1
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Abstract
Recent structures of DNA-bound bacterial and phage recombinases provide insights into homologous recombination and suggest relation to the eukaryotic Rad52 and identification of a Rad52 single strand annealing protein (SSAP) superfamily.
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Affiliation(s)
- Ali Al-Fatlawi
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47, 01307, Dresden, Germany
| | - Michael Schroeder
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47, 01307, Dresden, Germany.
| | - A Francis Stewart
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47, 01307, Dresden, Germany.
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia.
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2
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Grinat J, Kosel F, Goveas N, Kranz A, Alexopoulou D, Rajewsky K, Sigal M, Stewart AF, Heuberger J. Epigenetic modifier balances Mapk and Wnt signalling in differentiation of goblet and Paneth cells. Life Sci Alliance 2022; 5:5/4/e202101187. [PMID: 35064075 PMCID: PMC8807877 DOI: 10.26508/lsa.202101187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 12/24/2022] Open
Abstract
The histone methyltransferase Mll1 controls intestinal secretory cell fate by promoting Wnt-driven Paneth and restricting Mapk-dependent goblet cell differentiation through regulation of Gata4/6 transcription factors Differentiation and lineage specification are controlled by cooperation of growth factor signalling. The involvement of epigenetic regulators in lineage specification remains largely elusive. Here, we show that the histone methyltransferase Mll1 prevents intestinal progenitor cells from differentiation, whereas it is also involved in secretory lineage specification of Paneth and goblet cells. Using conditional mutagenesis in mice and intestinal organoids, we demonstrate that loss of Mll1 renders intestinal progenitor cells permissive for Wnt-driven secretory differentiation. However, Mll1-deficient crypt cells fail to segregate Paneth and goblet cell fates. Mll1 deficiency causes Paneth cell-determined crypt progenitors to exhibit goblet cell features by unleashing Mapk signalling, resulting in increased numbers of mixed Paneth/goblet cells. We show that loss of Mll1 abolishes the pro-proliferative effect of Mapk signalling in intestinal progenitor cells and promotes Mapk-induced goblet cell differentiation. Our data uncover Mll1 and its downstream targets Gata4/6 as a regulatory hub of Wnt and Mapk signalling in the control of lineage specification of intestinal secretory Paneth and goblet cells.
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Affiliation(s)
- Johanna Grinat
- Cancer Research Program, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Society, Berlin, Germany
| | - Frauke Kosel
- Cancer Research Program, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Society, Berlin, Germany
| | - Neha Goveas
- Genomics, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Andrea Kranz
- Genomics, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Dimitra Alexopoulou
- DRESDEN-concept Genome Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Klaus Rajewsky
- Cancer Research Program, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Society, Berlin, Germany
| | - Michael Sigal
- Medical Department, Division of Gastroenterology and Hepatology, Charité University Medicine, Berlin, Germany.,Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - A Francis Stewart
- Genomics, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Dresden, Germany.,Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Julian Heuberger
- Medical Department, Division of Gastroenterology and Hepatology, Charité University Medicine, Berlin, Germany .,Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
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3
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Michurina A, Sakib MS, Kerimoglu C, Krüger DM, Kaurani L, Islam MR, Joshi PD, Schröder S, Centeno TP, Zhou J, Pradhan R, Cha J, Xu X, Eichele G, Zeisberg EM, Kranz A, Stewart AF, Fischer A. Postnatal expression of the lysine methyltransferase SETD1B is essential for learning and the regulation of neuron-enriched genes. EMBO J 2022; 41:e106459. [PMID: 34806773 PMCID: PMC8724770 DOI: 10.15252/embj.2020106459] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/04/2021] [Accepted: 10/15/2021] [Indexed: 01/04/2023] Open
Abstract
In mammals, histone 3 lysine 4 methylation (H3K4me) is mediated by six different lysine methyltransferases. Among these enzymes, SETD1B (SET domain containing 1b) has been linked to syndromic intellectual disability in human subjects, but its role in the mammalian postnatal brain has not been studied yet. Here, we employ mice deficient for Setd1b in excitatory neurons of the postnatal forebrain, and combine neuron-specific ChIP-seq and RNA-seq approaches to elucidate its role in neuronal gene expression. We observe that Setd1b controls the expression of a set of genes with a broad H3K4me3 peak at their promoters, enriched for neuron-specific genes linked to learning and memory function. Comparative analyses in mice with conditional deletion of Kmt2a and Kmt2b histone methyltransferases show that SETD1B plays a more pronounced and potent role in regulating such genes. Moreover, postnatal loss of Setd1b leads to severe learning impairment, suggesting that SETD1B-dependent regulation of H3K4me levels in postnatal neurons is critical for cognitive function.
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Affiliation(s)
- Alexandra Michurina
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - M Sadman Sakib
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Cemil Kerimoglu
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Dennis Manfred Krüger
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Lalit Kaurani
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Md Rezaul Islam
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Parth Devesh Joshi
- Department for Gene and BehaviorMax Planck Institute for Biophysical ChemistryGöttingenGermany
| | - Sophie Schröder
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Tonatiuh Pena Centeno
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Jiayin Zhou
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Ranjit Pradhan
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Julia Cha
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Xingbo Xu
- Department of Cardiology and PneumologyUniversity Medical Center of GöttingenGeorg‐August UniversityGöttingenGermany
- German Centre for Cardiovascular Research (DZHK)Partner Site GöttingenGöttingenGermany
| | - Gregor Eichele
- Department for Gene and BehaviorMax Planck Institute for Biophysical ChemistryGöttingenGermany
| | - Elisabeth M Zeisberg
- Department of Cardiology and PneumologyUniversity Medical Center of GöttingenGeorg‐August UniversityGöttingenGermany
- German Centre for Cardiovascular Research (DZHK)Partner Site GöttingenGöttingenGermany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC)University of GöttingenGermany
| | - Andrea Kranz
- Biotechnology CenterCenter for Molecular and Cellular BioengineeringDresden University of TechnologyDresdenGermany
| | - A Francis Stewart
- Biotechnology CenterCenter for Molecular and Cellular BioengineeringDresden University of TechnologyDresdenGermany
- Max‐Planck‐Institute for Cell Biology and GeneticsDresdenGermany
| | - André Fischer
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC)University of GöttingenGermany
- Department of Psychiatry and PsychotherapyUniversity Medical Center GöttingenGöttingenGermany
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4
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Wang X, Zheng W, Zhou H, Tu Q, Tang YJ, Stewart AF, Zhang Y, Bian X. Improved dsDNA recombineering enables versatile multiplex genome engineering of kilobase-scale sequences in diverse bacteria. Nucleic Acids Res 2021; 50:e15. [PMID: 34792175 PMCID: PMC8860599 DOI: 10.1093/nar/gkab1076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 09/23/2021] [Accepted: 10/22/2021] [Indexed: 01/21/2023] Open
Abstract
Recombineering assisted multiplex genome editing generally uses single-stranded oligonucleotides for site directed mutational changes. It has proven highly efficient for functional screens and to optimize microbial cell factories. However, this approach is limited to relatively small mutational changes. Here, we addressed the challenges involved in the use of double-stranded DNA substrates for multiplex genome engineering. Recombineering is mediated by phage single-strand annealing proteins annealing ssDNAs into the replication fork. We apply this insight to facilitate the generation of ssDNA from the dsDNA substrate and to alter the speed of replication by elevating the available deoxynucleoside triphosphate (dNTP) levels. Intracellular dNTP concentration was elevated by ribonucleotide reductase overexpression or dNTP addition to establish double-stranded DNA Recombineering-assisted Multiplex Genome Engineering (dReaMGE), which enables rapid and flexible insertional and deletional mutagenesis at multiple sites on kilobase scales in diverse bacteria without the generation of double-strand breaks or disturbance of the mismatch repair system. dReaMGE can achieve combinatorial genome engineering works, for example, alterations to multiple biosynthetic pathways, multiple promoter or gene insertions, variations of transcriptional regulator combinations, within a few days. dReaMGE adds to the repertoire of bacterial genome engineering to facilitate discovery, functional genomics, strain optimization and directed evolution of microbial cell factories.
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Affiliation(s)
- Xue Wang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Wentao Zheng
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Haibo Zhou
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Qiang Tu
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Ya-Jie Tang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - A Francis Stewart
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47-51, 01307 Dresden, Germany
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
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5
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Lackner A, Sehlke R, Garmhausen M, Giuseppe Stirparo G, Huth M, Titz-Teixeira F, van der Lelij P, Ramesmayer J, Thomas HF, Ralser M, Santini L, Galimberti E, Sarov M, Stewart AF, Smith A, Beyer A, Leeb M. Cooperative genetic networks drive embryonic stem cell transition from naïve to formative pluripotency. EMBO J 2021; 40:e105776. [PMID: 33687089 PMCID: PMC8047444 DOI: 10.15252/embj.2020105776] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 12/11/2022] Open
Abstract
In the mammalian embryo, epiblast cells must exit the naïve state and acquire formative pluripotency. This cell state transition is recapitulated by mouse embryonic stem cells (ESCs), which undergo pluripotency progression in defined conditions in vitro. However, our understanding of the molecular cascades and gene networks involved in the exit from naïve pluripotency remains fragmentary. Here, we employed a combination of genetic screens in haploid ESCs, CRISPR/Cas9 gene disruption, large‐scale transcriptomics and computational systems biology to delineate the regulatory circuits governing naïve state exit. Transcriptome profiles for 73 ESC lines deficient for regulators of the exit from naïve pluripotency predominantly manifest delays on the trajectory from naïve to formative epiblast. We find that gene networks operative in ESCs are also active during transition from pre‐ to post‐implantation epiblast in utero. We identified 496 naïve state‐associated genes tightly connected to the in vivo epiblast state transition and largely conserved in primate embryos. Integrated analysis of mutant transcriptomes revealed funnelling of multiple gene activities into discrete regulatory modules. Finally, we delineate how intersections with signalling pathways direct this pivotal mammalian cell state transition.
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Affiliation(s)
- Andreas Lackner
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Robert Sehlke
- Cologne Excellence Cluster Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Marius Garmhausen
- Cologne Excellence Cluster Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Giuliano Giuseppe Stirparo
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.,Living Systems Institute, University of Exeter, Exeter, UK
| | - Michelle Huth
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Fabian Titz-Teixeira
- Cologne Excellence Cluster Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Petra van der Lelij
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Julia Ramesmayer
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Henry F Thomas
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Meryem Ralser
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Laura Santini
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Elena Galimberti
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Mihail Sarov
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - A Francis Stewart
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Austin Smith
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.,Living Systems Institute, University of Exeter, Exeter, UK
| | - Andreas Beyer
- Cologne Excellence Cluster Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Martin Leeb
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Vienna, Austria
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6
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Song C, Luan J, Li R, Jiang C, Hou Y, Cui Q, Cui T, Tan L, Ma Z, Tang YJ, Stewart AF, Fu J, Zhang Y, Wang H. RedEx: a method for seamless DNA insertion and deletion in large multimodular polyketide synthase gene clusters. Nucleic Acids Res 2021; 48:e130. [PMID: 33119745 PMCID: PMC7736807 DOI: 10.1093/nar/gkaa956] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/08/2020] [Accepted: 10/08/2020] [Indexed: 11/23/2022] Open
Abstract
Biosynthesis reprograming is an important way to diversify chemical structures. The large repetitive DNA sequences existing in polyketide synthase genes make seamless DNA manipulation of the polyketide biosynthetic gene clusters extremely challenging. In this study, to replace the ethyl group attached to the C-21 of the macrolide insecticide spinosad with a butenyl group by refactoring the 79-kb gene cluster, we developed a RedEx method by combining Redαβ mediated linear-circular homologous recombination, ccdB counterselection and exonuclease mediated in vitro annealing to insert an exogenous extension module in the polyketide synthase gene without any extra sequence. RedEx was also applied for seamless deletion of the rhamnose 3′-O-methyltransferase gene in the spinosad gene cluster to produce rhamnosyl-3′-desmethyl derivatives. The advantages of RedEx in seamless mutagenesis will facilitate rational design of complex DNA sequences for diverse purposes.
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Affiliation(s)
- Chaoyi Song
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
| | - Ji Luan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
| | - Ruijuan Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
| | - Chanjuan Jiang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
| | - Yu Hou
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
| | - Qingwen Cui
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
| | - Tianqi Cui
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
| | - Long Tan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
| | - Zaichao Ma
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
| | - Ya-Jie Tang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
| | - A Francis Stewart
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47-51, 01307 Dresden, Germany
| | - Jun Fu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
| | - Hailong Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
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7
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Grinat J, Heuberger J, Vidal RO, Goveas N, Kosel F, Berenguer-Llergo A, Kranz A, Wulf-Goldenberg A, Behrens D, Melcher B, Sauer S, Vieth M, Batlle E, Stewart AF, Birchmeier W. The epigenetic regulator Mll1 is required for Wnt-driven intestinal tumorigenesis and cancer stemness. Nat Commun 2020; 11:6422. [PMID: 33349639 PMCID: PMC7752919 DOI: 10.1038/s41467-020-20222-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 11/16/2020] [Indexed: 12/30/2022] Open
Abstract
Wnt/β-catenin signaling is crucial for intestinal carcinogenesis and the maintenance of intestinal cancer stem cells. Here we identify the histone methyltransferase Mll1 as a regulator of Wnt-driven intestinal cancer. Mll1 is highly expressed in Lgr5+ stem cells and human colon carcinomas with increased nuclear β-catenin. High levels of MLL1 are associated with poor survival of colon cancer patients. The genetic ablation of Mll1 in mice prevents Wnt/β-catenin-driven adenoma formation from Lgr5+ intestinal stem cells. Ablation of Mll1 decreases the self-renewal of human colon cancer spheres and halts tumor growth of xenografts. Mll1 controls the expression of stem cell genes including the Wnt/β-catenin target gene Lgr5. Upon the loss of Mll1, histone methylation at the stem cell promoters switches from activating H3K4 tri-methylation to repressive H3K27 tri-methylation, indicating that Mll1 sustains stem cell gene expression by antagonizing gene silencing through polycomb repressive complex 2 (PRC2)-mediated H3K27 tri-methylation. Transcriptome profiling of Wnt-mutated intestinal tumor-initiating cells reveals that Mll1 regulates Gata4/6 transcription factors, known to sustain cancer stemness and to control goblet cell differentiation. Our results demonstrate that Mll1 is an essential epigenetic regulator of Wnt/β-catenin-induced intestinal tumorigenesis and cancer stemness. Intestinal cancer stem cells (CSC) are associated with colon cancer. Here, the authors show that Wnt/beta-catenin signalling in CSC requires the epigenetic regulator Mll1 to promote stemness and tumourigenesis in murine and human colon cancer models.
