1
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Birkhoff JC, Brouwer RWW, Kolovos P, Korporaal AL, Bermejo-Santos A, Boltsis I, Nowosad K, van den Hout MCGN, Grosveld FG, van IJcken WFJ, Huylebroeck D, Conidi A. Targeted chromatin conformation analysis identifies novel distal neural enhancers of ZEB2 in pluripotent stem cell differentiation. Hum Mol Genet 2021; 29:2535-2550. [PMID: 32628253 PMCID: PMC7471508 DOI: 10.1093/hmg/ddaa141] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 12/25/2022] Open
Abstract
The transcription factor zinc finger E-box binding protein 2 (ZEB2) controls embryonic and adult cell fate decisions and cellular maturation in many stem/progenitor cell types. Defects in these processes in specific cell types underlie several aspects of Mowat–Wilson syndrome (MOWS), which is caused by ZEB2 haplo-insufficiency. Human ZEB2, like mouse Zeb2, is located on chromosome 2 downstream of a ±3.5 Mb-long gene-desert, lacking any protein-coding gene. Using temporal targeted chromatin capture (T2C), we show major chromatin structural changes based on mapping in-cis proximities between the ZEB2 promoter and this gene desert during neural differentiation of human-induced pluripotent stem cells, including at early neuroprogenitor cell (NPC)/rosette state, where ZEB2 mRNA levels increase significantly. Combining T2C with histone-3 acetylation mapping, we identified three novel candidate enhancers about 500 kb upstream of the ZEB2 transcription start site. Functional luciferase-based assays in heterologous cells and NPCs reveal co-operation between these three enhancers. This study is the first to document in-cis Regulatory Elements located in ZEB2’s gene desert. The results further show the usability of T2C for future studies of ZEB2 REs in differentiation and maturation of multiple cell types and the molecular characterization of newly identified MOWS patients that lack mutations in ZEB2 protein-coding exons.
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Affiliation(s)
- Judith C Birkhoff
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands
| | - Rutger W W Brouwer
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands.,Center for Biomics, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands
| | - Petros Kolovos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis 68100, Greece
| | - Anne L Korporaal
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands
| | - Ana Bermejo-Santos
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands
| | - Ilias Boltsis
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands
| | - Karol Nowosad
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands.,Department of Biochemistry and Molecular Biology, Medical University of Lublin, Lublin 20-093, Poland
| | - Mirjam C G N van den Hout
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands.,Center for Biomics, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands
| | - Frank G Grosveld
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands
| | - Wilfred F J van IJcken
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands.,Center for Biomics, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands
| | - Danny Huylebroeck
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands.,Department of Development and Regeneration, KU Leuven, Leuven B-3000, Belgium
| | - Andrea Conidi
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands
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2
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Papadopoulos P, Kafasi A, De Cuyper IM, Barroca V, Lewandowski D, Kadri Z, Veldthuis M, Berghuis J, Gillemans N, Benavente Cuesta CM, Grosveld FG, van Zwieten R, Philipsen S, Vernet M, Gutiérrez L, Patrinos GP. Mild dyserythropoiesis and β-like globin gene expression imbalance due to the loss of histone chaperone ASF1B. Hum Genomics 2020; 14:39. [PMID: 33066815 PMCID: PMC7566067 DOI: 10.1186/s40246-020-00283-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 07/18/2020] [Accepted: 09/10/2020] [Indexed: 01/09/2023] Open
Abstract
The expression of the human β-like globin genes follows a well-orchestrated developmental pattern, undergoing two essential switches, the first one during the first weeks of gestation (ε to γ), and the second one during the perinatal period (γ to β). The γ- to β-globin gene switching mechanism includes suppression of fetal (γ-globin, HbF) and activation of adult (β-globin, HbA) globin gene transcription. In hereditary persistence of fetal hemoglobin (HPFH), the γ-globin suppression mechanism is impaired leaving these individuals with unusual elevated levels of fetal hemoglobin (HbF) in adulthood. Recently, the transcription factors KLF1 and BCL11A have been established as master regulators of the γ- to β-globin switch. Previously, a genomic variant in the KLF1 gene, identified by linkage analysis performed on twenty-seven members of a Maltese family, was found to be associated with HPFH. However, variation in the levels of HbF among family members, and those from other reported families carrying genetic variants in KLF1, suggests additional contributors to globin switching. ASF1B was downregulated in the family members with HPFH. Here, we investigate the role of ASF1B in γ- to β-globin switching and erythropoiesis in vivo. Mouse-human interspecies ASF1B protein identity is 91.6%. By means of knockdown functional assays in human primary erythroid cultures and analysis of the erythroid lineage in Asf1b knockout mice, we provide evidence that ASF1B is a novel contributor to steady-state erythroid differentiation, and while its loss affects the balance of globin expression, it has no major role in hemoglobin switching.
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Affiliation(s)
- Petros Papadopoulos
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands.
- Department of Hematology, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain.
| | - Athanassia Kafasi
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, AMC, UvA, Amsterdam, The Netherlands
| | - Iris M De Cuyper
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, AMC, UvA, Amsterdam, The Netherlands
| | - Vilma Barroca
- UMR Stabilité Génétique Cellules Souches et Radiations, Université de Paris and Université de Paris-Saclay, CEA, 18 route du Panorama, 92260, Fontenay-aux-Roses, France
- U1274, Inserm, 18 route du Panorama, 92260, Fontenay-aux-Roses, France
| | - Daniel Lewandowski
- UMR Stabilité Génétique Cellules Souches et Radiations, Université de Paris and Université de Paris-Saclay, CEA, 18 route du Panorama, 92260, Fontenay-aux-Roses, France
- U1274, Inserm, 18 route du Panorama, 92260, Fontenay-aux-Roses, France
| | - Zahra Kadri
- Division of Innovative Therapies, UMR1184, Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses, France
| | - Martijn Veldthuis
- Laboratory of Red Blood Cell Diagnostics, Sanquin Diagnostics, Amsterdam, The Netherlands
| | - Jeffrey Berghuis
- Laboratory of Red Blood Cell Diagnostics, Sanquin Diagnostics, Amsterdam, The Netherlands
| | - Nynke Gillemans
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Celina María Benavente Cuesta
- Department of Hematology, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Frank G Grosveld
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Rob van Zwieten
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, AMC, UvA, Amsterdam, The Netherlands
- Laboratory of Red Blood Cell Diagnostics, Sanquin Diagnostics, Amsterdam, The Netherlands
| | - Sjaak Philipsen
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Muriel Vernet
- UMR Stabilité Génétique Cellules Souches et Radiations, Université de Paris and Université de Paris-Saclay, CEA, 18 route du Panorama, 92260, Fontenay-aux-Roses, France
| | - Laura Gutiérrez
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
- Department of Hematology, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, AMC, UvA, Amsterdam, The Netherlands
- Platelet Research Lab -Instituto de Investigación Sanitaria del Principado de Asturias (ISPA)-, Department of Medicine -University of Oviedo-, Oviedo, Spain
| | - George P Patrinos
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, University of Patras School of Health Sciences, Patras, Greece
- Department of Pathology, College of Medicine and Health Sciences and Zayed Center of Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
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3
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Deryckere A, Stappers E, Dries R, Peyre E, van den Berghe V, Conidi A, Zampeta FI, Francis A, Bresseleers M, Stryjewska A, Vanlaer R, Maas E, Smal IV, van IJcken WFJ, Grosveld FG, Nguyen L, Huylebroeck D, Seuntjens E. Multifaceted actions of Zeb2 in postnatal neurogenesis from the ventricular-subventricular zone to the olfactory bulb. Development 2020; 147:dev184861. [PMID: 32253238 DOI: 10.1242/dev.184861] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 03/23/2020] [Indexed: 03/01/2024]
Abstract
The transcription factor Zeb2 controls fate specification and subsequent differentiation and maturation of multiple cell types in various embryonic tissues. It binds many protein partners, including activated Smad proteins and the NuRD co-repressor complex. How Zeb2 subdomains support cell differentiation in various contexts has remained elusive. Here, we studied the role of Zeb2 and its domains in neurogenesis and neural differentiation in the young postnatal ventricular-subventricular zone (V-SVZ), in which neural stem cells generate olfactory bulb-destined interneurons. Conditional Zeb2 knockouts and separate acute loss- and gain-of-function approaches indicated that Zeb2 is essential for controlling apoptosis and neuronal differentiation of V-SVZ progenitors before and after birth, and we identified Sox6 as a potential downstream target gene of Zeb2. Zeb2 genetic inactivation impaired the differentiation potential of the V-SVZ niche in a cell-autonomous fashion. We also provide evidence that its normal function in the V-SVZ also involves non-autonomous mechanisms. Additionally, we demonstrate distinct roles for Zeb2 protein-binding domains, suggesting that Zeb2 partners co-determine neuronal output from the mouse V-SVZ in both quantitative and qualitative ways in early postnatal life.
