Zeng
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Tyler Kuhns
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Chul Min Yang
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Teresa Mohr
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Chengyu Liu
- Transgenic Core, National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Lothar Hennighausen
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland 20892, USA
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Nakagawa Y, Sakuma T, Nishimichi N, Yokosaki Y, Takeo T, Nakagata N, Yamamoto T. Culture time of vitrified/warmed zygotes before microinjection affects the production efficiency of CRISPR-Cas9-mediated knock-in mice. Biol Open 2017; 6:706-713. [PMID: 28396487 PMCID: PMC5450330 DOI: 10.1242/bio.025122] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Robust reproductive engineering techniques are required for the efficient and rapid production of genetically modified mice. We have reported the efficient production of genome-edited mice using reproductive engineering techniques, such as ultra-superovulation, in vitro fertilization (IVF) and vitrification/warming of zygotes. We usually use vitrified/warmed fertilized oocytes created by IVF for microinjection because of work efficiency and flexible scheduling. Here, we investigated whether the culture time of zygotes before microinjection influences the efficiency of producing knock-in mice. Knock-in mice were generated using clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) system and single-stranded oligodeoxynucleotide (ssODN) or PITCh (Precise Integration into Target Chromosome) system, a method of integrating a donor vector assisted by microhomology-mediated end-joining. The cryopreserved fertilized oocytes were warmed, cultured for several hours and microinjected at different timings. Microinjection was performed with Cas9 protein, guide RNA(s), and an ssODN or PITCh donor plasmid for the ssODN knock-in and the PITCh knock-in, respectively. Different production efficiencies of knock-in mice were observed by changing the timing of microinjection. Our study provides useful information for the CRISPR-Cas9-based generation of knock-in mice. Summary: We report variable production efficiencies of CRISPR-Cas9-mediated knock-in mice depending on a series of microinjection timings using vitrified, warmed, and cultured zygotes created via ultra-superovulation and in vitro fertilization.
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Affiliation(s)
- Yoshiko Nakagawa
- Center for Animal Resources and Development, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
| | - Tetsushi Sakuma
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Norihisa Nishimichi
- Cell-Matrix Frontier Laboratory, Health Administration Center, Hiroshima University, 1-2-3 Kasumi, Minamiku, Hiroshima 734-8551, Japan
| | - Yasuyuki Yokosaki
- Cell-Matrix Frontier Laboratory, Health Administration Center, Hiroshima University, 1-2-3 Kasumi, Minamiku, Hiroshima 734-8551, Japan.,Clinical Genetics, Hiroshima University Hospital, 1-2-3 Kasumi, Minamiku, Hiroshima 734-8551, Japan
| | - Toru Takeo
- Center for Animal Resources and Development, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
| | - Naomi Nakagata
- Center for Animal Resources and Development, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
| | - Takashi Yamamoto
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
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Halim D, Wilson MP, Oliver D, Brosens E, Verheij JB, Han Y, Nanda V, Lyu Q, Doukas M, Stoop H, Brouwer RW, van IJcken WF, Slivano OJ, Burns AJ, Christie CK, de Mesy Bentley KL, Brooks AS, Tibboel D, Xu S, Jin ZG, Djuwantono T, Yan W, Alves MM, Hofstra RM, Miano JM. Loss of LMOD1 impairs smooth muscle cytocontractility and causes megacystis microcolon intestinal hypoperistalsis syndrome in humans and mice. Proc Natl Acad Sci U S A 2017; 114:E2739-47. [PMID: 28292896 DOI: 10.1073/pnas.1620507114] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Megacystis microcolon intestinal hypoperistalsis syndrome (MMIHS) is a congenital visceral myopathy characterized by severe dilation of the urinary bladder and defective intestinal motility. The genetic basis of MMIHS has been ascribed to spontaneous and autosomal dominant mutations in actin gamma 2 (ACTG2), a smooth muscle contractile gene. However, evidence suggesting a recessive origin of the disease also exists. Using combined homozygosity mapping and whole exome sequencing, a genetically isolated family was found to carry a premature termination codon in Leiomodin1 (LMOD1), a gene preferentially expressed in vascular and visceral smooth muscle cells. Parents heterozygous for the mutation exhibited no abnormalities, but a child homozygous for the premature termination codon displayed symptoms consistent with MMIHS. We used CRISPR-Cas9 (CRISPR-associated protein) genome editing of Lmod1 to generate a similar premature termination codon. Mice homozygous for the mutation showed loss of LMOD1 protein and pathology consistent with MMIHS, including late gestation expansion of the bladder, hydronephrosis, and rapid demise after parturition. Loss of LMOD1 resulted in a reduction of filamentous actin, elongated cytoskeletal dense bodies, and impaired intestinal smooth muscle contractility. These results define LMOD1 as a disease gene for MMIHS and suggest its role in establishing normal smooth muscle cytoskeletal-contractile coupling.
