1
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Yamaguchi K, Chen X, Rodgers B, Miura F, Bashtrykov P, Bonhomme F, Salinas-Luypaert C, Haxholli D, Gutekunst N, Aygenli BÖ, Ferry L, Kirsh O, Laisné M, Scelfo A, Ugur E, Arimondo PB, Leonhardt H, Kanemaki MT, Bartke T, Fachinetti D, Jeltsch A, Ito T, Defossez PA. Non-canonical functions of UHRF1 maintain DNA methylation homeostasis in cancer cells. Nat Commun 2024; 15:2960. [PMID: 38580649 PMCID: PMC10997609 DOI: 10.1038/s41467-024-47314-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 03/25/2024] [Indexed: 04/07/2024] Open
Abstract
DNA methylation is an essential epigenetic chromatin modification, and its maintenance in mammals requires the protein UHRF1. It is yet unclear if UHRF1 functions solely by stimulating DNA methylation maintenance by DNMT1, or if it has important additional functions. Using degron alleles, we show that UHRF1 depletion causes a much greater loss of DNA methylation than DNMT1 depletion. This is not caused by passive demethylation as UHRF1-depleted cells proliferate more slowly than DNMT1-depleted cells. Instead, bioinformatics, proteomics and genetics experiments establish that UHRF1, besides activating DNMT1, interacts with DNMT3A and DNMT3B and promotes their activity. In addition, we show that UHRF1 antagonizes active DNA demethylation by TET2. Therefore, UHRF1 has non-canonical roles that contribute importantly to DNA methylation homeostasis; these findings have practical implications for epigenetics in health and disease.
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Affiliation(s)
- Kosuke Yamaguchi
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, Paris, France.
| | - Xiaoying Chen
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, Paris, France
| | - Brianna Rodgers
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, Paris, France
| | - Fumihito Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Pavel Bashtrykov
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Frédéric Bonhomme
- Institut Pasteur, Université Paris Cité, Epigenetic Chemical Biology, CNRS, UMR 3523, Chem4Life, Paris, France
| | | | - Deis Haxholli
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Nicole Gutekunst
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, Stuttgart, Germany
| | | | - Laure Ferry
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, Paris, France
| | - Olivier Kirsh
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, Paris, France
| | - Marthe Laisné
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, Paris, France
| | - Andrea Scelfo
- Institut Curie, PSL Research University, CNRS, UMR 144, Paris, France
| | - Enes Ugur
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Paola B Arimondo
- Institut Pasteur, Université Paris Cité, Epigenetic Chemical Biology, CNRS, UMR 3523, Chem4Life, Paris, France
| | - Heinrich Leonhardt
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Masato T Kanemaki
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima, Shizuoka, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
- Department of Biological Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Till Bartke
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | | | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Takashi Ito
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
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2
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Palikyras S, Sofiadis K, Stavropoulou A, Danieli‐Mackay A, Varamogianni‐Mamatsi V, Hörl D, Nasiscionyte S, Zhu Y, Papadionysiou I, Papadakis A, Josipovic N, Zirkel A, O'Connell A, Loughran G, Keane J, Michel A, Wagner W, Beyer A, Harz H, Leonhardt H, Lukinavicius G, Nikolaou C, Papantonis A. Rapid and synchronous chemical induction of replicative-like senescence via a small molecule inhibitor. Aging Cell 2024; 23:e14083. [PMID: 38196311 PMCID: PMC11019153 DOI: 10.1111/acel.14083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/07/2023] [Accepted: 01/03/2024] [Indexed: 01/11/2024] Open
Abstract
Cellular senescence is acknowledged as a key contributor to organismal ageing and late-life disease. Though popular, the study of senescence in vitro can be complicated by the prolonged and asynchronous timing of cells committing to it and by its paracrine effects. To address these issues, we repurposed a small molecule inhibitor, inflachromene (ICM), to induce senescence to human primary cells. Within 6 days of treatment with ICM, senescence hallmarks, including the nuclear eviction of HMGB1 and -B2, are uniformly induced across IMR90 cell populations. By generating and comparing various high throughput datasets from ICM-induced and replicative senescence, we uncovered a high similarity of the two states. Notably though, ICM suppresses the pro-inflammatory secretome associated with senescence, thus alleviating most paracrine effects. In summary, ICM rapidly and synchronously induces a senescent-like phenotype thereby allowing the study of its core regulatory program without confounding heterogeneity.
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Affiliation(s)
- Spiros Palikyras
- Institute of PathologyUniversity Medical Center GöttingenGöttingenGermany
| | - Konstantinos Sofiadis
- Institute of PathologyUniversity Medical Center GöttingenGöttingenGermany
- Present address:
Oncode InstituteHubrecht Institute‐KNAW and University Medical Center UtrechtUtrechtThe Netherlands
| | - Athanasia Stavropoulou
- Institute for BioinnovationBiomedical Sciences Research Center “Alexander Fleming”VariGreece
| | - Adi Danieli‐Mackay
- Institute of PathologyUniversity Medical Center GöttingenGöttingenGermany
- Clinical Research Unit 5002University Medical Center GöttingenGöttingenGermany
| | | | - David Hörl
- Faculty of BiologyLudwig Maximilians University MunichMunichGermany
| | | | - Yajie Zhu
- Institute of PathologyUniversity Medical Center GöttingenGöttingenGermany
| | | | - Antonis Papadakis
- Cluster of Excellence on Cellular Stress Responses in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany
| | - Natasa Josipovic
- Institute of PathologyUniversity Medical Center GöttingenGöttingenGermany
- Present address:
Single Cell DiscoveriesUtrechtThe Netherlands
| | - Anne Zirkel
- Center for Molecular Medicine CologneUniversity and University Hospital of CologneCologneGermany
| | | | | | | | | | - Wolfgang Wagner
- Helmholtz‐Institute for Biomedical EngineeringRWTH Aachen University Medical SchoolAachenGermany
- Institute for Stem Cell BiologyRWTH Aachen University Medical SchoolAachenGermany
| | - Andreas Beyer
- Cluster of Excellence on Cellular Stress Responses in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany
| | - Hartmann Harz
- Faculty of BiologyLudwig Maximilians University MunichMunichGermany
| | | | - Grazvydas Lukinavicius
- Department of NanoBiophotonicsMax Planck Institute for Multidisciplinary SciencesGöttingenGermany
| | - Christoforos Nikolaou
- Institute for BioinnovationBiomedical Sciences Research Center “Alexander Fleming”VariGreece
| | - Argyris Papantonis
- Institute of PathologyUniversity Medical Center GöttingenGöttingenGermany
- Clinical Research Unit 5002University Medical Center GöttingenGöttingenGermany
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3
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Bachem K, Li X, Ceolin S, Mühling B, Hörl D, Harz H, Leonhardt H, Arnoult L, Weber S, Matarlo B, Prud’homme B, Gompel N. Regulatory evolution tuning pigmentation intensity quantitatively in Drosophila. Sci Adv 2024; 10:eadl2616. [PMID: 38266088 PMCID: PMC10807792 DOI: 10.1126/sciadv.adl2616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 12/21/2023] [Indexed: 01/26/2024]
Abstract
Quantitative variation in attributes such as color, texture, or stiffness dominates morphological diversification. It results from combinations of alleles at many Mendelian loci. Here, we identify an additional source of quantitative variation among species, continuous evolution in a gene regulatory region. Specifically, we examined the modulation of wing pigmentation in a group of fly species and showed that inter-species variation correlated with the quantitative expression of the pigmentation gene yellow. This variation results from an enhancer of yellow determining darkness through species-specific activity. We mapped the divergent activities between two sister species and found the changes to be broadly distributed along the enhancer. Our results demonstrate that enhancers can act as dials fueling quantitative morphological diversification by modulating trait properties.
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Affiliation(s)
- Katharina Bachem
- Department of Evolutionary Ecology, Ludwig-Maximilians Universität München, München 82152, Germany
| | - Xinyi Li
- Department of Evolutionary Ecology, Ludwig-Maximilians Universität München, München 82152, Germany
| | - Stefano Ceolin
- Department of Evolutionary Ecology, Ludwig-Maximilians Universität München, München 82152, Germany
| | - Bettina Mühling
- Department of Evolutionary Ecology, Ludwig-Maximilians Universität München, München 82152, Germany
| | - David Hörl
- Human Biology and Bioimaging, Ludwig-Maximilians Universität München, München 82152, Germany
| | - Hartmann Harz
- Human Biology and Bioimaging, Ludwig-Maximilians Universität München, München 82152, Germany
| | - Heinrich Leonhardt
- Human Biology and Bioimaging, Ludwig-Maximilians Universität München, München 82152, Germany
| | - Laurent Arnoult
- Institut de Biologie du Développement de Marseille, Aix-Marseille Université, Marseille 13288, France
| | - Sabrina Weber
- Department of Evolutionary Ecology, Ludwig-Maximilians Universität München, München 82152, Germany
| | - Blair Matarlo
- Department of Evolutionary Ecology, Ludwig-Maximilians Universität München, München 82152, Germany
| | - Benjamin Prud’homme
- Institut de Biologie du Développement de Marseille, Aix-Marseille Université, Marseille 13288, France
| | - Nicolas Gompel
- Department of Evolutionary Ecology, Ludwig-Maximilians Universität München, München 82152, Germany
- Bonn Institute for Organismic Biology, University of Bonn, Bonn 53115, Germany
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4
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Abstract
The eukaryotic nucleus displays a variety of membraneless compartments with distinct biomolecular composition and specific cellular activities. Emerging evidence indicates that protein-based liquid-liquid phase separation (LLPS) plays an essential role in the formation and dynamic regulation of heterochromatin compartmentalization. This feature is especially conspicuous at the pericentric heterochromatin domains. In this review, we will describe our understanding of heterochromatin organization and LLPS. In addition, we will highlight the increasing importance of multivalent weak homo- and heteromolecular interactions in LLPS-mediated heterochromatin compartmentalization in the complex environment inside living cells.
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Affiliation(s)
- Hui Zhang
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Weihua Qin
- Human Biology and Bioimaging, Faculty of Biology, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - Hector Romero
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Heinrich Leonhardt
- Human Biology and Bioimaging, Faculty of Biology, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - M. Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany,CONTACT M. Cristina Cardoso Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287Darmstadt, Germany
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5
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Pabba MK, Ritter C, Chagin VO, Meyer J, Celikay K, Stear JH, Loerke D, Kolobynina K, Prorok P, Schmid AK, Leonhardt H, Rohr K, Cardoso MC. Replisome loading reduces chromatin motion independent of DNA synthesis. eLife 2023; 12:RP87572. [PMID: 37906089 PMCID: PMC10617993 DOI: 10.7554/elife.87572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023] Open
Abstract
Chromatin has been shown to undergo diffusional motion, which is affected during gene transcription by RNA polymerase activity. However, the relationship between chromatin mobility and other genomic processes remains unclear. Hence, we set out to label the DNA directly in a sequence unbiased manner and followed labeled chromatin dynamics in interphase human cells expressing GFP-tagged proliferating cell nuclear antigen (PCNA), a cell cycle marker and core component of the DNA replication machinery. We detected decreased chromatin mobility during the S-phase compared to G1 and G2 phases in tumor as well as normal diploid cells using automated particle tracking. To gain insight into the dynamical organization of the genome during DNA replication, we determined labeled chromatin domain sizes and analyzed their motion in replicating cells. By correlating chromatin mobility proximal to the active sites of DNA synthesis, we showed that chromatin motion was locally constrained at the sites of DNA replication. Furthermore, inhibiting DNA synthesis led to increased loading of DNA polymerases. This was accompanied by accumulation of the single-stranded DNA binding protein on the chromatin and activation of DNA helicases further restricting local chromatin motion. We, therefore, propose that it is the loading of replisomes but not their catalytic activity that reduces the dynamics of replicating chromatin segments in the S-phase as well as their accessibility and probability of interactions with other genomic regions.
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Affiliation(s)
| | - Christian Ritter
- Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg UniversityHeidelbergGermany
| | - Vadim O Chagin
- Department of Biology, Technical University of DarmstadtDarmstadtGermany
- Institute of Cytology RASSt. PetersburgRussian Federation
| | - Janis Meyer
- Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg UniversityHeidelbergGermany
| | - Kerem Celikay
- Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg UniversityHeidelbergGermany
| | - Jeffrey H Stear
- EMBL Australia Node in Single Molecule Science, University of New South WalesSydneyAustralia
| | - Dinah Loerke
- Department of Physics & Astronomy, University of DenverDenverUnited States
| | - Ksenia Kolobynina
- Department of Biology, Technical University of DarmstadtDarmstadtGermany
| | - Paulina Prorok
- Department of Biology, Technical University of DarmstadtDarmstadtGermany
| | - Alice Kristin Schmid
- Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg UniversityHeidelbergGermany
| | | | - Karl Rohr
- Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg UniversityHeidelbergGermany
| | - M Cristina Cardoso
- Department of Biology, Technical University of DarmstadtDarmstadtGermany
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6
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Ullrich S, Leidescher S, Feodorova Y, Thanisch K, Fini JB, Kaspers B, Weber F, Markova B, Führer D, Romitti M, Krebs S, Blum H, Leonhardt H, Costagliola S, Heuer H, Solovei I. The highly and perpetually upregulated thyroglobulin gene is a hallmark of functional thyrocytes. Front Cell Dev Biol 2023; 11:1265407. [PMID: 37860816 PMCID: PMC10582334 DOI: 10.3389/fcell.2023.1265407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 09/22/2023] [Indexed: 10/21/2023] Open
Abstract
Abnormalities are indispensable for studying normal biological processes and mechanisms. In the present work, we draw attention to the remarkable phenomenon of a perpetually and robustly upregulated gene, the thyroglobulin gene (Tg). The gene is expressed in the thyroid gland and, as it has been recently demonstrated, forms so-called transcription loops, easily observable by light microscopy. Using this feature, we show that Tg is expressed at a high level from the moment a thyroid cell acquires its identity and both alleles remain highly active over the entire life of the cell, i.e., for months or years depending on the species. We demonstrate that this high upregulation is characteristic of thyroglobulin genes in all major vertebrate groups. We provide evidence that Tg is not influenced by the thyroid hormone status, does not oscillate round the clock and is expressed during both the exocrine and endocrine phases of thyrocyte activity. We conclude that the thyroglobulin gene represents a unique and valuable model to study the maintenance of a high transcriptional upregulation.
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Affiliation(s)
- Simon Ullrich
- Biocenter, Ludwig Maximilians University Munich, Munich, Germany
| | | | - Yana Feodorova
- Biocenter, Ludwig Maximilians University Munich, Munich, Germany
| | | | - Jean-Baptiste Fini
- Département Adaptations du Vivant (AVIV), Physiologie Moléculaire et Adaptation (PhyMA UMR 7221 CNRS), Muséum National d’Histoire Naturelle, CNRS, CP 32, Paris, France
| | - Bernd Kaspers
- Department for Veterinary Sciences, Ludwig Maximilians University Munich, Planegg, Germany
| | - Frank Weber
- Department of General, Visceral and Transplantation Surgery, Section of Endocrine Surgery, University Duisburg-Essen, University Hospital Essen, Essen, Germany
| | - Boyka Markova
- Department of Endocrinology, Diabetes and Metabolism, University Duisburg-Essen, University Hospital Essen, Essen, Germany
| | - Dagmar Führer
- Department of Endocrinology, Diabetes and Metabolism, University Duisburg-Essen, University Hospital Essen, Essen, Germany
| | | | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig Maximilians University Munich, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig Maximilians University Munich, Munich, Germany
| | | | | | - Heike Heuer
- Department of Endocrinology, Diabetes and Metabolism, University Duisburg-Essen, University Hospital Essen, Essen, Germany
| | - Irina Solovei
- Biocenter, Ludwig Maximilians University Munich, Munich, Germany
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7
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Ziegler KA, Ahles A, Dueck A, Esfandyari D, Pichler P, Weber K, Kotschi S, Bartelt A, Sinicina I, Graw M, Leonhardt H, Weckbach LT, Massberg S, Schifferer M, Simons M, Hoeher L, Luo J, Ertürk A, Schiattarella GG, Sassi Y, Misgeld T, Engelhardt S. Immune-mediated denervation of the pineal gland underlies sleep disturbance in cardiac disease. Science 2023; 381:285-290. [PMID: 37471539 DOI: 10.1126/science.abn6366] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 06/01/2023] [Indexed: 07/22/2023]
Abstract
Disruption of the physiologic sleep-wake cycle and low melatonin levels frequently accompany cardiac disease, yet the underlying mechanism has remained enigmatic. Immunostaining of sympathetic axons in optically cleared pineal glands from humans and mice with cardiac disease revealed their substantial denervation compared with controls. Spatial, single-cell, nuclear, and bulk RNA sequencing traced this defect back to the superior cervical ganglia (SCG), which responded to cardiac disease with accumulation of inflammatory macrophages, fibrosis, and the selective loss of pineal gland-innervating neurons. Depletion of macrophages in the SCG prevented disease-associated denervation of the pineal gland and restored physiological melatonin secretion. Our data identify the mechanism by which diurnal rhythmicity in cardiac disease is disturbed and suggest a target for therapeutic intervention.