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Affiliation(s)
- Astrid Deryckere
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven 3000, Belgium
| | - Elke Stappers
- Laboratory of Molecular Biology (Celgen), Department of Development and Regeneration, KU Leuven, Leuven 3000, Belgium
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam 3015 CN, The Netherlands
| | - Ruben Dries
- Laboratory of Molecular Biology (Celgen), Department of Development and Regeneration, KU Leuven, Leuven 3000, Belgium
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam 3015 CN, The Netherlands
| | - Elise Peyre
- GIGA-Stem Cells and GIGA-Neurosciences, Liège University, Liège 4000, Belgium
| | - Veronique van den Berghe
- Laboratory of Molecular Biology (Celgen), Department of Development and Regeneration, KU Leuven, Leuven 3000, Belgium
- Department of Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, and MRC Centre for Neurodevelopmental Disorders, King's College London, London SE1 1UL, UK
| | - Andrea Conidi
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam 3015 CN, The Netherlands
| | - F Isabella Zampeta
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam 3015 CN, The Netherlands
| | - Annick Francis
- Laboratory of Molecular Biology (Celgen), Department of Development and Regeneration, KU Leuven, Leuven 3000, Belgium
| | - Marjolein Bresseleers
- Laboratory of Molecular Biology (Celgen), Department of Development and Regeneration, KU Leuven, Leuven 3000, Belgium
| | - Agata Stryjewska
- Laboratory of Molecular Biology (Celgen), Department of Development and Regeneration, KU Leuven, Leuven 3000, Belgium
| | - Ria Vanlaer
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven 3000, Belgium
| | - Elke Maas
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, KU Leuven, Leuven 3000, Belgium
| | - Ihor V Smal
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam 3015 CN, The Netherlands
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam 3015 CN, The Netherlands
| | - Wilfred F J van IJcken
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam 3015 CN, The Netherlands
- Center for Biomics-Genomics, Department of Cell Biology, Erasmus University Medical Center, Rotterdam 3015 CN, The Netherlands
| | - Frank G Grosveld
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam 3015 CN, The Netherlands
| | - Laurent Nguyen
- GIGA-Stem Cells and GIGA-Neurosciences, Liège University, Liège 4000, Belgium
| | - Danny Huylebroeck
- Laboratory of Molecular Biology (Celgen), Department of Development and Regeneration, KU Leuven, Leuven 3000, Belgium
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam 3015 CN, The Netherlands
| | - Eve Seuntjens
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven 3000, Belgium
- Laboratory of Molecular Biology (Celgen), Department of Development and Regeneration, KU Leuven, Leuven 3000, Belgium
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4
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Dries R, Stryjewska A, Coddens K, Okawa S, Notelaers T, Birkhoff J, Dekker M, Verfaillie CM, Del Sol A, Mulugeta E, Conidi A, Grosveld FG, Huylebroeck D. Integrative and perturbation-based analysis of the transcriptional dynamics of TGFβ/BMP system components in transition from embryonic stem cells to neural progenitors. Stem Cells 2019; 38:202-217. [PMID: 31675135 PMCID: PMC7027912 DOI: 10.1002/stem.3111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 08/02/2019] [Accepted: 10/09/2019] [Indexed: 01/05/2023]
Abstract
Cooperative actions of extrinsic signals and cell‐intrinsic transcription factors alter gene regulatory networks enabling cells to respond appropriately to environmental cues. Signaling by transforming growth factor type β (TGFβ) family ligands (eg, bone morphogenetic proteins [BMPs] and Activin/Nodal) exerts cell‐type specific and context‐dependent transcriptional changes, thereby steering cellular transitions throughout embryogenesis. Little is known about coordinated regulation and transcriptional interplay of the TGFβ system. To understand intrafamily transcriptional regulation as part of this system's actions during development, we selected 95 of its components and investigated their mRNA‐expression dynamics, gene‐gene interactions, and single‐cell expression heterogeneity in mouse embryonic stem cells transiting to neural progenitors. Interrogation at 24 hour intervals identified four types of temporal gene transcription profiles that capture all stages, that is, pluripotency, epiblast formation, and neural commitment. Then, between each stage we performed esiRNA‐based perturbation of each individual component and documented the effect on steady‐state mRNA levels of the remaining 94 components. This exposed an intricate system of multilevel regulation whereby the majority of gene‐gene interactions display a marked cell‐stage specific behavior. Furthermore, single‐cell RNA‐profiling at individual stages demonstrated the presence of detailed co‐expression modules and subpopulations showing stable co‐expression modules such as that of the core pluripotency genes at all stages. Our combinatorial experimental approach demonstrates how intrinsically complex transcriptional regulation within a given pathway is during cell fate/state transitions.