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Affiliation(s)
- Johanna Grinat
- Cancer Research Program, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Society, 13125, Berlin, Germany
| | - Julian Heuberger
- Cancer Research Program, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Society, 13125, Berlin, Germany. .,Division of Gastroenterology and Hepatology, Medical Department, Charité University Medicine, 13353, Berlin, Germany.
| | - Ramon Oliveira Vidal
- Laboratory of Functional Genomics, Nutrigenomics and Systems Biology, Scientific Genomics Platforms, Max Delbrück Center for Molecular Medicine (BIMSB/BIH), 13092, Berlin, Germany
| | - Neha Goveas
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, 01307, Dresden, Germany
| | - Frauke Kosel
- Cancer Research Program, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Society, 13125, Berlin, Germany
| | - Antoni Berenguer-Llergo
- Biostatistics and Bioinformatics Unit, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Andrea Kranz
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, 01307, Dresden, Germany
| | | | - Diana Behrens
- Experimental Pharmacology & Oncology (EPO), 13125, Berlin, Germany
| | - Bálint Melcher
- Institute for Pathology, Klinikum Bayreuth, 95445, Bayreuth, Germany
| | - Sascha Sauer
- Laboratory of Functional Genomics, Nutrigenomics and Systems Biology, Scientific Genomics Platforms, Max Delbrück Center for Molecular Medicine (BIMSB/BIH), 13092, Berlin, Germany
| | - Michael Vieth
- Institute for Pathology, Klinikum Bayreuth, 95445, Bayreuth, Germany
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,ICREA, Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - A Francis Stewart
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, 01307, Dresden, Germany
| | - Walter Birchmeier
- Cancer Research Program, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Society, 13125, Berlin, Germany.
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8
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Ramakrishnan S, Subramaniam S, Kielar C, Grundmeier G, Stewart AF, Keller A. Protein-Assisted Room-Temperature Assembly of Rigid, Immobile Holliday Junctions and Hierarchical DNA Nanostructures. Molecules 2020; 25:molecules25215099. [PMID: 33153073 PMCID: PMC7663122 DOI: 10.3390/molecules25215099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/28/2020] [Accepted: 10/30/2020] [Indexed: 12/30/2022] Open
Abstract
Immobile Holliday junctions represent not only the most fundamental building block of structural DNA nanotechnology but are also of tremendous importance for the in vitro investigation of genetic recombination and epigenetics. Here, we present a detailed study on the room-temperature assembly of immobile Holliday junctions with the help of the single-strand annealing protein Redβ. Individual DNA single strands are initially coated with protein monomers and subsequently hybridized to form a rigid blunt-ended four-arm junction. We investigate the efficiency of this approach for different DNA/protein ratios, as well as for different DNA sequence lengths. Furthermore, we also evaluate the potential of Redβ to anneal sticky-end modified Holliday junctions into hierarchical assemblies. We demonstrate the Redβ-mediated annealing of Holliday junction dimers, multimers, and extended networks several microns in size. While these hybrid DNA–protein nanostructures may find applications in the crystallization of DNA–protein complexes, our work shows the great potential of Redβ to aid in the synthesis of functional DNA nanostructures under mild reaction conditions.
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Affiliation(s)
- Saminathan Ramakrishnan
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany; (S.R.); (C.K.); (G.G.)
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Sivaraman Subramaniam
- Biotechnology Center, Department of Genomics, Technische Universität Dresden, Tatzberg 47-51, 01307 Dresden, Germany; (S.S.); (A.F.S.)
- Cluster of Excellence Physics of Life, Technische Universität Dresden, 01062 Dresden, Germany
| | - Charlotte Kielar
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany; (S.R.); (C.K.); (G.G.)
| | - Guido Grundmeier
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany; (S.R.); (C.K.); (G.G.)
| | - A. Francis Stewart
- Biotechnology Center, Department of Genomics, Technische Universität Dresden, Tatzberg 47-51, 01307 Dresden, Germany; (S.S.); (A.F.S.)
- Cluster of Excellence Physics of Life, Technische Universität Dresden, 01062 Dresden, Germany
| | - Adrian Keller
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany; (S.R.); (C.K.); (G.G.)
- Correspondence:
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9
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Ashokkumar D, Zhang Q, Much C, Bledau AS, Naumann R, Alexopoulou D, Dahl A, Goveas N, Fu J, Anastassiadis K, Stewart AF, Kranz A. MLL4 is required after implantation, whereas MLL3 becomes essential during late gestation. Development 2020; 147:dev186999. [PMID: 32439762 DOI: 10.1242/dev.186999] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/24/2020] [Indexed: 12/26/2022]
Abstract
Methylation of histone 3 lysine 4 (H3K4) is a major epigenetic system associated with gene expression. In mammals there are six H3K4 methyltransferases related to yeast Set1 and fly Trithorax, including two orthologs of fly Trithorax-related: MLL3 and MLL4. Exome sequencing has documented high frequencies of MLL3 and MLL4 mutations in many types of human cancer. Despite this emerging importance, the requirements of these paralogs in mammalian development have only been incompletely reported. Here, we examined the null phenotypes to establish that MLL3 is first required for lung maturation, whereas MLL4 is first required for migration of the anterior visceral endoderm that initiates gastrulation in the mouse. This collective cell migration is preceded by a columnar-to-squamous transition in visceral endoderm cells that depends on MLL4. Furthermore, Mll4 mutants display incompletely penetrant, sex-distorted, embryonic haploinsufficiency and adult heterozygous mutants show aspects of Kabuki syndrome, indicating that MLL4 action, unlike MLL3, is dosage dependent. The highly specific and discordant functions of these paralogs in mouse development argues against their action as general enhancer factors.
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Affiliation(s)
- Deepthi Ashokkumar
- Genomics, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47, 01307 Dresden, Germany
| | - Qinyu Zhang
- Genomics, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47, 01307 Dresden, Germany
| | - Christian Much
- Genomics, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47, 01307 Dresden, Germany
| | - Anita S Bledau
- Stem Cell Engineering, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47, 01307 Dresden, Germany
| | - Ronald Naumann
- Transgenic Core Facility, Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Dimitra Alexopoulou
- DRESDEN-concept Genome Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Fetscherstr. 105, 01307 Dresden, Germany
| | - Andreas Dahl
- DRESDEN-concept Genome Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Fetscherstr. 105, 01307 Dresden, Germany
| | - Neha Goveas
- Genomics, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47, 01307 Dresden, Germany
| | - Jun Fu
- Genomics, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47, 01307 Dresden, Germany
| | - Konstantinos Anastassiadis
- Stem Cell Engineering, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47, 01307 Dresden, Germany
| | - A Francis Stewart
- Genomics, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47, 01307 Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Andrea Kranz
- Genomics, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47, 01307 Dresden, Germany
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10
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Addicks GC, Brun CE, Sincennes MC, Saber J, Porter CJ, Francis Stewart A, Ernst P, Rudnicki MA. MLL1 is required for PAX7 expression and satellite cell self-renewal in mice. Nat Commun 2019; 10:4256. [PMID: 31534153 PMCID: PMC6751293 DOI: 10.1038/s41467-019-12086-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 08/16/2019] [Indexed: 01/16/2023] Open
Abstract
PAX7 is a paired-homeobox transcription factor that specifies the myogenic identity of muscle stem cells and acts as a nodal factor by stimulating proliferation while inhibiting differentiation. We previously found that PAX7 recruits the H3K4 methyltransferases MLL1/2 to epigenetically activate target genes. Here we report that in the absence of Mll1, myoblasts exhibit reduced H3K4me3 at both Pax7 and Myf5 promoters and reduced Pax7 and Myf5 expression. Mll1-deficient myoblasts fail to proliferate but retain their differentiation potential, while deletion of Mll2 had no discernable effect. Re-expression of PAX7 in committed Mll1 cKO myoblasts restored H3K4me3 enrichment at the Myf5 promoter and Myf5 expression. Deletion of Mll1 in satellite cells reduced satellite cell proliferation and self-renewal, and significantly impaired skeletal muscle regeneration. Pax7 expression was unaffected in quiescent satellite cells but was markedly downregulated following satellite cell activation. Therefore, MLL1 is required for PAX7 expression and satellite cell function in vivo. Furthermore, PAX7, but not MLL1, is required for Myf5 transcriptional activation in committed myoblasts. PAX7 transcription factor specifies the myogenic identity of muscle stem cells and acts as a nodal factor by stimulating proliferation while inhibiting differentiation. Here authors find that Mll1 deletion in myoblasts in mice results in reduced H3K4me3 at both Pax7 and Myf5 promoters, reduced Pax7 and Myf5 expression, and proliferation defects.
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Affiliation(s)
- Gregory C Addicks
- Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada.,Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Caroline E Brun
- Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada.,Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Marie-Claude Sincennes
- Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada.,Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - John Saber
- Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada.,Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Christopher J Porter
- Sprott Centre for Stem Cell Research, Ottawa Bioinformatics Core Facility, Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada
| | - A Francis Stewart
- Genomics, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47, Dresden, 01307, Germany
| | - Patricia Ernst
- Department of Pediatrics and Pharmacology, University of Colorado/Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Michael A Rudnicki
- Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada. .,Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada.
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11
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Bereshchenko O, Lo Re O, Nikulenkov F, Flamini S, Kotaskova J, Mazza T, Le Pannérer MM, Buschbeck M, Giallongo C, Palumbo G, Li Volti G, Pazienza V, Cervinek L, Riccardi C, Krejci L, Pospisilova S, Stewart AF, Vinciguerra M. Deficiency and haploinsufficiency of histone macroH2A1.1 in mice recapitulate hematopoietic defects of human myelodysplastic syndrome. Clin Epigenetics 2019; 11:121. [PMID: 31439048 PMCID: PMC6704528 DOI: 10.1186/s13148-019-0724-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 08/12/2019] [Indexed: 12/19/2022] Open
Abstract
Background Epigenetic regulation is important in hematopoiesis, but the involvement of histone variants is poorly understood. Myelodysplastic syndromes (MDS) are heterogeneous clonal hematopoietic stem cell (HSC) disorders characterized by ineffective hematopoiesis. MacroH2A1.1 is a histone H2A variant that negatively correlates with the self-renewal capacity of embryonic, adult, and cancer stem cells. MacroH2A1.1 is a target of the frequent U2AF1 S34F mutation in MDS. The role of macroH2A1.1 in hematopoiesis is unclear. Results MacroH2A1.1 mRNA levels are significantly decreased in patients with low-risk MDS presenting with chromosomal 5q deletion and myeloid cytopenias and tend to be decreased in MDS patients carrying the U2AF1 S34F mutation. Using an innovative mouse allele lacking the macroH2A1.1 alternatively spliced exon, we investigated whether macroH2A1.1 regulates HSC homeostasis and differentiation. The lack of macroH2A1.1 decreased while macroH2A1.1 haploinsufficiency increased HSC frequency upon irradiation. Moreover, bone marrow transplantation experiments showed that both deficiency and haploinsufficiency of macroH2A1.1 resulted in enhanced HSC differentiation along the myeloid lineage. Finally, RNA-sequencing analysis implicated macroH2A1.1-mediated regulation of ribosomal gene expression in HSC homeostasis. Conclusions Together, our findings suggest a new epigenetic process contributing to hematopoiesis regulation. By combining clinical data with a discrete mutant mouse model and in vitro studies of human and mouse cells, we identify macroH2A1.1 as a key player in the cellular and molecular features of MDS. These data justify the exploration of macroH2A1.1 and associated proteins as therapeutic targets in hematological malignancies. Electronic supplementary material The online version of this article (10.1186/s13148-019-0724-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Oxana Bereshchenko
- Department of Medicine, Department of Philosophy, Social Sciences and Education, University of Perugia, Perugia, Italy.
| | - Oriana Lo Re
- International Clinical Research Center, St'Anne University Hospital, Brno, Czech Republic.,Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Fedor Nikulenkov
- International Clinical Research Center, St'Anne University Hospital, Brno, Czech Republic.,Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Sara Flamini
- Department of Medicine, Department of Philosophy, Social Sciences and Education, University of Perugia, Perugia, Italy
| | - Jana Kotaskova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine - Hematology and Oncology, Faculty of Medicine, University Hospital Brno and Masaryk University, Brno, Czech Republic
| | - Tommaso Mazza
- IRCCS Casa Sollievo della Sofferenza, Bioinformatics unit, San Giovanni Rotondo, Italy
| | - Marguerite-Marie Le Pannérer
- Josep Carreras Leukemia Research Institute (IJC), Universitat Autònoma de Barcelona, Campus ICO-Germans Trias I Pujol, Badalona, Spain.,Programme of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Spain
| | - Marcus Buschbeck
- Josep Carreras Leukemia Research Institute (IJC), Universitat Autònoma de Barcelona, Campus ICO-Germans Trias I Pujol, Badalona, Spain.,Programme of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Spain
| | - Cesarina Giallongo
- Division of Hematology, A.O.U. Policlinico-OVE, University of Catania, Catania, Italy
| | - Giuseppe Palumbo
- Department of Medical and Surgical Sciences and Advanced Technologies "GF Ingrassia", University of Catania, Catania, Italy
| | - Giovanni Li Volti
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Valerio Pazienza
- Gastroenterology unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Libor Cervinek
- Department of Internal Medicine - Hematology and Oncology, Faculty of Medicine, University Hospital Brno and Masaryk University, Brno, Czech Republic
| | - Carlo Riccardi
- Department of Medicine, Department of Philosophy, Social Sciences and Education, University of Perugia, Perugia, Italy
| | - Lumir Krejci
- International Clinical Research Center, St'Anne University Hospital, Brno, Czech Republic.,Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Sarka Pospisilova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine - Hematology and Oncology, Faculty of Medicine, University Hospital Brno and Masaryk University, Brno, Czech Republic
| | - A Francis Stewart
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Manlio Vinciguerra
- International Clinical Research Center, St'Anne University Hospital, Brno, Czech Republic.
