1
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Ilık İA, Glažar P, Tse K, Brändl B, Meierhofer D, Müller FJ, Smith ZD, Aktaş T. Autonomous transposons tune their sequences to ensure somatic suppression. Nature 2024; 626:1116-1124. [PMID: 38355802 PMCID: PMC10901741 DOI: 10.1038/s41586-024-07081-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 01/16/2024] [Indexed: 02/16/2024]
Abstract
Transposable elements (TEs) are a major constituent of human genes, occupying approximately half of the intronic space. During pre-messenger RNA synthesis, intronic TEs are transcribed along with their host genes but rarely contribute to the final mRNA product because they are spliced out together with the intron and rapidly degraded. Paradoxically, TEs are an abundant source of RNA-processing signals through which they can create new introns1, and also functional2 or non-functional chimeric transcripts3. The rarity of these events implies the existence of a resilient splicing code that is able to suppress TE exonization without compromising host pre-mRNA processing. Here we show that SAFB proteins protect genome integrity by preventing retrotransposition of L1 elements while maintaining splicing integrity, via prevention of the exonization of previously integrated TEs. This unique dual role is possible because of L1's conserved adenosine-rich coding sequences that are bound by SAFB proteins. The suppressive activity of SAFB extends to tissue-specific, giant protein-coding cassette exons, nested genes and Tigger DNA transposons. Moreover, SAFB also suppresses LTR/ERV elements in species in which they are still active, such as mice and flies. A significant subset of splicing events suppressed by SAFB in somatic cells are activated in the testis, coinciding with low SAFB expression in postmeiotic spermatids. Reminiscent of the division of labour between innate and adaptive immune systems that fight external pathogens, our results uncover SAFB proteins as an RNA-based, pattern-guided, non-adaptive defence system against TEs in the soma, complementing the RNA-based, adaptive Piwi-interacting RNA pathway of the germline.
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Affiliation(s)
- İbrahim Avşar Ilık
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Petar Glažar
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Kevin Tse
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA
| | - Björn Brändl
- Universitätsklinikum Schleswig-Holstein Campus Kiel, Zentrum für Integrative Psychiatrie, Kiel, Germany
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - David Meierhofer
- Mass Spectrometry Joint Facilities Scientific Service, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Franz-Josef Müller
- Universitätsklinikum Schleswig-Holstein Campus Kiel, Zentrum für Integrative Psychiatrie, Kiel, Germany
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Zachary D Smith
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA
| | - Tuğçe Aktaş
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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2
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Hu W, Li M, Xiao H, Guan L. Essential genes identification model based on sequence feature map and graph convolutional neural network. BMC Genomics 2024; 25:47. [PMID: 38200437 PMCID: PMC10777564 DOI: 10.1186/s12864-024-09958-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 01/01/2024] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND Essential genes encode functions that play a vital role in the life activities of organisms, encompassing growth, development, immune system functioning, and cell structure maintenance. Conventional experimental techniques for identifying essential genes are resource-intensive and time-consuming, and the accuracy of current machine learning models needs further enhancement. Therefore, it is crucial to develop a robust computational model to accurately predict essential genes. RESULTS In this study, we introduce GCNN-SFM, a computational model for identifying essential genes in organisms, based on graph convolutional neural networks (GCNN). GCNN-SFM integrates a graph convolutional layer, a convolutional layer, and a fully connected layer to model and extract features from gene sequences of essential genes. Initially, the gene sequence is transformed into a feature map using coding techniques. Subsequently, a multi-layer GCN is employed to perform graph convolution operations, effectively capturing both local and global features of the gene sequence. Further feature extraction is performed, followed by integrating convolution and fully-connected layers to generate prediction results for essential genes. The gradient descent algorithm is utilized to iteratively update the cross-entropy loss function, thereby enhancing the accuracy of the prediction results. Meanwhile, model parameters are tuned to determine the optimal parameter combination that yields the best prediction performance during training. CONCLUSIONS Experimental evaluation demonstrates that GCNN-SFM surpasses various advanced essential gene prediction models and achieves an average accuracy of 94.53%. This study presents a novel and effective approach for identifying essential genes, which has significant implications for biology and genomics research.
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Affiliation(s)
- Wenxing Hu
- College of Physics and Electronic Information, Gannan Normal University, Ganzhou, Jiangxi, 341000, China
| | - Mengshan Li
- College of Physics and Electronic Information, Gannan Normal University, Ganzhou, Jiangxi, 341000, China.
| | - Haiyang Xiao
- College of Physics and Electronic Information, Gannan Normal University, Ganzhou, Jiangxi, 341000, China
| | - Lixin Guan
- College of Physics and Electronic Information, Gannan Normal University, Ganzhou, Jiangxi, 341000, China
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3
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Wu X, Li Z, Wang ZQ, Xu X. The neurological and non-neurological roles of the primary microcephaly-associated protein ASPM. Front Neurosci 2023; 17:1242448. [PMID: 37599996 PMCID: PMC10436222 DOI: 10.3389/fnins.2023.1242448] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 07/24/2023] [Indexed: 08/22/2023] Open
Abstract
Primary microcephaly (MCPH), is a neurological disorder characterized by small brain size that results in numerous developmental problems, including intellectual disability, motor and speech delays, and seizures. Hitherto, over 30 MCPH causing genes (MCPHs) have been identified. Among these MCPHs, MCPH5, which encodes abnormal spindle-like microcephaly-associated protein (ASPM), is the most frequently mutated gene. ASPM regulates mitotic events, cell proliferation, replication stress response, DNA repair, and tumorigenesis. Moreover, using a data mining approach, we have confirmed that high levels of expression of ASPM correlate with poor prognosis in several types of tumors. Here, we summarize the neurological and non-neurological functions of ASPM and provide insight into its implications for the diagnosis and treatment of MCPH and cancer.
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Affiliation(s)
- Xingxuan Wu
- Guangdong Key Laboratory for Genome Stability and Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, Guangdong, China
- Shenzhen University-Friedrich Schiller Universität Jena Joint PhD Program in Biomedical Sciences, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
- Laboratory of Genome Stability, Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
| | - Zheng Li
- Guangdong Key Laboratory for Genome Stability and Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, Guangdong, China
| | - Zhao-Qi Wang
- Shenzhen University-Friedrich Schiller Universität Jena Joint PhD Program in Biomedical Sciences, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
- Laboratory of Genome Stability, Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
| | - Xingzhi Xu
- Guangdong Key Laboratory for Genome Stability and Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, Guangdong, China
- Shenzhen University-Friedrich Schiller Universität Jena Joint PhD Program in Biomedical Sciences, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
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4
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Evke S, Lin Q, Melendez JA, Begley TJ. Epitranscriptomic Reprogramming Is Required to Prevent Stress and Damage from Acetaminophen. Genes (Basel) 2022; 13:genes13030421. [PMID: 35327975 PMCID: PMC8955276 DOI: 10.3390/genes13030421] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/13/2022] [Accepted: 02/16/2022] [Indexed: 02/06/2023] Open
Abstract
Epitranscriptomic marks, in the form of enzyme catalyzed RNA modifications, play important gene regulatory roles in response to environmental and physiological conditions. However, little is known with respect to how acute toxic doses of pharmaceuticals influence the epitranscriptome. Here we define how acetaminophen (APAP) induces epitranscriptomic reprogramming and how the writer Alkylation Repair Homolog 8 (Alkbh8) plays a key gene regulatory role in the response. Alkbh8 modifies tRNA selenocysteine (tRNASec) to translationally regulate the production of glutathione peroxidases (Gpx’s) and other selenoproteins, with Gpx enzymes known to play protective roles during APAP toxicity. We demonstrate that APAP increases toxicity and markers of damage, and decreases selenoprotein levels in Alkbh8 deficient mouse livers, when compared to wildtype. APAP also promotes large scale reprogramming of many RNA marks comprising the liver tRNA epitranscriptome including: 5-methoxycarbonylmethyluridine (mcm5U), isopentenyladenosine (i6A), pseudouridine (Ψ), and 1-methyladenosine (m1A) modifications linked to tRNASec and many other tRNA’s. Alkbh8 deficiency also leads to wide-spread epitranscriptomic dysregulation in response to APAP, demonstrating that a single writer defect can promote downstream changes to a large spectrum of RNA modifications. Our study highlights the importance of RNA modifications and translational responses to APAP, identifies writers as key modulators of stress responses in vivo and supports the idea that the epitranscriptome may play important roles in responses to pharmaceuticals.