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Lee MY, Park C, Ha SE, Park PJ, Berent RM, Jorgensen BG, Corrigan RD, Grainger N, Blair PJ, Slivano OJ, Miano JM, Ward SM, Smith TK, Sanders KM, Ro S. Serum response factor regulates smooth muscle contractility via myotonic dystrophy protein kinases and L-type calcium channels. PLoS One 2017; 12:e0171262. [PMID: 28152551 PMCID: PMC5289827 DOI: 10.1371/journal.pone.0171262] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 01/17/2017] [Indexed: 11/19/2022] Open
Abstract
Serum response factor (SRF) transcriptionally regulates expression of contractile genes in smooth muscle cells (SMC). Lack or decrease of SRF is directly linked to a phenotypic change of SMC, leading to hypomotility of smooth muscle in the gastrointestinal (GI) tract. However, the molecular mechanism behind SRF-induced hypomotility in GI smooth muscle is largely unknown. We describe here how SRF plays a functional role in the regulation of the SMC contractility via myotonic dystrophy protein kinase (DMPK) and L-type calcium channel CACNA1C. GI SMC expressed Dmpk and Cacna1c genes into multiple alternative transcriptional isoforms. Deficiency of SRF in SMC of Srf knockout (KO) mice led to reduction of SRF-dependent DMPK, which down-regulated the expression of CACNA1C. Reduction of CACNA1C in KO SMC not only decreased intracellular Ca2+ spikes but also disrupted their coupling between cells resulting in decreased contractility. The role of SRF in the regulation of SMC phenotype and function provides new insight into how SMC lose their contractility leading to hypomotility in pathophysiological conditions within the GI tract.
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Affiliation(s)
- Moon Young Lee
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada, United States of America
- Department of Physiology, Wonkwang Digestive Disease Research Institute and Institute of Wonkwang Medical Science, School of Medicine, Wonkwang University, Iksan, Chonbuk, Korea
| | - Chanjae Park
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada, United States of America
| | - Se Eun Ha
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada, United States of America
| | - Paul J. Park
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada, United States of America
| | - Robyn M. Berent
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada, United States of America
| | - Brian G. Jorgensen
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada, United States of America
| | - Robert D. Corrigan
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada, United States of America
| | - Nathan Grainger
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada, United States of America
| | - Peter J. Blair
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada, United States of America
| | - Orazio J. Slivano
- Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Joseph M. Miano
- Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Sean M. Ward
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada, United States of America
| | - Terence K. Smith
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada, United States of America
| | - Kenton M. Sanders
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada, United States of America
| | - Seungil Ro
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada, United States of America
- * E-mail:
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Abstract
Gene editing is a relatively recent concept in the molecular biology field. Traditional genetic modifications in animals relied on a classical toolbox that, aside from some technical improvements and additions, remained unchanged for many years. Classical methods involved direct delivery of DNA sequences into embryos or the use of embryonic stem cells for those few species (mice and rats) where it was possible to establish them. For livestock, the advent of somatic cell nuclear transfer platforms provided alternative, but technically challenging, approaches for the genetic alteration of loci at will. However, the entire landscape changed with the appearance of different classes of genome editors, from initial zinc finger nucleases, to transcription activator-like effector nucleases and, most recently, with the development of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas). Gene editing is currently achieved by CRISPR–Cas-mediated methods, and this technological advancement has boosted our capacity to generate almost any genetically altered animal that can be envisaged.