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12
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Wang H, Li Z, Jia R, Yin J, Li A, Xia L, Yin Y, Müller R, Fu J, Stewart AF, Zhang Y. ExoCET: exonuclease in vitro assembly combined with RecET recombination for highly efficient direct DNA cloning from complex genomes. Nucleic Acids Res 2019; 46:e28. [PMID: 29240926 PMCID: PMC5861427 DOI: 10.1093/nar/gkx1249] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 12/02/2017] [Indexed: 12/29/2022] Open
Abstract
The exponentially increasing volumes of DNA sequence data highlight the need for new DNA cloning methods to explore the new information. Here, we describe ‘ExoCET’ (Exonuclease Combined with RecET recombination) to directly clone any chosen region from bacterial and mammalian genomes with nucleotide precision into operational plasmids. ExoCET combines in vitro exonuclease and annealing with the remarkable capacity of full length RecET homologous recombination (HR) to retrieve specified regions from genomic DNA preparations. Using T4 polymerase (T4pol) as the in vitro exonuclease for ExoCET, we directly cloned large regions (>50 kb) from bacterial and mammalian genomes, including DNA isolated from blood. Employing RecET HR or Cas9 cleavage in vitro, the directly cloned region can be chosen with nucleotide precision to position, for example, a gene into an expression vector without the need for further subcloning. In addition to its utility for bioprospecting in bacterial genomes, ExoCET presents straightforward access to mammalian genomes for various applications such as region-specific DNA sequencing that retains haplotype phasing, the rapid construction of optimal, haplotypic, isogenic targeting constructs or a new way to genotype that presents advantages over Southern blotting or polymerase chain reaction. The direct cloning capacities of ExoCET present new freedoms in recombinant DNA technology.
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Affiliation(s)
- Hailong Wang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China
| | - Zhen Li
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China
| | - Ruonan Jia
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China
| | - Jia Yin
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China
| | - Aiying Li
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China
| | - Liqiu Xia
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, 410081 Changsha, People's Republic of China
| | - Yulong Yin
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China.,State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, 410081 Changsha, People's Republic of China.,Key Laboratory of Subtropical Agro-ecology, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, Hunan Province 410125, People's Republic of China
| | - Rolf Müller
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China.,Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Pharmaceutical Biotechnology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Jun Fu
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China
| | - A Francis Stewart
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47-51, 01307 Dresden, Germany
| | - Youming Zhang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China
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13
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Affiliation(s)
- A Francis Stewart
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, 01307 Dresden, Germany; Max-Planck-Institute for Cell Biology and Genetics, 01307 Dresden, Germany.
| | - Harald von Melchner
- Department for Molecular Hematology and Loewe Center for Cell and Gene Therapy, University of Frankfurt Medical School, Goethe University Medical School, 60590 Frankfurt am Main, Germany.
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14
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Yin J, Zheng W, Gao Y, Jiang C, Shi H, Diao X, Li S, Chen H, Wang H, Li R, Li A, Xia L, Yin Y, Stewart AF, Zhang Y, Fu J. Single-Stranded DNA-Binding Protein and Exogenous RecBCD Inhibitors Enhance Phage-Derived Homologous Recombination in Pseudomonas. iScience 2019; 14:1-14. [PMID: 30921732 PMCID: PMC6438905 DOI: 10.1016/j.isci.2019.03.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 12/28/2018] [Accepted: 03/07/2019] [Indexed: 12/25/2022] Open
Abstract
The limited efficiency of the available tools for genetic manipulation of Pseudomonas limits fundamental research and utilization of this genus. We explored the properties of a lambda Red-like operon (BAS) from Pseudomonas aeruginosa phage Ab31 and a Rac bacteriophage RecET-like operon (RecTEPsy) from Pseudomonas syringae pv. syringae B728a. Compared with RecTEPsy, the BAS operon was functional at a higher temperature indicating potential to be a generic system for Pseudomonas. Owing to the lack of RecBCD inhibitor in the BAS operon, we added Redγ or Pluγ and found increased recombineering efficiencies in P. aeruginosa and Pseudomonas fluorescens but not in Pseudomonas putida and P. syringae. Overexpression of single-stranded DNA-binding protein enhanced recombineering in several contexts including RecET recombination in E. coli. The utility of these systems was demonstrated by engineering P. aeruginosa genomes to create an attenuated rhamnolipid producer. Our work enhances the potential for functional genomics in Pseudomonas. The BAS operon is a generic recombineering system for Pseudomonas species Single-stranded DNA-binding proteins (SSBs) can stimulate homologous recombination The heterologous gam genes can inhibit RecBCD function in Pseudomonas
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Affiliation(s)
- Jia Yin
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235 Qingdao, China; Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, 410081 Changsha, China
| | - Wentao Zheng
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235 Qingdao, China
| | - Yunsheng Gao
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235 Qingdao, China
| | - Chanjuan Jiang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235 Qingdao, China
| | - Hongbo Shi
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235 Qingdao, China
| | - Xiaotong Diao
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235 Qingdao, China
| | - Shanshan Li
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235 Qingdao, China
| | - Hanna Chen
- Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, 410081 Changsha, China
| | - Hailong Wang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235 Qingdao, China
| | - Ruijuan Li
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235 Qingdao, China
| | - Aiying Li
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235 Qingdao, China
| | - Liqiu Xia
- Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, 410081 Changsha, China
| | - Yulong Yin
- Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, 410081 Changsha, China; Chinese Academy of Science, Institute of Subtropical Agriculture, Research Center for Healthy Breeding of Livestock and Poultry, Hunan Engineering and Research Center of Animal and Poultry Science and Key Laboratory for Agroecological Processes in Subtropical Region, Scientific Observation and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, 410125 Changsha, China
| | - A Francis Stewart
- Biotechnology Research Center, Center for Molecular and Cellular Bioengineering, Dresden University of Technology, BioInnovationsZentrum, Tatzberg 47-51, 01307 Dresden, Germany.
| | - Youming Zhang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235 Qingdao, China.
| | - Jun Fu
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235 Qingdao, China.
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15
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Choudhury R, Singh S, Arumugam S, Roguev A, Stewart AF. The Set1 complex is dimeric and acts with Jhd2 demethylation to convey symmetrical H3K4 trimethylation. Genes Dev 2019; 33:550-564. [PMID: 30842216 PMCID: PMC6499330 DOI: 10.1101/gad.322222.118] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 02/15/2019] [Indexed: 12/19/2022]
Abstract
In this study, Choudhury et al. report that yeast Set1C/COMPASS is dimeric and, consequently, symmetrically trimethylates histone 3 Lys4 (H3K4me3) on promoter nucleosomes. This presents a new paradigm for the establishment of epigenetic detail, in which dimeric methyltransferase and monomeric demethylase cooperate to eliminate asymmetry and focus symmetrical H3K4me3 onto selected nucleosomes. Epigenetic modifications can maintain or alter the inherent symmetry of the nucleosome. However, the mechanisms that deposit and/or propagate symmetry or asymmetry are not understood. Here we report that yeast Set1C/COMPASS (complex of proteins associated with Set1) is dimeric and, consequently, symmetrically trimethylates histone 3 Lys4 (H3K4me3) on promoter nucleosomes. Mutation of the dimer interface to make Set1C monomeric abolished H3K4me3 on most promoters. The most active promoters, particularly those involved in the oxidative phase of the yeast metabolic cycle, displayed H3K4me2, which is normally excluded from active promoters, and a subset of these also displayed H3K4me3. In wild-type yeast, deletion of the sole H3K4 demethylase, Jhd2, has no effect. However, in monomeric Set1C yeast, Jhd2 deletion increased H3K4me3 levels on the H3K4me2 promoters. Notably, the association of Set1C with the elongating polymerase was not perturbed by monomerization. These results imply that symmetrical H3K4 methylation is an embedded consequence of Set1C dimerism and that Jhd2 demethylates asymmetric H3K4me3. Consequently, rather than methylation and demethylation acting in opposition as logic would suggest, a dimeric methyltransferase and monomeric demethylase cooperate to eliminate asymmetry and focus symmetrical H3K4me3 onto selected nucleosomes. This presents a new paradigm for the establishment of epigenetic detail.
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Affiliation(s)
- Rupam Choudhury
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, University of Technology Dresden, 01307 Dresden, Germany
| | - Sukhdeep Singh
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, University of Technology Dresden, 01307 Dresden, Germany
| | - Senthil Arumugam
- European Molecular Biology Laboratory Australia Node for Single Molecule Science, ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| | - Assen Roguev
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, University of Technology Dresden, 01307 Dresden, Germany.,Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, California 94518, USA
| | - A Francis Stewart
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, University of Technology Dresden, 01307 Dresden, Germany
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16
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Song C, Luan J, Cui Q, Duan Q, Li Z, Gao Y, Li R, Li A, Shen Y, Li Y, Stewart AF, Zhang Y, Fu J, Wang H. Enhanced Heterologous Spinosad Production from a 79-kb Synthetic Multioperon Assembly. ACS Synth Biol 2019; 8:137-147. [PMID: 30590919 DOI: 10.1021/acssynbio.8b00402] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Refactoring biosynthetic pathways for enhanced secondary metabolite production is a central challenge for synthetic biology. Here we applied advanced DNA assembly methods and a uniform overexpression logic using constitutive promoters to achieve efficient heterologous production of the complex insecticidal macrolide spinosad. We constructed a 79-kb artificial gene cluster in which 23 biosynthetic genes were grouped into 7 operons, each with a strong constitutive promoter. Compared with the original gene cluster, the artificial gene cluster resulted in a 328-fold enhanced spinosad production in Streptomyces albus J1074. To achieve this goal, we applied the ExoCET DNA assembly method to build a plasmid from 13 GC-rich fragments with high efficiency in one step. Together with our previous direct cloning and recombineering tools, we present new synthetic biology options for refactoring large gene clusters for diverse applications.
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Affiliation(s)
- Chaoyi Song
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Ji Luan
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Qingwen Cui
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Qiuyue Duan
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Zhen Li
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Yunsheng Gao
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Ruijuan Li
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Aiying Li
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Yuemao Shen
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Yuezhong Li
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - A. Francis Stewart
- Genomics, Biotechnology Center, Technische Universität Dresden, Tatzberg 47-51, Dresden 01307, Germany
- GenArc GmbH, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Youming Zhang
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Jun Fu
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Hailong Wang
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
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17
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Tomizawa SI, Kobayashi Y, Shirakawa T, Watanabe K, Mizoguchi K, Hoshi I, Nakajima K, Nakabayashi J, Singh S, Dahl A, Alexopoulou D, Seki M, Suzuki Y, Royo H, Peters AHFM, Anastassiadis K, Stewart AF, Ohbo K. Kmt2b conveys monovalent and bivalent H3K4me3 in mouse spermatogonial stem cells at germline and embryonic promoters. Development 2018; 145:145/23/dev169102. [PMID: 30504434 DOI: 10.1242/dev.169102] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 11/01/2018] [Indexed: 12/20/2022]
Abstract
The mammalian male germline is sustained by a pool of spermatogonial stem cells (SSCs) that can transmit both genetic and epigenetic information to offspring. However, the mechanisms underlying epigenetic transmission remain unclear. The histone methyltransferase Kmt2b is highly expressed in SSCs and is required for the SSC-to-progenitor transition. At the stem-cell stage, Kmt2b catalyzes H3K4me3 at bivalent H3K27me3-marked promoters as well as at promoters of a new class of genes lacking H3K27me3, which we call monovalent. Monovalent genes are mainly activated in late spermatogenesis, whereas most bivalent genes are mainly not expressed until embryonic development. These data suggest that SSCs are epigenetically primed by Kmt2b in two distinguishable ways for the upregulation of gene expression both during the spermatogenic program and through the male germline into the embryo. Because Kmt2b is also the major H3K4 methyltransferase for bivalent promoters in embryonic stem cells, we also propose that Kmt2b has the capacity to prime stem cells epigenetically.
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Affiliation(s)
- Shin-Ichi Tomizawa
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Yuki Kobayashi
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Takayuki Shirakawa
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Kumiko Watanabe
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Keita Mizoguchi
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Ikue Hoshi
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Kuniko Nakajima
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Jun Nakabayashi
- Bioinformatics Laboratory, Advanced Medical Research Center, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Sukhdeep Singh
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47-51, 01307 Dresden, Germany
| | - Andreas Dahl
- Genome Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47-51, 01307 Dresden, Germany
| | - Dimitra Alexopoulou
- Genome Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47-51, 01307 Dresden, Germany
| | - Masahide Seki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Hélène Royo
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,Swiss Institute of Bioinformatics, 4056 Basel, Switzerland
| | - Antoine H F M Peters
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,Faculty of Sciences, University of Basel, 4058 Basel, Switzerland
| | - Konstantinos Anastassiadis
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47-51, 01307 Dresden, Germany
| | - A Francis Stewart
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47-51, 01307 Dresden, Germany
| | - Kazuyuki Ohbo
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
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18
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Li R, Helbig L, Fu J, Bian X, Herrmann J, Baumann M, Stewart AF, Müller R, Li A, Zips D, Zhang Y. Expressing cytotoxic compounds in Escherichia coli Nissle 1917 for tumor-targeting therapy. Res Microbiol 2018; 170:74-79. [PMID: 30447257 DOI: 10.1016/j.resmic.2018.11.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 10/16/2018] [Accepted: 11/03/2018] [Indexed: 10/27/2022]
Abstract
Abnormal blood vessels and hypoxic and necrotic regions are common features of solid tumors and related to the malignant phenotype and therapy resistance. Certain obligate or facultative anaerobic bacteria exhibit inherent ability to colonize and proliferate within solid tumors in vivo. Escherichia coli Nissle 1917 (EcN), a non-pathogenic probiotic in European markets, has been known to proliferate selectively in the interface between the viable and necrotic regions of solid tumors. The objective of this study was to establish a tumor-targeting therapy system using the genetically engineered EcN for targeted delivery of cytotoxic compounds, including colibactin, glidobactin and luminmide. Biosynthetic gene clusters of these cytotoxic compounds were introduced into EcN and the corresponding compounds were detected in the resultant recombinant EcN strains. The recombinant EcN showed significant cytotoxic activity in vitro and in vivo as well, and significantly suppressed the tumor growth. Together, this study confirmed efficient tumor-targeting colonization of EcN and demonstrated its potentiality in the tumor-specific delivery of cytotoxic compounds as a new tumor-targeting therapy system.