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Affiliation(s)
- Sara Evke
- Nanobioscience Constellation, College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY 12203, USA; (S.E.); (J.A.M.)
- The RNA Institute, University at Albany, Albany, NY 12222, USA;
| | - Qishan Lin
- The RNA Institute, University at Albany, Albany, NY 12222, USA;
- Department of Biological Sciences, University at Albany, Albany, NY 12222, USA
- RNA Epitranscriptomics and Proteomics Resource, University at Albany, Albany, NY 12222, USA
| | - Juan Andres Melendez
- Nanobioscience Constellation, College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY 12203, USA; (S.E.); (J.A.M.)
- The RNA Institute, University at Albany, Albany, NY 12222, USA;
| | - Thomas John Begley
- The RNA Institute, University at Albany, Albany, NY 12222, USA;
- Department of Biological Sciences, University at Albany, Albany, NY 12222, USA
- RNA Epitranscriptomics and Proteomics Resource, University at Albany, Albany, NY 12222, USA
- Correspondence:
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5
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Tchasovnikarova IA, Marr SK, Damle M, Kingston RE. TRACE generates fluorescent human reporter cell lines to characterize epigenetic pathways. Mol Cell 2022; 82:479-491.e7. [PMID: 34963054 PMCID: PMC8796053 DOI: 10.1016/j.molcel.2021.11.035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 09/14/2021] [Accepted: 11/29/2021] [Indexed: 01/22/2023]
Abstract
Genetically encoded biosensors are powerful tools to monitor cellular behavior, but the difficulty in generating appropriate reporters for chromatin factors hampers our ability to dissect epigenetic pathways. Here, we present TRACE (transgene reporters across chromatin environments), a high-throughput, genome-wide technique to generate fluorescent human reporter cell lines responsive to manipulation of epigenetic factors. By profiling GFP expression from a large pool of individually barcoded lentiviral integrants in the presence and absence of a perturbation, we identify reporters responsive to pharmacological inhibition of the histone lysine demethylase LSD1 and genetic ablation of the PRC2 subunit SUZ12. Furthermore, by manipulating the HIV-1 host factor LEDGF through targeted deletion or fusion to chromatin reader domains, we alter lentiviral integration site preferences, thus broadening the types of chromatin examined by TRACE. The phenotypic reporters generated through TRACE will allow the genetic interrogation of a broad range of epigenetic pathways, furthering our mechanistic understanding of chromatin biology.
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Affiliation(s)
- Iva A. Tchasovnikarova
- Department of Molecular Biology, Massachusetts General
Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02114,
USA,The Gurdon Institute, University of Cambridge, Tennis Court
Road, Cambridge, CB2 1QN, UK,Lead Contact,Correspondence should be addressed to:
,
| | - Sharon K. Marr
- Department of Molecular Biology, Massachusetts General
Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02114,
USA
| | - Manashree Damle
- Department of Molecular Biology, Massachusetts General
Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02114,
USA
| | - Robert E. Kingston
- Department of Molecular Biology, Massachusetts General
Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02114,
USA,Correspondence should be addressed to:
,
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6
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Applications of piggyBac Transposons for Genome Manipulation in Stem Cells. Stem Cells Int 2021; 2021:3829286. [PMID: 34567130 PMCID: PMC8460389 DOI: 10.1155/2021/3829286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/16/2021] [Indexed: 12/20/2022] Open
Abstract
Transposons are mobile genetic elements in the genome. The piggyBac (PB) transposon system is increasingly being used for stem cell research due to its high transposition efficiency and seamless excision capacity. Over the past few decades, forward genetic screens based on PB transposons have been successfully established to identify genes associated with drug resistance and stem cell-related characteristics. Moreover, PB transposon is regarded as a promising gene therapy vector and has been used in some clinically relevant stem cells. Here, we review the recent progress on the basic biology of PB, highlight its applications in current stem cell research, and discuss its advantages and challenges.
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7
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Campos TL, Korhonen PK, Hofmann A, Gasser RB, Young ND. Harnessing model organism genomics to underpin the machine learning-based prediction of essential genes in eukaryotes - Biotechnological implications. Biotechnol Adv 2021; 54:107822. [PMID: 34461202 DOI: 10.1016/j.biotechadv.2021.107822] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 08/17/2021] [Accepted: 08/24/2021] [Indexed: 12/17/2022]
Abstract
The availability of high-quality genomes and advances in functional genomics have enabled large-scale studies of essential genes in model eukaryotes, including the 'elegant worm' (Caenorhabditis elegans; Nematoda) and the 'vinegar fly' (Drosophila melanogaster; Arthropoda). However, this is not the case for other, much less-studied organisms, such as socioeconomically important parasites, for which functional genomic platforms usually do not exist. Thus, there is a need to develop innovative techniques or approaches for the prediction, identification and investigation of essential genes. A key approach that could enable the prediction of such genes is machine learning (ML). Here, we undertake an historical review of experimental and computational approaches employed for the characterisation of essential genes in eukaryotes, with a particular focus on model ecdysozoans (C. elegans and D. melanogaster), and discuss the possible applicability of ML-approaches to organisms such as socioeconomically important parasites. We highlight some recent results showing that high-performance ML, combined with feature engineering, allows a reliable prediction of essential genes from extensive, publicly available 'omic data sets, with major potential to prioritise such genes (with statistical confidence) for subsequent functional genomic validation. These findings could 'open the door' to fundamental and applied research areas. Evidence of some commonality in the essential gene-complement between these two organisms indicates that an ML-engineering approach could find broader applicability to ecdysozoans such as parasitic nematodes or arthropods, provided that suitably large and informative data sets become/are available for proper feature engineering, and for the robust training and validation of algorithms. This area warrants detailed exploration to, for example, facilitate the identification and characterisation of essential molecules as novel targets for drugs and vaccines against parasitic diseases. This focus is particularly important, given the substantial impact that such diseases have worldwide, and the current challenges associated with their prevention and control and with drug resistance in parasite populations.
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Affiliation(s)
- Tulio L Campos
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia; Bioinformatics Core Facility, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz (IAM-Fiocruz), Recife, Pernambuco, Brazil
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Andreas Hofmann
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
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8
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Clark JF, Dinsmore CJ, Soriano P. A most formidable arsenal: genetic technologies for building a better mouse. Genes Dev 2021; 34:1256-1286. [PMID: 33004485 PMCID: PMC7528699 DOI: 10.1101/gad.342089.120] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In this review, Clark et al. summarize the history of mice in genetic studies and the development of classic approaches to genome modification, and how they have been used and improved in recent years. They also discuss the recent surge of nuclease-mediated techniques and how they are changing the field of mouse genetics. The mouse is one of the most widely used model organisms for genetic study. The tools available to alter the mouse genome have developed over the preceding decades from forward screens to gene targeting in stem cells to the recent influx of CRISPR approaches. In this review, we first consider the history of mice in genetic study, the development of classic approaches to genome modification, and how such approaches have been used and improved in recent years. We then turn to the recent surge of nuclease-mediated techniques and how they are changing the field of mouse genetics. Finally, we survey common classes of alleles used in mice and discuss how they might be engineered using different methods.