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Affiliation(s)
- Ruben Dries
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Agata Stryjewska
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Kathleen Coddens
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Satoshi Okawa
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.,Integrated BioBank of Luxembourg, Dudelange, Luxembourg
| | - Tineke Notelaers
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Judith Birkhoff
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mike Dekker
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Antonio Del Sol
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.,CIC bioGUNE, Bizkaia Technology Park, Derio, Spain.,IKERBASQUE, Basque, Foundation for Science, Bilbao, Spain
| | - Eskeatnaf Mulugeta
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Andrea Conidi
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Frank G Grosveld
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Danny Huylebroeck
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Development and Regeneration, KU Leuven, Leuven, Belgium
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5
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Yu X, Martella A, Kolovos P, Stevens M, Stadhouders R, Grosveld FG, Andrieu-Soler C. The dynamic emergence of GATA1 complexes identified in in vitro embryonic stem cell differentiation and in vivo mouse fetal liver. Haematologica 2019; 105:1802-1812. [PMID: 31582556 PMCID: PMC7327653 DOI: 10.3324/haematol.2019.216010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 01/07/2019] [Accepted: 10/03/2019] [Indexed: 01/20/2023] Open
Abstract
GATA1 is an essential transcriptional regulator of myeloid hematopoietic differentiation towards red blood cells. During erythroid differentiation, GATA1 forms different complexes with other transcription factors such as LDB1, TAL1, E2A and LMO2 ("the LDB1 complex") or with FOG1. The functions of GATA1 complexes have been studied extensively in definitive erythroid differentiation; however, the temporal and spatial formation of these complexes during erythroid development is unknown. We applied proximity ligation assay (PLA) to detect, localize and quantify individual interactions during embryonic stem cell differentiation and in mouse fetal liver (FL) tissue. We show that GATA1/LDB1 interactions appear before the proerythroblast stage and increase in a subset of the CD71+/TER119- cells to activate the terminal erythroid differentiation program in 12.5 day FL. Using Ldb1 and Gata1 knockdown FL cells, we studied the functional contribution of the GATA1/LDB1 complex during differentiation. This shows that the active LDB1 complex appears quite late at the proerythroblast stage of differentiation and confirms the power of PLA in studying the dynamic interaction of proteins in cell differentiation at the single cell level. We provide dynamic insight into the temporal and spatial formation of the GATA1 and LDB1 transcription factor complexes during hematopoietic development and differentiation.
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Affiliation(s)
- Xiao Yu
- Department of Cell Biology, ErasmusMC, Rotterdam, the Netherlands.,Current address: Department of Medical Microbiology, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Andrea Martella
- Department of Cell Biology, ErasmusMC, Rotterdam, the Netherlands.,AstraZeneca, R&D Innovative Medicines, Cambridge Science Park, Milton Road, Cambridge, UK
| | - Petros Kolovos
- Department of Cell Biology, ErasmusMC, Rotterdam, the Netherlands.,Biotech Research & Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Mary Stevens
- Department of Cell Biology, ErasmusMC, Rotterdam, the Netherlands
| | - Ralph Stadhouders
- Department of Cell Biology, ErasmusMC, Rotterdam, the Netherlands.,Department of Pulmonary Medicine, Erasmus MC, Rotterdam, the Netherlands
| | - Frank G Grosveld
- Department of Cell Biology, ErasmusMC, Rotterdam, the Netherlands
| | - Charlotte Andrieu-Soler
- Department of Cell Biology, ErasmusMC, Rotterdam, the Netherlands .,Institut de Génétique Moléculaire Montpellier, Université de Montpellier, CNRS, Montpellier, France.,Université de Paris, Laboratoire d'excellence (LabEx) du globule rouge GR-Ex, Paris, France
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6
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Abstract
The last decade has radically renewed our understanding of higher order chromatin folding in the eukaryotic nucleus. As a result, most current models are in support of a mostly hierarchical and relatively stable folding of chromosomes dividing chromosomal territories into A‐ (active) and B‐ (inactive) compartments, which are then further partitioned into topologically associating domains (TADs), each of which is made up from multiple loops stabilized mainly by the CTCF and cohesin chromatin‐binding complexes. Nonetheless, the structure‐to‐function relationship of eukaryotic genomes is still not well understood. Here, we focus on recent work highlighting the biophysical and regulatory forces that contribute to the spatial organization of genomes, and we propose that the various conformations that chromatin assumes are not so much the result of a linear hierarchy, but rather of both converging and conflicting dynamic forces that act on it.
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Affiliation(s)
- Alvaro Rada-Iglesias
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany .,CECAD, University of Cologne, Cologne, Germany
| | - Frank G Grosveld
- Department of Cell Biology, Erasmus Medical Center, GE Rotterdam, Netherlands
| | - Argyris Papantonis
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
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7
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Knoch TA, Wachsmuth M, Kepper N, Lesnussa M, Abuseiris A, Ali Imam AM, Kolovos P, Zuin J, Kockx CEM, Brouwer RWW, van de Werken HJG, van IJcken WFJ, Wendt KS, Grosveld FG. The detailed 3D multi-loop aggregate/rosette chromatin architecture and functional dynamic organization of the human and mouse genomes. Epigenetics Chromatin 2016; 9:58. [PMID: 28035242 PMCID: PMC5192698 DOI: 10.1186/s13072-016-0089-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 09/01/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The dynamic three-dimensional chromatin architecture of genomes and its co-evolutionary connection to its function-the storage, expression, and replication of genetic information-is still one of the central issues in biology. Here, we describe the much debated 3D architecture of the human and mouse genomes from the nucleosomal to the megabase pair level by a novel approach combining selective high-throughput high-resolution chromosomal interaction capture (T2C), polymer simulations, and scaling analysis of the 3D architecture and the DNA sequence. RESULTS The genome is compacted into a chromatin quasi-fibre with ~5 ± 1 nucleosomes/11 nm, folded into stable ~30-100 kbp loops forming stable loop aggregates/rosettes connected by similar sized linkers. Minor but significant variations in the architecture are seen between cell types and functional states. The architecture and the DNA sequence show very similar fine-structured multi-scaling behaviour confirming their co-evolution and the above. CONCLUSIONS This architecture, its dynamics, and accessibility, balance stability and flexibility ensuring genome integrity and variation enabling gene expression/regulation by self-organization of (in)active units already in proximity. Our results agree with the heuristics of the field and allow "architectural sequencing" at a genome mechanics level to understand the inseparable systems genomic properties.