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Affiliation(s)
- Ruijuan Li
- Shandong University - Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Linda Helbig
- Experimental Radiotherapy of Tumours, OncoRay National Center for Radiation Research in Oncology, Medical Faculty and University Hospital, Dresden University of Technology, Germany
| | - Jun Fu
- Shandong University - Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China; Department of Genomics, Biotechnology Center, Dresden University of Technology, Dresden, Germany
| | - Xiaoying Bian
- Shandong University - Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China; Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Jennifer Herrmann
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Michael Baumann
- Experimental Radiotherapy of Tumours, OncoRay National Center for Radiation Research in Oncology, Medical Faculty and University Hospital, Dresden University of Technology, Germany
| | - A Francis Stewart
- Department of Genomics, Biotechnology Center, Dresden University of Technology, Dresden, Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Aiying Li
- Shandong University - Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China.
| | - Daniel Zips
- Experimental Radiotherapy of Tumours, OncoRay National Center for Radiation Research in Oncology, Medical Faculty and University Hospital, Dresden University of Technology, Germany.
| | - Youming Zhang
- Shandong University - Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China.
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19
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Chen Y, Jones KL, Anastassiadis K, Kranz A, Stewart AF, Grembecka J, Meyerson M, Ernst P. Distinct pathways affected by menin versus MLL1/MLL2 in MLL-rearranged acute myeloid leukemia. Exp Hematol 2018; 69:37-42. [PMID: 30315824 DOI: 10.1016/j.exphem.2018.10.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 10/05/2018] [Accepted: 10/06/2018] [Indexed: 01/08/2023]
Abstract
Disrupting the protein-protein interaction for molecularly targeted cancer therapeutics can be a challenging but promising strategy. Compounds that disrupt the interaction between menin, a chromatin-binding protein, and oncogenic mixed lineage leukemia fusion proteins (MLL-FPs) have shown significant promise in preclinical models of leukemia and have a high degree of selectivity for leukemia versus normal hematopoietic cells. Biochemical and structural studies demonstrate that, in addition to disrupting the menin-MLL-FP interaction, such compounds also inhibit menin-MLL1, menin-MLL2, and other menin-interacting proteins. Here, we address the degree to which disruption of menin-MLL-FP interactions or menin-MLL1/MLL2 interactions contribute to the antileukemia effect of menin inhibition. We show that Men1 deletion in MLL-AF9-transformed leukemia cells produces distinct cellular and molecular consequences compared with Mll1;Mll2 co-deletion and that compounds disrupting menin-MLL N-terminal interactions largely phenocopy menin loss. Moreover, we show that Mll1;Mll2-deficient leukemia cells exhibit enhanced sensitivity to menin interaction inhibitors, which is consistent with each regulating complementary genetic pathways. These data illustrate the heightened dependency of MLL-FPs on menin compared with wild-type MLL1/MLL2 for regulation of downstream target genes and argue that the predominant action of menin inhibitory compounds is through direct inhibition of MLL-FPs without significant contribution from MLL1/MLL2 inhibition.
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Affiliation(s)
- Yufei Chen
- Department of Pediatrics, University of Colorado, Denver/Anschutz Medical Campus. Aurora, CO, USA
| | - Kenneth L Jones
- Department of Pediatrics, University of Colorado, Denver/Anschutz Medical Campus. Aurora, CO, USA
| | - Konstantinos Anastassiadis
- Genomics and Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Andrea Kranz
- Genomics and Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - A Francis Stewart
- Genomics and Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | | | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Patricia Ernst
- Department of Pediatrics, University of Colorado, Denver/Anschutz Medical Campus. Aurora, CO, USA; Department of Pharmacology, University of Colorado, Denver/Anschutz Medical Campus. Aurora, CO, USA.
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20
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Liu J, Boehme P, Zhang W, Fu J, Yumul R, Mese K, Tsoukas R, Solanki M, Kaufmann M, Lu R, Schmidtko A, Stewart AF, Lieber A, Ehrhardt A. Human adenovirus type 17 from species D transduces endothelial cells and human CD46 is involved in cell entry. Sci Rep 2018; 8:13442. [PMID: 30194327 PMCID: PMC6128842 DOI: 10.1038/s41598-018-31713-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 08/03/2018] [Indexed: 11/09/2022] Open
Abstract
More than 70 human adenoviruses with type-dependent pathogenicity have been identified but biological information about the majority of these virus types is scarce. Here we employed multiple sequence alignments and structural information to predict receptor usage for the development of an adenoviral vector with novel biological features. We report the generation of a cloned adenovirus based on human adenovirus type 17 (HAdV17) with high sequence homology to the well characterized human adenovirus type 37 (HAdV37) that causes epidemic keratoconjunctivitis (EKC). Our study revealed that human CD46 (CD46) is involved in cell entry of HAdV17. Moreover, we found that HAdV17 infects endothelial cells (EC) in vitro including primary cells at higher efficiencies compared to the commonly used human adenovirus type 5 (HAdV5). Using a human CD46 transgenic mouse model, we observed that HAdV17 displays a broad tropism in vivo after systemic injection and that it transduces ECs in this mouse model. We conclude that the HAdV17-based vector may provide a novel platform for gene therapy.
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Affiliation(s)
- Jing Liu
- Institute for Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, Witten, Germany.,Department of Oncology and cancer immunotherapy, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Philip Boehme
- Institute for Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, Witten, Germany.,Medical Student, Department of Human Medicine, Faculty of Health, Witten/Herdecke University, Witten, Germany
| | - Wenli Zhang
- Institute for Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, Witten, Germany
| | - Jun Fu
- Shandong University-Helmholtz Institute of Biotechnoloy, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, People's Republic of China.,Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovations Zentrum, Dresden, Germany
| | - Roma Yumul
- Division for Medical Biochemistry, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, Witten, Germany
| | - Kemal Mese
- Institute for Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, Witten, Germany
| | - Raphael Tsoukas
- Institute for Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, Witten, Germany
| | - Manish Solanki
- Institute for Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, Witten, Germany.,Institute for Experimental Gene Therapy and Cancer Research (IEGT), Medical University Rostock, Rostock, Germany
| | - Michael Kaufmann
- University of Washington, Department of Medicine, Division of Medical Genetics, Seattle, USA
| | - Ruirui Lu
- Institute for Pharmakology and Toxicology, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, Witten, Germany.,Institute of Pharmacology, College of Pharmacy, Goethe University, Frankfurt am Main, Germany
| | - Achim Schmidtko
- Institute for Pharmakology and Toxicology, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, Witten, Germany.,Institute of Pharmacology, College of Pharmacy, Goethe University, Frankfurt am Main, Germany
| | - A Francis Stewart
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovations Zentrum, Dresden, Germany
| | - André Lieber
- Division for Medical Biochemistry, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, Witten, Germany
| | - Anja Ehrhardt
- Institute for Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, Witten, Germany.
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21
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Chakraborty D, Paszkowski-Rogacz M, Berger N, Ding L, Mircetic J, Fu J, Iesmantavicius V, Choudhary C, Anastassiadis K, Stewart AF, Buchholz F. lncRNA Panct1 Maintains Mouse Embryonic Stem Cell Identity by Regulating TOBF1 Recruitment to Oct-Sox Sequences in Early G1. Cell Rep 2018; 21:3012-3021. [PMID: 29241531 DOI: 10.1016/j.celrep.2017.11.045] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 10/13/2017] [Accepted: 11/13/2017] [Indexed: 11/25/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) have been implicated in diverse biological processes, including embryonic stem cell (ESC) maintenance. However, their functional mechanisms remain largely undefined. Here, we show that the lncRNA Panct1 regulates the transient recruitment of a putative X-chromosome-encoded protein A830080D01Rik, hereafter referred to as transient octamer binding factor 1 (TOBF1), to genomic sites resembling the canonical Oct-Sox motif. TOBF1 physically interacts with Panct1 and exhibits a cell-cycle-specific punctate localization in ESCs. At the chromatin level, this correlates with its recruitment to promoters of pluripotency genes. Strikingly, mutating an octamer-like motif in Panct1 RNA abrogates the strength of TOBF1 localization and recruitment to its targets. Taken together, our data reveal a tightly controlled spatial and temporal pattern of lncRNA-mediated gene regulation in a cell-cycle-dependent manner and suggest that lncRNAs might function as barcodes for identifying genomic addresses for maintaining cellular states.
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Affiliation(s)
- Debojyoti Chakraborty
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Maciej Paszkowski-Rogacz
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Nicolas Berger
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Li Ding
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Jovan Mircetic
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Jun Fu
- Genomics, Biotechnology Center, TU Dresden, BioInnovationsZentrum, Tatzberg 47, 01307 Dresden, Germany
| | - Vytautas Iesmantavicius
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Chunaram Choudhary
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Konstantinos Anastassiadis
- Stem Cell Engineering, Biotechnology Center, TU Dresden, BioInnovationsZentrum, Tatzberg 47, 01307 Dresden, Germany
| | - A Francis Stewart
- Genomics, Biotechnology Center, TU Dresden, BioInnovationsZentrum, Tatzberg 47, 01307 Dresden, Germany
| | - Frank Buchholz
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Fetscherstrasse 74, 01307 Dresden, Germany; Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany; German Cancer Research Center (DKFZ), Heidelberg and German Cancer Consortium (DKTK) partner site Dresden, 01307 Dresden, Germany; National Center for Tumor Diseases (NCT), University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany.
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22
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Zhang W, Fu J, Liu J, Wang H, Schiwon M, Janz S, Schaffarczyk L, von der Goltz L, Ehrke-Schulz E, Dörner J, Solanki M, Boehme P, Bergmann T, Lieber A, Lauber C, Dahl A, Petzold A, Zhang Y, Stewart AF, Ehrhardt A. An Engineered Virus Library as a Resource for the Spectrum-wide Exploration of Virus and Vector Diversity. Cell Rep 2018; 19:1698-1709. [PMID: 28538186 DOI: 10.1016/j.celrep.2017.05.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 04/12/2017] [Accepted: 05/02/2017] [Indexed: 12/18/2022] Open
Abstract
Adenoviruses (Ads) are large human-pathogenic double-stranded DNA (dsDNA) viruses presenting an enormous natural diversity associated with a broad variety of diseases. However, only a small fraction of adenoviruses has been explored in basic virology and biomedical research, highlighting the need to develop robust and adaptable methodologies and resources. We developed a method for high-throughput direct cloning and engineering of adenoviral genomes from different sources utilizing advanced linear-linear homologous recombination (LLHR) and linear-circular homologous recombination (LCHR). We describe 34 cloned adenoviral genomes originating from clinical samples, which were characterized by next-generation sequencing (NGS). We anticipate that this recombineering strategy and the engineered adenovirus library will provide an approach to study basic and clinical virology. High-throughput screening (HTS) of the reporter-tagged Ad library in a panel of cell lines including osteosarcoma disease-specific cell lines revealed alternative virus types with enhanced transduction and oncolysis efficiencies. This highlights the usefulness of this resource.
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Affiliation(s)
- Wenli Zhang
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Jun Fu
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, People's Republic of China; Genomics, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | - Jing Liu
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Hailong Wang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, People's Republic of China; Genomics, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | - Maren Schiwon
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Sebastian Janz
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Lukas Schaffarczyk
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Lukas von der Goltz
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Eric Ehrke-Schulz
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Johannes Dörner
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Manish Solanki
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Philip Boehme
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Thorsten Bergmann
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Andre Lieber
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195-7720, USA
| | - Chris Lauber
- Institute for Medical Informatics and Biometry, Carl Gustav Carus, Faculty of Medicine, Technische Universität Dresden, 01307 Dresden, Germany
| | - Andreas Dahl
- Deep Sequencing, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | - Andreas Petzold
- Deep Sequencing, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | - Youming Zhang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, People's Republic of China.
| | - A Francis Stewart
- Genomics, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany.
| | - Anja Ehrhardt
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany.