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Zhu QM, Ko KA, Ture S, Mastrangelo MA, Chen MH, Johnson AD, O'Donnell CJ, Morrell CN, Miano JM, Lowenstein CJ. Novel Thrombotic Function of a Human SNP in STXBP5 Revealed by CRISPR/Cas9 Gene Editing in Mice. Arterioscler Thromb Vasc Biol 2016; 37:264-270. [PMID: 28062498 DOI: 10.1161/atvbaha.116.308614] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 12/13/2016] [Indexed: 11/16/2022]
Abstract
OBJECTIVE To identify and characterize the effect of a SNP (single-nucleotide polymorphism) in the STXBP5 locus that is associated with altered thrombosis in humans. GWAS (genome-wide association studies) have identified numerous SNPs associated with human thrombotic phenotypes, but determining the functional significance of an individual candidate SNP can be challenging, particularly when in vivo modeling is required. Recent GWAS led to the discovery of STXBP5 as a regulator of platelet secretion in humans. Further clinical studies have identified genetic variants of STXBP5 that are linked to altered plasma von Willebrand factor levels and thrombosis in humans, but the functional significance of these variants in STXBP5 is not understood. APPROACH AND RESULTS We used CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated 9) techniques to produce a precise mouse model carrying a human coding SNP rs1039084 (encoding human p. N436S) in the STXBP5 locus associated with decreased thrombosis. Mice carrying the orthologous human mutation (encoding p. N437S in mouse STXBP5) have lower plasma von Willebrand factor levels, decreased thrombosis, and decreased platelet secretion compared with wild-type mice. This thrombosis phenotype recapitulates the phenotype of humans carrying the minor allele of rs1039084. Decreased plasma von Willebrand factor and platelet activation may partially explain the decreased thrombotic phenotype in mutant mice. CONCLUSIONS Using precise mammalian genome editing, we have identified a human nonsynonymous SNP rs1039084 in the STXBP5 locus as a causal variant for a decreased thrombotic phenotype. CRISPR/Cas9 genetic editing facilitates the rapid and efficient generation of animals to study the function of human genetic variation in vascular diseases.
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Affiliation(s)
- Qiuyu Martin Zhu
- From the Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester Medical Center, NY (Q.M.Z., K.A.K., S.T., M.A.M., C.N.M., J.M.M., C.J.L.); Division of Intramural Research, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health, and NHLBI Framingham Heart Study, Framingham, MA (M.-H.C., A.D.J., C.J.O.D.); and Cardiovascular Division, Massachusetts General Hospital, Harvard Medical School, Boston (C.J.O.D.)
| | - Kyung Ae Ko
- From the Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester Medical Center, NY (Q.M.Z., K.A.K., S.T., M.A.M., C.N.M., J.M.M., C.J.L.); Division of Intramural Research, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health, and NHLBI Framingham Heart Study, Framingham, MA (M.-H.C., A.D.J., C.J.O.D.); and Cardiovascular Division, Massachusetts General Hospital, Harvard Medical School, Boston (C.J.O.D.)
| | - Sara Ture
- From the Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester Medical Center, NY (Q.M.Z., K.A.K., S.T., M.A.M., C.N.M., J.M.M., C.J.L.); Division of Intramural Research, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health, and NHLBI Framingham Heart Study, Framingham, MA (M.-H.C., A.D.J., C.J.O.D.); and Cardiovascular Division, Massachusetts General Hospital, Harvard Medical School, Boston (C.J.O.D.)
| | - Michael A Mastrangelo
- From the Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester Medical Center, NY (Q.M.Z., K.A.K., S.T., M.A.M., C.N.M., J.M.M., C.J.L.); Division of Intramural Research, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health, and NHLBI Framingham Heart Study, Framingham, MA (M.-H.C., A.D.J., C.J.O.D.); and Cardiovascular Division, Massachusetts General Hospital, Harvard Medical School, Boston (C.J.O.D.)
| | - Ming-Huei Chen
- From the Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester Medical Center, NY (Q.M.Z., K.A.K., S.T., M.A.M., C.N.M., J.M.M., C.J.L.); Division of Intramural Research, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health, and NHLBI Framingham Heart Study, Framingham, MA (M.-H.C., A.D.J., C.J.O.D.); and Cardiovascular Division, Massachusetts General Hospital, Harvard Medical School, Boston (C.J.O.D.)
| | - Andrew D Johnson
- From the Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester Medical Center, NY (Q.M.Z., K.A.K., S.T., M.A.M., C.N.M., J.M.M., C.J.L.); Division of Intramural Research, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health, and NHLBI Framingham Heart Study, Framingham, MA (M.-H.C., A.D.J., C.J.O.D.); and Cardiovascular Division, Massachusetts General Hospital, Harvard Medical School, Boston (C.J.O.D.)
| | - Christopher J O'Donnell
- From the Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester Medical Center, NY (Q.M.Z., K.A.K., S.T., M.A.M., C.N.M., J.M.M., C.J.L.); Division of Intramural Research, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health, and NHLBI Framingham Heart Study, Framingham, MA (M.-H.C., A.D.J., C.J.O.D.); and Cardiovascular Division, Massachusetts General Hospital, Harvard Medical School, Boston (C.J.O.D.)