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Affiliation(s)
- Tobias A. Knoch
- Biophysical Genomics, Department of Cell Biology and Genetics, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Malte Wachsmuth
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Nick Kepper
- Biophysical Genomics, Department of Cell Biology and Genetics, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
- Genome Organization and Function, BioQuant and German Cancer Research Center, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Michael Lesnussa
- Biophysical Genomics, Department of Cell Biology and Genetics, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Anis Abuseiris
- Biophysical Genomics, Department of Cell Biology and Genetics, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - A. M. Ali Imam
- Biophysical Genomics, Department of Cell Biology and Genetics, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
- Cell Biology, Department Cell Biology and Genetics, Erasmus MC, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
| | - Petros Kolovos
- Biophysical Genomics, Department of Cell Biology and Genetics, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
- Cell Biology, Department Cell Biology and Genetics, Erasmus MC, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
| | - Jessica Zuin
- Cohesin in Chromatin Structure and Gene Regulation, Department of Cell Biology and Genetics, Erasmus MC, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
| | - Christel E. M. Kockx
- Center for Biomics, Department of Cell Biology and Genetics, Erasmus MC, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
| | - Rutger W. W. Brouwer
- Center for Biomics, Department of Cell Biology and Genetics, Erasmus MC, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
| | - Harmen J. G. van de Werken
- Cell Biology, Department Cell Biology and Genetics, Erasmus MC, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
| | - Wilfred F. J. van IJcken
- Center for Biomics, Department of Cell Biology and Genetics, Erasmus MC, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
| | - Kerstin S. Wendt
- Cohesin in Chromatin Structure and Gene Regulation, Department of Cell Biology and Genetics, Erasmus MC, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
| | - Frank G. Grosveld
- Cell Biology, Department Cell Biology and Genetics, Erasmus MC, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
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8
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Brant L, Georgomanolis T, Nikolic M, Brackley CA, Kolovos P, van Ijcken W, Grosveld FG, Marenduzzo D, Papantonis A. Exploiting native forces to capture chromosome conformation in mammalian cell nuclei. Mol Syst Biol 2016; 12:891. [PMID: 27940490 PMCID: PMC5199122 DOI: 10.15252/msb.20167311] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [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] [Indexed: 12/22/2022] Open
Abstract
Mammalian interphase chromosomes fold into a multitude of loops to fit the confines of cell nuclei, and looping is tightly linked to regulated function. Chromosome conformation capture (3C) technology has significantly advanced our understanding of this structure‐to‐function relationship. However, all 3C‐based methods rely on chemical cross‐linking to stabilize spatial interactions. This step remains a “black box” as regards the biases it may introduce, and some discrepancies between microscopy and 3C studies have now been reported. To address these concerns, we developed “i3C”, a novel approach for capturing spatial interactions without a need for cross‐linking. We apply i3C to intact nuclei of living cells and exploit native forces that stabilize chromatin folding. Using different cell types and loci, computational modeling, and a methylation‐based orthogonal validation method, “TALE‐iD”, we show that native interactions resemble cross‐linked ones, but display improved signal‐to‐noise ratios and are more focal on regulatory elements and CTCF sites, while strictly abiding to topologically associating domain restrictions.
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Affiliation(s)
- Lilija Brant
- Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | | | - Milos Nikolic
- Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Chris A Brackley
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Petros Kolovos
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Frank G Grosveld
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Davide Marenduzzo
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
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9
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Stryjewska A, Dries R, Pieters T, Verstappen G, Conidi A, Coddens K, Francis A, Umans L, van IJcken WFJ, Berx G, van Grunsven LA, Grosveld FG, Goossens S, Haigh JJ, Huylebroeck D. Zeb2 Regulates Cell Fate at the Exit from Epiblast State in Mouse Embryonic Stem Cells. Stem Cells 2016; 35:611-625. [PMID: 27739137 PMCID: PMC5396376 DOI: 10.1002/stem.2521] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 09/09/2016] [Accepted: 09/12/2016] [Indexed: 12/12/2022]
Abstract
In human embryonic stem cells (ESCs) the transcription factor Zeb2 regulates neuroectoderm versus mesendoderm formation, but it is unclear how Zeb2 affects the global transcriptional regulatory network in these cell‐fate decisions. We generated Zeb2 knockout (KO) mouse ESCs, subjected them as embryoid bodies (EBs) to neural and general differentiation and carried out temporal RNA‐sequencing (RNA‐seq) and reduced representation bisulfite sequencing (RRBS) analysis in neural differentiation. This shows that Zeb2 acts preferentially as a transcriptional repressor associated with developmental progression and that Zeb2 KO ESCs can exit from their naïve state. However, most cells in these EBs stall in an early epiblast‐like state and are impaired in both neural and mesendodermal differentiation. Genes involved in pluripotency, epithelial‐to‐mesenchymal transition (EMT), and DNA‐(de)methylation, including Tet1, are deregulated in the absence of Zeb2. The observed elevated Tet1 levels in the mutant cells and the knowledge of previously mapped Tet1‐binding sites correlate with loss‐of‐methylation in neural‐stimulating conditions, however, after the cells initially acquired the correct DNA‐methyl marks. Interestingly, cells from such Zeb2 KO EBs maintain the ability to re‐adapt to 2i + LIF conditions even after prolonged differentiation, while knockdown of Tet1 partially rescues their impaired differentiation. Hence, in addition to its role in EMT, Zeb2 is critical in ESCs for exit from the epiblast state, and links the pluripotency network and DNA‐methylation with irreversible commitment to differentiation. Stem Cells2017;35:611–625
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Affiliation(s)
- Agata Stryjewska
- Department of Development and Regeneration, KU Leuven, Leuven, 3000, Belgium
| | - Ruben Dries
- Department of Development and Regeneration, KU Leuven, Leuven, 3000, Belgium.,Department of Cell Biology, Erasmus University Medical Center, Rotterdam, 3015 CN, The Netherlands
| | - Tim Pieters
- VIB Inflammation Research Center (IRC), Unit Vascular Cell Biology.,Department of Biomedical Molecular Biology.,VIB-IRC, Unit Molecular and Cellular Oncology, Ghent University, Ghent, 9052, Belgium.,Center for Medical Genetics, Ghent University Hospital, Ghent, 9000, Belgium
| | - Griet Verstappen
- Department of Development and Regeneration, KU Leuven, Leuven, 3000, Belgium
| | - Andrea Conidi
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, 3015 CN, The Netherlands
| | - Kathleen Coddens
- Department of Development and Regeneration, KU Leuven, Leuven, 3000, Belgium
| | - Annick Francis
- Department of Development and Regeneration, KU Leuven, Leuven, 3000, Belgium
| | - Lieve Umans
- Department of Development and Regeneration, KU Leuven, Leuven, 3000, Belgium
| | - Wilfred F J van IJcken
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, 3015 CN, The Netherlands.,Center for Biomics, Erasmus University Medical Center, Rotterdam, 3015 CN, The Netherlands
| | - Geert Berx
- Department of Biomedical Molecular Biology.,VIB-IRC, Unit Molecular and Cellular Oncology, Ghent University, Ghent, 9052, Belgium
| | - Leo A van Grunsven
- Department of Cell Biology, Liver Cell Biology Lab, Vrije Universiteit Brussel, Jette, 1090, Belgium
| | - Frank G Grosveld
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, 3015 CN, The Netherlands
| | - Steven Goossens
- VIB Inflammation Research Center (IRC), Unit Vascular Cell Biology.,Department of Biomedical Molecular Biology.,VIB-IRC, Unit Molecular and Cellular Oncology, Ghent University, Ghent, 9052, Belgium.,ACBD - Blood Cancers and Stem Cells, Group Mammalian Functional Genetics, Monash University, Melbourne, VIC, 3004, Australia
| | - Jody J Haigh
- VIB Inflammation Research Center (IRC), Unit Vascular Cell Biology.,Department of Biomedical Molecular Biology.,ACBD - Blood Cancers and Stem Cells, Group Mammalian Functional Genetics, Monash University, Melbourne, VIC, 3004, Australia
| | - Danny Huylebroeck
- Department of Development and Regeneration, KU Leuven, Leuven, 3000, Belgium.,Department of Cell Biology, Erasmus University Medical Center, Rotterdam, 3015 CN, The Netherlands
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10
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Kolovos P, Georgomanolis T, Koeferle A, Larkin JD, Brant L, Nikolicć M, Gusmao EG, Zirkel A, Knoch TA, van Ijcken WF, Cook PR, Costa IG, Grosveld FG, Papantonis A. Binding of nuclear factor κB to noncanonical consensus sites reveals its multimodal role during the early inflammatory response. Genome Res 2016; 26:1478-1489. [PMID: 27633323 PMCID: PMC5088591 DOI: 10.1101/gr.210005.116] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [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: 05/19/2016] [Accepted: 09/14/2016] [Indexed: 01/25/2023]
Abstract
Mammalian cells have developed intricate mechanisms to interpret, integrate, and respond to extracellular stimuli. For example, tumor necrosis factor (TNF) rapidly activates proinflammatory genes, but our understanding of how this occurs against the ongoing transcriptional program of the cell is far from complete. Here, we monitor the early phase of this cascade at high spatiotemporal resolution in TNF-stimulated human endothelial cells. NF-κB, the transcription factor complex driving the response, interferes with the regulatory machinery by binding active enhancers already in interaction with gene promoters. Notably, >50% of these enhancers do not encode canonical NF-κB binding motifs. Using a combination of genomics tools, we find that binding site selection plays a key role in NF-κΒ–mediated transcriptional activation and repression. We demonstrate the latter by describing the synergy between NF-κΒ and the corepressor JDP2. Finally, detailed analysis of a 2.8-Mbp locus using sub-kbp-resolution targeted chromatin conformation capture and genome editing uncovers how NF-κΒ that has just entered the nucleus exploits pre-existing chromatin looping to exert its multimodal role. This work highlights the involvement of topology in cis-regulatory element function during acute transcriptional responses, where primary DNA sequence and its higher-order structure constitute a regulatory context leading to either gene activation or repression.