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Affiliation(s)
- Karin A Ziegler
- Institute of Pharmacology and Toxicology, Technical University Munich (TUM), Munich, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Andrea Ahles
- Institute of Pharmacology and Toxicology, Technical University Munich (TUM), Munich, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Anne Dueck
- Institute of Pharmacology and Toxicology, Technical University Munich (TUM), Munich, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Dena Esfandyari
- Institute of Pharmacology and Toxicology, Technical University Munich (TUM), Munich, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Pauline Pichler
- Institute of Pharmacology and Toxicology, Technical University Munich (TUM), Munich, Germany
| | - Karolin Weber
- Institute of Pharmacology and Toxicology, Technical University Munich (TUM), Munich, Germany
| | - Stefan Kotschi
- Institute for Cardiovascular Prevention (IPEK), Faculty of Medicine, Ludwig-Maximilians-Universität (LMU) München, Munich, Germany
| | - Alexander Bartelt
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
- Institute for Cardiovascular Prevention (IPEK), Faculty of Medicine, Ludwig-Maximilians-Universität (LMU) München, Munich, Germany
- Institute for Diabetes and Cancer, Helmholtz Center Munich, Neuherberg, Germany
- Department of Molecular Metabolism & Sabri Ülker Center for Metabolic Research, Harvard. T.H. Chan School of Public Health, Boston, MA, USA
| | - Inga Sinicina
- Institute of Legal Medicine, Faculty of Medicine, Ludwig-Maximilians-Universität (LMU) München, Munich, Germany
| | - Matthias Graw
- Institute of Legal Medicine, Faculty of Medicine, Ludwig-Maximilians-Universität (LMU) München, Munich, Germany
| | - Heinrich Leonhardt
- Human Biology & Bioimaging, Faculty of Biology, Ludwig-Maximilians-Universität (LMU) München, Munich, Germany
| | - Ludwig T Weckbach
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
- Medizinische Klinik und Poliklinik I, Klinikum der Universität München, Munich, Germany
- Institute of Cardiovascular Physiology and Pathophysiology, Biomedical Center, Ludwig-Maximilians-Universität (LMU), Planegg-Martinsried, Germany
| | - Steffen Massberg
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
- Medizinische Klinik und Poliklinik I, Klinikum der Universität München, Munich, Germany
| | - Martina Schifferer
- DZNE (German Center for Neurodegenerative Diseases), Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Mikael Simons
- DZNE (German Center for Neurodegenerative Diseases), Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- Institute of Neuronal Cell Biology, Technical University Munich (TUM), Munich, Germany
| | - Luciano Hoeher
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center Munich, Neuherberg, Germany
| | - Jie Luo
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center Munich, Neuherberg, Germany
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians-Universität (LMU) München, Munich, Germany
| | - Ali Ertürk
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center Munich, Neuherberg, Germany
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians-Universität (LMU) München, Munich, Germany
| | - Gabriele G Schiattarella
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
- Max Rubner Center for Cardiovascular Metabolic Renal Research (MRC), Deutsches Herzzentrum der Charité (DHZC), Charité-Universitätsmedizin Berlin, Berlin, Germany
- Translational Approaches in Heart Failure and Cardiometabolic Disease, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Yassine Sassi
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Roanoke, VA, USA
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA
- Department of Internal Medicine, Virginia Tech Carilion School of Medicine, Roanoke, VA, USA
| | - Thomas Misgeld
- DZNE (German Center for Neurodegenerative Diseases), Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- Institute of Neuronal Cell Biology, Technical University Munich (TUM), Munich, Germany
| | - Stefan Engelhardt
- Institute of Pharmacology and Toxicology, Technical University Munich (TUM), Munich, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
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8
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Nixdorf D, Sponheimer M, Berghammer D, Engert F, Bader U, Philipp N, Kazerani M, Straub T, Rohrbacher L, Wange L, Dapa S, Atar D, Seitz CM, Brandstetter K, Linder A, von Bergwelt M, Leonhardt H, Mittelstaet J, Kaiser A, Bücklein V, Subklewe M. Adapter CAR T cells to counteract T-cell exhaustion and enable flexible targeting in AML. Leukemia 2023:10.1038/s41375-023-01905-0. [PMID: 37106163 DOI: 10.1038/s41375-023-01905-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 04/11/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023]
Abstract
Although the landscape for treating acute myeloid leukemia (AML) patients has changed substantially in recent years, the majority of patients will eventually relapse and succumb to their disease. Allogeneic stem cell transplantation provides the best anti-AML treatment strategy, but is only suitable in a minority of patients. In contrast to B-cell neoplasias, chimeric antigen receptor (CAR) T-cell therapy in AML has encountered challenges in target antigen heterogeneity, safety, and T-cell dysfunction. We established a Fab-based adapter CAR (AdCAR) T-cell platform with flexibility of targeting and control of AdCAR T-cell activation. Utilizing AML cell lines and a long-term culture assay for primary AML cells, we were able to demonstrate AML-specific cytotoxicity using anti-CD33, anti-CD123, and anti-CLL1 adapter molecules in vitro and in vivo. Notably, we show for the first time the feasibility of sequential application of adapter molecules of different specificity in primary AML co-cultures. Importantly, using the AML platform, we were able to demonstrate that chronic T-cell stimulation and exhaustion can be counteracted through introduction of treatment-free intervals. As T-cell exhaustion and target antigen heterogeneity are well-known causes of resistance, the AdCAR platform might offer effective strategies to ameliorate these limitations.
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Affiliation(s)
- D Nixdorf
- Department of Medicine III, University Hospital, LMU, Munich, Germany
- Laboratory for Translational Cancer Immunology, LMU Gene Center, Munich, Germany
| | - M Sponheimer
- Department of Medicine III, University Hospital, LMU, Munich, Germany
- Laboratory for Translational Cancer Immunology, LMU Gene Center, Munich, Germany
| | - D Berghammer
- Laboratory for Translational Cancer Immunology, LMU Gene Center, Munich, Germany
| | - F Engert
- Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - U Bader
- Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - N Philipp
- Department of Medicine III, University Hospital, LMU, Munich, Germany
- Laboratory for Translational Cancer Immunology, LMU Gene Center, Munich, Germany
| | - M Kazerani
- Department of Medicine III, University Hospital, LMU, Munich, Germany
- Laboratory for Translational Cancer Immunology, LMU Gene Center, Munich, Germany
| | - T Straub
- Core Facility Bioinformatics, Biomedical Center, LMU, Munich, Germany
| | - L Rohrbacher
- Department of Medicine III, University Hospital, LMU, Munich, Germany
- Laboratory for Translational Cancer Immunology, LMU Gene Center, Munich, Germany
| | - L Wange
- Anthropology and Human Genomics, Faculty of Biology, LMU, Munich, Germany
| | - S Dapa
- Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - D Atar
- Department of General Pediatrics, Hematology and Oncology, University Children's Hospital Tuebingen, Tuebingen, Germany
| | - C M Seitz
- Department of General Pediatrics, Hematology and Oncology, University Children's Hospital Tuebingen, Tuebingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University Tuebingen, Tuebingen, Germany
| | | | - A Linder
- Gene Center and Department of Biochemistry, LMU, Munich, Germany
- Department of Medicine II, University Hospital, LMU, Munich, Germany
| | - M von Bergwelt
- Department of Medicine III, University Hospital, LMU, Munich, Germany
| | - H Leonhardt
- Department of Biology II, LMU, Munich, Germany
| | - J Mittelstaet
- Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - A Kaiser
- Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - V Bücklein
- Department of Medicine III, University Hospital, LMU, Munich, Germany
- Laboratory for Translational Cancer Immunology, LMU Gene Center, Munich, Germany
| | - M Subklewe
- Department of Medicine III, University Hospital, LMU, Munich, Germany.
- Laboratory for Translational Cancer Immunology, LMU Gene Center, Munich, Germany.
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.
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9
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Mirzaei N, Wärnberg F, Zaar P, Leonhardt H, Bagge RO. P221 Using an ultra-low dose of superparamagnetic iron oxide for sentinel lymph node detection in breast cancer patients - the MAGSNOW feasibility study. Breast 2023. [DOI: 10.1016/s0960-9776(23)00339-9] [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: 03/18/2023] Open
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10
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Roas M, Vick B, Kasper MA, Able M, Polzer H, Gerlach M, Kremmer E, Hecker JS, Schmitt S, Stengl A, Waller V, Hohmann N, Festini M, Ludwig A, Rohrbacher L, Herold T, Subklewe M, Götze KS, Hackenberger CPR, Schumacher D, Helma-Smets J, Jeremias I, Leonhardt H, Spiekermann K. Targeting FLT3 with a new-generation antibody-drug conjugate in combination with kinase inhibitors for treatment of AML. Blood 2023; 141:1023-1035. [PMID: 35981498 DOI: 10.1182/blood.2021015246] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 06/23/2022] [Accepted: 07/15/2022] [Indexed: 11/20/2022] Open
Abstract
Fms-like tyrosine kinase 3 (FLT3) is often overexpressed or constitutively activated by internal tandem duplication (ITD) and tyrosine kinase domain (TKD) mutations in acute myeloid leukemia (AML). Despite the use of receptor tyrosine kinase inhibitors (TKI) in FLT3-ITD-positive AML, the prognosis of patients is still poor, and further improvement of therapy is required. Targeting FLT3 independent of mutations by antibody-drug conjugates (ADCs) is a promising strategy for AML therapy. Here, we report the development and preclinical characterization of a novel FLT3-targeting ADC, 20D9-ADC, which was generated by applying the innovative P5 conjugation technology. In vitro, 20D9-ADC mediated potent cytotoxicity to Ba/F3 cells expressing transgenic FLT3 or FLT3-ITD, to AML cell lines, and to FLT3-ITD-positive patient-derived xenograft AML cells. In vivo, 20D9-ADC treatment led to a significant tumor reduction and even durable complete remission in AML xenograft models. Furthermore, 20D9-ADC demonstrated no severe hematotoxicity in in vitro colony formation assays using concentrations that were cytotoxic in AML cell line treatment. The combination of 20D9-ADC with the TKI midostaurin showed strong synergy in vitro and in vivo, leading to reduction of aggressive AML cells below the detection limit. Our data indicate that targeting FLT3 with an advanced new-generation ADC is a promising and potent antileukemic strategy, especially when combined with FLT3-TKI in FLT3-ITD-positive AML.
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Affiliation(s)
- Maike Roas
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site, Munich, Germany
- German Cancer Research Centre (DKFZ), Heidelberg, Germany
- Department of Biology II, Human Biology and Bioimaging, LMU Munich, Munich, Germany
| | - Binje Vick
- German Cancer Consortium (DKTK), Partner Site, Munich, Germany
- Research Unit Apoptosis in Hematopoietic Stem Cells (AHS), Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Munich, Germany
| | - Marc-André Kasper
- Chemical Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Campus Berlin, Berlin, Germany
- Department of Chemistry, Humboldt Universität zu Berlin, Berlin, Germany
- Tubulis GmbH, Munich, Germany
| | - Marina Able
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Harald Polzer
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site, Munich, Germany
- German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | | | - Elisabeth Kremmer
- Institute of Molecular Immunology, Helmholtz Zentrum München, German Research Center for Environmental Health, Core Facility Monoclonal Antibodies, Munich, Germany
| | - Judith S Hecker
- German Cancer Consortium (DKTK), Partner Site, Munich, Germany
- German Cancer Research Centre (DKFZ), Heidelberg, Germany
- Department of Medicine III, Technical University of Munich (TUM), Klinikum rechts der Isar, Munich, Germany
| | | | - Andreas Stengl
- Department of Biology II, Human Biology and Bioimaging, LMU Munich, Munich, Germany
| | - Verena Waller
- Department of Biology II, Human Biology and Bioimaging, LMU Munich, Munich, Germany
| | - Natascha Hohmann
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Moreno Festini
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Alexander Ludwig
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Lisa Rohrbacher
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
- Department of Translational Cancer Immunology, Gene Center Munich, LMU Munich, Munich, Germany
| | - Tobias Herold
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site, Munich, Germany
- German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Marion Subklewe
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site, Munich, Germany
- Department of Translational Cancer Immunology, Gene Center Munich, LMU Munich, Munich, Germany
| | - Katharina S Götze
- German Cancer Consortium (DKTK), Partner Site, Munich, Germany
- German Cancer Research Centre (DKFZ), Heidelberg, Germany
- Department of Medicine III, Technical University of Munich (TUM), Klinikum rechts der Isar, Munich, Germany
- Bavarian Cancer Research Center (BZKF), Munich, Germany
| | - Christian P R Hackenberger
- Chemical Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Campus Berlin, Berlin, Germany
- Department of Chemistry, Humboldt Universität zu Berlin, Berlin, Germany
| | - Dominik Schumacher
- Chemical Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Campus Berlin, Berlin, Germany
- Department of Chemistry, Humboldt Universität zu Berlin, Berlin, Germany
- Tubulis GmbH, Munich, Germany
| | - Jonas Helma-Smets
- Department of Biology II, Human Biology and Bioimaging, LMU Munich, Munich, Germany
- Tubulis GmbH, Munich, Germany
| | - Irmela Jeremias
- German Cancer Consortium (DKTK), Partner Site, Munich, Germany
- Research Unit Apoptosis in Hematopoietic Stem Cells (AHS), Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Munich, Germany
- Department of Pediatrics, Dr. von Hauner Children's Hospital, LMU Munich, Munich, Germany
| | - Heinrich Leonhardt
- Department of Biology II, Human Biology and Bioimaging, LMU Munich, Munich, Germany
- Tubulis GmbH, Munich, Germany
| | - Karsten Spiekermann
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site, Munich, Germany
- German Cancer Research Centre (DKFZ), Heidelberg, Germany
- Bavarian Cancer Research Center (BZKF), Munich, Germany
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11
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Ugur E, de la Porte A, Qin W, Bultmann S, Ivanova A, Drukker M, Mann M, Wierer M, Leonhardt H. Comprehensive chromatin proteomics resolves functional phases of pluripotency and identifies changes in regulatory components. Nucleic Acids Res 2023; 51:2671-2690. [PMID: 36806742 PMCID: PMC10085704 DOI: 10.1093/nar/gkad058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 01/11/2023] [Accepted: 01/19/2023] [Indexed: 02/22/2023] Open
Abstract
The establishment of cellular identity is driven by transcriptional and epigenetic regulators of the chromatin proteome - the chromatome. Comprehensive analyses of the chromatome composition and dynamics can therefore greatly improve our understanding of gene regulatory mechanisms. Here, we developed an accurate mass spectrometry (MS)-based proteomic method called Chromatin Aggregation Capture (ChAC) followed by Data-Independent Acquisition (DIA) and analyzed chromatome reorganizations during major phases of pluripotency. This enabled us to generate a comprehensive atlas of proteomes, chromatomes, and chromatin affinities for the ground, formative and primed pluripotency states, and to pinpoint the specific binding and rearrangement of regulatory components. These comprehensive datasets combined with extensive analyses identified phase-specific factors like QSER1 and JADE1/2/3 and provide a detailed foundation for an in-depth understanding of mechanisms that govern the phased progression of pluripotency. The technical advances reported here can be readily applied to other models in development and disease.