| | - Craig N Morrell
- From the Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester Medical Center, NY (Q.M.Z., K.A.K., S.T., M.A.M., C.N.M., J.M.M., C.J.L.); Division of Intramural Research, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health, and NHLBI Framingham Heart Study, Framingham, MA (M.-H.C., A.D.J., C.J.O.D.); and Cardiovascular Division, Massachusetts General Hospital, Harvard Medical School, Boston (C.J.O.D.)
| | - Joseph M Miano
- From the Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester Medical Center, NY (Q.M.Z., K.A.K., S.T., M.A.M., C.N.M., J.M.M., C.J.L.); Division of Intramural Research, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health, and NHLBI Framingham Heart Study, Framingham, MA (M.-H.C., A.D.J., C.J.O.D.); and Cardiovascular Division, Massachusetts General Hospital, Harvard Medical School, Boston (C.J.O.D.)
| | - Charles J Lowenstein
- From the Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester Medical Center, NY (Q.M.Z., K.A.K., S.T., M.A.M., C.N.M., J.M.M., C.J.L.); Division of Intramural Research, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health, and NHLBI Framingham Heart Study, Framingham, MA (M.-H.C., A.D.J., C.J.O.D.); and Cardiovascular Division, Massachusetts General Hospital, Harvard Medical School, Boston (C.J.O.D.).
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Dickel DE, Barozzi I, Zhu Y, Fukuda-Yuzawa Y, Osterwalder M, Mannion BJ, May D, Spurrell CH, Plajzer-Frick I, Pickle CS, Lee E, Garvin TH, Kato M, Akiyama JA, Afzal V, Lee AY, Gorkin DU, Ren B, Rubin EM, Visel A, Pennacchio LA. Genome-wide compendium and functional assessment of in vivo heart enhancers. Nat Commun 2016; 7:12923. [PMID: 27703156 PMCID: PMC5059478 DOI: 10.1038/ncomms12923] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 08/16/2016] [Indexed: 12/04/2022] Open
Abstract
Whole-genome sequencing is identifying growing numbers of non-coding variants in human disease studies, but the lack of accurate functional annotations prevents their interpretation. We describe the genome-wide landscape of distant-acting enhancers active in the developing and adult human heart, an organ whose impairment is a predominant cause of mortality and morbidity. Using integrative analysis of >35 epigenomic data sets from mouse and human pre- and postnatal hearts we created a comprehensive reference of >80,000 putative human heart enhancers. To illustrate the importance of enhancers in the regulation of genes involved in heart disease, we deleted the mouse orthologs of two human enhancers near cardiac myosin genes. In both cases, we observe in vivo expression changes and cardiac phenotypes consistent with human heart disease. Our study provides a comprehensive catalogue of human heart enhancers for use in clinical whole-genome sequencing studies and highlights the importance of enhancers for cardiac function. Identification of non-coding variants has outstripped our ability to annotate and interpret them. Dickel et al. present a compendium of over 80,000 putative human heart enhancers and demonstrate that two conserved enhancers are required for proper cardiac function in mice.
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Affiliation(s)
- Diane E Dickel
- Functional Genomics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Iros Barozzi
- Functional Genomics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Yiwen Zhu
- Functional Genomics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Yoko Fukuda-Yuzawa
- Functional Genomics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Marco Osterwalder
- Functional Genomics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Brandon J Mannion
- Functional Genomics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Dalit May
- Functional Genomics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Cailyn H Spurrell
- Functional Genomics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Ingrid Plajzer-Frick
- Functional Genomics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Catherine S Pickle
- Functional Genomics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Elizabeth Lee
- Functional Genomics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Tyler H Garvin
- Functional Genomics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Momoe Kato
- Functional Genomics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Jennifer A Akiyama
- Functional Genomics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Veena Afzal
- Functional Genomics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Ah Young Lee
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - David U Gorkin
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, USA.,Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, California 92093, USA
| | - Edward M Rubin
- Functional Genomics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA.,U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Axel Visel
- Functional Genomics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA.,U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.,School of Natural Sciences, University of California, Merced, Merced, California 95343, USA
| | - Len A Pennacchio
- Functional Genomics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA.,U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
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Abstract
Genome-editing tools, which include zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) systems, have emerged as an invaluable technology to achieve somatic and germline genomic manipulation in cells and model organisms for multiple applications, including the creation of knockout alleles, introducing desired mutations into genomic DNA, and inserting novel transgenes. Genome editing is being rapidly adopted into all fields of biomedical research, including the cardiovascular field, where it has facilitated a greater understanding of lipid metabolism, electrophysiology, cardiomyopathies, and other cardiovascular disorders, has helped to create a wider variety of cellular and animal models, and has opened the door to a new class of therapies. In this Review, we discuss the applications of genome-editing technology throughout cardiovascular disease research and the prospect of in vivo genome-editing therapies in the future. We also describe some of the existing limitations of genome-editing tools that will need to be addressed if cardiovascular genome editing is to achieve its full scientific and therapeutic potential.