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Affiliation(s)
- Petros Kolovos
- Department of Cell Biology, Erasmus Medical Centre, 3015 CN Rotterdam, The Netherlands
| | | | - Anna Koeferle
- Sir William Dunn School of Pathology, University of Oxford, OX1 3RE Oxford, United Kingdom
| | - Joshua D Larkin
- Sir William Dunn School of Pathology, University of Oxford, OX1 3RE Oxford, United Kingdom
| | - Lilija Brant
- Center for Molecular Medicine, University of Cologne, 50931 Cologne, Germany
| | - Miloš Nikolicć
- Center for Molecular Medicine, University of Cologne, 50931 Cologne, Germany
| | - Eduardo G Gusmao
- IZKF Computational Biology Research Group, RWTH Aachen University Medical School, 52062 Aachen, Germany
| | - Anne Zirkel
- Center for Molecular Medicine, University of Cologne, 50931 Cologne, Germany
| | - Tobias A Knoch
- Department of Cell Biology, Erasmus Medical Centre, 3015 CN Rotterdam, The Netherlands
| | | | - Peter R Cook
- Sir William Dunn School of Pathology, University of Oxford, OX1 3RE Oxford, United Kingdom
| | - Ivan G Costa
- IZKF Computational Biology Research Group, RWTH Aachen University Medical School, 52062 Aachen, Germany
| | - Frank G Grosveld
- Department of Cell Biology, Erasmus Medical Centre, 3015 CN Rotterdam, The Netherlands
| | - Argyris Papantonis
- Center for Molecular Medicine, University of Cologne, 50931 Cologne, Germany
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11
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Tresini M, Warmerdam DO, Kolovos P, Snijder L, Vrouwe MG, Demmers JAA, van IJcken WFJ, Grosveld FG, Medema RH, Hoeijmakers JHJ, Mullenders LHF, Vermeulen W, Marteijn JA. The core spliceosome as target and effector of non-canonical ATM signalling. Nature 2015; 523:53-8. [PMID: 26106861 PMCID: PMC4501432 DOI: 10.1038/nature14512] [Citation(s) in RCA: 182] [Impact Index Per Article: 20.2] [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: 04/14/2014] [Accepted: 05/11/2015] [Indexed: 01/19/2023]
Abstract
In response to DNA damage, tissue homoeostasis is ensured by protein networks promoting DNA repair, cell cycle arrest or apoptosis. DNA damage response signalling pathways coordinate these processes, partly by propagating gene-expression-modulating signals. DNA damage influences not only the abundance of messenger RNAs, but also their coding information through alternative splicing. Here we show that transcription-blocking DNA lesions promote chromatin displacement of late-stage spliceosomes and initiate a positive feedback loop centred on the signalling kinase ATM. We propose that initial spliceosome displacement and subsequent R-loop formation is triggered by pausing of RNA polymerase at DNA lesions. In turn, R-loops activate ATM, which signals to impede spliceosome organization further and augment ultraviolet-irradiation-triggered alternative splicing at the genome-wide level. Our findings define R-loop-dependent ATM activation by transcription-blocking lesions as an important event in the DNA damage response of non-replicating cells, and highlight a key role for spliceosome displacement in this process.
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Affiliation(s)
- Maria Tresini
- Department of Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, 3015 CN, The Netherlands
| | - Daniël O Warmerdam
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, 1066 CX, The Netherlands
| | - Petros Kolovos
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, 3015 CN, The Netherlands
| | - Loes Snijder
- Department of Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, 3015 CN, The Netherlands
| | - Mischa G Vrouwe
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZC, The Netherlands
| | - Jeroen A A Demmers
- Erasmus MC Proteomics Center, Erasmus University Medical Center, Rotterdam, 3015 CN, The Netherlands
| | - Wilfred F J van IJcken
- Erasmus Center for Biomics, Erasmus University Medical Center, Rotterdam, 3015 CN, The Netherlands
| | - Frank G Grosveld
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, 3015 CN, The Netherlands
| | - René H Medema
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, 1066 CX, The Netherlands
| | - Jan H J Hoeijmakers
- Department of Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, 3015 CN, The Netherlands
| | - Leon H F Mullenders
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZC, The Netherlands
| | - Wim Vermeulen
- Department of Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, 3015 CN, The Netherlands
| | - Jurgen A Marteijn
- Department of Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, 3015 CN, The Netherlands
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12
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Ochieng JK, Schilders K, Kool H, Boerema-De Munck A, Buscop-Van Kempen M, Gontan C, Smits R, Grosveld FG, Wijnen RMH, Tibboel D, Rottier RJ. Sox2 regulates the emergence of lung basal cells by directly activating the transcription of Trp63. Am J Respir Cell Mol Biol 2014; 51:311-22. [PMID: 24669837 DOI: 10.1165/rcmb.2013-0419oc] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Lung development is determined by the coordinated expression of several key genes. Previously, we and others have shown the importance of the sex determining region Y-box 2 (Sox2) gene in lung development. Transgenic expression of Sox2 during lung development resulted in cystic airways, and here we show that modulating the timing of ectopic Sox2 expression in the branching regions of the developing lung results in variable cystic lesions resembling the spectrum of the human congenital disorder congenital cystic adenomatoid malformation (CCAM). Sox2 dominantly differentiated naive epithelial cells into the proximal lineage irrespective of the presence of Fgf10. Sox2 directly induced the expression of Trp63, the master switch toward the basal cell lineage and induced the expression of Gata6, a factor involved in the emergence of bronchoalveolar stem cells. We showed that SOX2 and TRP63 are coexpressed in the lungs of human patients with type II CCAM. The combination of premature differentiation toward the proximal cell lineage and the induction of proliferation resulted in the cyst-like structures. Thus, we show that Sox2 is directly responsible for the emergence of two lung progenitor cells: basal cells by regulating the master gene Trp63 and bronchoalveolar stem cells by regulating Gata6.