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23
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Hanna CW, Taudt A, Huang J, Gahurova L, Kranz A, Andrews S, Dean W, Stewart AF, Colomé-Tatché M, Kelsey G. MLL2 conveys transcription-independent H3K4 trimethylation in oocytes. Nat Struct Mol Biol 2018; 25:73-82. [DOI: 10.1038/s41594-017-0013-5] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 11/15/2017] [Indexed: 01/03/2023]
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24
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Wang H, Li Z, Jia R, Yin J, Li A, Xia L, Yin Y, Müller R, Fu J, Stewart AF, Zhang Y. ExoCET: exonuclease in vitro assembly combined with RecET recombination for highly efficient direct DNA cloning from complex genomes. Nucleic Acids Res 2017; 46:2697. [PMID: 29272442 PMCID: PMC5861451 DOI: 10.1093/nar/gkx1296] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Hailong Wang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China
| | - Zhen Li
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China
| | - Ruonan Jia
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China
| | - Jia Yin
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China
| | - Aiying Li
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China
| | - Liqiu Xia
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, 410081 Changsha, People's Republic of China
| | - Yulong Yin
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China.,State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, 410081 Changsha, People's Republic of China.,Key Laboratory of Subtropical Agro-ecology, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, Hunan Province 410125, People's Republic of China
| | - Rolf Müller
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China.,Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Pharmaceutical Biotechnology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Jun Fu
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China
| | - A Francis Stewart
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47-51, 01307 Dresden, Germany
| | - Youming Zhang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China
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25
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Baker O, Tsurkan S, Fu J, Klink B, Rump A, Obst M, Kranz A, Schröck E, Anastassiadis K, Stewart AF. The contribution of homology arms to nuclease-assisted genome engineering. Nucleic Acids Res 2017; 45:8105-8115. [PMID: 28582546 PMCID: PMC5570031 DOI: 10.1093/nar/gkx497] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 05/30/2017] [Indexed: 01/29/2023] Open
Abstract
Designer nucleases like CRISPR/Cas9 enable fluent site-directed damage or small mutations in many genomes. Strategies for their use to achieve more complex tasks like regional exchanges for gene humanization or the establishment of conditional alleles are still emerging. To optimize Cas9-assisted targeting, we measured the relationship between targeting frequency and homology length in targeting constructs using a hypoxanthine-guanine phosphoribosyl-transferase assay in mouse embryonic stem cells. Targeting frequency with supercoiled plasmids improved steeply up to 2 kb total homology and continued to increase with even longer homology arms, thereby implying that Cas9-assisted targeting efficiencies can be improved using homology arms of 1 kb or greater. To humanize the Kmt2d gene, we built a hybrid mouse/human targeting construct in a bacterial artificial chromosome by recombineering. To simplify the possible outcomes, we employed a single Cas9 cleavage strategy and best achieved the intended 42 kb regional exchange with a targeting construct including a very long homology arm to recombine ∼42 kb away from the cleavage site. We recommend the use of long homology arm targeting constructs for accurate and efficient complex genome engineering, particularly when combined with the simplifying advantages of using just one Cas9 cleavage at the genome target site.
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Affiliation(s)
- Oliver Baker
- Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany.,Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Sarah Tsurkan
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Jun Fu
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany.,Shandong University-Helmholtz Joint Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China
| | - Barbara Klink
- Institute for Clinical Genetics, Faculty of Medicine, Carl Gustav Carus, Technische Universität Dresden, Fetscherstrasse 74, Dresden 01307, Germany
| | - Andreas Rump
- Institute for Clinical Genetics, Faculty of Medicine, Carl Gustav Carus, Technische Universität Dresden, Fetscherstrasse 74, Dresden 01307, Germany
| | - Mandy Obst
- Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany.,Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Andrea Kranz
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Evelin Schröck
- Institute for Clinical Genetics, Faculty of Medicine, Carl Gustav Carus, Technische Universität Dresden, Fetscherstrasse 74, Dresden 01307, Germany
| | - Konstantinos Anastassiadis
- Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - A Francis Stewart
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
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26
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Singh S, Hein MY, Stewart AF. msVolcano: A flexible web application for visualizing quantitative proteomics data. Proteomics 2017; 16:2491-4. [PMID: 27440201 PMCID: PMC5096246 DOI: 10.1002/pmic.201600167] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 07/06/2016] [Accepted: 07/15/2016] [Indexed: 02/05/2023]
Abstract
We introduce msVolcano, a web application for the visualization of label‐free mass spectrometric data. It is optimized for the output of the MaxQuant data analysis pipeline of interactomics experiments and generates volcano plots with lists of interacting proteins. The user can optimize the cutoff values to find meaningful significant interactors for the tagged protein of interest. Optionally, stoichiometries of interacting proteins can be calculated. Several customization options are provided to the user for flexibility, and publication‐quality outputs can also be downloaded (tabular and graphical). Availability: msVolcano is implemented in R Statistical language using Shiny. It can be accessed freely at http://projects.biotec.tu-dresden.de/msVolcano/
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Affiliation(s)
- Sukhdeep Singh
- Genomics, Biotechnology Center, Technische Universität Dresden, Dresden, Germany.
| | - Marco Y Hein
- Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - A Francis Stewart
- Genomics, Biotechnology Center, Technische Universität Dresden, Dresden, Germany
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27
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Bian X, Tang B, Yu Y, Tu Q, Gross F, Wang H, Li A, Fu J, Shen Y, Li YZ, Stewart AF, Zhao G, Ding X, Müller R, Zhang Y. Heterologous Production and Yield Improvement of Epothilones in Burkholderiales Strain DSM 7029. ACS Chem Biol 2017; 12:1805-1812. [PMID: 28467833 DOI: 10.1021/acschembio.7b00097] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The cloning of microbial natural product biosynthetic gene clusters and their heterologous expression in a suitable host have proven to be a feasible approach to improve the yield of valuable natural products and to begin mining cryptic natural products in microorganisms. Myxobacteria are a prolific source of novel bioactive natural products with only limited choices of heterologous hosts that have been exploited. Here, we describe the use of Burkholderiales strain DSM 7029 as a potential heterologous host for the functional expression of myxobacterial secondary metabolites. Using a newly established electroporation procedure, the 56 kb epothilone biosynthetic gene cluster from the myxobacterium Sorangium cellulosum was introduced into the chromosome of strain DSM 7029 by transposition. Production of epothilones A, B, C, and D was detected despite their yields being low. Optimization of the medium, introduction of the exogenous methylmalonyl-CoA biosynthetic pathway, and overexpression of rare tRNA genes resulted in an approximately 75-fold increase in the total yields of epothilones to 307 μg L-1. These results show that strain DSM 7029 has the potential to produce epothilones with reasonable titers and might be a broadly applicable host for the heterologous expression of other myxobacterial polyketide synthases and nonribosomal peptide synthetases, expediting the process of genome mining.
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Affiliation(s)
- Xiaoying Bian
- Shandong
University−Helmholtz Institute of Biotechnology, State Key
Laboratory of Microbial Technology, School of Life Science, Shandong University, Qingdao 266235, China
- Department
of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Saarland University, 66123 Saarbrücken, Germany
| | - Biao Tang
- Collaborative
Innovation Center for Genetics and Development, State Key Laboratory
of Genetic Engineering, Department of Microbiology, School of Life
Sciences, Fudan University, Shanghai 200433, China
| | - Yucong Yu
- Collaborative
Innovation Center for Genetics and Development, State Key Laboratory
of Genetic Engineering, Department of Microbiology, School of Life
Sciences, Fudan University, Shanghai 200433, China
| | - Qiang Tu
- Shandong
University−Helmholtz Institute of Biotechnology, State Key
Laboratory of Microbial Technology, School of Life Science, Shandong University, Qingdao 266235, China
- Department
of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Saarland University, 66123 Saarbrücken, Germany
| | - Frank Gross
- Genomics,
Biotechnology Center, Technische Universität Dresden, Dresden 01062, Germany
| | - Hailong Wang
- Shandong
University−Helmholtz Institute of Biotechnology, State Key
Laboratory of Microbial Technology, School of Life Science, Shandong University, Qingdao 266235, China
| | - Aiying Li
- Shandong
University−Helmholtz Institute of Biotechnology, State Key
Laboratory of Microbial Technology, School of Life Science, Shandong University, Qingdao 266235, China
| | - Jun Fu
- Shandong
University−Helmholtz Institute of Biotechnology, State Key
Laboratory of Microbial Technology, School of Life Science, Shandong University, Qingdao 266235, China
- Genomics,
Biotechnology Center, Technische Universität Dresden, Dresden 01062, Germany
| | - Yuemao Shen
- Shandong
University−Helmholtz Institute of Biotechnology, State Key
Laboratory of Microbial Technology, School of Life Science, Shandong University, Qingdao 266235, China
| | - Yue-zhong Li
- Shandong
University−Helmholtz Institute of Biotechnology, State Key
Laboratory of Microbial Technology, School of Life Science, Shandong University, Qingdao 266235, China
| | - A. Francis Stewart
- Genomics,
Biotechnology Center, Technische Universität Dresden, Dresden 01062, Germany
| | - Guoping Zhao
- Collaborative
Innovation Center for Genetics and Development, State Key Laboratory
of Genetic Engineering, Department of Microbiology, School of Life
Sciences, Fudan University, Shanghai 200433, China
- CAS
Key Laboratory of Synthetic Biology, Institute of Plant Physiology
and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xiaoming Ding
- Collaborative
Innovation Center for Genetics and Development, State Key Laboratory
of Genetic Engineering, Department of Microbiology, School of Life
Sciences, Fudan University, Shanghai 200433, China
| | - Rolf Müller
- Department
of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Saarland University, 66123 Saarbrücken, Germany
| | - Youming Zhang
- Shandong
University−Helmholtz Institute of Biotechnology, State Key
Laboratory of Microbial Technology, School of Life Science, Shandong University, Qingdao 266235, China
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28
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Brici D, Zhang Q, Reinhardt S, Dahl A, Hartmann H, Schmidt K, Goveas N, Huang J, Gahurova L, Kelsey G, Anastassiadis K, Stewart AF, Kranz A. Setd1b, encoding a histone 3 lysine 4 methyltransferase, is a maternal effect gene required for the oogenic gene expression program. Development 2017; 144:2606-2617. [PMID: 28619824 DOI: 10.1242/dev.143347] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 06/02/2017] [Indexed: 12/16/2022]
Abstract
Germ cell development involves major reprogramming of the epigenome to prime the zygote for totipotency. Histone 3 lysine 4 (H3K4) methylations are universal epigenetic marks mediated in mammals by six H3K4 methyltransferases related to fly Trithorax, including two yeast Set1 orthologs: Setd1a and Setd1b. Whereas Setd1a plays no role in oogenesis, we report that Setd1b deficiency causes female sterility in mice. Oocyte-specific Gdf9-iCre conditional knockout (Setd1bGdf9 cKO) ovaries develop through all stages; however, follicular loss accumulated with age and unfertilized metaphase II (MII) oocytes exhibited irregularities of the zona pellucida and meiotic spindle. Most Setd1bGdf9 cKO zygotes remained in the pronuclear stage and displayed polyspermy in the perivitelline space. Expression profiling of Setd1bGdf9 cKO MII oocytes revealed (1) that Setd1b promotes the expression of the major oocyte transcription factors including Obox1, 2, 5, 7, Meis2 and Sall4; and (2) twice as many mRNAs were upregulated than downregulated, suggesting that Setd1b also promotes the expression of negative regulators of oocyte development with multiple Zfp-KRAB factors implicated. Together, these findings indicate that Setd1b serves as maternal effect gene through regulation of the oocyte gene expression program.
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Affiliation(s)
- David Brici
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Qinyu Zhang
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Susanne Reinhardt
- Deep Sequencing Group SFB 655, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | - Andreas Dahl
- Deep Sequencing Group SFB 655, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | - Hella Hartmann
- Light Microscopy Core Facility of the Biotechnology Center/Center for Regenerative Therapies Dresden, Technische Universität Dresden, 01307 Dresden, Germany
| | - Kerstin Schmidt
- Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Neha Goveas
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Jiahao Huang
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Lenka Gahurova
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Gavin Kelsey
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Konstantinos Anastassiadis
- Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - A Francis Stewart
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Andrea Kranz
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
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29
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Chen Y, Anastassiadis K, Kranz A, Stewart AF, Arndt K, Waskow C, Yokoyama A, Jones K, Neff T, Lee Y, Ernst P. MLL2, Not MLL1, Plays a Major Role in Sustaining MLL-Rearranged Acute Myeloid Leukemia. Cancer Cell 2017; 31:755-770.e6. [PMID: 28609655 PMCID: PMC5598468 DOI: 10.1016/j.ccell.2017.05.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Revised: 03/09/2017] [Accepted: 05/05/2017] [Indexed: 01/11/2023]
Abstract
The MLL1 histone methyltransferase gene undergoes many distinct chromosomal rearrangements to yield poor-prognosis leukemia. The remaining wild-type allele is most commonly, but not always, retained. To what extent the wild-type allele contributes to leukemogenesis is unclear. Here we show, using rigorous, independent animal models, that endogenous MLL1 is dispensable for MLL-rearranged leukemia. Potential redundancy was addressed by co-deleting the closest paralog, Mll2. Surprisingly, Mll2 deletion alone had a significant impact on survival of MLL-AF9-transformed cells, and additional Mll1 loss further reduced viability and proliferation. We show that MLL1/MLL2 collaboration is not through redundancy, but regulation of distinct pathways. These findings highlight the relevance of MLL2 as a drug target in MLL-rearranged leukemia and suggest its broader significance in AML.
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Affiliation(s)
- Yufei Chen
- Department of Pediatrics, Section of Hematology/Oncology/BMT, University of Colorado, Denver/Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Konstantinos Anastassiadis
- Genomics and Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, BioInnovations Zentrum, Tatzberg 47, Dresden 01307, Germany
| | - Andrea Kranz
- Genomics and Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, BioInnovations Zentrum, Tatzberg 47, Dresden 01307, Germany
| | - A Francis Stewart
- Genomics and Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, BioInnovations Zentrum, Tatzberg 47, Dresden 01307, Germany
| | - Kathrin Arndt
- Regeneration in Hematopoiesis and Animal Models in Hematopoiesis, Institute for Immunology, Medical Faculty, Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Claudia Waskow
- Regeneration in Hematopoiesis and Animal Models in Hematopoiesis, Institute for Immunology, Medical Faculty, Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Akihiko Yokoyama
- Tsuruoka Metabolomics Laboratory, National Cancer Center, Mizukami 246-2, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Kenneth Jones
- Department of Pediatrics, Section of Hematology/Oncology/BMT, University of Colorado, Denver/Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Tobias Neff
- Department of Pediatrics, Section of Hematology/Oncology/BMT, University of Colorado, Denver/Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Yoo Lee
- Department of Pediatrics, Section of Hematology/Oncology/BMT, University of Colorado, Denver/Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Patricia Ernst
- Department of Pediatrics, Section of Hematology/Oncology/BMT, University of Colorado, Denver/Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pharmacology, University of Colorado, Denver/Anschutz Medical Campus, Aurora, CO 80045, USA.