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Affiliation(s)
- James F Clark
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mt. Sinai, New York, New York 10029, USA
| | - Colin J Dinsmore
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mt. Sinai, New York, New York 10029, USA
| | - Philippe Soriano
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mt. Sinai, New York, New York 10029, USA
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9
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Hansen J, von Melchner H, Wurst W. Mutant non-coding RNA resource in mouse embryonic stem cells. Dis Model Mech 2021; 14:14/2/dmm047803. [PMID: 33729986 PMCID: PMC7875499 DOI: 10.1242/dmm.047803] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 12/14/2020] [Indexed: 01/23/2023] Open
Abstract
Gene trapping is a high-throughput approach that has been used to introduce insertional mutations into the genome of mouse embryonic stem (ES) cells. It is performed with generic gene trap vectors that simultaneously mutate and report the expression of the endogenous gene at the site of insertion and provide a DNA sequence tag for the rapid identification of the disrupted gene. Large-scale international efforts assembled a gene trap library of 566,554 ES cell lines with single gene trap integrations distributed throughout the genome. Here, we re-investigated this unique library and identified mutations in 2202 non-coding RNA (ncRNA) genes, in addition to mutations in 12,078 distinct protein-coding genes. Moreover, we found certain types of gene trap vectors preferentially integrating into genes expressing specific long non-coding RNA (lncRNA) biotypes. Together with all other gene-trapped ES cell lines, lncRNA gene-trapped ES cell lines are readily available for functional in vitro and in vivo studies.
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Affiliation(s)
- Jens Hansen
- Institute of Developmental Genetics, Helmholtz Zentrum München GmbH, German Research Center for Environmental Health, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Harald von Melchner
- Department of Molecular Hematology, University Hospital Frankfurt, Goethe University, D-60590 Frankfurt am Main, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München GmbH, German Research Center for Environmental Health, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany .,Technische Universität München-Weihenstephan, c/o Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany.,German Center for Neurodegenerative Diseases (DZNE), Site Munich, Feodor-Lynen-Str. 17, D-81377 Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Adolf-Butenandt-Institut, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 17, D-81377 München, Germany
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10
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Wolter JM, Mao H, Fragola G, Simon JM, Krantz JL, Bazick HO, Oztemiz B, Stein JL, Zylka MJ. Cas9 gene therapy for Angelman syndrome traps Ube3a-ATS long non-coding RNA. Nature 2020; 587:281-284. [PMID: 33087932 PMCID: PMC8020672 DOI: 10.1038/s41586-020-2835-2] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 07/28/2020] [Indexed: 12/15/2022]
Abstract
Angelman syndrome (AS) is a severe neurodevelopmental disorder caused by a mutation or deletion of the maternally inherited UBE3A allele. In neurons, the paternally inherited UBE3A allele is silenced in cis by a long non-coding RNA called UBE3A-ATS. Here, as part of a systematic screen, we found that Cas9 can be used to activate ('unsilence') paternal Ube3a in cultured mouse and human neurons when targeted to Snord115 genes, which are small nucleolar RNAs that are clustered in the 3' region of Ube3a-ATS. A short Cas9 variant and guide RNA that target about 75 Snord115 genes were packaged into an adeno-associated virus and administered to a mouse model of AS during the embryonic and early postnatal stages, when the therapeutic benefit of restoring Ube3a is predicted to be greatest1,2. This early treatment unsilenced paternal Ube3a throughout the brain for at least 17 months and rescued anatomical and behavioural phenotypes in AS mice. Genomic integration of the adeno-associated virus vector into Cas9 target sites caused premature termination of Ube3a-ATS at the vector-derived polyA cassette, or when integrated in the reverse orientation, by transcriptional collision with the vector-derived Cas9 transcript. Our study shows that targeted genomic integration of a gene therapy vector can restore the function of paternally inherited UBE3A throughout life, providing a path towards a disease-modifying treatment for a syndromic neurodevelopmental disorder.
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Affiliation(s)
- Justin M Wolter
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hanqian Mao
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Giulia Fragola
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeremy M Simon
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - James L Krantz
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hannah O Bazick
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Baris Oztemiz
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jason L Stein
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mark J Zylka
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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11
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Li Z, Oh H, Cung M, Marquez SJ, Sun J, Hammad H, Janssens S, Pouliot P, Lambrecht BN, Yang YS, Shim JH, Greenblatt MB. TAOK3 is a MAP3K contributing to osteoblast differentiation and skeletal mineralization. Biochem Biophys Res Commun 2020; 531:497-502. [PMID: 32807497 PMCID: PMC7494564 DOI: 10.1016/j.bbrc.2020.07.060] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 07/12/2020] [Indexed: 11/18/2022]
Abstract
Current anabolic drugs to treat osteoporosis and other disorders of low bone mass all have important limitations in terms of toxicity, contraindications, or poor efficacy in certain contexts. Addressing these limitations will require a better understanding of the molecular pathways, such as the mitogen activated protein kinase (MAPK) pathways, that govern osteoblast differentiation and, thereby, skeletal mineralization. Whereas MAP3Ks functioning in the extracellular signal-regulated kinases (ERK) and p38 pathways have been identified in osteoblasts, MAP3Ks mediating proximal activation of the c-Jun N-terminal kinase (JNK) pathway have yet to be identified. Here, we demonstrate that thousand-and-one kinase 3 (TAOK3, MAP3K18) functions as an upstream activator of the JNK pathway in osteoblasts both in vitro and in vivo. Taok3-deficient osteoblasts displayed defective JNK pathway activation and a marked decrease in osteoblast differentiation markers and defective mineralization, which was also confirmed using TAOK3 deficient osteoblasts derived from human MSCs. Additionally, reduced expression of Taok3 in a murine model resulted in osteopenia that phenocopies aspects of the Jnk1-associated skeletal phenotype such as occipital hypomineralization. Thus, in vitro and in vivo evidence supports TAOK3 as a proximal activator of the JNK pathway in osteoblasts that plays a critical role in skeletal mineralization.
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Affiliation(s)
- Zan Li
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA; Department of Sports Medicine & Research Center of Sports Medicine, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China
| | - Hwanhee Oh
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Michelle Cung
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Sofia Jenia Marquez
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Jun Sun
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Hamida Hammad
- VIB Inflammation Research Center, Department of Respiratory Medicine, Ghent University, Ghent, Belgium; Department of Pulmonary Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Sophie Janssens
- VIB Inflammation Research Center, Department of Respiratory Medicine, Ghent University, Ghent, Belgium; Department of Pulmonary Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Philippe Pouliot
- VIB Inflammation Research Center, Department of Respiratory Medicine, Ghent University, Ghent, Belgium
| | - Bart N Lambrecht
- VIB Inflammation Research Center, Department of Respiratory Medicine, Ghent University, Ghent, Belgium; Department of Pulmonary Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Yeon-Suk Yang
- Division of Rheumatology, Department of Medicine, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA01605, USA
| | - Jae-Hyuck Shim
- Division of Rheumatology, Department of Medicine, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA01605, USA.
| | - Matthew B Greenblatt
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA.
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12
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Awwad DA. Beyond classic editing: innovative CRISPR approaches for functional studies of long non-coding RNA. Biol Methods Protoc 2019; 4:bpz017. [PMID: 32161809 PMCID: PMC6994087 DOI: 10.1093/biomethods/bpz017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 09/06/2019] [Accepted: 11/19/2019] [Indexed: 12/26/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) makeup a considerable part of the non-coding human genome and had been well-established as crucial players in an array of biological processes. In spite of their abundance and versatile roles, their functional characteristics remain largely undiscovered mainly due to the lack of suitable genetic manipulation tools. The emerging CRISPR/Cas9 technology has been widely adapted in several studies that aim to screen and identify novel lncRNAs as well as interrogate the functional properties of specific lncRNAs. However, the complexity of lncRNAs genes and the regulatory mechanisms that govern their transcription, as well as their unique functionality pose several limitations the utilization of classic CRISPR methods in lncRNAs functional studies. Here, we overview the unique characteristics of lncRNAs transcription and function and the suitability of the CRISPR toolbox for applications in functional characterization of lncRNAs. We discuss some of the novel variations to the classic CRISPR/Cas9 system that have been tailored and applied previously to study several aspects of lncRNAs functionality. Finally, we share perspectives on the potential applications of various CRISPR systems, including RNA-targeting, in the direct editing and manipulation of lncRNAs.