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Nakagawa Y, Sakuma T, Nishimichi N, Yokosaki Y, Yanaka N, Takeo T, Nakagata N, Yamamoto T. Ultra-superovulation for the CRISPR-Cas9-mediated production of gene-knockout, single-amino-acid-substituted, and floxed mice. Biol Open 2016; 5:1142-8. [PMID: 27387532 PMCID: PMC5004614 DOI: 10.1242/bio.019349] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Current advances in producing genetically modified mice using genome-editing technologies have indicated the need for improvement of limiting factors including zygote collection for microinjection and their cryopreservation. Recently, we developed a novel superovulation technique using inhibin antiserum and equine chorionic gonadotropin to promote follicle growth. This method enabled the increased production of fertilized oocytes via in vitro fertilization compared with the conventional superovulation method. Here, we verify that the ultra-superovulation technique can be used for the efficient generation of clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9)-mediated knockout mice by microinjection of plasmid vector or ribonucleoprotein into zygotes. We also investigated whether single-amino-acid-substituted mice and conditional knockout mice could be generated. Founder mice bearing base substitutions were generated more efficiently by co-microinjection of Cas9 protein, a guide RNA and single-stranded oligodeoxynucleotide (ssODN) than by plasmid microinjection with ssODN. The conditional allele was successfully introduced by the one-step insertion of an ssODN designed to carry an exon flanked by two loxP sequences and homology arms using a double-cut CRISPR-Cas9 strategy. Our study presents a useful method for the CRISPR-Cas9-based generation of genetically modified mice from the viewpoints of animal welfare and work efficiency. Summary: We demonstrate the production of CRISPR-Cas9-mediated knockout and knock-in mice using a recently developed ultra-superovulation technique to obtain greater numbers of oocytes compared with conventional methods.
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Affiliation(s)
- Yoshiko Nakagawa
- Center for Animal Resources and Development, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
| | - Tetsushi Sakuma
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Norihisa Nishimichi
- Cell-Matrix Frontier Laboratory, Health Administration Center, Hiroshima University, 1-2-3 Kasumi, Minamiku, Hiroshima 734-8551, Japan
| | - Yasuyuki Yokosaki
- Cell-Matrix Frontier Laboratory, Health Administration Center, Hiroshima University, 1-2-3 Kasumi, Minamiku, Hiroshima 734-8551, Japan Clinical Genetics, Hiroshima University Hospital, 1-2-3 Kasumi, Minamiku, Hiroshima 734-8551, Japan
| | - Noriyuki Yanaka
- Department of Molecular and Applied Bioscience, Graduate School of Biosphere Science, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Toru Takeo
- Center for Animal Resources and Development, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
| | - Naomi Nakagata
- Center for Animal Resources and Development, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
| | - Takashi Yamamoto
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
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34
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Miller CL, Pjanic M, Wang T, Nguyen T, Cohain A, Lee JD, Perisic L, Hedin U, Kundu RK, Majmudar D, Kim JB, Wang O, Betsholtz C, Ruusalepp A, Franzén O, Assimes TL, Montgomery SB, Schadt EE, Björkegren JLM, Quertermous T. Integrative functional genomics identifies regulatory mechanisms at coronary artery disease loci. Nat Commun 2016; 7:12092. [PMID: 27386823 DOI: 10.1038/ncomms12092] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/28/2016] [Indexed: 12/22/2022] Open
Abstract
Coronary artery disease (CAD) is the leading cause of mortality and morbidity, driven by both genetic and environmental risk factors. Meta-analyses of genome-wide association studies have identified >150 loci associated with CAD and myocardial infarction susceptibility in humans. A majority of these variants reside in non-coding regions and are co-inherited with hundreds of candidate regulatory variants, presenting a challenge to elucidate their functions. Herein, we use integrative genomic, epigenomic and transcriptomic profiling of perturbed human coronary artery smooth muscle cells and tissues to begin to identify causal regulatory variation and mechanisms responsible for CAD associations. Using these genome-wide maps, we prioritize 64 candidate variants and perform allele-specific binding and expression analyses at seven top candidate loci: 9p21.3, SMAD3, PDGFD, IL6R, BMP1, CCDC97/TGFB1 and LMOD1. We validate our findings in expression quantitative trait loci cohorts, which together reveal new links between CAD associations and regulatory function in the appropriate disease context. Coronary heart disease is the leading cause of death worldwide with multiple environmental and genetic risk factors. Here the authors integrate genomic, epigenomic and transcriptomic mapping to elucidate causal variation and mechanisms of known genetic associations.