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Affiliation(s)
- Enes Ugur
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany.,Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried 82152, Germany
| | | | - Weihua Qin
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Sebastian Bultmann
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Alina Ivanova
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Micha Drukker
- Institute of Stem Cell Research, Helmholtz Center Munich, Neuherberg 85764, Germany.,Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Gorlaeus Building, 2333 CC RA Leiden, The Netherlands
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried 82152, Germany.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried 82152, Germany.,Proteomics Research Infrastructure, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Heinrich Leonhardt
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
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12
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Abuhasanein S, Hansen C, Vojinovic D, Jahnson S, Leonhardt H, Kjölhede H. Computed tomography urography with corticomedullary phase can exclude urinary bladder cancer with high accuracy. Eur Urol 2023. [DOI: 10.1016/s0302-2838(23)00644-9] [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: 02/12/2023]
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13
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Miyashita R, Nishiyama A, Qin W, Chiba Y, Kori S, Kato N, Konishi C, Kumamoto S, Kozuka-Hata H, Oyama M, Kawasoe Y, Tsurimoto T, Takahashi TS, Leonhardt H, Arita K, Nakanishi M. The termination of UHRF1-dependent PAF15 ubiquitin signaling is regulated by USP7 and ATAD5. eLife 2023; 12:79013. [PMID: 36734974 PMCID: PMC9943068 DOI: 10.7554/elife.79013] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 02/02/2023] [Indexed: 02/04/2023] Open
Abstract
UHRF1-dependent ubiquitin signaling plays an integral role in the regulation of maintenance DNA methylation. UHRF1 catalyzes transient dual mono-ubiquitylation of PAF15 (PAF15Ub2), which regulates the localization and activation of DNMT1 at DNA methylation sites during DNA replication. Although the initiation of UHRF1-mediated PAF15 ubiquitin signaling has been relatively well characterized, the mechanisms underlying its termination and how they are coordinated with the completion of maintenance DNA methylation have not yet been clarified. This study shows that deubiquitylation by USP7 and unloading by ATAD5 (ELG1 in yeast) are pivotal processes for the removal of PAF15 from chromatin. On replicating chromatin, USP7 specifically interacts with PAF15Ub2 in a complex with DNMT1. USP7 depletion or inhibition of the interaction between USP7 and PAF15 results in abnormal accumulation of PAF15Ub2 on chromatin. Furthermore, we also find that the non-ubiquitylated form of PAF15 (PAF15Ub0) is removed from chromatin in an ATAD5-dependent manner. PAF15Ub2 was retained at high levels on chromatin when the catalytic activity of DNMT1 was inhibited, suggesting that the completion of maintenance DNA methylation is essential for the termination of UHRF1-mediated ubiquitin signaling. This finding provides a molecular understanding of how the maintenance DNA methylation machinery is disassembled at the end of the S phase.
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Affiliation(s)
- Ryota Miyashita
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of TokyoTokyoJapan
| | - Atsuya Nishiyama
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of TokyoTokyoJapan
| | - Weihua Qin
- Faculty of Biology, Ludwig-Maximilians-Universität MünchenMunichGermany
| | - Yoshie Chiba
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of TokyoTokyoJapan
| | - Satomi Kori
- Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City UniversityYokohamaJapan
| | - Norie Kato
- Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City UniversityYokohamaJapan
| | - Chieko Konishi
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of TokyoTokyoJapan
| | - Soichiro Kumamoto
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of TokyoTokyoJapan
| | - Hiroko Kozuka-Hata
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of TokyoTokyoJapan
| | - Masaaki Oyama
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of TokyoTokyoJapan
| | - Yoshitaka Kawasoe
- Laboratory of Chromosome Biology, Department of Biology, Faculty of Science, Kyushu UniversityFukuokaJapan
| | - Toshiki Tsurimoto
- Laboratory of Chromosome Biology, Department of Biology, Faculty of Science, Kyushu UniversityFukuokaJapan
| | - Tatsuro S Takahashi
- Laboratory of Chromosome Biology, Department of Biology, Faculty of Science, Kyushu UniversityFukuokaJapan
| | | | - Kyohei Arita
- Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City UniversityYokohamaJapan
| | - Makoto Nakanishi
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of TokyoTokyoJapan
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14
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Palmér M, Åkesson Å, Marcickiewicz J, Blank E, Hogström L, Torle M, Mateoiu C, Dahm-Kähler P, Leonhardt H. Accuracy of transvaginal ultrasound versus MRI in the PreOperative Diagnostics of low-grade Endometrial Cancer (PODEC) study: a prospective multicentre study. Clin Radiol 2023; 78:70-79. [PMID: 36270868 DOI: 10.1016/j.crad.2022.09.118] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 09/01/2022] [Accepted: 09/02/2022] [Indexed: 01/07/2023]
Abstract
AIM To investigate if the diagnostic accuracy of transvaginal ultrasound (TVUS) performed by gynaecologists is sufficient for preoperative assessment of low-grade endometrial cancer (EC) compared to magnetic resonance imaging (MRI). MATERIALS AND METHODS MRI and TVUS performed by gynaecologists were assessed at the participating centres. The MRI examinations were interpreted by two radiologists at the tertiary centre. Deep myometrial and cervical stroma invasion were visually assessed and compared to postoperative histopathology. RESULTS Two hundred and fifty-nine patients were included. There was a statistically significant difference in specificity assessing deep myometrial invasion between MRI and TVUS (MRI 0.88, TVUS 0.68). There was no difference in sensitivity (MRI 0.73, TVUS 0.68). When assessing cervical stroma infiltration, MRI had a higher specificity (MRI 0.96, TVUS 0.90), but there was no difference in sensitivity (MRI 0.41, TVUS 0.32). CONCLUSION MRI has higher specificity than TVUS performed by gynaecologists for assessing deep MI and CSI in low-grade EC, but similar sensitivities. The use of TVUS as a first-line test, rather than MRI, may be supported by this study in centres where access to MRI may be limited.
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Affiliation(s)
- M Palmér
- Department of Radiology, Institute of Clinical Sciences, Sahlgrenska Academy at University of Gothenburg, Sweden
| | - Å Åkesson
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy at University of Gothenburg, Sweden
| | - J Marcickiewicz
- Department of Obstetrics and Gynaecology, Varberg Hospital, Varberg, Sweden
| | - E Blank
- Department of Obstetrics and Gynaecology, NU Hospital Group, Trollhättan, Sweden
| | - L Hogström
- Department of Obstetrics and Gynaecology, Skaraborg Hospital, Skövde, Sweden
| | - M Torle
- Department of Obstetrics and Gynaecology, Södra Älvsborg Hospital, Borås, Sweden
| | - C Mateoiu
- Department of Pathology, Sahlgrenska University Hospital, Göteborg, Sweden
| | - P Dahm-Kähler
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy at University of Gothenburg, Sweden
| | - H Leonhardt
- Department of Radiology, Institute of Clinical Sciences, Sahlgrenska Academy at University of Gothenburg, Sweden.
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15
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Schmacke NA, O'Duill F, Gaidt MM, Szymanska I, Kamper JM, Schmid-Burgk JL, Mädler SC, Mackens-Kiani T, Kozaki T, Chauhan D, Nagl D, Stafford CA, Harz H, Fröhlich AL, Pinci F, Ginhoux F, Beckmann R, Mann M, Leonhardt H, Hornung V. IKKβ primes inflammasome formation by recruiting NLRP3 to the trans-Golgi network. Immunity 2022; 55:2271-2284.e7. [PMID: 36384135 PMCID: PMC7614333 DOI: 10.1016/j.immuni.2022.10.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 07/17/2022] [Accepted: 10/26/2022] [Indexed: 11/17/2022]
Abstract
The NLRP3 inflammasome plays a central role in antimicrobial defense as well as in the context of sterile inflammatory conditions. NLRP3 activity is governed by two independent signals: the first signal primes NLRP3, rendering it responsive to the second signal, which then triggers inflammasome formation. Our understanding of how NLRP3 priming contributes to inflammasome activation remains limited. Here, we show that IKKβ, a kinase activated during priming, induces recruitment of NLRP3 to phosphatidylinositol-4-phosphate (PI4P), a phospholipid enriched on the trans-Golgi network. NEK7, a mitotic spindle kinase that had previously been thought to be indispensable for NLRP3 activation, was redundant for inflammasome formation when IKKβ recruited NLRP3 to PI4P. Studying iPSC-derived human macrophages revealed that the IKKβ-mediated NEK7-independent pathway constitutes the predominant NLRP3 priming mechanism in human myeloid cells. Our results suggest that PI4P binding represents a primed state into which NLRP3 is brought by IKKβ activity.
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Affiliation(s)
- Niklas A Schmacke
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Fionan O'Duill
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Moritz M Gaidt
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Inga Szymanska
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Julia M Kamper
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Jonathan L Schmid-Burgk
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Sophia C Mädler
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Timur Mackens-Kiani
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Tatsuya Kozaki
- Singapore Immunology Network (SIgN), Agency for Science, Technology & Research (A∗STAR), 8A Biomedical Grove, Immunos Building #3-4, Biopolis, Singapore 138648, Singapore
| | - Dhruv Chauhan
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Dennis Nagl
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Che A Stafford
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Hartmann Harz
- Faculty of Biology, Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Adrian L Fröhlich
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Francesca Pinci
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), Agency for Science, Technology & Research (A∗STAR), 8A Biomedical Grove, Immunos Building #3-4, Biopolis, Singapore 138648, Singapore; Shanghai Institute of Immunology, Shanghai JiaoTong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, China; Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore 169856, Singapore
| | - Roland Beckmann
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Heinrich Leonhardt
- Faculty of Biology, Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Veit Hornung
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany.
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16
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Hata K, Kobayashi N, Sugimura K, Qin W, Haxholli D, Chiba Y, Yoshimi S, Hayashi G, Onoda H, Ikegami T, Mulholland C, Nishiyama A, Nakanishi M, Leonhardt H, Konuma T, Arita K. Structural basis for the unique multifaceted interaction of DPPA3 with the UHRF1 PHD finger. Nucleic Acids Res 2022; 50:12527-12542. [PMID: 36420895 PMCID: PMC9757060 DOI: 10.1093/nar/gkac1082] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 06/03/2022] [Revised: 09/20/2022] [Accepted: 10/27/2022] [Indexed: 11/27/2022] Open
Abstract
Ubiquitin-like with PHD and RING finger domain-containing protein 1 (UHRF1)-dependent DNA methylation is essential for maintaining cell fate during cell proliferation. Developmental pluripotency-associated 3 (DPPA3) is an intrinsically disordered protein that specifically interacts with UHRF1 and promotes passive DNA demethylation by inhibiting UHRF1 chromatin localization. However, the molecular basis of how DPPA3 interacts with and inhibits UHRF1 remains unclear. We aimed to determine the structure of the mouse UHRF1 plant homeodomain (PHD) complexed with DPPA3 using nuclear magnetic resonance. Induced α-helices in DPPA3 upon binding of UHRF1 PHD contribute to stable complex formation with multifaceted interactions, unlike canonical ligand proteins of the PHD domain. Mutations in the binding interface and unfolding of the DPPA3 helical structure inhibited binding to UHRF1 and its chromatin localization. Our results provide structural insights into the mechanism and specificity underlying the inhibition of UHRF1 by DPPA3.
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Affiliation(s)
| | | | - Keita Sugimura
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Weihua Qin
- Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Deis Haxholli
- Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Yoshie Chiba
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Sae Yoshimi
- Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Gosuke Hayashi
- Department of Biomolecular Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Hiroki Onoda
- Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Takahisa Ikegami
- Structural Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | | | - Atsuya Nishiyama
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Makoto Nakanishi
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Heinrich Leonhardt
- Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Tsuyoshi Konuma
- Correspondence may also be addressed to Tsuyoshi Konuma. Tel: +81 45 508 7218; Fax: +81 45 508 7362;
| | - Kyohei Arita
- To whom correspondence should be addressed. Tel: +81 45 508 7225; Fax: +81 45 508 7365;
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17
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Perucca P, Cazzalini O, Mortusewicz O, Necchi D, Savio M, Nardo T, Stivala LA, Leonhardt H, Cardoso MC, Prosperi E. Expression of Concern: Spatiotemporal dynamics of p21CDKN1A protein recruitment to DNA-damage sites and interaction with proliferating cell nuclear antigen. J Cell Sci 2022; 135:279744. [DOI: 10.1242/jcs.260709] [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: 11/07/2022] Open
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18
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Qin W, Steinek C, Kolobynina K, Forné I, Imhof A, Cardoso M, Leonhardt H. Probing protein ubiquitination in live cells. Nucleic Acids Res 2022; 50:e125. [PMID: 36189882 PMCID: PMC9757074 DOI: 10.1093/nar/gkac805] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 03/08/2022] [Revised: 08/26/2022] [Accepted: 09/08/2022] [Indexed: 12/24/2022] Open
Abstract
The reversible attachment of ubiquitin governs the interaction, activity and degradation of proteins whereby the type and target of this conjugation determine the biological response. The investigation of this complex and multi-faceted protein ubiquitination mostly relies on painstaking biochemical analyses. Here, we employ recombinant binding domains to probe the ubiquitination of proteins in living cells. We immobilize GFP-fused proteins of interest at a distinct cellular structure and detect their ubiquitination state with red fluorescent ubiquitin binders. With this ubiquitin fluorescent three-hybrid (ubiF3H) assay we identified HP1β as a novel ubiquitination target of UHRF1. The use of linkage specific ubiquitin binding domains enabled the discrimination of K48 and K63 linked protein ubiquitination. To enhance signal-to-noise ratio, we implemented fluorescence complementation (ubiF3Hc) with split YFP. Using in addition a cell cycle marker we could show that HP1β is mostly ubiquitinated by UHRF1 during S phase and deubiquitinated by the protease USP7. With this complementation assay we could also directly detect the ubiquitination of the tumor suppressor p53 and monitor its inhibition by the anti-cancer drug Nutlin-3. Altogether, we demonstrate the utility of the ubiF3H assay to probe the ubiquitination of specific proteins and to screen for ligases, proteases and small molecules controlling this posttranslational modification.
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Affiliation(s)
- Weihua Qin
- Correspondence may also be addressed to Weihua Qin. Tel: +49 89 2180 71132; Fax: +49 89 2180 74236;
| | - Clemens Steinek
- Faculty of Biology, Ludwig-Maximilians-Universität München, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
| | - Ksenia Kolobynina
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Ignasi Forné
- Biomedical Center Munich, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Planegg-Martinsried, Germany
| | - Axel Imhof
- Biomedical Center Munich, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Planegg-Martinsried, Germany
| | - M Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Heinrich Leonhardt
- To whom correspondence should be addressed. Tel: +49 89 2180 74232; Fax: +49 89 2180 74236;
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19
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Stolz P, Mantero AS, Tvardovskiy A, Ugur E, Wange LE, Mulholland CB, Cheng Y, Wierer M, Enard W, Schneider R, Bartke T, Leonhardt H, Elsässer SJ, Bultmann S. TET1 regulates gene expression and repression of endogenous retroviruses independent of DNA demethylation. Nucleic Acids Res 2022; 50:8491-8511. [PMID: 35904814 PMCID: PMC9410877 DOI: 10.1093/nar/gkac642] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 04/25/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
DNA methylation (5-methylcytosine (5mC)) is critical for genome stability and transcriptional regulation in mammals. The discovery that ten-eleven translocation (TET) proteins catalyze the oxidation of 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) revolutionized our perspective on the complexity and regulation of DNA modifications. However, to what extent the regulatory functions of TET1 can be attributed to its catalytic activity remains unclear. Here, we use genome engineering and quantitative multi-omics approaches to dissect the precise catalytic vs. non-catalytic functions of TET1 in murine embryonic stem cells (mESCs). Our study identifies TET1 as an essential interaction hub for multiple chromatin modifying complexes and a global regulator of histone modifications. Strikingly, we find that the majority of transcriptional regulation depends on non-catalytic functions of TET1. In particular, we show that TET1 is critical for the establishment of H3K9me3 and H4K20me3 at endogenous retroviral elements (ERVs) and their silencing that is independent of its canonical role in DNA demethylation. Furthermore, we provide evidence that this repression of ERVs depends on the interaction between TET1 and SIN3A. In summary, we demonstrate that the non-catalytic functions of TET1 are critical for regulation of gene expression and the silencing of endogenous retroviruses in mESCs.