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Affiliation(s)
- Dahlia A Awwad
- Center of X-Ray Determination of Structure of Matter (CXDS), Helmi Institute of Biomedical Research, Zewail City of Science and Technology, Giza, Cairo, Egypt
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13
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Tolson KP, Marooki N, Wolfe A, Smith JT, Kauffman AS. Cre/lox generation of a novel whole-body Kiss1r KO mouse line recapitulates a hypogonadal, obese, and metabolically-impaired phenotype. Mol Cell Endocrinol 2019; 498:110559. [PMID: 31442544 PMCID: PMC6814569 DOI: 10.1016/j.mce.2019.110559] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/24/2019] [Accepted: 08/19/2019] [Indexed: 10/26/2022]
Abstract
Kisspeptin and its receptor, Kiss1r, act centrally to stimulate reproduction. Recent evidence indicates that kisspeptin is also important for body weight and metabolism, as whole-body Kiss1r KO mice, developed with gene trap technology, display obesity and reduced metabolism. Kiss1r is expressed in brain and multiple peripheral tissues, but it is unknown which is responsible for the metabolic phenotype. Here, we sought to confirm that 1) the metabolic phenotype of the gene trap Kiss1r KOs is due to disruption of kisspeptin signaling and not off-target effects of viral mutagenesis, and 2) the Kiss1r flox line is suitable for creating conditional KOs to study the metabolic phenotype. We used Cre/lox technology (Zp3-Cre/Kiss1r flox) to develop a new global Kiss1r KO ("Kiss1r gKO") to compare with the original gene trap KO phenotype. We confirmed that deleting exon 2 of Kiss1r from the entire body induces hypogonadism in both sexes. Moreover, global deletion of Kiss1r induced obesity in females, but not males, along with increased adiposity and impaired glucose tolerance, similar to the gene trap Kiss1r KOs. Likewise, Kiss1r gKO females had decreased VO2 and VCO2, likely underlying their obesity. These findings support that our previous results in gene trap Kiss1r KOs are due to disrupted kisspeptin signaling, and further highlight a role for Kiss1r signaling in energy expenditure and metabolism besides controlling reproduction. Moreover, given Kiss1r expression in multiple cell-types, our findings indicate that the Kiss1r flox line is viable for future investigations to isolate specific target cells of kisspeptin's metabolic effects.
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Affiliation(s)
- Kristen P Tolson
- Department of OBGYN and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Nuha Marooki
- Department of OBGYN and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Andrew Wolfe
- Department of Pediatrics and Physiology, Johns Hopkins University, Baltimore, MD, USA
| | - Jeremy T Smith
- School of Human Sciences, University of Western Australia, Perth, Australia
| | - Alexander S Kauffman
- Department of OBGYN and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA.
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14
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Gurumurthy CB, Lloyd KCK. Generating mouse models for biomedical research: technological advances. Dis Model Mech 2019; 12:dmm029462. [PMID: 30626588 PMCID: PMC6361157 DOI: 10.1242/dmm.029462] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Over the past decade, new methods and procedures have been developed to generate genetically engineered mouse models of human disease. This At a Glance article highlights several recent technical advances in mouse genome manipulation that have transformed our ability to manipulate and study gene expression in the mouse. We discuss how conventional gene targeting by homologous recombination in embryonic stem cells has given way to more refined methods that enable allele-specific manipulation in zygotes. We also highlight advances in the use of programmable endonucleases that have greatly increased the feasibility and ease of editing the mouse genome. Together, these and other technologies provide researchers with the molecular tools to functionally annotate the mouse genome with greater fidelity and specificity, as well as to generate new mouse models using faster, simpler and less costly techniques.
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Affiliation(s)
- Channabasavaiah B Gurumurthy
- Developmental Neuroscience, Munroe Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Center, Omaha, NE 68106-5915, USA
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE 68106-5915, USA
| | - Kevin C Kent Lloyd
- Department of Surgery, School of Medicine, University of California, Davis, CA 95618, USA
- Mouse Biology Program, University of California, Davis, CA 95618, USA
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15
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Reid W, Pilitt K, Alford R, Cervantes-Medina A, Yu H, Aluvihare C, Harrell R, O'Brochta DA. An Anopheles stephensi Promoter-Trap: Augmenting Genome Annotation and Functional Genomics. G3 (BETHESDA, MD.) 2018; 8:3119-3130. [PMID: 30135106 PMCID: PMC6169391 DOI: 10.1534/g3.118.200347] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 08/15/2018] [Indexed: 12/20/2022]
Abstract
The piggyBac transposon was modified to generate gene trap constructs, which were then incorporated into the genome of the Asian malaria vector, Anopheles stephensi and remobilized through genetic crosses using a piggyBac transposase expressing line. A total of 620 remobilization events were documented, and 73 were further characterized at the DNA level to identify patterns in insertion site preferences, remobilization frequencies, and remobilization patterns. Overall, the use of the tetameric AmCyan reporter as the fusion peptide displayed a preference for insertion into the 5'-end of transcripts. Notably 183 - 44882 bp upstream of the An. stephensi v1.0 ab initio gene models, which demonstrated that the promoter regions for the genes of An. stephensi are further upstream of the 5'-proximal regions of the genes in the ab inito models than may be otherwise predicted. RNA-Seq transcript coverage supported the insertion of the splice acceptor gene trap element into 5'-UTR introns for nearly half of all insertions identified. The use of a gene trap element that prefers insertion into the 5'-end of genes supports the use of this technology for the random generation of knock-out mutants, as well as the experimental confirmation of 5'-UTR introns in An. stephensi.
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Affiliation(s)
- William Reid
- Institute for Bioscience and Biotechnology Research, University of Maryland College Park, 9600 Gudelsky Drive, Rockville, MD 20850-3467
| | - Kristina Pilitt
- Institute for Bioscience and Biotechnology Research, University of Maryland College Park, 9600 Gudelsky Drive, Rockville, MD 20850-3467
| | - Robert Alford
- Institute for Bioscience and Biotechnology Research, University of Maryland College Park, 9600 Gudelsky Drive, Rockville, MD 20850-3467
- Insect Transformation Facility, Institute for Bioscience and Biotechnology Research, University of Maryland College Park, 9600 Gudelsky Drive, Rockville, MD 20850-3467
| | - Adriana Cervantes-Medina
- Institute for Bioscience and Biotechnology Research, University of Maryland College Park, 9600 Gudelsky Drive, Rockville, MD 20850-3467
| | - Hao Yu
- Department of Plant Protection, Henan Institute of Science and Technology, East Street Huan-Lan, Xinxiang City, Henan Province 453003, CHINA
| | - Channa Aluvihare
- Insect Transformation Facility, Institute for Bioscience and Biotechnology Research, University of Maryland College Park, 9600 Gudelsky Drive, Rockville, MD 20850-3467
| | - Rob Harrell
- Insect Transformation Facility, Institute for Bioscience and Biotechnology Research, University of Maryland College Park, 9600 Gudelsky Drive, Rockville, MD 20850-3467
| | - David A O'Brochta
- Institute for Bioscience and Biotechnology Research, University of Maryland College Park, 9600 Gudelsky Drive, Rockville, MD 20850-3467
- Department of Entomology, University of Maryland College Park, 4112 Plant Sciences Building, College Park, MD 20742-4454
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16
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Morris SM, Mhyre AJ, Carmack SS, Myers CH, Burns C, Ye W, Ferrer M, Olson JM, Klinghoffer RA. A modified gene trap approach for improved high-throughput cancer drug discovery. Oncogene 2018; 37:4226-4238. [PMID: 29717260 PMCID: PMC6076322 DOI: 10.1038/s41388-018-0274-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 03/01/2018] [Accepted: 03/23/2018] [Indexed: 01/22/2023]
Abstract
While advances in laboratory automation has dramatically increased throughout of compound screening efforts, development of robust cell-based assays in relevant disease models remain resource-intensive and time-consuming, presenting a bottleneck to drug discovery campaigns. To address this issue, we present a modified gene trap approach to efficiently generate pathway-specific reporters that result in a robust "on" signal when the pathway of interest is inhibited. In this proof-of-concept study, we used vemurafenib and trametinib to identify traps that specifically detect inhibition of the mitogen-activated protein kinase (MAPK) pathway in a model of BRAFV600E driven human malignant melanoma. We demonstrate that insertion of our trap into particular loci results in remarkably specific detection of MAPK pathway inhibitors over compounds targeting any other pathway or cellular function. The accuracy of our approach was highlighted in a pilot screen of ~6000 compounds where 40 actives were detected, including 18 MEK, 10 RAF, and 3 ERK inhibitors along with a few compounds representing previously under-characterized inhibitors of the MAPK pathway. One such compound, bafetinib, a second generation BCR/ABL inhibitor, reduced phosphorylation of ERK and when combined with trametinib, both in vitro and in vivo, reduced growth of vemurafenib resistant melanoma cells. While piloted in a model of BRAF-driven melanoma, our results set the stage for using this approach to rapidly generate reporters against any transcriptionally active pathway across a wide variety of disease-relevant cell-based models to expedite drug discovery efforts.