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Affiliation(s)
- Joshua K Ochieng
- Departments of 1 Pediatric Surgery of the Erasmus MC-Sophia Children's Hospital
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13
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Giraud G, Stadhouders R, Conidi A, Dekkers DHW, Huylebroeck D, Demmers JAA, Soler E, Grosveld FG. NLS-tagging: an alternative strategy to tag nuclear proteins. Nucleic Acids Res 2014; 42:gku869. [PMID: 25260593 PMCID: PMC4245968 DOI: 10.1093/nar/gku869] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The characterization of transcription factor complexes and their binding sites in the genome by affinity purification has yielded tremendous new insights into how genes are regulated. The affinity purification requires either the use of antibodies raised against the factor of interest itself or by high-affinity binding of a C- or N-terminally added tag sequence to the factor. Unfortunately, fusing extra amino acids to the termini of a factor can interfere with its biological function or the tag may be inaccessible inside the protein. Here, we describe an effective solution to that problem by integrating the ‘tag’ close to the nuclear localization sequence domain of the factor. We demonstrate the effectiveness of this approach with the transcription factors Fli-1 and Irf2bp2, which cannot be tagged at their extremities without loss of function. This resulted in the identification of novel proteins partners and a new hypothesis on the contribution of Fli-1 to hematopoiesis.
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Affiliation(s)
- Guillaume Giraud
- Department of Cell Biology, Erasmus Medical Center, Faculty building, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Ralph Stadhouders
- Department of Cell Biology, Erasmus Medical Center, Faculty building, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Andrea Conidi
- Department of Cell Biology, Erasmus Medical Center, Faculty building, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Dick H W Dekkers
- Proteomics Center, Erasmus University Medical Center, Faculty building, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Danny Huylebroeck
- Department of Cell Biology, Erasmus Medical Center, Faculty building, PO Box 2040, 3000 CA Rotterdam, The Netherlands Laboratory of Molecular Biology (Celgen), Department of Development and Regeneration, KU Leuven, Herestraat 49, B-3000 Leuven, Belgium
| | - Jeroen A A Demmers
- Proteomics Center, Erasmus University Medical Center, Faculty building, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Eric Soler
- Department of Cell Biology, Erasmus Medical Center, Faculty building, PO Box 2040, 3000 CA Rotterdam, The Netherlands Laboratory of Hematopoiesis and Leukemic Stem Cells (LSHL), CEA/INSERM U967, Fontenay-aux-Roses, France Center for Biomedical Genetics and Medical Epigenetics Consortium, Erasmus Medical Center, Faculty building, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Frank G Grosveld
- Department of Cell Biology, Erasmus Medical Center, Faculty building, PO Box 2040, 3000 CA Rotterdam, The Netherlands Center for Biomedical Genetics and Medical Epigenetics Consortium, Erasmus Medical Center, Faculty building, PO Box 2040, 3000 CA Rotterdam, The Netherlands Center for Biomedical Genetics, Erasmus Medical Center, Faculty building, PO Box 2040, 3000 CA Rotterdam, The Netherlands
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14
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15
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Zuin J, Dixon JR, van der Reijden MIJA, Ye Z, Kolovos P, Brouwer RWW, van de Corput MPC, van de Werken HJG, Knoch TA, van IJcken WFJ, Grosveld FG, Ren B, Wendt KS. Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells. Proc Natl Acad Sci U S A 2014; 111:996-1001. [PMID: 24335803 PMCID: PMC3903193 DOI: 10.1073/pnas.1317788111] [Citation(s) in RCA: 564] [Impact Index Per Article: 56.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Recent studies of genome-wide chromatin interactions have revealed that the human genome is partitioned into many self-associating topological domains. The boundary sequences between domains are enriched for binding sites of CTCC-binding factor (CTCF) and the cohesin complex, implicating these two factors in the establishment or maintenance of topological domains. To determine the role of cohesin and CTCF in higher-order chromatin architecture in human cells, we depleted the cohesin complex or CTCF and examined the consequences of loss of these factors on higher-order chromatin organization, as well as the transcriptome. We observed a general loss of local chromatin interactions upon disruption of cohesin, but the topological domains remain intact. However, we found that depletion of CTCF not only reduced intradomain interactions but also increased interdomain interactions. Furthermore, distinct groups of genes become misregulated upon depletion of cohesin and CTCF. Taken together, these observations suggest that CTCF and cohesin contribute differentially to chromatin organization and gene regulation.
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Affiliation(s)
| | - Jesse R. Dixon
- Laboratory of Gene Regulation, Ludwig Institute for Cancer Research, La Jolla, CA 92093
- Medical Scientist Training Program
- Biomedical Sciences Graduate Program
| | | | - Zhen Ye
- Laboratory of Gene Regulation, Ludwig Institute for Cancer Research, La Jolla, CA 92093
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, Moores Cancer Center, San Diego School of Medicine, University of California, San Diego, La Jolla, CA 92093
| | | | - Rutger W. W. Brouwer
- Center for Biomics
- Netherlands Bioinformatics Centre, 6500 HB, Nijmegen, The Netherlands; and
| | | | | | - Tobias A. Knoch
- Biophysical Genomics, Department of Cell Biology
- Genome Organization and Function, Bioquant Centre/German Cancer Research Center, 69120 Heidelberg, Germany
| | | | - Frank G. Grosveld
- Department of Cell Biology
- Cancer Genomics Center, Erasmus Medical Center, 3015 GE, Rotterdam, The Netherlands
| | - Bing Ren
- Laboratory of Gene Regulation, Ludwig Institute for Cancer Research, La Jolla, CA 92093
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, Moores Cancer Center, San Diego School of Medicine, University of California, San Diego, La Jolla, CA 92093
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16
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Francius C, Harris A, Rucchin V, Hendricks TJ, Stam FJ, Barber M, Kurek D, Grosveld FG, Pierani A, Goulding M, Clotman F. Identification of multiple subsets of ventral interneurons and differential distribution along the rostrocaudal axis of the developing spinal cord. PLoS One 2013; 8:e70325. [PMID: 23967072 PMCID: PMC3744532 DOI: 10.1371/journal.pone.0070325] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 06/17/2013] [Indexed: 01/06/2023] Open
Abstract
The spinal cord contains neuronal circuits termed Central Pattern Generators (CPGs) that coordinate rhythmic motor activities. CPG circuits consist of motor neurons and multiple interneuron cell types, many of which are derived from four distinct cardinal classes of ventral interneurons, called V0, V1, V2 and V3. While significant progress has been made on elucidating the molecular and genetic mechanisms that control ventral interneuron differentiation, little is known about their distribution along the antero-posterior axis of the spinal cord and their diversification. Here, we report that V0, V1 and V2 interneurons exhibit distinct organizational patterns at brachial, thoracic and lumbar levels of the developing spinal cord. In addition, we demonstrate that each cardinal class of ventral interneurons can be subdivided into several subsets according to the combinatorial expression of different sets of transcription factors, and that these subsets are differentially distributed along the rostrocaudal axis of the spinal cord. This comprehensive molecular profiling of ventral interneurons provides an important resource for investigating neuronal diversification in the developing spinal cord and for understanding the contribution of specific interneuron subsets on CPG circuits and motor control.