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Affiliation(s)
- Paul Stolz
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Angelo Salazar Mantero
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet 17165 Stockholm, Sweden, Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet 17177 Stockholm, Sweden
| | - Andrey Tvardovskiy
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Enes Ugur
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany.,Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Lucas E Wange
- Faculty of Biology, Anthropology and Human Genomics, Ludwig-Maximilians-Universität München 82152, Planegg-Martinsried, Germany
| | - Christopher B Mulholland
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Yuying Cheng
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet 17165 Stockholm, Sweden, Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet 17177 Stockholm, Sweden
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Wolfgang Enard
- Faculty of Biology, Anthropology and Human Genomics, Ludwig-Maximilians-Universität München 82152, Planegg-Martinsried, Germany
| | - Robert Schneider
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Till Bartke
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Heinrich Leonhardt
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Simon J Elsässer
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet 17165 Stockholm, Sweden, Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet 17177 Stockholm, Sweden
| | - Sebastian Bultmann
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
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20
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Zhang L, Isselstein M, Köhler J, Eleftheriadis N, Huisjes NM, Guirao‐Ortiz M, Narducci A, Smit JH, Stoffels J, Harz H, Leonhardt H, Herrmann A, Cordes T. Inside Back Cover: Linker Molecules Convert Commercial Fluorophores into Tailored Functional Probes during Biolabelling (Angew. Chem. Int. Ed. 19/2022). Angew Chem Int Ed Engl 2022. [DOI: 10.1002/anie.202205055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Lei Zhang
- Physical and Synthetic Biology Faculty of Biology Ludwig-Maximilians-Universität München Großhadernerstr. 2–4 82152 Planegg-Martinsried Germany
- Institute of Advanced Synthesis School of Chemistry and Molecular Engineering Nanjing Tech University Nanjing 211816 China
| | - Michael Isselstein
- Physical and Synthetic Biology Faculty of Biology Ludwig-Maximilians-Universität München Großhadernerstr. 2–4 82152 Planegg-Martinsried Germany
| | - Jens Köhler
- (DWI) Leibniz Institute for Interactive Materials Forckenbeckstr. 50 52056 Aachen Germany
- & Institute of Technical and Macromolecular Chemistry (RWTH) Aachen University Worringerweg 2 52074 Aachen Germany
| | - Nikolaos Eleftheriadis
- Molecular Microscopy Research Group Zernike Institute for Advanced Materials University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Nadia M. Huisjes
- Physical and Synthetic Biology Faculty of Biology Ludwig-Maximilians-Universität München Großhadernerstr. 2–4 82152 Planegg-Martinsried Germany
- Molecular Microscopy Research Group Zernike Institute for Advanced Materials University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Miguel Guirao‐Ortiz
- Human Biology & Bioimaging Faculty of Biology Ludwig-Maximilians-Universität München Großhadernerstr. 2–4 82152 Planegg-Martinsried Germany
| | - Alessandra Narducci
- Physical and Synthetic Biology Faculty of Biology Ludwig-Maximilians-Universität München Großhadernerstr. 2–4 82152 Planegg-Martinsried Germany
| | - Jochem H. Smit
- Molecular Microscopy Research Group Zernike Institute for Advanced Materials University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Janko Stoffels
- (DWI) Leibniz Institute for Interactive Materials Forckenbeckstr. 50 52056 Aachen Germany
- & Institute of Technical and Macromolecular Chemistry (RWTH) Aachen University Worringerweg 2 52074 Aachen Germany
| | - Hartmann Harz
- Human Biology & Bioimaging Faculty of Biology Ludwig-Maximilians-Universität München Großhadernerstr. 2–4 82152 Planegg-Martinsried Germany
| | - Heinrich Leonhardt
- Human Biology & Bioimaging Faculty of Biology Ludwig-Maximilians-Universität München Großhadernerstr. 2–4 82152 Planegg-Martinsried Germany
| | - Andreas Herrmann
- (DWI) Leibniz Institute for Interactive Materials Forckenbeckstr. 50 52056 Aachen Germany
- & Institute of Technical and Macromolecular Chemistry (RWTH) Aachen University Worringerweg 2 52074 Aachen Germany
| | - Thorben Cordes
- Physical and Synthetic Biology Faculty of Biology Ludwig-Maximilians-Universität München Großhadernerstr. 2–4 82152 Planegg-Martinsried Germany
- Molecular Microscopy Research Group Zernike Institute for Advanced Materials University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
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21
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Zhang L, Isselstein M, Köhler J, Eleftheriadis N, Huisjes NM, Guirao-Ortiz M, Narducci A, Smit JH, Stoffels J, Harz H, Leonhardt H, Herrmann A, Cordes T. Linker Molecules Convert Commercial Fluorophores into Tailored Functional Probes during Biolabelling. Angew Chem Int Ed Engl 2022; 61:e202112959. [PMID: 35146855 PMCID: PMC9305292 DOI: 10.1002/anie.202112959] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Indexed: 12/27/2022]
Abstract
Many life‐science techniques and assays rely on selective labeling of biological target structures with commercial fluorophores that have specific yet invariant properties. Consequently, a fluorophore (or dye) is only useful for a limited range of applications, e.g., as a label for cellular compartments, super‐resolution imaging, DNA sequencing or for a specific biomedical assay. Modifications of fluorophores with the goal to alter their bioconjugation chemistry, photophysical or functional properties typically require complex synthesis schemes. We here introduce a general strategy that allows to customize these properties during biolabelling with the goal to introduce the fluorophore in the last step of biolabelling. For this, we present the design and synthesis of ‘linker’ compounds, that bridge biotarget, fluorophore and a functional moiety via well‐established labeling protocols. Linker molecules were synthesized via the Ugi four‐component reaction (Ugi‐4CR) which facilitates a modular design of linkers with diverse functional properties and bioconjugation‐ and fluorophore attachment moieties. To demonstrate the possibilities of different linkers experimentally, we characterized the ability of commercial fluorophores from the classes of cyanines, rhodamines, carbopyronines and silicon‐rhodamines to become functional labels on different biological targets in vitro and in vivo via thiol‐maleimide chemistry. With our strategy, we showed that the same commercial dye can become a photostable self‐healing dye or a sensor for bivalent ions subject to the linker used. Finally, we quantified the photophysical performance of different self‐healing linker–fluorophore conjugates and demonstrated their applications in super‐resolution imaging and single‐molecule spectroscopy.
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Affiliation(s)
- Lei Zhang
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany.,Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Michael Isselstein
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Jens Köhler
- (DWI) Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany.,& Institute of Technical and Macromolecular Chemistry, (RWTH) Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Nikolaos Eleftheriadis
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Nadia M Huisjes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany.,Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Miguel Guirao-Ortiz
- Human Biology & Bioimaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Alessandra Narducci
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Jochem H Smit
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Janko Stoffels
- (DWI) Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany.,& Institute of Technical and Macromolecular Chemistry, (RWTH) Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Hartmann Harz
- Human Biology & Bioimaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Heinrich Leonhardt
- Human Biology & Bioimaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Andreas Herrmann
- (DWI) Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany.,& Institute of Technical and Macromolecular Chemistry, (RWTH) Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany.,Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
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22
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Zhang L, Isselstein M, Köhler J, Eleftheriadis N, Huisjes NM, Guirao‐Ortiz M, Narducci A, Smit JH, Stoffels J, Harz H, Leonhardt H, Herrmann A, Cordes T. Innenrücktitelbild: Linker Molecules Convert Commercial Fluorophores into Tailored Functional Probes during Biolabelling (Angew. Chem. 19/2022). Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202205055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Lei Zhang
- Physical and Synthetic Biology Faculty of Biology Ludwig-Maximilians-Universität München Großhadernerstr. 2–4 82152 Planegg-Martinsried Germany
- Institute of Advanced Synthesis School of Chemistry and Molecular Engineering Nanjing Tech University Nanjing 211816 China
| | - Michael Isselstein
- Physical and Synthetic Biology Faculty of Biology Ludwig-Maximilians-Universität München Großhadernerstr. 2–4 82152 Planegg-Martinsried Germany
| | - Jens Köhler
- (DWI) Leibniz Institute for Interactive Materials Forckenbeckstr. 50 52056 Aachen Germany
- & Institute of Technical and Macromolecular Chemistry (RWTH) Aachen University Worringerweg 2 52074 Aachen Germany
| | - Nikolaos Eleftheriadis
- Molecular Microscopy Research Group Zernike Institute for Advanced Materials University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Nadia M. Huisjes
- Physical and Synthetic Biology Faculty of Biology Ludwig-Maximilians-Universität München Großhadernerstr. 2–4 82152 Planegg-Martinsried Germany
- Molecular Microscopy Research Group Zernike Institute for Advanced Materials University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Miguel Guirao‐Ortiz
- Human Biology & Bioimaging Faculty of Biology Ludwig-Maximilians-Universität München Großhadernerstr. 2–4 82152 Planegg-Martinsried Germany
| | - Alessandra Narducci
- Physical and Synthetic Biology Faculty of Biology Ludwig-Maximilians-Universität München Großhadernerstr. 2–4 82152 Planegg-Martinsried Germany
| | - Jochem H. Smit
- Molecular Microscopy Research Group Zernike Institute for Advanced Materials University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Janko Stoffels
- (DWI) Leibniz Institute for Interactive Materials Forckenbeckstr. 50 52056 Aachen Germany
- & Institute of Technical and Macromolecular Chemistry (RWTH) Aachen University Worringerweg 2 52074 Aachen Germany
| | - Hartmann Harz
- Human Biology & Bioimaging Faculty of Biology Ludwig-Maximilians-Universität München Großhadernerstr. 2–4 82152 Planegg-Martinsried Germany
| | - Heinrich Leonhardt
- Human Biology & Bioimaging Faculty of Biology Ludwig-Maximilians-Universität München Großhadernerstr. 2–4 82152 Planegg-Martinsried Germany
| | - Andreas Herrmann
- (DWI) Leibniz Institute for Interactive Materials Forckenbeckstr. 50 52056 Aachen Germany
- & Institute of Technical and Macromolecular Chemistry (RWTH) Aachen University Worringerweg 2 52074 Aachen Germany
| | - Thorben Cordes
- Physical and Synthetic Biology Faculty of Biology Ludwig-Maximilians-Universität München Großhadernerstr. 2–4 82152 Planegg-Martinsried Germany
- Molecular Microscopy Research Group Zernike Institute for Advanced Materials University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
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23
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Brandstetter K, Zülske T, Ragoczy T, Hörl D, Guirao-Ortiz M, Steinek C, Barnes T, Stumberger G, Schwach J, Haugen E, Rynes E, Korber P, Stamatoyannopoulos JA, Leonhardt H, Wedemann G, Harz H. Differences in nanoscale organization of regulatory active and inactive human chromatin. Biophys J 2022; 121:977-990. [PMID: 35150617 PMCID: PMC8943813 DOI: 10.1016/j.bpj.2022.02.009] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 12/11/2021] [Accepted: 02/07/2022] [Indexed: 11/25/2022] Open
Abstract
Methodological advances in conformation capture techniques have fundamentally changed our understanding of chromatin architecture. However, the nanoscale organization of chromatin and its cell-to-cell variance are less studied. Analyzing genome-wide data from 733 human cell and tissue samples, we identified 2 prototypical regions that exhibit high or absent hypersensitivity to deoxyribonuclease I, respectively. These regulatory active or inactive regions were examined in the lymphoblast cell line K562 by using high-throughput super-resolution microscopy. In both regions, we systematically measured the physical distance of 2 fluorescence in situ hybridization spots spaced by only 5 kb of DNA. Unexpectedly, the resulting distance distributions range from very compact to almost elongated configurations of more than 200-nm length for both the active and inactive regions. Monte Carlo simulations of a coarse-grained model of these chromatin regions based on published data of nucleosome occupancy in K562 cells were performed to understand the underlying mechanisms. There was no parameter set for the simulation model that can explain the microscopically measured distance distributions. Obviously, the chromatin state given by the strength of internucleosomal interaction, nucleosome occupancy, or amount of histone H1 differs from cell to cell, which results in the observed broad distance distributions. This large variability was not expected, especially in inactive regions. The results for the mechanisms for different distance distributions on this scale are important for understanding the contacts that mediate gene regulation. Microscopic measurements show that the inactive region investigated here is expected to be embedded in a more compact chromatin environment. The simulation results of this region require an increase in the strength of internucleosomal interactions. It may be speculated that the higher density of chromatin is caused by the increased internucleosomal interaction strength.
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Affiliation(s)
- Katharina Brandstetter
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Tilo Zülske
- Competence Center Bioinformatics, Institute for Applied Computer Science, Hochschule Stralsund, Stralsund, Germany
| | - Tobias Ragoczy
- Altius Institute for Biomedical Sciences, Seattle, Washington
| | - David Hörl
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Miguel Guirao-Ortiz
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Clemens Steinek
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Toby Barnes
- Biomedical Center (BMC), Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Gabriela Stumberger
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jonathan Schwach
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Eric Haugen
- Altius Institute for Biomedical Sciences, Seattle, Washington
| | - Eric Rynes
- Altius Institute for Biomedical Sciences, Seattle, Washington
| | - Philipp Korber
- Biomedical Center (BMC), Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - John A Stamatoyannopoulos
- Altius Institute for Biomedical Sciences, Seattle, Washington; Department of Genome Sciences, University of Washington, Seattle, Washington; Department of Medicine, Division of Oncology, University of Washington, Seattle, Washington
| | - Heinrich Leonhardt
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gero Wedemann
- Competence Center Bioinformatics, Institute for Applied Computer Science, Hochschule Stralsund, Stralsund, Germany.
| | - Hartmann Harz
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany.
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24
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Leidescher S, Ribisel J, Ullrich S, Feodorova Y, Hildebrand E, Galitsyna A, Bultmann S, Link S, Thanisch K, Mulholland C, Dekker J, Leonhardt H, Mirny L, Solovei I. Spatial organization of transcribed eukaryotic genes. Nat Cell Biol 2022; 24:327-339. [PMID: 35177821 DOI: 10.1038/s41556-022-00847-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 01/10/2022] [Indexed: 12/19/2022]
Abstract
Despite the well-established role of nuclear organization in the regulation of gene expression, little is known about the reverse: how transcription shapes the spatial organization of the genome. Owing to the small sizes of most previously studied genes and the limited resolution of microscopy, the structure and spatial arrangement of a single transcribed gene are still poorly understood. Here we study several long highly expressed genes and demonstrate that they form open-ended transcription loops with polymerases moving along the loops and carrying nascent RNAs. Transcription loops can span across micrometres, resembling lampbrush loops and polytene puffs. The extension and shape of transcription loops suggest their intrinsic stiffness, which we attribute to decoration with multiple voluminous nascent ribonucleoproteins. Our data contradict the model of transcription factories and suggest that although microscopically resolvable transcription loops are specific for long highly expressed genes, the mechanisms underlying their formation could represent a general aspect of eukaryotic transcription.
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Affiliation(s)
- Susanne Leidescher
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany
| | - Johannes Ribisel
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Simon Ullrich
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany
| | - Yana Feodorova
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany.,Department of Medical Biology, Medical University of Plovdiv; Division of Molecular and Regenerative Medicine, Research Institute at Medical University of Plovdiv, Plovdiv, Bulgaria
| | - Erica Hildebrand
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | | | - Sebastian Bultmann
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany
| | - Stephanie Link
- BioMedizinisches Center, Ludwig-Maximilians University Munich, Planegg-Martinsried, Germany
| | - Katharina Thanisch
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany.,Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Christopher Mulholland
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Heinrich Leonhardt
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany
| | - Leonid Mirny
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Irina Solovei
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany.