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Affiliation(s)
- Shelli M Morris
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Andrew J Mhyre
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Savanna S Carmack
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Carrie H Myers
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | | | | | - James M Olson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Division of Pediatric Hematology/Oncology, University of Washington School of Medicine, Seattle, WA, USA.
- Seattle Children's Hospital, Seattle, WA, USA.
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17
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Kwon NH, Lee JY, Ryu YL, Kim C, Kong J, Oh S, Kang BS, Ahn HW, Ahn SG, Jeong J, Kim HK, Kim JH, Han DY, Park MC, Kim D, Takase R, Masuda I, Hou YM, Jang SI, Chang YS, Lee DK, Kim Y, Wang MW, Basappa, Kim S. Stabilization of Cyclin-Dependent Kinase 4 by Methionyl-tRNA Synthetase in p16 INK4a-Negative Cancer. ACS Pharmacol Transl Sci 2018; 1:21-31. [PMID: 32219202 DOI: 10.1021/acsptsci.8b00001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Indexed: 12/23/2022]
Abstract
Although abnormal increases in the level or activity of cyclin-dependent kinase 4 (CDK4) occur frequently in cancer, the underlying mechanism is not fully understood. Here, we show that methionyl-tRNA synthetase (MRS) specifically stabilizes CDK4 by enhancing the formation of the complex between CDK4 and a chaperone protein. Knockdown of MRS reduced the CDK4 level, resulting in G0/G1 cell cycle arrest. The effects of MRS on CDK4 stability were more prominent in the tumor suppressor p16INK4a-negative cancer cells because of the competitive relationship of the two proteins for binding to CDK4. Suppression of MRS reduced cell transformation and the tumorigenic ability of a p16INK4a-negative breast cancer cell line in vivo. Further, the MRS levels showed a positive correlation with those of CDK4 and the downstream signals at high frequency in p16INK4a-negative human breast cancer tissues. This work revealed an unexpected functional connection between the two enzymes involving protein synthesis and the cell cycle.
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Affiliation(s)
- Nam Hoon Kwon
- Medicinal Bioconvergence Research Center, Seoul National University, Suwon, 16229, Korea.,Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, 08826, Korea
| | - Jin Young Lee
- Medicinal Bioconvergence Research Center, Seoul National University, Suwon, 16229, Korea
| | - Ye-Lim Ryu
- Medicinal Bioconvergence Research Center, Seoul National University, Suwon, 16229, Korea
| | - Chanhee Kim
- Medicinal Bioconvergence Research Center, Seoul National University, Suwon, 16229, Korea
| | - Jiwon Kong
- Medicinal Bioconvergence Research Center, Seoul National University, Suwon, 16229, Korea
| | - Seongeun Oh
- Medicinal Bioconvergence Research Center, Seoul National University, Suwon, 16229, Korea
| | - Beom Sik Kang
- School of Life Science and Biotechnology, Kyungpook National University, Daegu, 41566, Korea
| | - Hye Won Ahn
- Medicinal Bioconvergence Research Center, Seoul National University, Suwon, 16229, Korea
| | - Sung Gwe Ahn
- Breast Cancer Center, Department of Surgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Joon Jeong
- Breast Cancer Center, Department of Surgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Hoi Kyoung Kim
- Medicinal Bioconvergence Research Center, Seoul National University, Suwon, 16229, Korea
| | - Jong Hyun Kim
- Medicinal Bioconvergence Research Center, Seoul National University, Suwon, 16229, Korea
| | - Dae Young Han
- Medicinal Bioconvergence Research Center, Seoul National University, Suwon, 16229, Korea
| | - Min Chul Park
- Medicinal Bioconvergence Research Center, Seoul National University, Suwon, 16229, Korea
| | - Doyeun Kim
- Medicinal Bioconvergence Research Center, Seoul National University, Suwon, 16229, Korea
| | - Ryuichi Takase
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, United States
| | - Isao Masuda
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, United States
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, United States
| | - Sung Ill Jang
- Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Yoon Soo Chang
- Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Dong Ki Lee
- Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Youngeun Kim
- Medicinal Bioconvergence Research Center, Seoul National University, Suwon, 16229, Korea
| | - Ming-Wei Wang
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Basappa
- Laboratory of Chemical Biology, Department of Chemistry, Bangalore University, Palace Road, Bangalore, 560 001, India
| | - Sunghoon Kim
- Medicinal Bioconvergence Research Center, Seoul National University, Suwon, 16229, Korea.,Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, 08826, Korea
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18
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Strassman A, Schnütgen F, Dai Q, Jones JC, Gomez AC, Pitstick L, Holton NE, Moskal R, Leslie ER, von Melchner H, Beier DR, Bjork BC. Generation of a multipurpose Prdm16 mouse allele by targeted gene trapping. Dis Model Mech 2017; 10:909-922. [PMID: 28424158 PMCID: PMC5536910 DOI: 10.1242/dmm.029561] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 04/18/2017] [Indexed: 12/17/2022] Open
Abstract
Gene trap mutagenesis is a powerful tool to create loss-of-function mutations in mice and other model organisms. Modifications of traditional gene trap cassettes, including addition of conditional features in the form of Flip-excision (FlEx) arrays to enable directional gene trap cassette inversions by Cre and Flpe site-specific recombinases, greatly enhanced their experimental potential. By taking advantage of these conditional gene trap cassettes, we developed a generic strategy for generating conditional mutations and validated this strategy in mice carrying a multipurpose allele of the Prdm16 transcription factor gene. We demonstrate that the gene trap insertion creates a null mutation replicating the Pierre Robin sequence-type cleft palate phenotype of other Prdm16 mutant mice. Consecutive breeding to Flpe and Emx1IREScre deleter mice spatially restricted Prdm16 loss to regions of the forebrain expressing the homeobox gene Emx1, demonstrating the utility of the technology for the analysis of tissue-specific gene functions. Summary: Described is the first targeting of an invertible gene trap to generate a conditional Prdm16 mouse allele and its use to assess phenotypic consequences of Prdm16 loss during craniofacial and brain development.