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Affiliation(s)
- Cédric Francius
- Université catholique de Louvain, Institute of Neuroscience, Laboratory of Neural Differentiation, Brussels, Belgium
| | - Audrey Harris
- Université catholique de Louvain, Institute of Neuroscience, Laboratory of Neural Differentiation, Brussels, Belgium
| | - Vincent Rucchin
- Université catholique de Louvain, Institute of Neuroscience, Laboratory of Neural Differentiation, Brussels, Belgium
| | - Timothy J. Hendricks
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Floor J. Stam
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Melissa Barber
- CNRS UMR 7592, Institut Jacques Monod, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Dorota Kurek
- Erasmus MC Stem Cell Institute, Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Frank G. Grosveld
- Erasmus MC Stem Cell Institute, Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Alessandra Pierani
- CNRS UMR 7592, Institut Jacques Monod, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Martyn Goulding
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Frédéric Clotman
- Université catholique de Louvain, Institute of Neuroscience, Laboratory of Neural Differentiation, Brussels, Belgium
- * E-mail:
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17
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Thongjuea S, Stadhouders R, Grosveld FG, Soler E, Lenhard B. r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data. Nucleic Acids Res 2013; 41:e132. [PMID: 23671339 PMCID: PMC3711450 DOI: 10.1093/nar/gkt373] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [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] [Indexed: 12/26/2022] Open
Abstract
The coupling of chromosome conformation capture (3C) with next-generation sequencing technologies enables the high-throughput detection of long-range genomic interactions, via the generation of ligation products between DNA sequences, which are closely juxtaposed in vivo. These interactions involve promoter regions, enhancers and other regulatory and structural elements of chromosomes and can reveal key details of the regulation of gene expression. 3C-seq is a variant of the method for the detection of interactions between one chosen genomic element (viewpoint) and the rest of the genome. We present r3Cseq, an R/Bioconductor package designed to perform 3C-seq data analysis in a number of different experimental designs. The package reads a common aligned read input format, provides data normalization, allows the visualization of candidate interaction regions and detects statistically significant chromatin interactions, thus greatly facilitating hypothesis generation and the interpretation of experimental results. We further demonstrate its use on a series of real-world applications.
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Affiliation(s)
- Supat Thongjuea
- Computational Biology Unit, Uni Computing, Uni Research AS, N-5020 Bergen, Norway
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18
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Ghamari A, van de Corput MP, Thongjuea S, van Cappellen WA, van IJcken W, van Haren J, Soler E, Eick D, Lenhard B, Grosveld FG. In vivo live imaging of RNA polymerase II transcription factories in primary cells. Genes Dev 2013; 27:767-77. [PMID: 23592796 PMCID: PMC3639417 DOI: 10.1101/gad.216200.113] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 03/18/2013] [Indexed: 11/24/2022]
Abstract
Transcription steps are marked by different modifications of the C-terminal domain of RNA polymerase II (RNAPII). Phosphorylation of Ser5 and Ser7 by cyclin-dependent kinase 7 (CDK7) as part of TFIIH marks initiation, whereas phosphorylation of Ser2 by CDK9 marks elongation. These processes are thought to take place in localized transcription foci in the nucleus, known as "transcription factories," but it has been argued that the observed clusters/foci are mere fixation or labeling artifacts. We show that transcription factories exist in living cells as distinct foci by live-imaging fluorescently labeled CDK9, a kinase known to associate with active RNAPII. These foci were observed in different cell types derived from CDK9-mCherry knock-in mice. We show that these foci are very stable while highly dynamic in exchanging CDK9. Chromatin immunoprecipitation (ChIP) coupled with deep sequencing (ChIP-seq) data show that the genome-wide binding sites of CDK9 and initiating RNAPII overlap on transcribed genes. Immunostaining shows that CDK9-mCherry foci colocalize with RNAPII-Ser5P, much less with RNAPII-Ser2P, and not with CDK12 (a kinase reported to be involved in the Ser2 phosphorylation) or with splicing factor SC35. In conclusion, transcription factories exist in living cells, and initiation and elongation of transcripts takes place in different nuclear compartments.
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Affiliation(s)
- Alireza Ghamari
- Department of Cell Biology, Erasmus Medical Center, 3015GE Rotterdam, the Netherlands
| | | | - Supat Thongjuea
- Computational Biology Unit-Bergen Centre for Computational Science
- Sars Centre for Marine Molecular Biology, University of Bergen, N-5008 Bergen, Norway
| | - Wiggert A. van Cappellen
- Department of Reproduction and Development, Erasmus Medical Center, 3015GE Rotterdam, the Netherlands
| | - Wilfred van IJcken
- Biomics Department, Erasmus Medical Center, 3015GE, Rotterdam, the Netherlands
| | - Jeffrey van Haren
- Department of Cell Biology, Erasmus Medical Center, 3015GE Rotterdam, the Netherlands
| | - Eric Soler
- Department of Cell Biology, Erasmus Medical Center, 3015GE Rotterdam, the Netherlands
| | - Dirk Eick
- Department of Molecular Epigenetics, Helmholtz Zentrum München, Center of Integrated Protein Science (CIPSM), D-81377 Munich, Germany
| | - Boris Lenhard
- Computational Biology Unit-Bergen Centre for Computational Science
- Sars Centre for Marine Molecular Biology, University of Bergen, N-5008 Bergen, Norway
| | - Frank G. Grosveld
- Department of Cell Biology, Erasmus Medical Center, 3015GE Rotterdam, the Netherlands
- Centre for Biomedical Genetics, 3015GE Rotterdam, the Netherlands
- Cancer Genomics Centre, 3015GE Rotterdam, the Netherlands
- Netherlands Consortium for Systems Biology, 3015GE Rotterdam, the Netherlands
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19
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Borg J, Phylactides M, Bartsakoulia M, Tafrali C, Lederer C, Felice AE, Papachatzopoulou A, Kourakli A, Stavrou EF, Christou S, Hou J, Karkabouna S, Lappa-Manakou C, Ozgur Z, van Ijcken W, von Lindern M, Grosveld FG, Georgitsi M, Kleanthous M, Philipsen S, Patrinos GP. KLF10 gene expression is associated with high fetal hemoglobin levels and with response to hydroxyurea treatment in β-hemoglobinopathy patients. Pharmacogenomics 2013; 13:1487-500. [PMID: 23057549 DOI: 10.2217/pgs.12.125] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
AIM In humans, fetal hemoglobin (HbF) production is controlled by many intricate mechanisms that, to date, remain only partly understood. PATIENTS & METHODS Pharmacogenomic analysis of the effects of hydroxyurea (HU) on HbF production was undertaken in a collection of Hellenic β-thalassemia and sickle cell disease (SCD) compound heterozygotes and a collection of healthy and KLF1-haploinsufficient Maltese adults, to identify genomic signatures that follow high HbF patterns. RESULTS KLF10 emerged as a top candidate. Moreover, genotype analysis of β-thalassemia major and intermedia patients and an independent cohort of β-thalassemia/SCD compound heterozygous patients that do or do not respond to HU treatment showed that the homozygous mutant state of a tagSNP in the KLF10 3'UTR is not present in β-thalassemia intermedia patients and is underrepresented in β-thalassemia/SCD compound heterozygous patients that respond well to HU treatment. CONCLUSION These data suggest that KLF10 may constitute a pharmacogenomic marker to discriminate between response and nonresponse to HU treatment.