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25
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Zhang H, Romero H, Schmidt A, Gagova K, Qin W, Bertulat B, Lehmkuhl A, Milden M, Eck M, Meckel T, Leonhardt H, Cardoso MC. MeCP2-induced heterochromatin organization is driven by oligomerization-based liquid–liquid phase separation and restricted by DNA methylation. Nucleus 2022; 13:1-34. [PMID: 35156529 PMCID: PMC8855868 DOI: 10.1080/19491034.2021.2024691] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Hui Zhang
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Hector Romero
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Annika Schmidt
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Katalina Gagova
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Weihua Qin
- Faculty of Biology, Ludwig Maximilians University Munich, Munich, Germany
| | - Bianca Bertulat
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Anne Lehmkuhl
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Manuela Milden
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Malte Eck
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Tobias Meckel
- Department of Chemistry, Technical University of Darmstadt, Darmstadt, Germany
| | - Heinrich Leonhardt
- Faculty of Biology, Ludwig Maximilians University Munich, Munich, Germany
| | - M. Cristina Cardoso
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
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26
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Zhang L, Isselstein M, Köhler J, Eleftheriadis N, Huisjes N, Guirao M, Narducci A, Smit J, Stoffels J, Harz H, Leonhardt H, Herrmann A, Cordes T. Linker Molecules Convert Commercial Fluorophores into Tailored Functional Probes during Bio‐labeling. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202112959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Lei Zhang
- LMU München: Ludwig-Maximilians-Universitat Munchen Biocenter GERMANY
| | | | - Jens Köhler
- DWI-Leibniz-Institut für Interaktive Materialien: DWI-Leibniz-Institut fur Interaktive Materialien Chemie GERMANY
| | | | - Nadia Huisjes
- RUG: Rijksuniversiteit Groningen Zernike NETHERLANDS
| | - Miguel Guirao
- LMU München: Ludwig-Maximilians-Universitat Munchen Biocenter GERMANY
| | | | - Jochem Smit
- RUG: Rijksuniversiteit Groningen Zernike NETHERLANDS
| | - Janko Stoffels
- DWI-Leibniz-Institut für Interaktive Materialien: DWI-Leibniz-Institut fur Interaktive Materialien Chemistry GERMANY
| | - Hartmann Harz
- LMU München: Ludwig-Maximilians-Universitat Munchen Biocenter GERMANY
| | | | - Andreas Herrmann
- DWI-Leibniz-Institut für Interaktive Materialien: DWI-Leibniz-Institut fur Interaktive Materialien Chemistry GERMANY
| | - Thorben Cordes
- Ludwig-Maximilians-Universitat Munchen Faculty of Biology Großhadernerstr. 2-4 82152 Planegg-Martiensried GERMANY
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27
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Jakubke C, Roussou R, Maiser A, Schug C, Thoma F, Bunk D, Hörl D, Leonhardt H, Walter P, Klecker T, Osman C. Cristae-dependent quality control of the mitochondrial genome. Sci Adv 2021; 7:eabi8886. [PMID: 34516914 PMCID: PMC8442932 DOI: 10.1126/sciadv.abi8886] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/08/2021] [Indexed: 06/10/2023]
Abstract
Mitochondrial genomes (mtDNA) encode essential subunits of the mitochondrial respiratory chain. Mutations in mtDNA can cause a shortage in cellular energy supply, which can lead to numerous mitochondrial diseases. How cells secure mtDNA integrity over generations has remained unanswered. Here, we show that the single-celled yeast Saccharomyces cerevisiae can intracellularly distinguish between functional and defective mtDNA and promote generation of daughter cells with increasingly healthy mtDNA content. Purifying selection for functional mtDNA occurs in a continuous mitochondrial network and does not require mitochondrial fission but necessitates stable mitochondrial subdomains that depend on intact cristae morphology. Our findings support a model in which cristae-dependent proximity between mtDNA and the proteins it encodes creates a spatial “sphere of influence,” which links a lack of functional fitness to clearance of defective mtDNA.
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Affiliation(s)
- Christopher Jakubke
- Faculty of Biology, Ludwig-Maximilian-Universität München, 82152 Planegg-Martinsried, Germany
- Graduate School Life Science Munich, Planegg, Germany
| | - Rodaria Roussou
- Faculty of Biology, Ludwig-Maximilian-Universität München, 82152 Planegg-Martinsried, Germany
- Graduate School Life Science Munich, Planegg, Germany
| | - Andreas Maiser
- Faculty of Biology, Ludwig-Maximilian-Universität München, 82152 Planegg-Martinsried, Germany
| | | | - Felix Thoma
- Faculty of Biology, Ludwig-Maximilian-Universität München, 82152 Planegg-Martinsried, Germany
- Graduate School Life Science Munich, Planegg, Germany
| | - David Bunk
- Faculty of Biology, Ludwig-Maximilian-Universität München, 82152 Planegg-Martinsried, Germany
| | - David Hörl
- Faculty of Biology, Ludwig-Maximilian-Universität München, 82152 Planegg-Martinsried, Germany
| | - Heinrich Leonhardt
- Faculty of Biology, Ludwig-Maximilian-Universität München, 82152 Planegg-Martinsried, Germany
| | - Peter Walter
- Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Physiology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Till Klecker
- Zellbiologie, Universität Bayreuth, 95440 Bayreuth, Germany
| | - Christof Osman
- Faculty of Biology, Ludwig-Maximilian-Universität München, 82152 Planegg-Martinsried, Germany
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28
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Qin W, Ugur E, Mulholland CB, Bultmann S, Solovei I, Modic M, Smets M, Wierer M, Forné I, Imhof A, Cardoso MC, Leonhardt H. Phosphorylation of the HP1β hinge region sequesters KAP1 in heterochromatin and promotes the exit from naïve pluripotency. Nucleic Acids Res 2021; 49:7406-7423. [PMID: 34214177 PMCID: PMC8287961 DOI: 10.1093/nar/gkab548] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/31/2021] [Accepted: 06/11/2021] [Indexed: 12/26/2022] Open
Abstract
Heterochromatin binding protein HP1β plays an important role in chromatin organization and cell differentiation, however the underlying mechanisms remain unclear. Here, we generated HP1β−/− embryonic stem cells and observed reduced heterochromatin clustering and impaired differentiation. We found that during stem cell differentiation, HP1β is phosphorylated at serine 89 by CK2, which creates a binding site for the pluripotency regulator KAP1. This phosphorylation dependent sequestration of KAP1 in heterochromatin compartments causes a downregulation of pluripotency factors and triggers pluripotency exit. Accordingly, HP1β−/− and phospho-mutant cells exhibited impaired differentiation, while ubiquitination-deficient KAP1−/− cells had the opposite phenotype with enhanced differentiation. These results suggest that KAP1 regulates pluripotency via its ubiquitination activity. We propose that the formation of subnuclear membraneless heterochromatin compartments may serve as a dynamic reservoir to trap or release cellular factors. The sequestration of essential regulators defines a novel and active role of heterochromatin in gene regulation and represents a dynamic mode of remote control to regulate cellular processes like cell fate decisions.
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Affiliation(s)
- Weihua Qin
- Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstraße 1, D-81377 Munich, Germany
| | - Enes Ugur
- Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstraße 1, D-81377 Munich, Germany.,Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Christopher B Mulholland
- Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstraße 1, D-81377 Munich, Germany
| | - Sebastian Bultmann
- Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstraße 1, D-81377 Munich, Germany
| | - Irina Solovei
- Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstraße 1, D-81377 Munich, Germany
| | - Miha Modic
- The Francis Crick Institute and UCL Queen Square Institute of Neurology, London NW1 1AT, United Kingdom
| | - Martha Smets
- Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstraße 1, D-81377 Munich, Germany
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Ignasi Forné
- Biomedical Center Munich, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Planegg-Martinsried, Germany
| | - Axel Imhof
- Biomedical Center Munich, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Planegg-Martinsried, Germany
| | - M Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Heinrich Leonhardt
- Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstraße 1, D-81377 Munich, Germany
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29
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Duan N, Arroyo M, Deng W, Cardoso MC, Leonhardt H. Visualization and characterization of RNA-protein interactions in living cells. Nucleic Acids Res 2021; 49:e107. [PMID: 34313753 PMCID: PMC8501972 DOI: 10.1093/nar/gkab614] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 05/14/2021] [Accepted: 07/07/2021] [Indexed: 12/26/2022] Open
Abstract
RNA–protein interactions are the structural and functional basis of significant numbers of RNA molecules. RNA–protein interaction assays though, still mainly depend on biochemical tests in vitro. Here, we establish a convenient and reliable RNA fluorescent three-hybrid (rF3H) method to detect/interrogate the interactions between RNAs and proteins in cells. A GFP tagged highly specific RNA trap is constructed to anchor the RNA of interest to an artificial or natural subcellular structure, and RNA–protein interactions can be detected and visualized by the enrichment of RNA binding proteins (RBPs) at these structures. Different RNA trapping systems are developed and detection of RNA–protein complexes at multiple subcellular structures are assayed. With this new toolset, interactions between proteins and mRNA or noncoding RNAs are characterized, including the interaction between a long noncoding RNA and an epigenetic modulator. Our approach provides a flexible and reliable method for the characterization of RNA–protein interactions in living cells.
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Affiliation(s)
- Ningjun Duan
- Department of Biology II, Ludwig Maximilians University Munich, Munich 81377, Germany.,Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Maria Arroyo
- Department of Biology, Technical University of Darmstadt, Darmstadt 64287, Germany
| | - Wen Deng
- Department of Biology II, Ludwig Maximilians University Munich, Munich 81377, Germany.,College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - M Cristina Cardoso
- Department of Biology, Technical University of Darmstadt, Darmstadt 64287, Germany
| | - Heinrich Leonhardt
- Department of Biology II, Ludwig Maximilians University Munich, Munich 81377, Germany
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30
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Levone BR, Lenzken SC, Antonaci M, Maiser A, Rapp A, Conte F, Reber S, Mechtersheimer J, Ronchi AE, Mühlemann O, Leonhardt H, Cardoso MC, Ruepp MD, Barabino SM. FUS-dependent liquid-liquid phase separation is important for DNA repair initiation. J Cell Biol 2021; 220:e202008030. [PMID: 33704371 PMCID: PMC7953258 DOI: 10.1083/jcb.202008030] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 01/17/2021] [Accepted: 02/04/2021] [Indexed: 12/17/2022] Open
Abstract
RNA-binding proteins (RBPs) are emerging as important effectors of the cellular DNA damage response (DDR). The RBP FUS is implicated in RNA metabolism and DNA repair, and it undergoes reversible liquid-liquid phase separation (LLPS) in vitro. Here, we demonstrate that FUS-dependent LLPS is necessary for the initiation of the DDR. Using laser microirradiation in FUS-knockout cells, we show that FUS is required for the recruitment to DNA damage sites of the DDR factors KU80, NBS1, and 53BP1 and of SFPQ, another RBP implicated in the DDR. The relocation of KU80, NBS1, and SFPQ is similarly impaired by LLPS inhibitors, or LLPS-deficient FUS variants. We also show that LLPS is necessary for efficient γH2AX foci formation. Finally, using superresolution structured illumination microscopy, we demonstrate that the absence of FUS impairs the proper arrangement of γH2AX nanofoci into higher-order clusters. These findings demonstrate the early requirement for FUS-dependent LLPS in the activation of the DDR and the proper assembly of DSB repair complexes.
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Affiliation(s)
- Brunno R. Levone
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Silvia C. Lenzken
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Marco Antonaci
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Andreas Maiser
- Department of Biology II, Center for Integrated Protein Science Munich, Ludwig Maximilian University of Munich, Planegg-Martinsried, Germany
| | - Alexander Rapp
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Francesca Conte
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Stefan Reber
- UK Dementia Research Institute, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, UK
| | - Jonas Mechtersheimer
- UK Dementia Research Institute, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, UK
| | - Antonella E. Ronchi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Oliver Mühlemann
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Heinrich Leonhardt
- Department of Biology II, Center for Integrated Protein Science Munich, Ludwig Maximilian University of Munich, Planegg-Martinsried, Germany
| | - M. Cristina Cardoso
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Marc-David Ruepp
- UK Dementia Research Institute, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, UK
| | - Silvia M.L. Barabino
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
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31
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Lei J, Ma-Lauer Y, Han Y, Thoms M, Buschauer R, Jores J, Thiel V, Beckmann R, Deng W, Leonhardt H, Hilgenfeld R, von Brunn A. The SARS-unique domain (SUD) of SARS-CoV and SARS-CoV-2 interacts with human Paip1 to enhance viral RNA translation. EMBO J 2021; 40:e102277. [PMID: 33876849 PMCID: PMC8167360 DOI: 10.15252/embj.2019102277] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [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: 04/18/2019] [Revised: 03/04/2021] [Accepted: 03/17/2021] [Indexed: 02/05/2023] Open
Abstract
The ongoing outbreak of severe acute respiratory syndrome (SARS) coronavirus 2 (SARS‐CoV‐2) demonstrates the continuous threat of emerging coronaviruses (CoVs) to public health. SARS‐CoV‐2 and SARS‐CoV share an otherwise non‐conserved part of non‐structural protein 3 (Nsp3), therefore named as “SARS‐unique domain” (SUD). We previously found a yeast‐2‐hybrid screen interaction of the SARS‐CoV SUD with human poly(A)‐binding protein (PABP)‐interacting protein 1 (Paip1), a stimulator of protein translation. Here, we validate SARS‐CoV SUD:Paip1 interaction by size‐exclusion chromatography, split‐yellow fluorescent protein, and co‐immunoprecipitation assays, and confirm such interaction also between the corresponding domain of SARS‐CoV‐2 and Paip1. The three‐dimensional structure of the N‐terminal domain of SARS‐CoV SUD (“macrodomain II”, Mac2) in complex with the middle domain of Paip1, determined by X‐ray crystallography and small‐angle X‐ray scattering, provides insights into the structural determinants of the complex formation. In cellulo, SUD enhances synthesis of viral but not host proteins via binding to Paip1 in pBAC‐SARS‐CoV replicon‐transfected cells. We propose a possible mechanism for stimulation of viral translation by the SUD of SARS‐CoV and SARS‐CoV‐2.
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Affiliation(s)
- Jian Lei
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Lübeck, Germany.,German Center for Infection Research (DZIF), Hamburg-Lübeck- Borstel-Riems Site, University of Lübeck, Lübeck, Germany.,State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Yue Ma-Lauer
- Max-von-Pettenkofer Institute, Ludwig-Maximilians-University Munich, Munich, Germany.,German Center for Infection Research (DZIF), Munich, Germany
| | - Yinze Han
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Matthias Thoms
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Robert Buschauer
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Joerg Jores
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Volker Thiel
- Institute of Virology and Immunology, University of Bern, Bern, Switzerland
| | - Roland Beckmann
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Wen Deng
- Department of Biology and Center for Integrated Protein Science, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany.,College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Heinrich Leonhardt
- Department of Biology and Center for Integrated Protein Science, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Rolf Hilgenfeld
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Lübeck, Germany.,German Center for Infection Research (DZIF), Hamburg-Lübeck- Borstel-Riems Site, University of Lübeck, Lübeck, Germany.,Institute of Molecular Medicine, University of Lübeck, Lübeck, Germany
| | - Albrecht von Brunn
- Max-von-Pettenkofer Institute, Ludwig-Maximilians-University Munich, Munich, Germany.,German Center for Infection Research (DZIF), Munich, Germany
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32
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Schwach J, Kolobynina K, Brandstetter K, Gerlach M, Ochtrop P, Helma J, Hackenberger CPR, Harz H, Cardoso MC, Leonhardt H, Stengl A. Site-Specific Antibody Fragment Conjugates for Reversible Staining in Fluorescence Microscopy. Chembiochem 2021; 22:1205-1209. [PMID: 33207032 PMCID: PMC8048457 DOI: 10.1002/cbic.202000727] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 10/21/2020] [Revised: 11/17/2020] [Indexed: 12/16/2022]
Abstract
Antibody conjugates have taken a great leap forward as tools in basic and applied molecular life sciences that was enabled by the development of chemoselective reactions for the site-specific modification of proteins. Antibody-oligonucleotide conjugates combine the antibody's target specificity with the reversible, sequence-encoded binding properties of oligonucleotides like DNAs or peptide nucleic acids (PNAs), allowing sequential imaging of large numbers of targets in a single specimen. In this report, we use the Tub-tag® technology in combination with Cu-catalyzed azide-alkyne cycloaddition for the site-specific conjugation of single DNA and PNA strands to an eGFP-binding nanobody. We show binding of the conjugate to recombinant eGFP and subsequent sequence-specific annealing of fluorescently labelled imager strands. Furthermore, we reversibly stain eGFP-tagged proteins in human cells, thus demonstrating the suitability of our conjugation strategy to generate antibody-oligonucleotides for reversible immunofluorescence imaging.