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Affiliation(s)
- Alexander Strassman
- Department of Biochemistry, Chicago College of Osteopathic Medicine, Midwestern University, Downers Grove, IL 60515, USA
| | - Frank Schnütgen
- Department for Molecular Hematology, University Hospital Frankfurt, Goethe University, 60590 Frankfurt am Main, Germany
| | - Qi Dai
- Department of Molecular Biosciences, The Wenner-Gren Institute, The University of Stockholm, SE-106 91 Stockholm, Sweden
| | - Jennifer C Jones
- Department of Biochemistry, Chicago College of Osteopathic Medicine, Midwestern University, Downers Grove, IL 60515, USA
| | - Angela C Gomez
- Department of Biochemistry, Chicago College of Osteopathic Medicine, Midwestern University, Downers Grove, IL 60515, USA
| | - Lenore Pitstick
- Department of Biochemistry, Chicago College of Osteopathic Medicine, Midwestern University, Downers Grove, IL 60515, USA
| | - Nathan E Holton
- Department of Orthodontics, College of Dentistry, The University of Iowa, Iowa City, IA 52242, USA
| | - Russell Moskal
- Department of Anatomy, Chicago College of Osteopathic Medicine, Midwestern University, Downers Grove, IL 60515, USA
| | - Erin R Leslie
- Department of Anatomy, Chicago College of Osteopathic Medicine, Midwestern University, Downers Grove, IL 60515, USA
| | - Harald von Melchner
- Department for Molecular Hematology, University Hospital Frankfurt, Goethe University, 60590 Frankfurt am Main, Germany
| | - David R Beier
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98105, USA.,Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Bryan C Bjork
- Department of Biochemistry, Chicago College of Osteopathic Medicine, Midwestern University, Downers Grove, IL 60515, USA
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19
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Tian Q, Smart JL, Clement JH, Wang Y, Derkatch A, Schubert H, Danilchik MV, Marks DL, Fedorov LM. RHEB1 expression in embryonic and postnatal mouse. Histochem Cell Biol 2015; 145:561-72. [PMID: 26708151 DOI: 10.1007/s00418-015-1394-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2015] [Indexed: 12/16/2022]
Abstract
Ras homolog enriched in brain (RHEB1) is a member within the superfamily of GTP-binding proteins encoded by the RAS oncogenes. RHEB1 is located at the crossroad of several important pathways including the insulin-signaling pathways and thus plays an important role in different physiological processes. To understand better the physiological relevance of RHEB1 protein, the expression pattern of RHEB1 was analyzed in both embryonic (at E3.5-E16.5) and adult (1-month old) mice. RHEB1 immunostaining and X-gal staining were used for wild-type and Rheb1 gene trap mutant mice, respectively. These independent methods revealed similar RHEB1 expression patterns during both embryonic and postnatal developments. Ubiquitous uniform RHEB1/β-gal and/or RHEB1 expression was seen in preimplantation embryos at E3.5 and postimplantation embryos up to E12.5. Between stages E13.5 and E16.5, RHEB1 expression levels became complex: In particular, strong expression was identified in neural tissues, including the neuroepithelial layer of the mesencephalon, telencephalon, and neural tube of CNS and dorsal root ganglia. In addition, strong expression was seen in certain peripheral tissues including heart, intestine, muscle, and urinary bladder. Postnatal mice have broad spatial RHEB1 expression in different regions of the cerebral cortex, subcortical regions (including hippocampus), olfactory bulb, medulla oblongata, and cerebellum (particularly in Purkinje cells). Significant RHEB1 expression was also viewed in internal organs including the heart, intestine, urinary bladder, and muscle. Moreover, adult animals have complex tissue- and organ-specific RHEB1 expression patterns with different intensities observed throughout postnatal development. Its expression level is in general comparable in CNS and other organs of mouse. Thus, the expression pattern of RHEB1 suggests that it likely plays a ubiquitous role in the development of the early embryo with more tissue-specific roles in later development.
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Affiliation(s)
- Qi Tian
- OHSU Transgenic Mouse Models Shared Resource, Knight Cancer Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239, USA
| | | | - Joachim H Clement
- Department of Hematology and Oncology, Jena University Hospital, 07747, Jena, Germany
| | - Yingming Wang
- OHSU Transgenic Mouse Models Shared Resource, Knight Cancer Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239, USA
| | - Alex Derkatch
- OHSU Transgenic Mouse Models Shared Resource, Knight Cancer Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239, USA
| | | | - Michael V Danilchik
- Department of Integrative Biosciences, Oregon Health and Science University, Portland, OR, USA
| | - Daniel L Marks
- Department of Pediatrics, Oregon Health and Science University, Portland, OR, USA
| | - Lev M Fedorov
- OHSU Transgenic Mouse Models Shared Resource, Knight Cancer Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239, USA.
- Friedrich-Schiller-University, 07740, Jena, Germany.
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20
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Abstract
Most animal genomes are diploid, and mammalian development depends on specific adaptations that have evolved secondary to diploidy. Genomic imprinting and dosage compensation restrict haploid development to early embryos. Recently, haploid mammalian development has been reinvestigated since the establishment of haploid embryonic stem cells (ESCs) from mouse embryos. Haploid cells possess one copy of each gene, facilitating the generation of loss-of-function mutations in a single step. Recessive mutations can then be assessed in forward genetic screens. Applications of haploid mammalian cell systems in screens have been illustrated in several recent publications. Haploid ESCs are characterized by a wide developmental potential and can contribute to chimeric embryos and mice. Different strategies for introducing genetic modifications from haploid ESCs into the mouse germline have been further developed. Haploid ESCs therefore introduce new possibilities in mammalian genetics and could offer an unprecedented tool for genome exploration in the future.
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Affiliation(s)
- Anton Wutz
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Zürich, Hönggerberg, 8049 Zürich, Switzerland;
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21
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Jungke P, Hammer J, Hans S, Brand M. Isolation of Novel CreERT2-Driver Lines in Zebrafish Using an Unbiased Gene Trap Approach. PLoS One 2015; 10:e0129072. [PMID: 26083735 PMCID: PMC4471347 DOI: 10.1371/journal.pone.0129072] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 05/04/2015] [Indexed: 01/01/2023] Open
Abstract
Gene manipulation using the Cre/loxP-recombinase system has been successfully employed in zebrafish to study gene functions and lineage relationships. Recently, gene trapping approaches have been applied to produce large collections of transgenic fish expressing conditional alleles in various tissues. However, the limited number of available cell- and tissue-specific Cre/CreERT2-driver lines still constrains widespread application in this model organism. To enlarge the pool of existing CreERT2-driver lines, we performed a genome-wide gene trap screen using a Tol2-based mCherry-T2a-CreERT2 (mCT2aC) gene trap vector. This cassette consists of a splice acceptor and a mCherry-tagged variant of CreERT2 which enables simultaneous labeling of the trapping event, as well as CreERT2 expression from the endogenous promoter. Using this strategy, we generated 27 novel functional CreERT2-driver lines expressing in a cell- and tissue-specific manner during development and adulthood. This study summarizes the analysis of the generated CreERT2-driver lines with respect to functionality, expression, integration, as well as associated phenotypes. Our results significantly enlarge the existing pool of CreERT2-driver lines in zebrafish and combined with Cre-dependent effector lines, the new CreERT2-driver lines will be important tools to manipulate the zebrafish genome.
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Affiliation(s)
- Peggy Jungke
- Biotechnology Center and Center for Regenerative Therapies Dresden, Dresden University of Technology, Fetscherstrasse 105, 01307 Dresden, Germany
| | - Juliane Hammer
- Biotechnology Center and Center for Regenerative Therapies Dresden, Dresden University of Technology, Fetscherstrasse 105, 01307 Dresden, Germany
| | - Stefan Hans
- Biotechnology Center and Center for Regenerative Therapies Dresden, Dresden University of Technology, Fetscherstrasse 105, 01307 Dresden, Germany
| | - Michael Brand
- Biotechnology Center and Center for Regenerative Therapies Dresden, Dresden University of Technology, Fetscherstrasse 105, 01307 Dresden, Germany
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22
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Exploring new gene integration sites for gene knock-in by gene-trapping strategy. Transgenic Res 2015; 24:549-59. [DOI: 10.1007/s11248-015-9872-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 03/23/2015] [Indexed: 10/23/2022]
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23
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Abstract
The CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 (CRISPR-associated nuclease 9) system is poised to transform developmental biology by providing a simple, efficient method to precisely manipulate the genome of virtually any developing organism. This RNA-guided nuclease (RGN)-based approach already has been effectively used to induce targeted mutations in multiple genes simultaneously, create conditional alleles, and generate endogenously tagged proteins. Illustrating the adaptability of RGNs, the genomes of >20 different plant and animal species as well as multiple cell lines and primary cells have been successfully modified. Here we review the current and potential uses of RGNs to investigate genome function during development.