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30
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Tasdogan A, Kumar S, Allies G, Bausinger J, Beckel F, Hofemeister H, Mulaw M, Madan V, Scharffetter-Kochanek K, Feuring-Buske M, Doehner K, Speit G, Stewart AF, Fehling HJ. DNA Damage-Induced HSPC Malfunction Depends on ROS Accumulation Downstream of IFN-1 Signaling and Bid Mobilization. Cell Stem Cell 2017; 20:415. [DOI: 10.1016/j.stem.2017.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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31
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Shen EY, Jiang Y, Javidfar B, Kassim B, Loh YHE, Ma Q, Mitchell AC, Pothula V, Stewart AF, Ernst P, Yao WD, Martin G, Shen L, Jakovcevski M, Akbarian S. Neuronal Deletion of Kmt2a/Mll1 Histone Methyltransferase in Ventral Striatum is Associated with Defective Spike-Timing-Dependent Striatal Synaptic Plasticity, Altered Response to Dopaminergic Drugs, and Increased Anxiety. Neuropsychopharmacology 2016; 41:3103-3113. [PMID: 27485686 PMCID: PMC5101561 DOI: 10.1038/npp.2016.144] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 07/25/2016] [Accepted: 07/27/2016] [Indexed: 12/27/2022]
Abstract
Lysine (K) methyltransferase 2a (Kmt2a) and other regulators of H3 lysine 4 methylation, a histone modification enriched at promoters and enhancers, are widely expressed throughout the brain, but molecular and cellular phenotypes in subcortical areas remain poorly explored. We report that Kmt2a conditional deletion in postnatal forebrain is associated with excessive nocturnal activity and with absent or blunted responses to stimulant and dopaminergic agonist drugs, in conjunction with near-complete loss of spike-timing-dependent long-term potentiation in medium spiny neurons (MSNs). Selective ablation of Kmt2a, but not the ortholog Kmt2b, in adult ventral striatum/nucleus accumbens neurons markedly increased anxiety scores in multiple behavioral paradigms. Striatal transcriptome sequencing in adult mutants identified 262 Kmt2a-sensitive genes, mostly downregulated in Kmt2a-deficient mice. Transcriptional repression includes the 5-Htr2a serotonin receptor, strongly associated with anxiety- and depression-related disorders in human and animal models. Consistent with the role of Kmt2a in promoting gene expression, the transcriptional regulators Bahcc1, Isl1, and Sp9 were downregulated and affected by H3K4 promoter hypomethylation. Therefore, Kmt2a regulates synaptic plasticity in striatal neurons and provides an epigenetic drug target for anxiety and dopamine-mediated behaviors.
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Affiliation(s)
| | - Yan Jiang
- Department of Psychiatry, New York, NY, USA
| | | | | | - Yong-Hwee E Loh
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, Hess Center for Science and Medicine, New York, NY, USA
| | - Qi Ma
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | | | | | | | - Patricia Ernst
- University of Colorado School of Medicine, Department of Pediatrics, Aurora, CO, USA
| | - Wei-Dong Yao
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Gilles Martin
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Li Shen
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, Hess Center for Science and Medicine, New York, NY, USA
| | - Mira Jakovcevski
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany,Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Kraepelinstrasse 2, 80804 Munich, Germany, Tel: +49 89 30622 643, E-mail:
| | - Schahram Akbarian
- Department of Psychiatry, New York, NY, USA,Icahn School of Medicine at Mount Sinai, Hess Center for Science and Medicine, Floor 9 Room 105, 1470 Madison Avenue, New York, NY 10029, USA, Tel: +1 212 824 8984, E-mail:
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32
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Ramakrishnan S, Subramaniam S, Stewart AF, Grundmeier G, Keller A. Regular Nanoscale Protein Patterns via Directed Adsorption through Self-Assembled DNA Origami Masks. ACS Appl Mater Interfaces 2016; 8:31239-31247. [PMID: 27779405 DOI: 10.1021/acsami.6b10535] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
DNA origami has become a widely used method for synthesizing well-defined nanostructures with promising applications in various areas of nanotechnology, biophysics, and medicine. Recently, the possibility to transfer the shape of single DNA origami nanostructures into different materials via molecular lithography approaches has received growing interest due to the great structural control provided by the DNA origami technique. Here, we use ordered monolayers of DNA origami nanostructures with internal cavities on mica surfaces as molecular lithography masks for the fabrication of regular protein patterns over large surface areas. Exposure of the masked sample surface to negatively charged proteins results in the directed adsorption of the proteins onto the exposed surface areas in the holes of the mask. By controlling the buffer and adsorption conditions, the protein coverage of the exposed areas can be varied from single proteins to densely packed monolayers. To demonstrate the versatility of this approach, regular nanopatterns of four different proteins are fabricated: the single-strand annealing proteins Redβ and Sak, the iron-storage protein ferritin, and the blood protein bovine serum albumin (BSA). We furthermore demonstrate the desorption of the DNA origami mask after directed protein adsorption, which may enable the fabrication of hierarchical patterns composed of different protein species. Because selectivity in adsorption is achieved by electrostatic interactions between the proteins and the exposed surface areas, this approach may enable also the large-scale patterning of other charged molecular species or even nanoparticles.
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Affiliation(s)
- Saminathan Ramakrishnan
- Technical and Macromolecular Chemistry, Paderborn University , Warburger Strasse 100, 33098 Paderborn, Germany
| | - Sivaraman Subramaniam
- Department of Genomics, Biotechnology Center, Technische Universität Dresden , Tatzberg 47-51, 01307 Dresden, Germany
| | - A Francis Stewart
- Department of Genomics, Biotechnology Center, Technische Universität Dresden , Tatzberg 47-51, 01307 Dresden, Germany
| | - Guido Grundmeier
- Technical and Macromolecular Chemistry, Paderborn University , Warburger Strasse 100, 33098 Paderborn, Germany
| | - Adrian Keller
- Technical and Macromolecular Chemistry, Paderborn University , Warburger Strasse 100, 33098 Paderborn, Germany
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33
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Subramaniam S, Erler A, Fu J, Kranz A, Tang J, Gopalswamy M, Ramakrishnan S, Keller A, Grundmeier G, Müller D, Sattler M, Stewart AF. DNA annealing by Redβ is insufficient for homologous recombination and the additional requirements involve intra- and inter-molecular interactions. Sci Rep 2016; 6:34525. [PMID: 27708411 PMCID: PMC5052646 DOI: 10.1038/srep34525] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 08/15/2016] [Indexed: 01/09/2023] Open
Abstract
Single strand annealing proteins (SSAPs) like Redβ initiate homologous recombination by annealing complementary DNA strands. We show that C-terminally truncated Redβ, whilst still able to promote annealing and nucleoprotein filament formation, is unable to mediate homologous recombination. Mutations of the C-terminal domain were evaluated using both single- and double stranded (ss and ds) substrates in recombination assays. Mutations of critical amino acids affected either dsDNA recombination or both ssDNA and dsDNA recombination indicating two separable functions, one of which is critical for dsDNA recombination and the second for recombination per se. As evaluated by co-immunoprecipitation experiments, the dsDNA recombination function relates to the Redα-Redβ protein-protein interaction, which requires not only contacts in the C-terminal domain but also a region near the N-terminus. Because the nucleoprotein filament formed with C-terminally truncated Redβ has altered properties, the second C-terminal function could be due to an interaction required for functional filaments. Alternatively the second C-terminal function could indicate a requirement for a Redβ-host factor interaction. These data further advance the model for Red recombination and the proposition that Redβ and RAD52 SSAPs share ancestral and mechanistic roots.
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Affiliation(s)
| | - Axel Erler
- Genomics, Biotechnology Center, TU Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Jun Fu
- Genomics, Biotechnology Center, TU Dresden, Tatzberg 47/49, 01307 Dresden, Germany.,Shandong University-Helmholtz Joint Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China
| | - Andrea Kranz
- Genomics, Biotechnology Center, TU Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Jing Tang
- Genomics, Biotechnology Center, TU Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Mohanraj Gopalswamy
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany and Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technische Universität München, Lichtenbergstr.4, 85747 Garching, Germany
| | - Saminathan Ramakrishnan
- Technical and Macromolecular Chemistry, University of Paderborn, Warburger Str. 100 33098 Paderborn, Germany
| | - Adrian Keller
- Technical and Macromolecular Chemistry, University of Paderborn, Warburger Str. 100 33098 Paderborn, Germany
| | - Guido Grundmeier
- Technical and Macromolecular Chemistry, University of Paderborn, Warburger Str. 100 33098 Paderborn, Germany
| | - Daniel Müller
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstraße 26, 4058 Basel, Switzerland
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany and Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technische Universität München, Lichtenbergstr.4, 85747 Garching, Germany
| | - A Francis Stewart
- Genomics, Biotechnology Center, TU Dresden, Tatzberg 47/49, 01307 Dresden, Germany
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Tasdogan A, Kumar S, Allies G, Bausinger J, Beckel F, Hofemeister H, Mulaw M, Madan V, Scharffetter-Kochanek K, Feuring-Buske M, Doehner K, Speit G, Stewart AF, Fehling HJ. DNA Damage-Induced HSPC Malfunction Depends on ROS Accumulation Downstream of IFN-1 Signaling and Bid Mobilization. Cell Stem Cell 2016; 19:752-767. [PMID: 27641306 DOI: 10.1016/j.stem.2016.08.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 06/12/2016] [Accepted: 08/09/2016] [Indexed: 01/02/2023]
Abstract
Mouse mutants with an impaired DNA damage response frequently exhibit a set of remarkably similar defects in the HSPC compartment that are of largely unknown molecular basis. Using Mixed-Lineage-Leukemia-5 (Mll5)-deficient mice as prototypical examples, we have identified a mechanistic pathway linking DNA damage and HSPC malfunction. We show that Mll5 deficiency results in accumulation of DNA damage and reactive oxygen species (ROS) in HSPCs. Reduction of ROS efficiently reverses hematopoietic defects, establishing ROS as a major cause of impaired HSPC function. The Ink4a/Arf locus also contributes to HSPC phenotypes, at least in part via promotion of ROS. Strikingly, toxic ROS levels in Mll5-/- mice are critically dependent on type 1 interferon (IFN-1) signaling, which triggers mitochondrial accumulation of full-length Bid. Genetic inactivation of Bid diminishes ROS levels and reverses HSPC defects in Mll5-/- mice. Overall, therefore, our findings highlight an unexpected IFN-1 > Bid > ROS pathway underlying DNA damage-associated HSPC malfunction.
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Affiliation(s)
- Alpaslan Tasdogan
- Institute of Immunology, University Hospital, 89081 Ulm, Germany; Department of Dermatology, University Hospital, 89081 Ulm, Germany
| | - Suresh Kumar
- Institute of Immunology, University Hospital, 89081 Ulm, Germany
| | - Gabriele Allies
- Institute of Immunology, University Hospital, 89081 Ulm, Germany
| | - Julia Bausinger
- Institute of Human Genetics, University Hospital, 89081 Ulm, Germany
| | - Franziska Beckel
- Institute of Immunology, University Hospital, 89081 Ulm, Germany
| | - Helmut Hofemeister
- Genomics, BioInnovations Zentrum, Technische Universität, 01307 Dresden, Germany
| | - Medhanie Mulaw
- Institute of Experimental Cancer Research, University Clinics, 89081 Ulm, Germany
| | - Vikas Madan
- Institute of Immunology, University Hospital, 89081 Ulm, Germany
| | | | | | - Konstanze Doehner
- Department of Internal Medicine III, University Hospital, 89081 Ulm, Germany
| | - Günter Speit
- Institute of Human Genetics, University Hospital, 89081 Ulm, Germany
| | - A Francis Stewart
- Genomics, BioInnovations Zentrum, Technische Universität, 01307 Dresden, Germany
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Baker O, Gupta A, Obst M, Zhang Y, Anastassiadis K, Fu J, Stewart AF. RAC-tagging: Recombineering And Cas9-assisted targeting for protein tagging and conditional analyses. Sci Rep 2016; 6:25529. [PMID: 27216209 PMCID: PMC4877586 DOI: 10.1038/srep25529] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 04/13/2016] [Indexed: 11/30/2022] Open
Abstract
A fluent method for gene targeting to establish protein tagged and ligand inducible conditional loss-of-function alleles is described. We couple new recombineering applications for one-step cloning of gRNA oligonucleotides and rapid generation of short-arm (~1 kb) targeting constructs with the power of Cas9-assisted targeting to establish protein tagged alleles in embryonic stem cells at high efficiency. RAC (Recombineering And Cas9)-tagging with Venus, BirM, APEX2 and the auxin degron is facilitated by a recombineering-ready plasmid series that permits the reuse of gene-specific reagents to insert different tags. Here we focus on protein tagging with the auxin degron because it is a ligand-regulated loss-of-function strategy that is rapid and reversible. Furthermore it includes the additional challenge of biallelic targeting. Despite high frequencies of monoallelic RAC-targeting, we found that simultaneous biallelic targeting benefits from long-arm (>4 kb) targeting constructs. Consequently an updated recombineering pipeline for fluent generation of long arm targeting constructs is also presented.
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Affiliation(s)
- Oliver Baker
- Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Ashish Gupta
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Mandy Obst
- Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Youming Zhang
- Shandong University–Helmholtz Joint Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Shanda Nanlu 27, 250100 Jinan, People’s Republic of China
| | - Konstantinos Anastassiadis
- Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Jun Fu
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
- Shandong University–Helmholtz Joint Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Shanda Nanlu 27, 250100 Jinan, People’s Republic of China
| | - A. Francis Stewart
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
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36
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Kantidakis T, Saponaro M, Mitter R, Horswell S, Kranz A, Boeing S, Aygün O, Kelly GP, Matthews N, Stewart A, Stewart AF, Svejstrup JQ. Mutation of cancer driver MLL2 results in transcription stress and genome instability. Genes Dev 2016; 30:408-20. [PMID: 26883360 PMCID: PMC4762426 DOI: 10.1101/gad.275453.115] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 01/15/2016] [Indexed: 12/12/2022]
Abstract
Genome instability is a recurring feature of tumorigenesis. Mutation in MLL2, encoding a histone methyltransferase, is a driver in numerous different cancer types, but the mechanism is unclear. Here, we present evidence that MLL2 mutation results in genome instability. Mouse cells in which MLL2 gene deletion can be induced display elevated levels of sister chromatid exchange, gross chromosomal aberrations, 53BP1 foci, and micronuclei. Human MLL2 knockout cells are characterized by genome instability as well. Interestingly, MLL2 interacts with RNA polymerase II (RNAPII) and RECQL5, and, although MLL2 mutated cells have normal overall H3K4me levels in genes, nucleosomes in the immediate vicinity of RNAPII are hypomethylated. Importantly, MLL2 mutated cells display signs of substantial transcription stress, and the most affected genes overlap with early replicating fragile sites, show elevated levels of γH2AX, and suffer frequent mutation. The requirement for MLL2 in the maintenance of genome stability in genes helps explain its widespread role in cancer and points to transcription stress as a strong driver in tumorigenesis.