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Affiliation(s)
- Jonathan Schwach
- Ludwig-Maximilians-Universität MünchenDepartment of Biology II, Human Biology and BioImaging82152Planegg-MartinsriedGermany
| | - Ksenia Kolobynina
- Technical University of DarmstadtDepartment of Biology, Cell Biology and EpigeneticsSchnittspahnstr. 1064287DarmstadtGermany
| | - Katharina Brandstetter
- Ludwig-Maximilians-Universität MünchenDepartment of Biology II, Human Biology and BioImaging82152Planegg-MartinsriedGermany
| | - Marcus Gerlach
- Tubulis GmbH, BioSysMButenandtstrasse 181377MunichGermany
| | - Philipp Ochtrop
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Department Chemical BiologyRobert-Rössle-Strasse 1013125BerlinGermany
| | - Jonas Helma
- Tubulis GmbH, BioSysMButenandtstrasse 181377MunichGermany
| | - Christian P. R. Hackenberger
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Department Chemical BiologyRobert-Rössle-Strasse 1013125BerlinGermany
- Humboldt Universität zu BerlinDepartment of ChemistryBrook-Taylor-Strasse 212489BerlinGermany
| | - Hartmann Harz
- Ludwig-Maximilians-Universität MünchenDepartment of Biology II, Human Biology and BioImaging82152Planegg-MartinsriedGermany
| | - M. Cristina Cardoso
- Technical University of DarmstadtDepartment of Biology, Cell Biology and EpigeneticsSchnittspahnstr. 1064287DarmstadtGermany
| | - Heinrich Leonhardt
- Ludwig-Maximilians-Universität MünchenDepartment of Biology II, Human Biology and BioImaging82152Planegg-MartinsriedGermany
| | - Andreas Stengl
- Ludwig-Maximilians-Universität MünchenDepartment of Biology II, Human Biology and BioImaging82152Planegg-MartinsriedGermany
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33
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Schwach J, Kolobynina K, Brandstetter K, Gerlach M, Ochtrop P, Helma J, Hackenberger CPR, Harz H, Cardoso MC, Leonhardt H, Stengl A. Cover Feature: Site‐Specific Antibody Fragment Conjugates for Reversible Staining in Fluorescence Microscopy (7/2021). Chembiochem 2021. [DOI: 10.1002/cbic.202100115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jonathan Schwach
- Ludwig-Maximilians-Universität München Department of Biology II, Human Biology and BioImaging 82152 Planegg-Martinsried Germany
| | - Ksenia Kolobynina
- Technical University of Darmstadt Department of Biology, Cell Biology and Epigenetics Schnittspahnstrasse 10 64287 Darmstadt Germany
| | - Katharina Brandstetter
- Ludwig-Maximilians-Universität München Department of Biology II, Human Biology and BioImaging 82152 Planegg-Martinsried Germany
| | - Marcus Gerlach
- Tubulis GmbH, BioSysM Butenandtstrasse 1 81377 Munich Germany
| | - Philipp Ochtrop
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Department Chemical Biology Robert-Rössle-Strasse 10 13125 Berlin Germany
| | - Jonas Helma
- Tubulis GmbH, BioSysM Butenandtstrasse 1 81377 Munich Germany
| | - Christian P. R. Hackenberger
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Department Chemical Biology Robert-Rössle-Strasse 10 13125 Berlin Germany
- Humboldt Universität zu Berlin Department of Chemistry Brook-Taylor-Strasse 2 12489 Berlin Germany
| | - Hartmann Harz
- Ludwig-Maximilians-Universität München Department of Biology II, Human Biology and BioImaging 82152 Planegg-Martinsried Germany
| | - M. Cristina Cardoso
- Technical University of Darmstadt Department of Biology, Cell Biology and Epigenetics Schnittspahnstrasse 10 64287 Darmstadt Germany
| | - Heinrich Leonhardt
- Ludwig-Maximilians-Universität München Department of Biology II, Human Biology and BioImaging 82152 Planegg-Martinsried Germany
| | - Andreas Stengl
- Ludwig-Maximilians-Universität München Department of Biology II, Human Biology and BioImaging 82152 Planegg-Martinsried Germany
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34
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Abstract
Liquid-liquid phase separation (LLPS) mediated formation of membraneless organelles has been proposed to coordinate biological processes in space and time. Previously, the formation of phase-separated droplets was described as a unique property of HP1α. Here, we demonstrate that the positive net charge of the intrinsically disordered hinge region (IDR-H) of HP1 proteins is critical for phase separation and that the exchange of four acidic amino acids is sufficient to confer LLPS properties to HP1β. Surprisingly, the addition of mono-nucleosomes promoted H3K9me3-dependent LLPS of HP1β which could be specifically disrupted with methylated but not acetylated H3K9 peptides. HP1β mutants defective in H3K9me3 binding were less efficient in phase separationin vitro and failed to accumulate at heterochromatin in vivo. We propose that multivalent interactions of HP1β with H3K9me3-modified nucleosomes via its chromodomain and dimerization via its chromoshadow domain enable phase separation and contribute to the formation of heterochromatin compartments in vivo.
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Affiliation(s)
- Weihua Qin
- Center for Molecular Biosystems (BioSysM), Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Andreas Stengl
- Center for Molecular Biosystems (BioSysM), Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Enes Ugur
- Center for Molecular Biosystems (BioSysM), Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
| | - Susanne Leidescher
- Center for Molecular Biosystems (BioSysM), Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Joel Ryan
- Center for Molecular Biosystems (BioSysM), Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - M Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Heinrich Leonhardt
- Center for Molecular Biosystems (BioSysM), Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
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35
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Rausch C, Weber P, Prorok P, Hörl D, Maiser A, Lehmkuhl A, Chagin VO, Casas-Delucchi CS, Leonhardt H, Cardoso MC. Developmental differences in genome replication program and origin activation. Nucleic Acids Res 2021; 48:12751-12777. [PMID: 33264404 PMCID: PMC7736824 DOI: 10.1093/nar/gkaa1124] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 06/30/2020] [Revised: 10/09/2020] [Accepted: 11/04/2020] [Indexed: 12/17/2022] Open
Abstract
To ensure error-free duplication of all (epi)genetic information once per cell cycle, DNA replication follows a cell type and developmental stage specific spatio-temporal program. Here, we analyze the spatio-temporal DNA replication progression in (un)differentiated mouse embryonic stem (mES) cells. Whereas telomeres replicate throughout S-phase, we observe mid S-phase replication of (peri)centromeric heterochromatin in mES cells, which switches to late S-phase replication upon differentiation. This replication timing reversal correlates with and depends on an increase in condensation and a decrease in acetylation of chromatin. We further find synchronous duplication of the Y chromosome, marking the end of S-phase, irrespectively of the pluripotency state. Using a combination of single-molecule and super-resolution microscopy, we measure molecular properties of the mES cell replicon, the number of replication foci active in parallel and their spatial clustering. We conclude that each replication nanofocus in mES cells corresponds to an individual replicon, with up to one quarter representing unidirectional forks. Furthermore, with molecular combing and genome-wide origin mapping analyses, we find that mES cells activate twice as many origins spaced at half the distance than somatic cells. Altogether, our results highlight fundamental developmental differences on progression of genome replication and origin activation in pluripotent cells.
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Affiliation(s)
- Cathia Rausch
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Patrick Weber
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Paulina Prorok
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - David Hörl
- Department of Biology II, LMU Munich, 81377 Munich, Germany
| | - Andreas Maiser
- Department of Biology II, LMU Munich, 81377 Munich, Germany
| | - Anne Lehmkuhl
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Vadim O Chagin
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany.,Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | | | | | - M Cristina Cardoso
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
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36
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Schmitt S, Tahk S, Lohner A, Hänel G, Maiser A, Hauke M, Patel L, Rothe M, Josenhans C, Leonhardt H, Griffioen M, Deiser K, Fenn NC, Hopfner KP, Subklewe M. Fusion of Bacterial Flagellin to a Dendritic Cell-Targeting αCD40 Antibody Construct Coupled With Viral or Leukemia-Specific Antigens Enhances Dendritic Cell Maturation and Activates Peptide-Responsive T Cells. Front Immunol 2020; 11:602802. [PMID: 33281829 PMCID: PMC7689061 DOI: 10.3389/fimmu.2020.602802] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 09/22/2020] [Accepted: 10/19/2020] [Indexed: 12/30/2022] Open
Abstract
Conventional dendritic cell (DC) vaccine strategies, in which DCs are loaded with antigens ex vivo, suffer biological issues such as impaired DC migration capacity and laborious GMP production procedures. In a promising alternative, antigens are targeted to DC-associated endocytic receptors in vivo with antibody–antigen conjugates co-administered with toll-like receptor (TLR) agonists as adjuvants. To combine the potential advantages of in vivo targeting of DCs with those of conjugated TLR agonists, we generated a multifunctional antibody construct integrating the DC-specific delivery of viral- or tumor-associated antigens and DC activation by TLR ligation in one molecule. We validated its functionality in vitro and determined if TLR ligation might improve the efficacy of such a molecule. In proof-of-principle studies, an αCD40 antibody containing a CMV pp65-derived peptide as an antigen domain (αCD40CMV) was genetically fused to the TLR5-binding D0/D1 domain of bacterial flagellin (αCD40.FlgCMV). The analysis of surface maturation markers on immature DCs revealed that fusion of flagellin to αCD40CMV highly increased DC maturation (3.4-fold elevation of CD80 expression compared to αCD40CMV alone) by specifically interacting with TLR5. Immature DCs loaded with αCD40.FlgCMV induced significantly higher CMVNLV-specific T cell activation and proliferation compared to αCD40CMV in co-culture experiments with allogeneic and autologous T cells (1.8-fold increase in % IFN-γ/TNF-α+ CD8+ T cells and 3.9-fold increase in % CMVNLV-specific dextramer+ CD8+ T cells). More importantly, we confirmed the beneficial effects of flagellin-dependent DC stimulation using a tumor-specific neoantigen as the antigen domain. Specifically, the acute myeloid leukemia (AML)-specific mutated NPM1 (mNPM1)-derived neoantigen CLAVEEVSL was delivered to DCs in the form of αCD40mNPM1 and αCD40.FlgmNPM1 antibody constructs, making this study the first to investigate mNPM1 in a DC vaccination context. Again, αCD40.FlgmNPM1-loaded DCs more potently activated allogeneic mNPM1CLA-specific T cells compared to αCD40mNPM1. These in vitro results confirmed the functionality of our multifunctional antibody construct and demonstrated that TLR5 ligation improved the efficacy of the molecule. Future mouse studies are required to examine the T cell-activating potential of αCD40.FlgmNPM1 after targeting of dendritic cells in vivo using AML xenograft models.
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Affiliation(s)
- Saskia Schmitt
- Gene Center and Department of Biochemistry, Ludwig Maximilians University Munich, Munich, Germany
| | - Siret Tahk
- Gene Center and Department of Biochemistry, Ludwig Maximilians University Munich, Munich, Germany
| | - Alina Lohner
- Department of Medicine III, University Hospital, Ludwig Maximilians University Munich, Munich, Germany.,Gene Center Munich, Laboratory for Translational Cancer Immunology, Ludwig Maximilians University Munich, Munich, Germany
| | - Gerulf Hänel
- Department of Medicine III, University Hospital, Ludwig Maximilians University Munich, Munich, Germany.,Gene Center Munich, Laboratory for Translational Cancer Immunology, Ludwig Maximilians University Munich, Munich, Germany
| | - Andreas Maiser
- Department of Biology II, Center for Integrated Protein Science, Ludwig Maximilians University Munich, Munich, Germany
| | - Martina Hauke
- Max von Pettenkofer Institute, Ludwig Maximilians University Munich, Munich, Germany
| | - Lubna Patel
- Max von Pettenkofer Institute, Ludwig Maximilians University Munich, Munich, Germany
| | - Maurine Rothe
- Department of Medicine III, University Hospital, Ludwig Maximilians University Munich, Munich, Germany.,Gene Center Munich, Laboratory for Translational Cancer Immunology, Ludwig Maximilians University Munich, Munich, Germany
| | - Christine Josenhans
- Max von Pettenkofer Institute, Ludwig Maximilians University Munich, Munich, Germany.,German Center of Infection Research, DZIF, Munich, Germany
| | - Heinrich Leonhardt
- Department of Biology II, Center for Integrated Protein Science, Ludwig Maximilians University Munich, Munich, Germany
| | - Marieke Griffioen
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Katrin Deiser
- Department of Medicine III, University Hospital, Ludwig Maximilians University Munich, Munich, Germany.,Gene Center Munich, Laboratory for Translational Cancer Immunology, Ludwig Maximilians University Munich, Munich, Germany
| | - Nadja C Fenn
- Gene Center and Department of Biochemistry, Ludwig Maximilians University Munich, Munich, Germany
| | - Karl-Peter Hopfner
- Gene Center and Department of Biochemistry, Ludwig Maximilians University Munich, Munich, Germany
| | - Marion Subklewe
- Department of Medicine III, University Hospital, Ludwig Maximilians University Munich, Munich, Germany.,Gene Center Munich, Laboratory for Translational Cancer Immunology, Ludwig Maximilians University Munich, Munich, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
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37
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Le Poul Y, Xin Y, Ling L, Mühling B, Jaenichen R, Hörl D, Bunk D, Harz H, Leonhardt H, Wang Y, Osipova E, Museridze M, Dharmadhikari D, Murphy E, Rohs R, Preibisch S, Prud'homme B, Gompel N. Regulatory encoding of quantitative variation in spatial activity of a Drosophila enhancer. Sci Adv 2020; 6:6/49/eabe2955. [PMID: 33268361 PMCID: PMC7821883 DOI: 10.1126/sciadv.abe2955] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 10/20/2020] [Indexed: 06/12/2023]
Abstract
Developmental enhancers control the expression of genes prefiguring morphological patterns. The activity of an enhancer varies among cells of a tissue, but collectively, expression levels in individual cells constitute a spatial pattern of gene expression. How the spatial and quantitative regulatory information is encoded in an enhancer sequence is elusive. To link spatial pattern and activity levels of an enhancer, we used systematic mutations of the yellow spot enhancer, active in developing Drosophila wings, and tested their effect in a reporter assay. Moreover, we developed an analytic framework based on the comprehensive quantification of spatial reporter activity. We show that the quantitative enhancer activity results from densely packed regulatory information along the sequence, and that a complex interplay between activators and multiple tiers of repressors carves the spatial pattern. Our results shed light on how an enhancer reads and integrates trans-regulatory landscape information to encode a spatial quantitative pattern.