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Affiliation(s)
- Melissa M Harrison
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, USA
| | - Brian V Jenkins
- Biochemistry Department, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Kate M O'Connor-Giles
- Laboratory of Genetics, Laboratory of Cell and Molecular Biology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Jill Wildonger
- Biochemistry Department, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
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24
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Abstract
Haploid genetics holds great promise for understanding genome evolution and function. Much of the work on haploid genetics has previously been limited to microbes, but possibilities now extend to animal species, including mammals. Whereas haploid animals were described decades ago, only very recent advances in culture techniques have facilitated haploid embryonic stem cell derivation in mammals. This article examines the potential use of haploid cells and puts haploid animal cells into a historical and biological context. Application of haploid cells in genetic screening holds promise for advancing the genetic exploration of mammalian genomes.
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Affiliation(s)
- Anton Wutz
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Hoenggerberg, Schafmattstrasse 22, 8049 Zurich, Switzerland
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25
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Csaki LS, Dwyer JR, Li X, Nguyen MHK, Dewald J, Brindley DN, Lusis AJ, Yoshinaga Y, de Jong P, Fong L, Young SG, Reue K. Lipin-1 and lipin-3 together determine adiposity in vivo. Mol Metab 2013; 3:145-54. [PMID: 24634820 DOI: 10.1016/j.molmet.2013.11.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 11/17/2013] [Accepted: 11/21/2013] [Indexed: 12/17/2022] Open
Abstract
The lipin protein family of phosphatidate phosphatases has an established role in triacylglycerol synthesis and storage. Physiological roles for lipin-1 and lipin-2 have been identified, but the role of lipin-3 has remained mysterious. Using lipin single- and double-knockout models we identified a cooperative relationship between lipin-3 and lipin-1 that influences adipogenesis in vitro and adiposity in vivo. Furthermore, natural genetic variations in Lpin1 and Lpin3 expression levels across 100 mouse strains correlate with adiposity. Analysis of PAP activity in additional metabolic tissues from lipin single- and double-knockout mice also revealed roles for lipin-1 and lipin-3 in spleen, kidney, and liver, for lipin-1 alone in heart and skeletal muscle, and for lipin-1 and lipin-2 in lung and brain. Our findings establish that lipin-1 and lipin-3 cooperate in vivo to determine adipose tissue PAP activity and adiposity, and may have implications in understanding the protection of lipin-1-deficient humans from overt lipodystrophy.
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Affiliation(s)
- Lauren S Csaki
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Jennifer R Dwyer
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Xia Li
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Michael H K Nguyen
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Jay Dewald
- Signal Transduction Research Group, Department of Biochemistry, University of Alberta, Alberta, Canada
| | - David N Brindley
- Signal Transduction Research Group, Department of Biochemistry, University of Alberta, Alberta, Canada
| | - Aldons J Lusis
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA ; Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA ; Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Yuko Yoshinaga
- Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA ; Current address: Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Pieter de Jong
- Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA
| | - Loren Fong
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Stephen G Young
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA ; Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA ; Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Karen Reue
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA ; Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA ; Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
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26
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Chaiyachati BH, Kaundal RK, Zhao J, Wu J, Flavell R, Chi T. LoxP-FRT Trap (LOFT): a simple and flexible system for conventional and reversible gene targeting. BMC Biol 2012. [PMID: 23198860 PMCID: PMC3529186 DOI: 10.1186/1741-7007-10-96] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Background Conditional gene knockout (cKO) mediated by the Cre/LoxP system is indispensable for exploring gene functions in mice. However, a major limitation of this method is that gene KO is not reversible. A number of methods have been developed to overcome this, but each method has its own limitations. Results We describe a simple method we have named LOFT [LoxP-flippase (FLP) recognition target (FRT) Trap], which is capable of reversible cKO and free of the limitations associated with existing techniques. This method involves two alleles of a target gene: a standard floxed allele, and a multi-functional allele bearing an FRT-flanked gene-trap cassette, which inactivates the target gene while reporting its expression with green fluorescent protein (GFP); the trapped allele is thus a null and GFP reporter by default, but is convertible into a wild-type allele. The floxed and trapped alleles can typically be generated using a single construct bearing a gene-trap cassette doubly flanked by LoxP and FRT sites, and can be used independently to achieve conditional and constitutive gene KO, respectively. More importantly, in mice bearing both alleles and also expressing the Cre and FLP recombinases, sequential function of the two enzymes should lead to deletion of the target gene, followed by restoration of its expression, thus achieving reversible cKO. LOFT should be generally applicable to mouse genes, including the growing numbers of genes already floxed; in the latter case, only the trapped alleles need to be generated to confer reversibility to the pre-existing cKO models. LOFT has other applications, including the creation and reversal of hypomorphic mutations. In this study we proved the principle of LOFT in the context of T-cell development, at a hypomorphic allele of Baf57/Smarce1 encoding a subunit of the chromatin-remodeling Brg/Brahma-associated factor (BAF) complex. Interestingly, the FLP used in the current work caused efficient reversal in peripheral T cells but not thymocytes, which is advantageous for studying developmental epigenetic programming of T-cell functions, a fundamental issue in immunology. Conclusions LOFT combines well-established basic genetic methods into a simple and reliable method for reversible gene targeting, with the flexibility of achieving traditional constitutive and conditional KO.
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Affiliation(s)
- Barbara H Chaiyachati
- Department of Immunobiology, Yale University Medical School, 300 Cedar Street, New Haven, CT 06520, USA
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Ermann J, Glimcher LH. After GWAS: mice to the rescue? Curr Opin Immunol 2012; 24:564-70. [PMID: 23031443 DOI: 10.1016/j.coi.2012.09.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 09/04/2012] [Accepted: 09/05/2012] [Indexed: 12/12/2022]
Abstract
The genetic basis of human autoimmune diseases remains incompletely understood, despite significant progress from genome-wide association studies (GWAS). In this review we outline how studies in mice may help filling these knowledge gaps. Forward genetic approaches including mutagenesis screens and quantitative trait locus (QTL) mapping studies can identify candidate genes for in depth analysis in human patient populations. Reverse genetic approaches utilize genetically engineered mice to analyze the function of disease-associated genes and their variants. Inbred strains are a distinctive feature of mouse genetics and we discuss their history, advantages and disadvantages. Three factors need to be considered when comparing experimental results from studies in mice and humans: In addition to species-specific differences, phenotypes are affected by the genetic background of the mouse strain being analyzed, and by microbial factors. Despite of these complexities, mice are essential discovery tools in the post GWAS era.
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Affiliation(s)
- Joerg Ermann
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Robert Brigham Arthritis Center, Boston, MA 02215, USA.
