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Takamura N, Seo H, Ohta K. TET3 dioxygenase modulates gene conversion at the avian immunoglobulin variable region via demethylation of non-CpG sites in pseudogene templates. Genes Cells 2021; 26:121-135. [PMID: 33421268 PMCID: PMC7986818 DOI: 10.1111/gtc.12828] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 12/20/2022]
Abstract
Diversification of the avian primary immunoglobulin (Ig) repertoire is achieved in developing B cells by somatic hypermutation (SHM) and gene conversion (GCV). GCV is a type of homologous recombination that unidirectionally transfers segments of Ig pseudogenes to Ig variable domains. It is regulated by epigenetic mechanisms like histone modifications, but the role of DNA methylation remains unclear. Here, we demonstrate that the chicken B‐cell line DT40 lacking TET3, a member of the TET (Ten‐eleven translocation) family dioxygenases that facilitate DNA demethylation, exhibited a marked reduction in GCV activity in Ig variable regions. This was accompanied by a drop in the bulk levels of 5‐hydroxymethylcytosine, an oxidized derivative of 5‐methylcytosine, whereas TET1‐deficient or TET2‐deficient DT40 strains did not exhibit such effects. Deletion of TET3 caused little effects on the expression of proteins required for SHM and GCV, but induced hypermethylation in some Ig pseudogene templates. Notably, the enhanced methylation occurred preferably on non‐CpG cytosines. Disruption of both TET1 and TET3 significantly inhibited the expression of activation‐induced cytidine deaminase (AID), an essential player in Ig diversification. These results uncover unique roles of TET proteins in avian Ig diversification, highlighting the potential importance of TET3 in maintaining hypomethylation In Ig pseudogenes.
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Affiliation(s)
- Natsuki Takamura
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Japan
| | - Hidetaka Seo
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Japan
| | - Kunihiro Ohta
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Japan.,Universal Biology Institute, The University of Tokyo, Bunkyo-ku, Japan
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van Tol N, van der Zaal BJ. Artificial transcription factor-mediated regulation of gene expression. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 225:58-67. [PMID: 25017160 DOI: 10.1016/j.plantsci.2014.05.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 05/22/2014] [Accepted: 05/23/2014] [Indexed: 06/03/2023]
Abstract
The transcriptional regulation of endogenous genes with artificial transcription factors (TFs) can offer new tools for plant biotechnology. Three systems are available for mediating site-specific DNA recognition of artificial TFs: those based on zinc fingers, TALEs, and on the CRISPR/Cas9 technology. Artificial TFs require an effector domain that controls the frequency of transcription initiation at endogenous target genes. These effector domains can be transcriptional activators or repressors, but can also have enzymatic activities involved in chromatin remodeling or epigenetic regulation. Artificial TFs are able to regulate gene expression in trans, thus allowing them to evoke dominant mutant phenotypes. Large scale changes in transcriptional activity are induced when the DNA binding domain is deliberately designed to have lower binding specificity. This technique, known as genome interrogation, is a powerful tool for generating novel mutant phenotypes. Genome interrogation has clear mechanistic and practical advantages over activation tagging, which is the technique most closely resembling it. Most notably, genome interrogation can lead to the discovery of mutant phenotypes that are unlikely to be found when using more conventional single gene-based approaches.
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Affiliation(s)
- Niels van Tol
- Department of Molecular and Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Bert J van der Zaal
- Department of Molecular and Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2333 BE Leiden, The Netherlands.
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Epigenetic modification of the repair donor regulates targeted gene correction. MOLECULAR THERAPY. NUCLEIC ACIDS 2012; 1:e49. [PMID: 23344649 PMCID: PMC3499697 DOI: 10.1038/mtna.2012.42] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Optimizing design of vectors is critical to effective gene therapy. In targeted gene correction (TGC), cleavage of chromosomal DNA near a mutation stimulates homology-directed repair of a target gene using a donor provided in trans. We have systematically addressed epigenetic parameters of donor design, using a flow-based assay to quantify correction frequencies and expression levels of a green fluorescent protein (GFP) reporter gene in a human cell line. We show that active transcription of the donor increased correction frequency by threefold, establishing that a proximal promoter enhances donor use. Conversely, CpG methylation of the donor diminished correction frequency and reduced expression of the repaired gene. However, bisulfite sequencing of the target revealed no transfer of methylation marks during repair with a methylated donor. Treatment with histone deacetylase (HDAC) inhibitors can partially compensate for epigenetic inactivation, suggesting a role for class I and II HDACs in regulation of donor use. These results establish that epigenetic status of a trans-donor determines both the efficiency and outcome of gene correction, and identify and clarify parameters that should guide donor design for targeted gene therapy.Molecular Therapy - Nucleic Acids (2012) 1, e49; doi:10.1038/mtna.2012.42; published online 23 October 2012.
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Abstract
Many devastating human diseases are caused by mutations in a single gene that prevent a somatic cell from carrying out its essential functions, or by genetic changes acquired as a result of infectious disease or in the course of cell transformation. Targeted gene therapies have emerged as potential strategies for treatment of such diseases. These therapies depend upon rare-cutting endonucleases to cleave at specific sites in or near disease genes. Targeted gene correction provides a template for homology-directed repair, enabling the cell's own repair pathways to erase the mutation and replace it with the correct sequence. Targeted gene disruption ablates the disease gene, disabling its function. Gene targeting can also promote other kinds of genome engineering, including mutation, insertion, or gene deletion. Targeted gene therapies present significant advantages compared to approaches to gene therapy that depend upon delivery of stably expressing transgenes. Recent progress has been fueled by advances in nuclease discovery and design, and by new strategies that maximize efficiency of targeting and minimize off-target damage. Future progress will build on deeper mechanistic understanding of critical factors and pathways.