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Affiliation(s)
- Theodoros Kantidakis
- Mechanisms of Transcription Laboratory, Clare Hall Laboratories, The Francis Crick Institute, South Mimms EN6 3LD, United Kingdom
| | - Marco Saponaro
- Mechanisms of Transcription Laboratory, Clare Hall Laboratories, The Francis Crick Institute, South Mimms EN6 3LD, United Kingdom
| | - Richard Mitter
- Bioinformatics and Biostatistics Group, The Francis Crick Institute, London WC2A 3LY, United Kingdom
| | - Stuart Horswell
- Bioinformatics and Biostatistics Group, The Francis Crick Institute, London WC2A 3LY, United Kingdom
| | - Andrea Kranz
- Biotechnologisches Zentrum, Technische Universität Dresden, 01062 Dresden, Germany
| | - Stefan Boeing
- Mechanisms of Transcription Laboratory, Clare Hall Laboratories, The Francis Crick Institute, South Mimms EN6 3LD, United Kingdom
| | - Ozan Aygün
- Mechanisms of Transcription Laboratory, Clare Hall Laboratories, The Francis Crick Institute, South Mimms EN6 3LD, United Kingdom
| | - Gavin P Kelly
- Bioinformatics and Biostatistics Group, The Francis Crick Institute, London WC2A 3LY, United Kingdom
| | - Nik Matthews
- Advanced Sequencing Facility, The Francis Crick Institute, London WC2A 3LY, United Kingdom
| | - Aengus Stewart
- Bioinformatics and Biostatistics Group, The Francis Crick Institute, London WC2A 3LY, United Kingdom
| | - A Francis Stewart
- Biotechnologisches Zentrum, Technische Universität Dresden, 01062 Dresden, Germany
| | - Jesper Q Svejstrup
- Mechanisms of Transcription Laboratory, Clare Hall Laboratories, The Francis Crick Institute, South Mimms EN6 3LD, United Kingdom
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Yin J, Wang H, Li R, Ravichandran V, Bian X, Li A, Tu Q, Francis Stewart A, Fu J, Zhang Y. A Practical Guide to Recombineering in Photorhabdus and Xenorhabdus. Curr Top Microbiol Immunol 2016; 402:195-213. [PMID: 28154939 DOI: 10.1007/82_2016_57] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Fluent genetic manipulation of prokaryote genomes is still limited to only a few commonly used hosts. Ideally the advanced technologies available for cloning into recombinant Escherichia coli should also be applicable in other prokaryotes. In particular, 'recombineering' is mediated by the lambda Red operon that permits fluent and precise engineering of the E. coli genome and associated recombinant DNA. The major limitation is that host-specific phage-derived recombination systems are also required in more distant species. Recently, an endogenous Red-like operon Pluγβα has been reported to be effective in both Photorhabdus and Xenorhabdus bacteria. The Pluγβα recombineering system is based on three host-specific phage proteins from Photorhabdus luminescens, Plu2935, Plu2936, and Plu2934, which are functional analogs of Redβ, Redα, and Redγ, respectively. In this chapter, we provide a comprehensive and up-to-date method for P. luminescens and Xenorhabdus stockiae genome engineering via the Pluγβα recombineering system. In order to facilitate the rapid construction of knock-in vectors, recET-mediated recombineering is incorporated in the pipeline. Concerted recET system in E. coli with Pluγβα system in Photorhabdus and Xenorhabdus could promote reverse genetics, functional genomics, and bioprospecting research for these two genera.
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Affiliation(s)
- Jia Yin
- Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, Jinan, 250100, People's Republic of China
| | - Hailong Wang
- Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, Jinan, 250100, People's Republic of China
| | - Ruijuan Li
- Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, Jinan, 250100, People's Republic of China
| | - Vinothkannan Ravichandran
- Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, Jinan, 250100, People's Republic of China
| | - Xiaoying Bian
- Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, Jinan, 250100, People's Republic of China
| | - Aiying Li
- Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, Jinan, 250100, People's Republic of China
| | - Qiang Tu
- Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, Jinan, 250100, People's Republic of China
| | - A Francis Stewart
- Department of Genomics, Dresden University of Technology, BioInnovations-Zentrum, Tatzberg 47-51, 01307, Dresden, Germany
| | - Jun Fu
- Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, Jinan, 250100, People's Republic of China. .,Department of Genomics, Dresden University of Technology, BioInnovations-Zentrum, Tatzberg 47-51, 01307, Dresden, Germany.
| | - Youming Zhang
- Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, Jinan, 250100, People's Republic of China.
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Bögershausen N, Tsai IC, Pohl E, Kiper PÖS, Beleggia F, Percin EF, Keupp K, Matchan A, Milz E, Alanay Y, Kayserili H, Liu Y, Banka S, Kranz A, Zenker M, Wieczorek D, Elcioglu N, Prontera P, Lyonnet S, Meitinger T, Stewart AF, Donnai D, Strom TM, Boduroglu K, Yigit G, Li Y, Katsanis N, Wollnik B. RAP1-mediated MEK/ERK pathway defects in Kabuki syndrome. J Clin Invest 2015; 125:3585-99. [PMID: 26280580 DOI: 10.1172/jci80102] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 07/09/2015] [Indexed: 02/06/2023] Open
Abstract
The genetic disorder Kabuki syndrome (KS) is characterized by developmental delay and congenital anomalies. Dominant mutations in the chromatin regulators lysine (K)-specific methyltransferase 2D (KMT2D) (also known as MLL2) and lysine (K)-specific demethylase 6A (KDM6A) underlie the majority of cases. Although the functions of these chromatin-modifying proteins have been studied extensively, the physiological systems regulated by them are largely unknown. Using whole-exome sequencing, we identified a mutation in RAP1A that was converted to homozygosity as the result of uniparental isodisomy (UPD) in a patient with KS and a de novo, dominant mutation in RAP1B in a second individual with a KS-like phenotype. We elucidated a genetic and functional interaction between the respective KS-associated genes and their products in zebrafish models and patient cell lines. Specifically, we determined that dysfunction of known KS genes and the genes identified in this study results in aberrant MEK/ERK signaling as well as disruption of F-actin polymerization and cell intercalation. Moreover, these phenotypes could be rescued in zebrafish models by rebalancing MEK/ERK signaling via administration of small molecule inhibitors of MEK. Taken together, our studies suggest that the KS pathophysiology overlaps with the RASopathies and provide a potential direction for treatment design.
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Wong FK, Fei JF, Mora-Bermúdez F, Taverna E, Haffner C, Fu J, Anastassiadis K, Stewart AF, Huttner WB. Sustained Pax6 Expression Generates Primate-like Basal Radial Glia in Developing Mouse Neocortex. PLoS Biol 2015; 13:e1002217. [PMID: 26252244 PMCID: PMC4529158 DOI: 10.1371/journal.pbio.1002217] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 06/30/2015] [Indexed: 11/21/2022] Open
Abstract
The evolutionary expansion of the neocortex in mammals has been linked to enlargement of the subventricular zone (SVZ) and increased proliferative capacity of basal progenitors (BPs), notably basal radial glia (bRG). The transcription factor Pax6 is known to be highly expressed in primate, but not mouse, BPs. Here, we demonstrate that sustaining Pax6 expression selectively in BP-genic apical radial glia (aRG) and their BP progeny of embryonic mouse neocortex suffices to induce primate-like progenitor behaviour. Specifically, we conditionally expressed Pax6 by in utero electroporation using a novel, Tis21–CreERT2 mouse line. This expression altered aRG cleavage plane orientation to promote bRG generation, increased cell-cycle re-entry of BPs, and ultimately increased upper-layer neuron production. Upper-layer neuron production was also increased in double-transgenic mouse embryos with sustained Pax6 expression in the neurogenic lineage. Strikingly, increased BPs existed not only in the SVZ but also in the intermediate zone of the neocortex of these double-transgenic mouse embryos. In mutant mouse embryos lacking functional Pax6, the proportion of bRG among BPs was reduced. Our data identify specific Pax6 effects in BPs and imply that sustaining this Pax6 function in BPs could be a key aspect of SVZ enlargement and, consequently, the evolutionary expansion of the neocortex. "Humanizing" the expression of the transcription factor Pax6 in cortical progenitors in the developing mouse brain is sufficient to endow these progenitors with a primate-like proliferative capacity. During development, neural progenitors generate all cells that make up the mammalian brain. Differences in brain size among the various mammalian species are attributed to differences in the abundance and proliferative capacity of a specific class of neural progenitors called basal progenitors. Among these, a specific progenitor type called basal radial glia is thought to have played an important role during evolution in the expansion of the neocortex, the part of the brain associated with higher cognitive functions like conscious thought and language. In the neocortex, the expression of the transcription factor Pax6 in basal progenitors is low in rodents, but high in primates, including humans. In this study, we aimed to mimic the elevated expression pattern of Pax6 seen in humans in basal progenitors of the embryonic mouse neocortex. To this end, we generated a novel, transgenic mouse line that allows sustained expression of the Pax6 gene in basal progenitors. This elevated expression resulted in an increase in the generation of basal radial glia, in the proliferative capacity of basal progenitors, and, ultimately, in the number of neurons produced. Our findings demonstrate that altering the expression of a single transcription factor from a mouse to a human-like pattern suffices to induce a primate-like proliferative behaviour in neural progenitors, which is thought to underlie the evolutionary expansion of the neocortex.
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Affiliation(s)
- Fong Kuan Wong
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Ji-Feng Fei
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Elena Taverna
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Christiane Haffner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Jun Fu
- Biotechnology Center of the Technische Universität Dresden, Dresden, Germany
| | | | - A. Francis Stewart
- Biotechnology Center of the Technische Universität Dresden, Dresden, Germany
| | - Wieland B. Huttner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- * E-mail:
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Ander M, Subramaniam S, Fahmy K, Stewart AF, Schäffer E. A Single-Strand Annealing Protein Clamps DNA to Detect and Secure Homology. PLoS Biol 2015; 13:e1002213. [PMID: 26271032 PMCID: PMC4535883 DOI: 10.1371/journal.pbio.1002213] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 06/26/2015] [Indexed: 11/24/2022] Open
Abstract
Repair of DNA breaks by single-strand annealing (SSA) is a major mechanism for the maintenance of genomic integrity. SSA is promoted by proteins (single-strand-annealing proteins [SSAPs]), such as eukaryotic RAD52 and λ phage Redβ. These proteins use a short single-stranded region to find sequence identity and initiate homologous recombination. However, it is unclear how SSAPs detect homology and catalyze annealing. Using single-molecule experiments, we provide evidence that homology is recognized by Redβ monomers that weakly hold single DNA strands together. Once annealing begins, dimerization of Redβ clamps the double-stranded region and nucleates nucleoprotein filament growth. In this manner, DNA clamping ensures and secures a successful detection for DNA sequence homology. The clamp is characterized by a structural change of Redβ and a remarkable stability against force up to 200 pN. Our findings not only present a detailed explanation for SSAP action but also identify the DNA clamp as a very stable, noncovalent, DNA-protein interaction.
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Affiliation(s)
- Marcel Ander
- Nanomechanics Group, Biotechnology Center, TU Dresden, Dresden, Germany
| | | | - Karim Fahmy
- Division of Biophysics, Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - A. Francis Stewart
- Department of Genomics, Biotechnology Center, TU Dresden, Dresden, Germany
| | - Erik Schäffer
- Nanomechanics Group, Biotechnology Center, TU Dresden, Dresden, Germany
- Cellular Nanoscience, Center for Plant Molecular Biology (ZMBP), Universität Tübingen, Tübingen, Germany
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Reddy TR, Fevat LMS, Munson SE, Stewart AF, Cowley SM. Lambda red mediated gap repair utilizes a novel replicative intermediate in Escherichia coli. PLoS One 2015; 10:e0120681. [PMID: 25803509 PMCID: PMC4372340 DOI: 10.1371/journal.pone.0120681] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 02/05/2015] [Indexed: 11/19/2022] Open
Abstract
The lambda phage Red recombination system can mediate efficient homologous recombination in Escherichia coli, which is the basis of the DNA engineering technique termed recombineering. Red mediated insertion of DNA requires DNA replication, involves a single-stranded DNA intermediate and is more efficient on the lagging strand of the replication fork. Lagging strand recombination has also been postulated to explain the Red mediated repair of gapped plasmids by an Okazaki fragment gap filling model. Here, we demonstrate that gap repair involves a different strand independent mechanism. Gap repair assays examining the strand asymmetry of recombination did not show a lagging strand bias. Directly testing an ssDNA plasmid showed lagging strand recombination is possible but dsDNA plasmids did not employ this mechanism. Insertional recombination combined with gap repair also did not demonstrate preferential lagging strand bias, supporting a different gap repair mechanism. The predominant recombination route involved concerted insertion and subcloning though other routes also operated at lower frequencies. Simultaneous insertion of DNA resulted in modification of both strands and was unaffected by mutations to DNA polymerase I, responsible for Okazaki fragment maturation. The lower efficiency of an alternate Red mediated ends-in recombination pathway and the apparent lack of a Holliday junction intermediate suggested that gap repair does not involve a different Red recombination pathway. Our results may be explained by a novel replicative intermediate in gap repair that does not involve a replication fork. We exploited these observations by developing a new recombineering application based on concerted insertion and gap repair, termed SPI (subcloning plus insertion). SPI selected against empty vector background and selected for correct gap repair recombinants. We used SPI to simultaneously insert up to four different gene cassettes in a single recombineering reaction. Consequently, our findings have important implications for the understanding of E. coli replication and Red recombination.