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28
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Smith CL, Eppig JT. The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data. Mamm Genome 2012; 23:653-68. [PMID: 22961259 PMCID: PMC3463787 DOI: 10.1007/s00335-012-9421-3] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 07/24/2012] [Indexed: 01/16/2023]
Abstract
The Mammalian Phenotype Ontology (MP) is a structured vocabulary for describing mammalian phenotypes and serves as a critical tool for efficient annotation and comprehensive retrieval of phenotype data. Importantly, the ontology contains broad and specific terms, facilitating annotation of data from initial observations or screens and detailed data from subsequent experimental research. Using the ontology structure, data are retrieved inclusively, i.e., data annotated to chosen terms and to terms subordinate in the hierarchy. Thus, searching for "abnormal craniofacial morphology" also returns annotations to "megacephaly" and "microcephaly," more specific terms in the hierarchy path. The development and refinement of the MP is ongoing, with new terms and modifications to its organization undergoing continuous assessment as users and expert reviewers propose expansions and revisions. A wealth of phenotype data on mouse mutations and variants annotated to the MP already exists in the Mouse Genome Informatics database. These data, along with data curated to the MP by many mouse mutagenesis programs and mouse repositories, provide a platform for comparative analyses and correlative discoveries. The MP provides a standard underpinning to mouse phenotype descriptions for existing and future experimental and large-scale phenotyping projects. In this review we describe the MP as it presently exists, its application to phenotype annotations, the relationship of the MP to other ontologies, and the integration of the MP within large-scale phenotyping projects. Finally we discuss future application of the MP in providing standard descriptors of the phenotype pipeline test results from the International Mouse Phenotype Consortium projects.
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29
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Mouse lipin-1 and lipin-2 cooperate to maintain glycerolipid homeostasis in liver and aging cerebellum. Proc Natl Acad Sci U S A 2012; 109:E2486-95. [PMID: 22908270 DOI: 10.1073/pnas.1205221109] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The three lipin phosphatidate phosphatase (PAP) enzymes catalyze a step in glycerolipid biosynthesis, the conversion of phosphatidate to diacylglycerol. Lipin-1 is critical for lipid synthesis and homeostasis in adipose tissue, liver, muscle, and peripheral nerves. Little is known about the physiological role of lipin-2, the predominant lipin protein present in liver and the deficient gene product in the rare disorder Majeed syndrome. By using lipin-2-deficient mice, we uncovered a functional relationship between lipin-1 and lipin-2 that operates in a tissue-specific and age-dependent manner. In liver, lipin-2 deficiency led to a compensatory increase in hepatic lipin-1 protein and elevated PAP activity, which maintained lipid homeostasis under basal conditions, but led to diet-induced hepatic triglyceride accumulation. As lipin-2-deficient mice aged, they developed ataxia and impaired balance. This was associated with the combination of lipin-2 deficiency and an age-dependent reduction in cerebellar lipin-1 levels, resulting in altered cerebellar phospholipid composition. Similar to patients with Majeed syndrome, lipin-2-deficient mice developed anemia, but did not show evidence of osteomyelitis, suggesting that additional environmental or genetic components contribute to the bone abnormalities observed in patients. Combined lipin-1 and lipin-2 deficiency caused embryonic lethality. Our results reveal functional interactions between members of the lipin family in vivo, and a unique role for lipin-2 in central nervous system biology that may be particularly important with advancing age. Additionally, as has been observed in mice and humans with lipin-1 deficiency, the pathophysiology in lipin-2 deficiency is associated with dysregulation of lipid intermediates.
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30
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Massart A, Lissens W, Tournaye H, Stouffs K. Genetic causes of spermatogenic failure. Asian J Androl 2012; 14:40-8. [PMID: 22138898 PMCID: PMC3735159 DOI: 10.1038/aja.2011.67] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Revised: 08/01/2011] [Accepted: 08/11/2011] [Indexed: 01/16/2023] Open
Abstract
Approximately 10%-15% of couples are infertile, and a male factor is involved in almost half of these cases. This observation is due in part to defects in spermatogenesis, and the underlying causes, including genetic abnormalities, remain largely unknown. Until recently, the only genetic tests used in the diagnosis of male infertility were aimed at detecting the presence of microdeletions of the long arm of the Y chromosome and/or chromosomal abnormalities. Various other single-gene or polygenic defects have been proposed to be involved in male fertility. However, their causative effects often remain unproven. The recent evolution in the development of whole-genome-based techniques and the large-scale analysis of mouse models might help in this process. Through knockout mouse models, at least 388 genes have been shown to be associated with spermatogenesis in mice. However, problems often arise when translating this information from mice to humans.
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Affiliation(s)
- Annelien Massart
- Center for Medical Genetics, Universitair Ziekenhuis Brussel, Brussels, Belgium
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31
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Abstract
Genome walking is a molecular procedure for the direct identification of nucleotide sequences from purified genomes. The only requirement is the availability of a known nucleotide sequence from which to start. Several genome walking methods have been developed in the last 20 years, with continuous improvements added to the first basic strategies, including the recent coupling with next generation sequencing technologies. This review focuses on the use of genome walking strategies in several aspects of the study of eukaryotic genomes. In a first part, the analysis of the numerous strategies available is reported. The technical aspects involved in genome walking are particularly intriguing, also because they represent the synthesis of the talent, the fantasy and the intelligence of several scientists. Applications in which genome walking can be employed are systematically examined in the second part of the review, showing the large potentiality of this technique, including not only the simple identification of nucleotide sequences but also the analysis of large collections of mutants obtained from the insertion of DNA of viral origin, transposons and transfer DNA (T-DNA) constructs. The enormous amount of data obtained indicates that genome walking, with its large range of applicability, multiplicity of strategies and recent developments, will continue to have much to offer for the rapid identification of unknown sequences in several fields of genomic research.
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Affiliation(s)
- Claudia Leoni
- Department of Biochemistry and Molecular Biology, University of Bari, Bari, Italy
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32
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Abstract
Large-scale projects are providing rapid global access to a wealth of mouse genetic resources to help discover disease genes and to manipulate their function.
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Affiliation(s)
| | | | - David J Adams
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Darren W Logan
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
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33
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Affiliation(s)
- Mary C Mullins
- University of Pennsylvania School of Medicine, Department of Cell and Developmental Biology, Philadelphia, Pennsylvania, USA.
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34
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Clark KJ, Balciunas D, Pogoda HM, Ding Y, Westcot SE, Bedell VM, Greenwood TM, Urban MD, Skuster KJ, Petzold AM, Ni J, Nielsen AL, Patowary A, Scaria V, Sivasubbu S, Xu X, Hammerschmidt M, Ekker SC. In vivo protein trapping produces a functional expression codex of the vertebrate proteome. Nat Methods 2011; 8:506-15. [PMID: 21552255 PMCID: PMC3306164 DOI: 10.1038/nmeth.1606] [Citation(s) in RCA: 135] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Accepted: 04/08/2011] [Indexed: 12/25/2022]
Abstract
We describe a conditional in vivo protein-trap mutagenesis system that reveals spatiotemporal protein expression dynamics and can be used to assess gene function in the vertebrate Danio rerio. Integration of pGBT-RP2.1 (RP2), a gene-breaking transposon containing a protein trap, efficiently disrupts gene expression with >97% knockdown of normal transcript amounts and simultaneously reports protein expression for each locus. The mutant alleles are revertible in somatic tissues via Cre recombinase or splice-site-blocking morpholinos and are thus to our knowledge the first systematic conditional mutant alleles outside the mouse model. We report a collection of 350 zebrafish lines that include diverse molecular loci. RP2 integrations reveal the complexity of genomic architecture and gene function in a living organism and can provide information on protein subcellular localization. The RP2 mutagenesis system is a step toward a unified 'codex' of protein expression and direct functional annotation of the vertebrate genome.
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35
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[Applications of DNA transposons to the study of gene function in mice]. YI CHUAN = HEREDITAS 2011; 33:485-93. [PMID: 21586395 DOI: 10.3724/sp.j.1005.2011.00485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In the past decade, transposon-mediated insertional mutagenesis has been widely used in mammalian molecular genetics. As a convenient and efficient tool for genetic manipulation, transposon has played an important role in making transgenic animal models, performing gene therapy, and annotating gene function at the cellular level and by animal studies in vivo. This review focuses on the structure, function and latest research progress of DNA transposons applied in mouse genetics.
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