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Affiliation(s)
- Yann Le Poul
- Evolutionary Ecology, Ludwig-Maximilians Universität München, Fakultät für Biologie, Biozentrum, Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Yaqun Xin
- Evolutionary Ecology, Ludwig-Maximilians Universität München, Fakultät für Biologie, Biozentrum, Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Liucong Ling
- Evolutionary Ecology, Ludwig-Maximilians Universität München, Fakultät für Biologie, Biozentrum, Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Bettina Mühling
- Evolutionary Ecology, Ludwig-Maximilians Universität München, Fakultät für Biologie, Biozentrum, Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Rita Jaenichen
- Evolutionary Ecology, Ludwig-Maximilians Universität München, Fakultät für Biologie, Biozentrum, Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - David Hörl
- Human Biology and Bioimaging, Ludwig-Maximilians Universität München, Fakultät für Biologie, Biozentrum, Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - David Bunk
- Human Biology and Bioimaging, Ludwig-Maximilians Universität München, Fakultät für Biologie, Biozentrum, Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Hartmann Harz
- Human Biology and Bioimaging, Ludwig-Maximilians Universität München, Fakultät für Biologie, Biozentrum, Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Heinrich Leonhardt
- Human Biology and Bioimaging, Ludwig-Maximilians Universität München, Fakultät für Biologie, Biozentrum, Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Yingfei Wang
- Quantitative and Computational Biology, Departments of Biological Sciences, Chemistry, Physics and Astronomy, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Elena Osipova
- Evolutionary Ecology, Ludwig-Maximilians Universität München, Fakultät für Biologie, Biozentrum, Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Mariam Museridze
- Evolutionary Ecology, Ludwig-Maximilians Universität München, Fakultät für Biologie, Biozentrum, Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Deepak Dharmadhikari
- Evolutionary Ecology, Ludwig-Maximilians Universität München, Fakultät für Biologie, Biozentrum, Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Eamonn Murphy
- Evolutionary Ecology, Ludwig-Maximilians Universität München, Fakultät für Biologie, Biozentrum, Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Remo Rohs
- Quantitative and Computational Biology, Departments of Biological Sciences, Chemistry, Physics and Astronomy, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Stephan Preibisch
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13092 Berlin, Germany
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Benjamin Prud'homme
- Aix-Marseille Université, CNRS, IBDM, Institut de Biologie du Développement de Marseille, Campus de Luminy Case 907, 13288 Marseille Cedex 9, France.
| | - Nicolas Gompel
- Evolutionary Ecology, Ludwig-Maximilians Universität München, Fakultät für Biologie, Biozentrum, Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany.
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38
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Cremer M, Brandstetter K, Maiser A, Rao SSP, Schmid VJ, Guirao-Ortiz M, Mitra N, Mamberti S, Klein KN, Gilbert DM, Leonhardt H, Cardoso MC, Aiden EL, Harz H, Cremer T. Cohesin depleted cells rebuild functional nuclear compartments after endomitosis. Nat Commun 2020; 11:6146. [PMID: 33262376 PMCID: PMC7708632 DOI: 10.1038/s41467-020-19876-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [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: 12/12/2019] [Accepted: 10/28/2020] [Indexed: 01/05/2023] Open
Abstract
Cohesin plays an essential role in chromatin loop extrusion, but its impact on a compartmentalized nuclear architecture, linked to nuclear functions, is less well understood. Using live-cell and super-resolved 3D microscopy, here we find that cohesin depletion in a human colon cancer derived cell line results in endomitosis and a single multilobulated nucleus with chromosome territories pervaded by interchromatin channels. Chromosome territories contain chromatin domain clusters with a zonal organization of repressed chromatin domains in the interior and transcriptionally competent domains located at the periphery. These clusters form microscopically defined, active and inactive compartments, which likely correspond to A/B compartments, which are detected with ensemble Hi-C. Splicing speckles are observed nearby within the lining channel system. We further observe that the multilobulated nuclei, despite continuous absence of cohesin, pass through S-phase with typical spatio-temporal patterns of replication domains. Evidence for structural changes of these domains compared to controls suggests that cohesin is required for their full integrity.
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Affiliation(s)
- Marion Cremer
- Anthropology and Human Genomics, Department Biology II, Ludwig-Maximilians-Universität München, München, Germany.
| | - Katharina Brandstetter
- Human Biology & BioImaging, Center for Molecular Biosystems, Department Biology II, Ludwig-Maximilians-Universität München, München, Germany
| | - Andreas Maiser
- Human Biology & BioImaging, Center for Molecular Biosystems, Department Biology II, Ludwig-Maximilians-Universität München, München, Germany
| | - Suhas S P Rao
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Structural Biology, Stanford University School of Medicine, California, USA
| | - Volker J Schmid
- Bayesian Imaging and Spatial Statistics Group, Department of Statistics, Ludwig-Maximilians-Universität München, München, Germany
| | - Miguel Guirao-Ortiz
- Human Biology & BioImaging, Center for Molecular Biosystems, Department Biology II, Ludwig-Maximilians-Universität München, München, Germany
| | - Namita Mitra
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Stefania Mamberti
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Kyle N Klein
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Heinrich Leonhardt
- Human Biology & BioImaging, Center for Molecular Biosystems, Department Biology II, Ludwig-Maximilians-Universität München, München, Germany
| | - M Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Erez Lieberman Aiden
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX, USA
| | - Hartmann Harz
- Human Biology & BioImaging, Center for Molecular Biosystems, Department Biology II, Ludwig-Maximilians-Universität München, München, Germany.
| | - Thomas Cremer
- Anthropology and Human Genomics, Department Biology II, Ludwig-Maximilians-Universität München, München, Germany.
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39
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Mulholland CB, Nishiyama A, Ryan J, Nakamura R, Yiğit M, Glück IM, Trummer C, Qin W, Bartoschek MD, Traube FR, Parsa E, Ugur E, Modic M, Acharya A, Stolz P, Ziegenhain C, Wierer M, Enard W, Carell T, Lamb DC, Takeda H, Nakanishi M, Bultmann S, Leonhardt H. Recent evolution of a TET-controlled and DPPA3/STELLA-driven pathway of passive DNA demethylation in mammals. Nat Commun 2020; 11:5972. [PMID: 33235224 PMCID: PMC7686362 DOI: 10.1038/s41467-020-19603-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [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: 03/24/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022] Open
Abstract
Genome-wide DNA demethylation is a unique feature of mammalian development and naïve pluripotent stem cells. Here, we describe a recently evolved pathway in which global hypomethylation is achieved by the coupling of active and passive demethylation. TET activity is required, albeit indirectly, for global demethylation, which mostly occurs at sites devoid of TET binding. Instead, TET-mediated active demethylation is locus-specific and necessary for activating a subset of genes, including the naïve pluripotency and germline marker Dppa3 (Stella, Pgc7). DPPA3 in turn drives large-scale passive demethylation by directly binding and displacing UHRF1 from chromatin, thereby inhibiting maintenance DNA methylation. Although unique to mammals, we show that DPPA3 alone is capable of inducing global DNA demethylation in non-mammalian species (Xenopus and medaka) despite their evolutionary divergence from mammals more than 300 million years ago. Our findings suggest that the evolution of Dppa3 facilitated the emergence of global DNA demethylation in mammals.
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Affiliation(s)
- Christopher B Mulholland
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Atsuya Nishiyama
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Joel Ryan
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Ryohei Nakamura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Merve Yiğit
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Ivo M Glück
- Physical Chemistry, Department of Chemistry, Center for Nanoscience, Nanosystems Initiative Munich and Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Carina Trummer
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Weihua Qin
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Michael D Bartoschek
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Franziska R Traube
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Edris Parsa
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Enes Ugur
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Miha Modic
- The Francis Crick Institute and UCL Queen Square Institute of Neurology, London, UK
| | - Aishwarya Acharya
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Paul Stolz
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Christoph Ziegenhain
- Department of Biology II, Anthropology and Human Genomics, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Wolfgang Enard
- Department of Biology II, Anthropology and Human Genomics, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Thomas Carell
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Center for Nanoscience, Nanosystems Initiative Munich and Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Makoto Nakanishi
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Sebastian Bultmann
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
| | - Heinrich Leonhardt
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
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40
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Pandya-Jones A, Markaki Y, Serizay J, Chitiashvili T, Leon WRM, Damianov A, Chronis C, Papp B, Chen CK, McKee R, Wang XJ, Chau A, Sabri S, Leonhardt H, Zheng S, Guttman M, Black DL, Plath K. Publisher Correction: A protein assembly mediates Xist localization and gene silencing. Nature 2020; 586:E30. [PMID: 33005055 DOI: 10.1038/s41586-020-2790-y] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Amy Pandya-Jones
- Department of Biological Chemistry at the David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Yolanda Markaki
- Department of Biological Chemistry at the David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Biology and Center for Integrated Protein Science, LMU Munich, Munich, Germany
| | - Jacques Serizay
- Department of Biological Chemistry at the David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- École Normale Supérieure de Cachan, Université Paris-Saclay, Saclay, France
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Tsotne Chitiashvili
- Department of Biological Chemistry at the David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Biology and Center for Integrated Protein Science, LMU Munich, Munich, Germany
| | - Walter R Mancia Leon
- Department of Biological Chemistry at the David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Andrey Damianov
- Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA
| | - Constantinos Chronis
- Department of Biological Chemistry at the David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Bernadett Papp
- Department of Biological Chemistry at the David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Chun-Kan Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Robin McKee
- Department of Biological Chemistry at the David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Xiao-Jun Wang
- Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA
| | - Anthony Chau
- Department of Biological Chemistry at the David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Shan Sabri
- Department of Biological Chemistry at the David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Heinrich Leonhardt
- Department of Biology and Center for Integrated Protein Science, LMU Munich, Munich, Germany
| | - Sika Zheng
- Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA
- Division of Biomedical Science, University of California Riverside, Riverside, CA, USA
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Douglas L Black
- Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA.
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA, USA.
- Brain Research Institute, University of California Los Angeles, Los Angeles, CA, USA.
- Graduate Program in the Biosciences, University of California Los Angeles, Los Angeles, CA, USA.
| | - Kathrin Plath
- Department of Biological Chemistry at the David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA, USA.
- Brain Research Institute, University of California Los Angeles, Los Angeles, CA, USA.
- Graduate Program in the Biosciences, University of California Los Angeles, Los Angeles, CA, USA.
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA, USA.
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41
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Schreck C, Bassermann F, Beauvarlet J, Brandstetter K, Götze K, Hameister E, Hettler F, Istvanffy R, Leonhardt H, Oostendorp R, Marquez SR, Yamaguchi T, Sippenauer T. 3034 – CYTOSTATIC STRESS CAUSES DEFECTS IN ACTIN-DEPENDENT AUTOPHAGY OF WNT5A-DELETED STROMAL CELLS. Exp Hematol 2020. [DOI: 10.1016/j.exphem.2020.09.054] [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: 11/28/2022]
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42
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Maiser A, Dillinger S, Längst G, Schermelleh L, Leonhardt H, Németh A. Super-resolution in situ analysis of active ribosomal DNA chromatin organization in the nucleolus. Sci Rep 2020; 10:7462. [PMID: 32366902 PMCID: PMC7198602 DOI: 10.1038/s41598-020-64589-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [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: 08/12/2019] [Accepted: 04/01/2020] [Indexed: 12/21/2022] Open
Abstract
Ribosomal RNA (rRNA) transcription by RNA polymerase I (Pol I) is the first key step of ribosome biogenesis. While the molecular mechanisms of rRNA transcription regulation have been elucidated in great detail, the functional organization of the multicopy rRNA gene clusters (rDNA) in the nucleolus is less well understood. Here we apply super-resolution 3D structured illumination microscopy (3D-SIM) to investigate the spatial organization of transcriptionally competent active rDNA chromatin at size scales well below the diffraction limit by optical microscopy. We identify active rDNA chromatin units exhibiting uniformly ring-shaped conformations with diameters of ~240 nm in mouse and ~170 nm in human fibroblasts, consistent with rDNA looping. The active rDNA chromatin units are clearly separated from each other and from the surrounding areas of rRNA processing. Simultaneous imaging of all active genes bound by Pol I and the architectural chromatin protein Upstream Binding Transcription Factor (UBF) reveals a random spatial orientation of regular repeats of rDNA coding sequences within the nucleoli. These observations imply rDNA looping and exclude potential formation of systematic spatial assemblies of the well-ordered repetitive arrays of transcription units. Collectively, this study uncovers key features of the 3D organization of active rDNA chromatin units and their nucleolar clusters providing a spatial framework of nucleolar chromatin organization at unprecedented detail.
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Affiliation(s)
- Andreas Maiser
- Department of Biology II, Ludwig-Maximilians-Universität München, München, Germany
| | - Stefan Dillinger
- Department of Biochemistry III, University of Regensburg, Regensburg, Germany
| | - Gernot Längst
- Department of Biochemistry III, University of Regensburg, Regensburg, Germany
| | - Lothar Schermelleh
- Micron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, Oxford, UK
| | - Heinrich Leonhardt
- Department of Biology II, Ludwig-Maximilians-Universität München, München, Germany
| | - Attila Németh
- Department of Biochemistry III, University of Regensburg, Regensburg, Germany.
- Institute of Neuropathology, Justus Liebig University, Giessen, Germany.
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43
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Nishiyama A, Mulholland CB, Bultmann S, Kori S, Endo A, Saeki Y, Qin W, Trummer C, Chiba Y, Yokoyama H, Kumamoto S, Kawakami T, Hojo H, Nagae G, Aburatani H, Tanaka K, Arita K, Leonhardt H, Nakanishi M. Two distinct modes of DNMT1 recruitment ensure stable maintenance DNA methylation. Nat Commun 2020; 11:1222. [PMID: 32144273 PMCID: PMC7060239 DOI: 10.1038/s41467-020-15006-4] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [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: 04/24/2019] [Accepted: 02/10/2020] [Indexed: 12/31/2022] Open
Abstract
Stable inheritance of DNA methylation is critical for maintaining differentiated phenotypes in multicellular organisms. We have recently identified dual mono-ubiquitylation of histone H3 (H3Ub2) by UHRF1 as an essential mechanism to recruit DNMT1 to chromatin. Here, we show that PCNA-associated factor 15 (PAF15) undergoes UHRF1-dependent dual mono-ubiquitylation (PAF15Ub2) on chromatin in a DNA replication-coupled manner. This event will, in turn, recruit DNMT1. During early S-phase, UHRF1 preferentially ubiquitylates PAF15, whereas H3Ub2 predominates during late S-phase. H3Ub2 is enhanced under PAF15 compromised conditions, suggesting that H3Ub2 serves as a backup for PAF15Ub2. In mouse ES cells, loss of PAF15Ub2 results in DNA hypomethylation at early replicating domains. Together, our results suggest that there are two distinct mechanisms underlying replication timing-dependent recruitment of DNMT1 through PAF15Ub2 and H3Ub2, both of which are prerequisite for high fidelity DNA methylation inheritance. Ubiquitylation of histone H3 (H3Ub2) by UHRF1 recruits DNMT1 to chromatin, which is essential for DNA methylation inheritance. Here, the authors provide evidence that there are two distinct mechanisms underlying replication timing-dependent recruitment of DNMT1 through PAF15Ub2 and H3Ub2, both of which are required for high fidelity DNA methylation inheritance.
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Affiliation(s)
- Atsuya Nishiyama
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, Japan.
| | - Christopher B Mulholland
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
| | - Sebastian Bultmann
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
| | - Satomi Kori
- Structure Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Akinori Endo
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, Japan
| | - Yasushi Saeki
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, Japan
| | - Weihua Qin
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
| | - Carina Trummer
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
| | - Yoshie Chiba
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, Japan
| | - Haruka Yokoyama
- Structure Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Soichiro Kumamoto
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, Japan
| | - Toru Kawakami
- Laboratory of Protein Organic Chemistry, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Hironobu Hojo
- Laboratory of Protein Organic Chemistry, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Genta Nagae
- The Research Center for Advanced Science and Technology, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, Japan
| | - Hiroyuki Aburatani
- The Research Center for Advanced Science and Technology, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, Japan
| | - Keiji Tanaka
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, Japan
| | - Kyohei Arita
- Structure Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan.
| | - Heinrich Leonhardt
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany.
| | - Makoto Nakanishi
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, Japan.
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44
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Schneider M, Trummer C, Stengl A, Zhang P, Szwagierczak A, Cardoso MC, Leonhardt H, Bauer C, Antes I. Systematic analysis of the binding behaviour of UHRF1 towards different methyl- and carboxylcytosine modification patterns at CpG dyads. PLoS One 2020; 15:e0229144. [PMID: 32084194 PMCID: PMC7034832 DOI: 10.1371/journal.pone.0229144] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 01/30/2020] [Indexed: 01/24/2023] Open
Abstract
The multi-domain protein UHRF1 is essential for DNA methylation maintenance and binds DNA via a base-flipping mechanism with a preference for hemi-methylated CpG sites. We investigated its binding to hemi- and symmetrically modified DNA containing either 5-methylcytosine (mC), 5-hydroxymethylcytosine (hmC), 5-formylcytosine (fC), or 5-carboxylcytosine (caC). Our experimental results indicate that UHRF1 binds symmetrically carboxylated and hybrid methylated/carboxylated CpG dyads in addition to its previously reported substrates. Complementary molecular dynamics simulations provide a possible mechanistic explanation of how the protein could differentiate between modification patterns. First, we observe different local binding modes in the nucleotide binding pocket as well as the protein's NKR finger. Second, both DNA modification sites are coupled through key residues within the NKR finger, suggesting a communication pathway affecting protein-DNA binding for carboxylcytosine modifications. Our results suggest a possible additional function of the hemi-methylation reader UHRF1 through binding of carboxylated CpG sites. This opens the possibility of new biological roles of UHRF1 beyond DNA methylation maintenance and of oxidised methylcytosine derivates in epigenetic regulation.