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Coll-Bonfill N, de la Cruz-Thea B, Pisano MV, Musri MM. Noncoding RNAs in smooth muscle cell homeostasis: implications in phenotypic switch and vascular disorders. Pflugers Arch 2016; 468:1071-87. [PMID: 27109570 DOI: 10.1007/s00424-016-1821-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 04/04/2016] [Indexed: 12/16/2022]
Abstract
Vascular smooth muscle cells (SMC) are a highly specialized cell type that exhibit extraordinary plasticity in adult animals in response to a number of environmental cues. Upon vascular injury, SMC undergo phenotypic switch from a contractile-differentiated to a proliferative/migratory-dedifferentiated phenotype. This process plays a major role in vascular lesion formation and during the development of vascular remodeling. Vascular remodeling comprises the accumulation of dedifferentiated SMC in the intima of arteries and is central to a number of vascular diseases such as arteriosclerosis, chronic obstructive pulmonary disease or pulmonary hypertension. Therefore, it is critical to understand the molecular mechanisms that govern SMC phenotype. In the last decade, a number of new classes of noncoding RNAs have been described. These molecules have emerged as key factors controlling tissue homeostasis during physiological and pathological conditions. In this review, we will discuss the role of noncoding RNAs, including microRNAs and long noncoding RNAs, in the regulation of SMC plasticity.
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Affiliation(s)
- N Coll-Bonfill
- Department of Pulmonary Medicine Hospital Clínic-Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Barcelona, Spain
| | - B de la Cruz-Thea
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, INIMEC-CONICET, Universidad Nacional de Córdoba, Friuli 2434, 5016, Córdoba, Argentina
| | - M V Pisano
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, INIMEC-CONICET, Universidad Nacional de Córdoba, Friuli 2434, 5016, Córdoba, Argentina
| | - M M Musri
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, INIMEC-CONICET, Universidad Nacional de Córdoba, Friuli 2434, 5016, Córdoba, Argentina.
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Miano JM, Zhu QM, Lowenstein CJ. A CRISPR Path to Engineering New Genetic Mouse Models for Cardiovascular Research. Arterioscler Thromb Vasc Biol 2016; 36:1058-75. [PMID: 27102963 DOI: 10.1161/atvbaha.116.304790] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 04/06/2016] [Indexed: 12/26/2022]
Abstract
Previous efforts to target the mouse genome for the addition, subtraction, or substitution of biologically informative sequences required complex vector design and a series of arduous steps only a handful of laboratories could master. The facile and inexpensive clustered regularly interspaced short palindromic repeats (CRISPR) method has now superseded traditional means of genome modification such that virtually any laboratory can quickly assemble reagents for developing new mouse models for cardiovascular research. Here, we briefly review the history of CRISPR in prokaryotes, highlighting major discoveries leading to its formulation for genome modification in the animal kingdom. Core components of CRISPR technology are reviewed and updated. Practical pointers for 2-component and 3-component CRISPR editing are summarized with many applications in mice including frameshift mutations, deletion of enhancers and noncoding genes, nucleotide substitution of protein-coding and gene regulatory sequences, incorporation of loxP sites for conditional gene inactivation, and epitope tag integration. Genotyping strategies are presented and topics of genetic mosaicism and inadvertent targeting discussed. Finally, clinical applications and ethical considerations are addressed as the biomedical community eagerly embraces this astonishing innovation in genome editing to tackle previously intractable questions.
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Affiliation(s)
- Joseph M Miano
- From the Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, NY (J.M.M., Q.M.Z., C.J.L.); and Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA (Q.M.Z.).
| | - Qiuyu Martin Zhu
- From the Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, NY (J.M.M., Q.M.Z., C.J.L.); and Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA (Q.M.Z.)
| | - Charles J Lowenstein
- From the Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, NY (J.M.M., Q.M.Z., C.J.L.); and Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA (Q.M.Z.)