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Affiliation(s)
- Olivier Humbert
- Departments of Immunology and Biochemistry, University of Washington School of Medicine, Seattle, WA 98195, USA
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Yabuki M, Cummings WJ, Leppard JB, Immormino RM, Wood CL, Allison DS, Gray PW, Tjoelker LW, Maizels N. Antibody discovery ex vivo accelerated by the LacO/LacI regulatory network. PLoS One 2012; 7:e36032. [PMID: 22558313 PMCID: PMC3338700 DOI: 10.1371/journal.pone.0036032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 03/27/2012] [Indexed: 11/18/2022] Open
Abstract
Monoclonal antibodies (mAbs) can be potent and highly specific therapeutics, diagnostics and research reagents. Nonetheless, mAb discovery using current in vivo or in vitro approaches can be costly and time-consuming, with no guarantee of success. We have established a platform for rapid discovery and optimization of mAbs ex vivo. This DTLacO platform derives from a chicken B cell line that has been engineered to enable rapid selection and seamless maturation of high affinity mAbs. We have validated the DTLacO platform by generation of high affinity and specific mAbs to five cell surface targets, the receptor tyrosine kinases VEGFR2 and TIE2, the glycoprotein TROP2, the small TNF receptor family member FN14, and the G protein-coupled receptor FZD10. mAb discovery is rapid and humanization is straightforward, establishing the utility of the DTLacO platform for identification of mAbs for therapeutic and other applications.
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Affiliation(s)
- Munehisa Yabuki
- Department of Immunology, University of Washington School of Medicine, Seattle, Washington, United States of America
- XORI Corporation, Seattle, Washington, United States of America
| | - W. Jason Cummings
- Department of Immunology, University of Washington School of Medicine, Seattle, Washington, United States of America
- XORI Corporation, Seattle, Washington, United States of America
| | - John B. Leppard
- XORI Corporation, Seattle, Washington, United States of America
| | - Robert M. Immormino
- Department of Immunology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Christi L. Wood
- XORI Corporation, Seattle, Washington, United States of America
| | | | - Patrick W. Gray
- Accelerator Corporation, Seattle, Washington, United States of America
| | | | - Nancy Maizels
- Department of Immunology, University of Washington School of Medicine, Seattle, Washington, United States of America
- Department of Biochemistry, University of Washington School of Medicine, Seattle, Washington, United States of America
- * E-mail:
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Antigenic variation and the generation of diversity in malaria parasites. Curr Opin Microbiol 2012; 15:456-62. [PMID: 22503815 DOI: 10.1016/j.mib.2012.03.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Accepted: 03/08/2012] [Indexed: 11/27/2022]
Abstract
Investigations into the genetic basis underlying antigenic variation in malaria parasites have primarily described transcriptional regulation of the large, multi-copy gene families that encode red cell surface antigens. In particular, extensive alterations to chromatin structure and subnuclear localization have been shown to play key roles in mutually exclusive expression, gene silencing and activation, and epigenetic memory. However the mechanisms responsible for the generation of sequence diversity within these gene families, a characteristic that is equally important for a parasite's ability to avoid the host's immune response, remains poorly understood in malaria. Recent work in model organisms suggests that the mechanisms controlling gene activation and silencing might also contribute to preferential recombination between antigen encoding genes, thus linking these two key processes.
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Jensen BC, Kifer CT, Parsons M. Trypanosoma brucei: Two mitogen activated protein kinase kinases are dispensable for growth and virulence of the bloodstream form. Exp Parasitol 2011; 128:250-5. [PMID: 21396364 DOI: 10.1016/j.exppara.2011.03.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Revised: 03/03/2011] [Accepted: 03/03/2011] [Indexed: 01/01/2023]
Abstract
Mitogen activated protein kinase cascades function in eukaryotic responses to the environment and stress. Trypanosomatid parasites possess protein kinases with sequences characteristic of kinases in such cascades. In this report we use gene knockouts to demonstrate that two mitogen activated kinase kinase genes, MKK1 (Tb927.3.4860) and MKK5 (Tb927.10.5270), are not essential in the pathogenic bloodstream stage of Trypanosoma brucei, either in vitro or in vivo. Bloodstream forms lacking MKK1 showed decreased growth at 39°C as compared to the parental line. However, unlike its Leishmania orthologue, T. brucei MKK1 does not appear to play a significant role in flagellar biogenesis.
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Affiliation(s)
- Bryan C Jensen
- Seattle Biomedical Research Institute, 307 Westlake Ave. N., Seattle, WA 98109, USA
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Johnson LJ, Tricker PJ. Epigenomic plasticity within populations: its evolutionary significance and potential. Heredity (Edinb) 2010; 105:113-21. [PMID: 20332811 DOI: 10.1038/hdy.2010.25] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Epigenetics has progressed rapidly from an obscure quirk of heredity into a data-heavy 'omic' science. Our understanding of the molecular mechanisms of epigenomic regulation, and the extent of its importance in nature, are far from complete, but in spite of such drawbacks, population-level studies are extremely valuable: epigenomic regulation is involved in several processes central to evolutionary biology including phenotypic plasticity, evolvability and the mediation of intragenomic conflicts. The first studies of epigenomic variation within populations suggest high levels of phenotypically relevant variation, with the patterns of epigenetic regulation varying between individuals and genome regions as well as with environment. Epigenetic mechanisms appear to function primarily as genome defences, but result in the maintenance of plasticity together with a degree of buffering of developmental programmes; periodic breakdown of epigenetic buffering could potentially cause variation in rates of phenotypic evolution.
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Affiliation(s)
- L J Johnson
- School of Biological Sciences, University of Reading, Reading, UK.
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