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Affiliation(s)
- Markus Schneider
- Center for Integrated Protein Science Munich at the TUM School of Life Sciences, Technische Universität München, Freising, Germany
| | - Carina Trummer
- Center for Integrated Protein Science Munich at the Department of Biology II, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - Andreas Stengl
- Center for Integrated Protein Science Munich at the Department of Biology II, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - Peng Zhang
- Center for Integrated Protein Science Munich at the Department of Biology II, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
- Cell Biology and Epigenetics at the Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Aleksandra Szwagierczak
- Center for Integrated Protein Science Munich at the Department of Biology II, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - M. Cristina Cardoso
- Cell Biology and Epigenetics at the Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Heinrich Leonhardt
- Center for Integrated Protein Science Munich at the Department of Biology II, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - Christina Bauer
- Center for Integrated Protein Science Munich at the Department of Biology II, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - Iris Antes
- Center for Integrated Protein Science Munich at the TUM School of Life Sciences, Technische Universität München, Freising, Germany
- * E-mail:
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45
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Abstract
Biological processes in development and disease are controlled by the abundance, localization and modification of cellular proteins. We have developed versatile tools based on recombinant E3 ubiquitin ligases that are controlled by light or drug induced heterodimerization for nanobody or DARPin targeted depletion of endogenous proteins in cells and organisms. We use this rapid, tunable and reversible protein depletion for functional studies of essential proteins like PCNA in DNA repair and to investigate the role of CED-3 in apoptosis during Caenorhabditis elegans development. These independent tools can be combined for spatial and temporal depletion of different sets of proteins, can help to distinguish immediate cellular responses from long-term adaptation effects and can facilitate the exploration of complex networks.
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Affiliation(s)
- Wen Deng
- Department of Biology II, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jack A Bates
- Department of Biology II, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Hai Wei
- Department of Biology II, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michael D Bartoschek
- Department of Biology II, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Barbara Conradt
- Department of Biology II, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Heinrich Leonhardt
- Department of Biology II, Ludwig-Maximilians-Universität München, Munich, Germany.
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46
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Kasper M, Gerlach M, Schneider AFL, Groneberg C, Ochtrop P, Boldt S, Schumacher D, Helma J, Leonhardt H, Christmann M, Hackenberger CPR. N-Hydroxysuccinimide-Modified Ethynylphosphonamidates Enable the Synthesis of Configurationally Defined Protein Conjugates. Chembiochem 2020; 21:113-119. [PMID: 31661184 PMCID: PMC7003776 DOI: 10.1002/cbic.201900587] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 09/20/2019] [Indexed: 12/15/2022]
Abstract
Herein, the application of N-hydroxysuccinimide-modified phosphonamidate building blocks for the incorporation of cysteine-selective ethynylphosphonamidates into lysine residues of proteins, followed by thiol addition with small molecules and proteins, is reported. It is demonstrated that the building blocks significantly lower undesired homo-crosslinking side products that can occur with commonly applied succinimidyl 4-(N-maleimidomethyl)cyclohexane-1-carboxylate (SMCC) under physiological pH. The previously demonstrated stability of the phosphonamidate moiety additionally solves the problem of premature maleimide hydrolysis, which can hamper the efficiency of subsequent thiol addition. Furthermore, a method to separate the phosphonamidate enantiomers to be able to synthesize protein conjugates in a defined configuration has been developed. Finally, the building blocks are applied to the construction of functional antibody-drug conjugates, analogously to FDA-approved, SMCC-linked Kadcyla, and to the synthesis of a functional antibody-protein conjugate.
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Affiliation(s)
- Marc‐André Kasper
- Chemical Biology DepartmentLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 1013125BerlinGermany
- Department of ChemistryHumboldt Universität zu BerlinBrook-Taylor-Strasse 212489BerlinGermany
- Tubulis GmbHBioSysMButenandtstrasse 181377MunichGermany
| | - Marcus Gerlach
- Department of Biology II andCenter for Integrated Protein Science MunichLudwig-Maximilians-Universität MünchenGroßhadernerstrasse 282152MartinsriedGermany
- Tubulis GmbHBioSysMButenandtstrasse 181377MunichGermany
| | - Anselm F. L. Schneider
- Chemical Biology DepartmentLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 1013125BerlinGermany
- Institut für Chemie und BiochemieFreie Universität BerlinTakustrasse. 314195BerlinGermany
| | - Christiane Groneberg
- Institut für Chemie und BiochemieFreie Universität BerlinTakustrasse. 314195BerlinGermany
| | - Philipp Ochtrop
- Chemical Biology DepartmentLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 1013125BerlinGermany
- Tubulis GmbHBioSysMButenandtstrasse 181377MunichGermany
| | - Stefanie Boldt
- Department of Biology II andCenter for Integrated Protein Science MunichLudwig-Maximilians-Universität MünchenGroßhadernerstrasse 282152MartinsriedGermany
- Tubulis GmbHBioSysMButenandtstrasse 181377MunichGermany
| | - Dominik Schumacher
- Chemical Biology DepartmentLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 1013125BerlinGermany
- Department of ChemistryHumboldt Universität zu BerlinBrook-Taylor-Strasse 212489BerlinGermany
- Department of Biology II andCenter for Integrated Protein Science MunichLudwig-Maximilians-Universität MünchenGroßhadernerstrasse 282152MartinsriedGermany
- Tubulis GmbHBioSysMButenandtstrasse 181377MunichGermany
| | - Jonas Helma
- Department of Biology II andCenter for Integrated Protein Science MunichLudwig-Maximilians-Universität MünchenGroßhadernerstrasse 282152MartinsriedGermany
- Tubulis GmbHBioSysMButenandtstrasse 181377MunichGermany
| | - Heinrich Leonhardt
- Department of Biology II andCenter for Integrated Protein Science MunichLudwig-Maximilians-Universität MünchenGroßhadernerstrasse 282152MartinsriedGermany
| | - Mathias Christmann
- Institut für Chemie und BiochemieFreie Universität BerlinTakustrasse. 314195BerlinGermany
| | - Christian P. R. Hackenberger
- Chemical Biology DepartmentLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 1013125BerlinGermany
- Department of ChemistryHumboldt Universität zu BerlinBrook-Taylor-Strasse 212489BerlinGermany
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47
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Abstract
Biotin proximity labeling has largely extended the toolbox of mass spectrometry-based interactomics. To date, BirA, engineered BirA variants, or other biotinylating enzymes have been widely applied to characterize protein interactions. By implementing chromatin purification-based methods the genome-wide interactome of proteins can be defined. However, acquiring a high-resolution interactome of a single genomic locus preferably by multiplexed measurements of several distinct genomic loci in parallel remains challenging. We recently developed CasID, a novel approach where the catalytically inactive Cas9 (dCas9) is coupled to the promiscuous biotin ligase BirA (BirA∗). With CasID, first the local proteome at repetitive telomeric, major satellite, and minor satellite regions was determined. With more efficient biotin ligases and sensitive mass spectrometry, others have successfully identified the chromatin composition at even smaller genomic, non-repetitive regions of a few hundred base pairs in length. Here, we summarize the most recent developments towards interactomics at a single genomic locus and provide a step-by-step protocol based on the CasID approach.
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Affiliation(s)
- Enes Ugur
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michael D Bartoschek
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Heinrich Leonhardt
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich, Germany.
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48
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Kasper M, Gerlach M, Schneider AFL, Groneberg C, Ochtrop P, Boldt S, Schumacher D, Helma J, Leonhardt H, Christmann M, Hackenberger CPR. Front Cover:
N
‐Hydroxysuccinimide‐Modified Ethynylphosphonamidates Enable the Synthesis of Configurationally Defined Protein Conjugates (ChemBioChem 1‐2/2020). Chembiochem 2019. [DOI: 10.1002/cbic.201900760] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Marc‐André Kasper
- Chemical Biology DepartmentLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Strasse 10 13125 Berlin Germany
- Department of ChemistryHumboldt Universität zu Berlin Brook-Taylor-Strasse 2 12489 Berlin Germany
- Tubulis GmbH BioSysM Butenandtstrasse 1 81377 Munich Germany
| | - Marcus Gerlach
- Department of Biology II andCenter for Integrated Protein Science MunichLudwig-Maximilians-Universität München Großhadernerstrasse 2 82152 Martinsried Germany
- Tubulis GmbH BioSysM Butenandtstrasse 1 81377 Munich Germany
| | - Anselm F. L. Schneider
- Chemical Biology DepartmentLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Strasse 10 13125 Berlin Germany
- Institut für Chemie und BiochemieFreie Universität Berlin Takustrasse. 3 14195 Berlin Germany
| | - Christiane Groneberg
- Institut für Chemie und BiochemieFreie Universität Berlin Takustrasse. 3 14195 Berlin Germany
| | - Philipp Ochtrop
- Chemical Biology DepartmentLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Strasse 10 13125 Berlin Germany
- Tubulis GmbH BioSysM Butenandtstrasse 1 81377 Munich Germany
| | - Stefanie Boldt
- Department of Biology II andCenter for Integrated Protein Science MunichLudwig-Maximilians-Universität München Großhadernerstrasse 2 82152 Martinsried Germany
- Tubulis GmbH BioSysM Butenandtstrasse 1 81377 Munich Germany
| | - Dominik Schumacher
- Chemical Biology DepartmentLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Strasse 10 13125 Berlin Germany
- Department of ChemistryHumboldt Universität zu Berlin Brook-Taylor-Strasse 2 12489 Berlin Germany
- Department of Biology II andCenter for Integrated Protein Science MunichLudwig-Maximilians-Universität München Großhadernerstrasse 2 82152 Martinsried Germany
- Tubulis GmbH BioSysM Butenandtstrasse 1 81377 Munich Germany
| | - Jonas Helma
- Department of Biology II andCenter for Integrated Protein Science MunichLudwig-Maximilians-Universität München Großhadernerstrasse 2 82152 Martinsried Germany
- Tubulis GmbH BioSysM Butenandtstrasse 1 81377 Munich Germany
| | - Heinrich Leonhardt
- Department of Biology II andCenter for Integrated Protein Science MunichLudwig-Maximilians-Universität München Großhadernerstrasse 2 82152 Martinsried Germany
| | - Mathias Christmann
- Institut für Chemie und BiochemieFreie Universität Berlin Takustrasse. 3 14195 Berlin Germany
| | - Christian P. R. Hackenberger
- Chemical Biology DepartmentLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Strasse 10 13125 Berlin Germany
- Department of ChemistryHumboldt Universität zu Berlin Brook-Taylor-Strasse 2 12489 Berlin Germany
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49
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Tepper S, Mortusewicz O, Członka E, Bello A, Schmidt A, Jeschke J, Fischbach A, Pfeil I, Petersen-Mahrt SK, Mangerich A, Helleday T, Leonhardt H, Jungnickel B. Restriction of AID activity and somatic hypermutation by PARP-1. Nucleic Acids Res 2019; 47:7418-7429. [PMID: 31127309 PMCID: PMC6698665 DOI: 10.1093/nar/gkz466] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 03/19/2019] [Revised: 05/13/2019] [Accepted: 05/16/2019] [Indexed: 12/20/2022] Open
Abstract
Affinity maturation of the humoral immune response depends on somatic hypermutation (SHM) of immunoglobulin (Ig) genes, which is initiated by targeted lesion introduction by activation-induced deaminase (AID), followed by error-prone DNA repair. Stringent regulation of this process is essential to prevent genetic instability, but no negative feedback control has been identified to date. Here we show that poly(ADP-ribose) polymerase-1 (PARP-1) is a key factor restricting AID activity during somatic hypermutation. Poly(ADP-ribose) (PAR) chains formed at DNA breaks trigger AID-PAR association, thus preventing excessive DNA damage induction at sites of AID action. Accordingly, AID activity and somatic hypermutation at the Ig variable region is decreased by PARP-1 activity. In addition, PARP-1 regulates DNA lesion processing by affecting strand biased A:T mutagenesis. Our study establishes a novel function of the ancestral genome maintenance factor PARP-1 as a critical local feedback regulator of both AID activity and DNA repair during Ig gene diversification.
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Affiliation(s)
- Sandra Tepper
- Department of Cell Biology, Institute of Biochemistry and Biophysics, School of Biology and Pharmacy, Friedrich Schiller University, 07745 Jena, Germany
| | - Oliver Mortusewicz
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany.,Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Ewelina Członka
- Department of Cell Biology, Institute of Biochemistry and Biophysics, School of Biology and Pharmacy, Friedrich Schiller University, 07745 Jena, Germany
| | - Amanda Bello
- Department of Cell Biology, Institute of Biochemistry and Biophysics, School of Biology and Pharmacy, Friedrich Schiller University, 07745 Jena, Germany
| | - Angelika Schmidt
- Department of Cell Biology, Institute of Biochemistry and Biophysics, School of Biology and Pharmacy, Friedrich Schiller University, 07745 Jena, Germany
| | - Julia Jeschke
- Department of Cell Biology, Institute of Biochemistry and Biophysics, School of Biology and Pharmacy, Friedrich Schiller University, 07745 Jena, Germany
| | - Arthur Fischbach
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Ines Pfeil
- Institute of Clinical Molecular Biology, Helmholtz Center Munich, German Research Center for Environmental Health, 81377 Munich, Germany
| | - Svend K Petersen-Mahrt
- DNA Editing in Immunity and Epigenetics, IFOM-Fondazione Instituto FIRC di Oncologia Molecolare, Milano, Italy
| | - Aswin Mangerich
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Thomas Helleday
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Heinrich Leonhardt
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
| | - Berit Jungnickel
- Department of Cell Biology, Institute of Biochemistry and Biophysics, School of Biology and Pharmacy, Friedrich Schiller University, 07745 Jena, Germany.,Department of Biology, University of Konstanz, 78457 Konstanz, Germany
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50
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Chagin VO, Reinhart B, Becker A, Mortusewicz O, Jost KL, Rapp A, Leonhardt H, Cardoso MC. Processive DNA synthesis is associated with localized decompaction of constitutive heterochromatin at the sites of DNA replication and repair. Nucleus 2019; 10:231-253. [PMID: 31744372 PMCID: PMC6949026 DOI: 10.1080/19491034.2019.1688932] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 04/11/2019] [Revised: 09/01/2019] [Accepted: 10/22/2019] [Indexed: 12/18/2022] Open
Abstract
Constitutive heterochromatin is considered as a functionally inert genome compartment, important for its architecture and stability. How such stable structure is maintained is not well understood. Here, we apply four different visualization schemes to label it and investigate its dynamics during DNA replication and repair. We show that replisomes assemble over the heterochromatin in a temporally ordered manner. Furthermore, heterochromatin undergoes transient decompaction locally at the active sites of DNA synthesis. Using selective laser microirradiation conditions that lead to damage repaired via processive DNA synthesis, we measured similarly local decompaction of heterochromatin. In both cases, we could not observe large-scale movement of heterochromatin to the domain surface. Instead, the processive DNA synthesis machinery assembled at the replication/repair sites. Altogether, our data are compatible with a progression of DNA replication/repair along the chromatin in a dynamic mode with localized and transient decompaction that does not globally remodels the whole heterochromatin compartment.
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Affiliation(s)
- Vadim O. Chagin
- Cell Biology & Epigenetics, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Britta Reinhart
- Cell Biology & Epigenetics, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Annette Becker
- Cell Biology & Epigenetics, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | | | - K. Laurence Jost
- Cell Biology & Epigenetics, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Alexander Rapp
- Cell Biology & Epigenetics, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | | | - M. Cristina Cardoso
- Cell Biology & Epigenetics, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
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