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Yan W, Chen D, Kaufmann K. Molecular mechanisms of floral organ specification by MADS domain proteins. Curr Opin Plant Biol 2016; 29:154-62. [PMID: 26802807 DOI: 10.1016/j.pbi.2015.12.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 11/23/2015] [Accepted: 12/06/2015] [Indexed: 05/11/2023]
Abstract
Flower development is a model system to understand organ specification in plants. The identities of different types of floral organs are specified by homeotic MADS transcription factors that interact in a combinatorial fashion. Systematic identification of DNA-binding sites and target genes of these key regulators show that they have shared and unique sets of target genes. DNA binding by MADS proteins is not based on 'simple' recognition of a specific DNA sequence, but depends on DNA structure and combinatorial interactions. Homeotic MADS proteins regulate gene expression via alternative mechanisms, one of which may be to modulate chromatin structure and accessibility in their target gene promoters.
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Affiliation(s)
- Wenhao Yan
- Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Dijun Chen
- Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Kerstin Kaufmann
- Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany.
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Abstract
Sea urchin embryos are a useful model system for investigating early developmental processes and the underlying gene regulatory networks. Most functional studies using sea urchin embryos rely on antisense morpholino oligonucleotides to knockdown gene functions. However, major concerns related to this technique include off-target effects, variations in morpholino efficiency, and potential morpholino toxicity; furthermore, such problems are difficult to discern. Recent advances in genome editing technologies have introduced the prospect of not only generating sequence-specific knockouts, but also providing genome-engineering applications. Two genome editing tools, zinc-finger nuclease (ZFN) and transcription activator-like effector nucleases (TALENs), have been utilized in sea urchin embryos, but the resulting efficiencies are far from satisfactory. The CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 (CRISPR-associated nuclease 9) system serves as an easy and efficient method with which to edit the genomes of several established and emerging model organisms in the field of developmental biology. Here, we apply the CRISPR/Cas9 system to the sea urchin embryo. We designed six guide RNAs (gRNAs) against the well-studied nodal gene and discovered that five of the gRNAs induced the expected phenotype in 60-80% of the injected embryos. In addition, we developed a simple method for isolating genomic DNA from individual embryos, enabling phenotype to be precisely linked to genotype, and revealed that the mutation rates were 67-100% among the sequenced clones. Of the two potential off-target sites we examined, no off-target effects were observed. The detailed procedures described herein promise to accelerate the usage of CRISPR/Cas9 system for genome editing in sea urchin embryos.
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Affiliation(s)
- Che-Yi Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yi-Hsien Su
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan.
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Tak YG, Farnham PJ. Making sense of GWAS: using epigenomics and genome engineering to understand the functional relevance of SNPs in non-coding regions of the human genome. Epigenetics Chromatin 2015; 8:57. [PMID: 26719772 PMCID: PMC4696349 DOI: 10.1186/s13072-015-0050-4] [Citation(s) in RCA: 206] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 12/09/2015] [Indexed: 12/13/2022] Open
Abstract
Considerable progress towards an understanding of complex diseases has been made in recent years due to the development of high-throughput genotyping technologies. Using microarrays that contain millions of single-nucleotide polymorphisms (SNPs), Genome Wide Association Studies (GWASs) have identified SNPs that are associated with many complex diseases or traits. For example, as of February 2015, 2111 association studies have identified 15,396 SNPs for various diseases and traits, with the number of identified SNP-disease/trait associations increasing rapidly in recent years. However, it has been difficult for researchers to understand disease risk from GWAS results. This is because most GWAS-identified SNPs are located in non-coding regions of the genome. It is important to consider that the GWAS-identified SNPs serve only as representatives for all SNPs in the same haplotype block, and it is equally likely that other SNPs in high linkage disequilibrium (LD) with the array-identified SNPs are causal for the disease. Because it was hoped that disease-associated coding variants would be identified if the true casual SNPs were known, investigators have expanded their analyses using LD calculation and fine-mapping. However, such analyses also identified risk-associated SNPs located in non-coding regions. Thus, the GWAS field has been left with the conundrum as to how a single-nucleotide change in a non-coding region could confer increased risk for a specific disease. One possible answer to this puzzle is that the variant SNPs cause changes in gene expression levels rather than causing changes in protein function. This review provides a description of (1) advances in genomic and epigenomic approaches that incorporate functional annotation of regulatory elements to prioritize the disease risk-associated SNPs that are located in non-coding regions of the genome for follow-up studies, (2) various computational tools that aid in identifying gene expression changes caused by the non-coding disease-associated SNPs, and (3) experimental approaches to identify target genes of, and study the biological phenotypes conferred by, non-coding disease-associated SNPs.