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Affiliation(s)
- Thimma R. Reddy
- Department of Biochemistry, University of Leicester, Leicester, United Kingdom
| | - Léna M. S. Fevat
- Center for Fisheries, Environment and Aquaculture Sciences, Lowestoft, United Kingdom
| | - Sarah E. Munson
- ES Cell Facility, Centre for Core Biotechnology Services, University of Leicester, Leicester, United Kingdom
| | - A. Francis Stewart
- Genomics, BioInnovationsZentrum, Technische Universitaet Dresden, Dresden, Germany
| | - Shaun M. Cowley
- Department of Biochemistry, University of Leicester, Leicester, United Kingdom
- * E-mail:
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Xu K, Stewart AF, Porter AC. Stimulation of oligonucleotide-directed gene correction by Redβ expression and MSH2 depletion in human HT1080 cells. Mol Cells 2015; 38:33-9. [PMID: 25431426 PMCID: PMC4314130 DOI: 10.14348/molcells.2015.2163] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 10/14/2014] [Accepted: 10/15/2014] [Indexed: 01/30/2023] Open
Abstract
The correction of disease-causing mutations by single-strand oligonucleotide-templated DNA repair (ssOR) is an attractive approach to gene therapy, but major improvements in ssOR efficiency and consistency are needed. The mechanism of ssOR is poorly understood but may involve annealing of oligonucleotides to transiently exposed single-stranded regions in the target duplex. In bacteria and yeast it has been shown that ssOR is promoted by expression of Redβ, a single-strand DNA annealing protein from bacteriophage lambda. Here we show that Redβ expression is well tolerated in a human cell line where it consistently promotes ssOR. By use of short interfering RNA, we also show that ssOR is stimulated by the transient depletion of the endogenous DNA mismatch repair protein MSH2. Furthermore, we find that the effects of Redβ expression and MSH2 depletion on ssOR can be combined with a degree of cooperativity. These results suggest that oligonucleotide annealing and mismatch recognition are distinct but interdependent events in ssOR that can be usefully modulated in gene correction strategies.
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Affiliation(s)
- Ke Xu
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenviroment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin 300052,
China
- Gene Targeting Group, Department of Hematology, Faculty of Medicine, Imperial College London, London W12 0NN,
UK
| | - A. Francis Stewart
- Genomics, Bio Innovations Zentrum, Technische Universitaet Dresden, 01307 Dresden,
Germany
| | - Andrew C.G. Porter
- Gene Targeting Group, Department of Hematology, Faculty of Medicine, Imperial College London, London W12 0NN,
UK
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Yin J, Zhu H, Xia L, Ding X, Hoffmann T, Hoffmann M, Bian X, Müller R, Fu J, Stewart AF, Zhang Y. A new recombineering system for Photorhabdus and Xenorhabdus. Nucleic Acids Res 2014; 43:e36. [PMID: 25539914 PMCID: PMC4381043 DOI: 10.1093/nar/gku1336] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 12/10/2014] [Indexed: 01/09/2023] Open
Abstract
Precise and fluent genetic manipulation is still limited to only a few prokaryotes. Ideally the highly advanced technologies available in Escherichia coli could be broadly applied. Our efforts to apply lambda Red technology, widely termed ‘recombineering’, in Photorhabdus and Xenorhabdus yielded only limited success. Consequently we explored the properties of an endogenous Photorhabdus luminescens lambda Red-like operon, Plu2934/Plu2935/Plu2936. Bioinformatic and functional tests indicate that Plu2936 is a 5’-3’ exonuclease equivalent to Redα and Plu2935 is a single strand annealing protein equivalent to Redβ. Plu2934 dramatically enhanced recombineering efficiency. Results from bioinformatic analysis and recombineering assays suggest that Plu2934 may be functionally equivalent to Redγ, which inhibits the major endogenous E. coli nuclease, RecBCD. The recombineering utility of Plu2934/Plu2935/Plu2936 was demonstrated by engineering Photorhabdus and Xenorhabdus genomes, including the activation of the 49-kb non-ribosomal peptide synthase (NRPS) gene cluster plu2670 by insertion of a tetracycline inducible promoter. After tetracycline induction, novel secondary metabolites were identified. Our work unlocks the potential for bioprospecting and functional genomics in the Photorhabdus, Xenorhabdus and related genomes.
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Affiliation(s)
- Jia Yin
- Hunan Provincial Key Laboratory for Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, College of Life Science, Hunan Normal University, 410081 Changsha, People's Republic of China
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China
- Department of Genomics, Dresden University of Technology, BioInnovations-Zentrum, Tatzberg 47-51, 01307 Dresden, Germany
- Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, PO Box 151150, 66041 Saarbrücken, Germany
| | - Hongbo Zhu
- Department of Protein Evolution, Max-Planck Institute for Developmental Biology, Spemannstr. 35, 72076 Tübingen, Germany
| | - Liqiu Xia
- Hunan Provincial Key Laboratory for Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, College of Life Science, Hunan Normal University, 410081 Changsha, People's Republic of China
| | - Xuezhi Ding
- Hunan Provincial Key Laboratory for Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, College of Life Science, Hunan Normal University, 410081 Changsha, People's Republic of China
| | - Thomas Hoffmann
- Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, PO Box 151150, 66041 Saarbrücken, Germany
| | - Michael Hoffmann
- Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, PO Box 151150, 66041 Saarbrücken, Germany
| | - Xiaoying Bian
- Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, PO Box 151150, 66041 Saarbrücken, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, PO Box 151150, 66041 Saarbrücken, Germany
| | - Jun Fu
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China
- Department of Genomics, Dresden University of Technology, BioInnovations-Zentrum, Tatzberg 47-51, 01307 Dresden, Germany
| | - A. Francis Stewart
- Department of Genomics, Dresden University of Technology, BioInnovations-Zentrum, Tatzberg 47-51, 01307 Dresden, Germany
| | - Youming Zhang
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China
- To whom correspondence should be addressed. Tel: +86 531 88363082; Fax: +86 531 88363203;
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Bledau AS, Schmidt K, Neumann K, Hill U, Ciotta G, Gupta A, Torres DC, Fu J, Kranz A, Stewart AF, Anastassiadis K. The H3K4 methyltransferase Setd1a is first required at the epiblast stage, whereas Setd1b becomes essential after gastrulation. Development 2014; 141:1022-35. [PMID: 24550110 DOI: 10.1242/dev.098152] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Histone 3 lysine 4 (H3K4) methylation is a universal epigenetic mark. In mammals, there are six H3K4 methyltransferases related to yeast Set1 and fly Trithorax, including two orthologs of Set1: Setd1a and Setd1b. Here we show that mouse Setd1a is required for gastrulation, whereas Setd1b-deficient embryos survive to E11.5 but are grossly retarded. Setd1a knockout embryos implant but do not proceed past the epiblast. Furthermore, Setd1a is not required until the inner cell mass has formed, at which stage it has replaced Mll2 as the major H3K4 methyltransferase. Setd1a is required for embryonic, epiblast and neural stem cell survival and neural stem cell reprogramming, whereas Setd1b is dispensable. Deletion of Setd1a in embryonic stem cells resulted in rapid losses of bulk H3K4 methylation, pluripotency gene expression and proliferation, with G1 pileup. Setd1b overexpression could not rescue the proliferation defects caused by loss of Setd1a in embryonic stem cells. The precise developmental requirement for Setd1a suggests that gastrulation is regulated by a switch between the major H3K4 methyltransferases.
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Affiliation(s)
- Anita S Bledau
- Stem Cell Engineering, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
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45
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Denissov S, Hofemeister H, Marks H, Kranz A, Ciotta G, Singh S, Anastassiadis K, Stunnenberg HG, Stewart AF. Mll2 is required for H3K4 trimethylation on bivalent promoters in embryonic stem cells, whereas Mll1 is redundant. Development 2014; 141:526-37. [PMID: 24423662 DOI: 10.1242/dev.102681] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Trimethylation of histone H3 lysine 4 (H3K4me3) at the promoters of actively transcribed genes is a universal epigenetic mark and a key product of Trithorax group action. Here, we show that Mll2, one of the six Set1/Trithorax-type H3K4 methyltransferases in mammals, is required for trimethylation of bivalent promoters in mouse embryonic stem cells. Mll2 is bound to bivalent promoters but also to most active promoters, which do not require Mll2 for H3K4me3 or mRNA expression. By contrast, the Set1 complex (Set1C) subunit Cxxc1 is primarily bound to active but not bivalent promoters. This indicates that bivalent promoters rely on Mll2 for H3K4me3 whereas active promoters have more than one bound H3K4 methyltransferase, including Set1C. Removal of Mll1, sister to Mll2, had almost no effect on any promoter unless Mll2 was also removed, indicating functional backup between these enzymes. Except for a subset, loss of H3K4me3 on bivalent promoters did not prevent responsiveness to retinoic acid, thereby arguing against a priming model for bivalency. In contrast, we propose that Mll2 is the pioneer trimethyltransferase for promoter definition in the naïve epigenome and that Polycomb group action on bivalent promoters blocks the premature establishment of active, Set1C-bound, promoters.
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Affiliation(s)
- Sergei Denissov
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences (NCMLS), Radboud University, PO Box 9101, 6500 HB Nijmegen, The Netherlands
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Ander M, Subramaniam S, Fahmy K, Stewart AF, Schäffer E. A Single-Strand Annealing Protein Clamps DNA to Detect Homology. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.3831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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47
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Wang H, Bian X, Xia L, Ding X, Müller R, Zhang Y, Fu J, Stewart AF. Improved seamless mutagenesis by recombineering using ccdB for counterselection. Nucleic Acids Res 2013; 42:e37. [PMID: 24369425 PMCID: PMC3950717 DOI: 10.1093/nar/gkt1339] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Recombineering, which is the use of homologous recombination for DNA engineering in Escherichia coli, usually uses antibiotic selection to identify the intended recombinant. When combined in a second step with counterselection using a small molecule toxin, seamless products can be obtained. Here, we report the advantages of a genetic strategy using CcdB as the counterselectable agent. Expression of CcdB is toxic to E. coli in the absence of the CcdA antidote so counterselection is initiated by the removal of CcdA expression. CcdB counterselection is robust and does not require titrations or experiment-to-experiment optimization. Because counterselection strategies necessarily differ according to the copy number of the target, we describe two variations. For multi-copy targets, we use two E. coli hosts so that counterselection is exerted by the transformation step that is needed to separate the recombined and unrecombined plasmids. For single copy targets, we put the ccdA gene onto the temperature-sensitive pSC101 Red expression plasmid so that counterselection is exerted by the standard temperature shift to remove the expression plasmid. To reduce unwanted intramolecular recombination, we also combined CcdB counterselection with Redα omission. These options improve the use of counterselection in recombineering with BACs, plasmids and the E. coli chromosome.
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Affiliation(s)
- Hailong Wang
- Hunan Provincial Key Laboratory for Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, College of Life Science, Hunan Normal University, 410081 Changsha, People's Republic of China, Department of Genomics, Dresden University of Technology, BioInnovations-Zentrum, Tatzberg 47-51, 01307 Dresden, Germany, Shandong University-Helmholtz Joint Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China, Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, PO Box 151150, 66041 Saarbrücken, Germany and Gene Bridges GmbH, Building C2.3, Saarland University, 66123 Saarbrücken, Germany
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48
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Hu S, Fu J, Huang F, Ding X, Stewart AF, Xia L, Zhang Y. Genome engineering of Agrobacterium tumefaciens using the lambda Red recombination system. Appl Microbiol Biotechnol 2013; 98:2165-72. [DOI: 10.1007/s00253-013-5412-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 11/01/2013] [Accepted: 11/10/2013] [Indexed: 10/26/2022]
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49
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Bian X, Fu J, Plaza A, Herrmann J, Pistorius D, Stewart AF, Zhang Y, Müller R. In vivo evidence for a prodrug activation mechanism during colibactin maturation. Chembiochem 2013; 14:1194-7. [PMID: 23744512 DOI: 10.1002/cbic.201300208] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Indexed: 01/19/2023]
Abstract
Releasing the cytopath: We have identified an N-myristoyl-D-asparagine (1) as the free N-terminal prodrug scaffold in cytopathogenic Escherichia coli strains expressing the colibactin gene cluster. Colibactin is released in vivo upon cleavage of precolibactin. We provide for the first time in vivo evidence of the prodrug-like release mechanism of colibactin.
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Affiliation(s)
- Xiaoying Bian
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland HIPS, Helmholtz Centre for Infection Research HZI and Department of Pharmaceutical Biotechnology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
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50
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Rostovskaya M, Naumann R, Fu J, Obst M, Mueller D, Stewart AF, Anastassiadis K. Transposon mediated BAC transgenesis via pronuclear injection of mouse zygotes. Genesis 2013; 51:135-41. [PMID: 23225373 DOI: 10.1002/dvg.22362] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 12/05/2012] [Indexed: 11/09/2022]
Abstract
Pronuclear microinjection of bacterial artificial chromosomes (BACs) is the preferred way to generate transgenic mice because the transgene accurately recapitulates expression of the endogenous gene. However, the method is demanding and the integrity and copy number of the BAC transgene is difficult to control. Here, we describe a simpler pronuclear injection method that relies on transposition to introduce full-length BACs into the mouse genome. The bacterial backbone of a hPAX6-GFP reporter BAC was retrofitted with PiggyBac transposon inverted terminal repeats and co-injected with PiggyBac transposase mRNA. Both the frequency of transgenic founders as well as intact, full-length, single copy integrations were increased. Transposition was determined by a rapid PCR screen for a transpositional signature and confirmation by splinkerette sequencing to show that the BACs were integrated as a single copy either in one or two different genomic sites. BAC transposons displayed improved functional accuracy over random integrants as evaluated by expression of the hPAX6-GFP reporter in embryonic neural tube and absence of ectopic expression. This method involves less work to achieve increased frequencies of both transgenesis and single copy, full-length integrations. These advantages are not only relevant to rodents but also for transgenesis in all systems.
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Affiliation(s)
- Maria Rostovskaya
- Stem Cell Engineering, Biotechnology Center, Technische Universitaet Dresden, Dresden, Germany
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