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Affiliation(s)
- Yu Gyoung Tak
- Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 USA
| | - Peggy J Farnham
- Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 USA
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Miano JM, Long X. The short and long of noncoding sequences in the control of vascular cell phenotypes. Cell Mol Life Sci 2015; 72:3457-88. [PMID: 26022065 DOI: 10.1007/s00018-015-1936-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 05/21/2015] [Accepted: 05/22/2015] [Indexed: 12/13/2022]
Abstract
The two principal cell types of importance for normal vessel wall physiology are smooth muscle cells and endothelial cells. Much progress has been made over the past 20 years in the discovery and function of transcription factors that coordinate proper differentiation of these cells and the maintenance of vascular homeostasis. More recently, the converging fields of bioinformatics, genomics, and next generation sequencing have accelerated discoveries in a number of classes of noncoding sequences, including transcription factor binding sites (TFBS), microRNA genes, and long noncoding RNA genes, each of which mediates vascular cell differentiation through a variety of mechanisms. Alterations in the nucleotide sequence of key TFBS or deviations in transcription of noncoding RNA genes likely have adverse effects on normal vascular cell phenotype and function. Here, the subject of noncoding sequences that influence smooth muscle cell or endothelial cell phenotype will be summarized as will future directions to further advance our understanding of the increasingly complex molecular circuitry governing normal vascular cell differentiation and how such information might be harnessed to combat vascular diseases.
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Affiliation(s)
- Joseph M Miano
- Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester, NY, 14642, USA,
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Nakagawa Y, Sakuma T, Sakamoto T, Ohmuraya M, Nakagata N, Yamamoto T. Production of knockout mice by DNA microinjection of various CRISPR/Cas9 vectors into freeze-thawed fertilized oocytes. BMC Biotechnol 2015; 15:33. [PMID: 25997509 PMCID: PMC4440308 DOI: 10.1186/s12896-015-0144-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 04/17/2015] [Indexed: 12/26/2022] Open
Abstract
Background Clustered regulatory interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)-mediated genome editing permits the rapid production of genetically engineered mice. To make the most of this innovative technology, a streamlined procedure is needed for the robust construction of CRISPR/Cas9 vectors, the efficient preparation of mouse oocytes, and refined genotyping strategies. Although we previously demonstrated the applicability of oocyte cryopreservation technologies and various genotyping methods in the production of transcription activator-like effector nuclease-mediated genome editing in mice, it has not yet been clarified whether these techniques can be applied to the CRISPR/Cas9-mediated generation of knockout mice. In this study, we investigated easy, efficient, and robust methods of creating knockout mice using several CRISPR/Cas9 systems. Results We constructed three types of CRISPR/Cas9 vectors expressing: 1) single guide RNA (gRNA) and Cas9 nuclease, 2) two gRNAs and Cas9 nickase, and 3) two gRNAs and FokI-dCas9, targeting the same genomic locus. These vectors were directly microinjected into the pronucleus of freeze-thawed fertilized oocytes, and surviving oocytes were transferred to pseudopregnant ICR mice. Cas9 nuclease resulted in the highest mutation rates with the lowest birth rates, while Cas9 nickase resulted in the highest birth rates with the lowest mutation rates. FokI-dCas9 presented well-balanced mutation and birth rates. Furthermore, we constructed a single all-in-one FokI-dCas9 vector targeting two different genomic loci, and validated its efficacy by blastocyst analysis, resulting in highly efficient simultaneous targeted mutagenesis. Conclusions Our report offers several choices of researcher-friendly consolidated procedures for making CRISPR/Cas9-mediated knockout mice, with sophisticated construction systems for various types of CRISPR vectors, convenient preparation of in vitro fertilized or mated freeze-thawed oocytes, and an efficient method of mutant screening. Electronic supplementary material The online version of this article (doi:10.1186/s12896-015-0144-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yoshiko Nakagawa
- Center for Animal Resources and Development, Kumamoto University, Kumamoto, 860-0811, Japan.
| | - Tetsushi Sakuma
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, 739-8526, Japan.
| | - Takuya Sakamoto
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, 739-8526, Japan.
| | - Masaki Ohmuraya
- Center for Animal Resources and Development, Kumamoto University, Kumamoto, 860-0811, Japan.
| | - Naomi Nakagata
- Center for Animal Resources and Development, Kumamoto University, Kumamoto, 860-0811, Japan.
| | - Takashi Yamamoto
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, 739-8526, Japan.
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Musunuru K. Genome editing of a CArG element in the mouse genome establishes its role in gene expression. Arterioscler Thromb Vasc Biol 2015; 35:496-7. [PMID: 25717176 DOI: 10.1161/atvbaha.115.305175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Kiran Musunuru
- From the Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA; and Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA.
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