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Affiliation(s)
- Joseph Borg
- Erasmus University Medical Center, Department of Cell Biology, Rotterdam, The Netherlands
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20
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van den Berghe V, Stappers E, Vandesande B, Dimidschstein J, Kroes R, Francis A, Conidi A, Lesage F, Dries R, Cazzola S, Berx G, Kessaris N, Vanderhaeghen P, van Ijcken W, Grosveld FG, Goossens S, Haigh JJ, Fishell G, Goffinet A, Aerts S, Huylebroeck D, Seuntjens E. Directed migration of cortical interneurons depends on the cell-autonomous action of Sip1. Neuron 2013; 77:70-82. [PMID: 23312517 DOI: 10.1016/j.neuron.2012.11.009] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2012] [Indexed: 12/23/2022]
Abstract
GABAergic interneurons mainly originate in the medial ganglionic eminence (MGE) of the embryonic ventral telencephalon (VT) and migrate tangentially to the cortex, guided by membrane-bound and secreted factors. We found that Sip1 (Zfhx1b, Zeb2), a transcription factor enriched in migrating cortical interneurons, is required for their proper differentiation and correct guidance. The majority of Sip1 knockout interneurons fail to migrate to the neocortex and stall in the VT. RNA sequencing reveals that Sip1 knockout interneurons do not acquire a fully mature cortical interneuron identity and contain increased levels of the repulsive receptor Unc5b. Focal electroporation of Unc5b-encoding vectors in the MGE of wild-type brain slices disturbs migration to the neocortex, whereas reducing Unc5b levels in Sip1 knockout slices and brains rescues the migration defect. Our results reveal that Sip1, through tuning of Unc5b levels, is essential for cortical interneuron guidance.
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Affiliation(s)
- Veronique van den Berghe
- Laboratory of Molecular Biology (Celgen), Department of Development and Regeneration, University of Leuven, 3000 Leuven, Belgium
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21
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Bradley A, Anastassiadis K, Ayadi A, Battey JF, Bell C, Birling MC, Bottomley J, Brown SD, Bürger A, Bult CJ, Bushell W, Collins FS, Desaintes C, Doe B, Economides A, Eppig JT, Finnell RH, Fletcher C, Fray M, Frendewey D, Friedel RH, Grosveld FG, Hansen J, Hérault Y, Hicks G, Hörlein A, Houghton R, Hrabé de Angelis M, Huylebroeck D, Iyer V, de Jong PJ, Kadin JA, Kaloff C, Kennedy K, Koutsourakis M, Kent Lloyd KC, Marschall S, Mason J, McKerlie C, McLeod MP, von Melchner H, Moore M, Mujica AO, Nagy A, Nefedov M, Nutter LM, Pavlovic G, Peterson JL, Pollock J, Ramirez-Solis R, Rancourt DE, Raspa M, Remacle JE, Ringwald M, Rosen B, Rosenthal N, Rossant J, Ruiz Noppinger P, Ryder E, Schick JZ, Schnütgen F, Schofield P, Seisenberger C, Selloum M, Simpson EM, Skarnes WC, Smedley D, Stanford WL, Francis Stewart A, Stone K, Swan K, Tadepally H, Teboul L, Tocchini-Valentini GP, Valenzuela D, West AP, Yamamura KI, Yoshinaga Y, Wurst W. The mammalian gene function resource: the International Knockout Mouse Consortium. Mamm Genome 2012; 23:580-6. [PMID: 22968824 PMCID: PMC3463800 DOI: 10.1007/s00335-012-9422-2] [Citation(s) in RCA: 234] [Impact Index Per Article: 19.5] [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: 04/06/2012] [Accepted: 07/20/2012] [Indexed: 11/16/2022]
Abstract
In 2007, the International Knockout Mouse Consortium (IKMC) made the ambitious promise to generate mutations in virtually every protein-coding gene of the mouse genome in a concerted worldwide action. Now, 5 years later, the IKMC members have developed high-throughput gene trapping and, in particular, gene-targeting pipelines and generated more than 17,400 mutant murine embryonic stem (ES) cell clones and more than 1,700 mutant mouse strains, most of them conditional. A common IKMC web portal (www.knockoutmouse.org) has been established, allowing easy access to this unparalleled biological resource. The IKMC materials considerably enhance functional gene annotation of the mammalian genome and will have a major impact on future biomedical research.
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Affiliation(s)
- Allan Bradley
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
| | | | - Abdelkader Ayadi
- Institut Clinique de la Souris and Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France
| | - James F. Battey
- National Institute on Deafness and Other Communication Disorders (NIH), Bethesda, MD 20892 USA
| | - Cindy Bell
- Genome Canada, Ottawa, ON K2P 1P1 Canada
| | - Marie-Christine Birling
- Institut Clinique de la Souris and Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France
| | - Joanna Bottomley
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
| | - Steve D. Brown
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD UK
| | - Antje Bürger
- Institute of Developmental Genetics, Helmholtz Zentrum München, Technische Universität München, 85764 Neuherberg, Germany
| | | | - Wendy Bushell
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
| | | | - Christian Desaintes
- Infectious Diseases and Public Health, European Commission, DG Research & Innovation, 1049 Brussels, Belgium
| | - Brendan Doe
- Istituto di Biologia Cellulare, Consiglio Nazionale delle Ricerche (CNR), Monterotondo-Scalo, 00015 Rome, Italy
| | - Aris Economides
- Velocigene Division, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591 USA
| | | | - Richard H. Finnell
- The Texas A&M Institute for Genomic Medicine, College Station, TX 77843-4485 USA
- University of Texas at Austin, Austin, TX 78712 USA
| | | | - Martin Fray
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD UK
| | - David Frendewey
- Velocigene Division, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591 USA
| | - Roland H. Friedel
- Institute of Developmental Genetics, Helmholtz Zentrum München, Technische Universität München, 85764 Neuherberg, Germany
- Icahn Medical Institute, The Mount Sinai Hospital, New York, NY 10029 USA
| | - Frank G. Grosveld
- Department of Cell Biology, Center of Biomedical Genetics, Erasmus University Medical Center, 3015 GE Rotterdam, The Netherlands
| | - Jens Hansen
- Institute of Developmental Genetics, Helmholtz Zentrum München, Technische Universität München, 85764 Neuherberg, Germany
| | - Yann Hérault
- Institut Clinique de la Souris and Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France
| | - Geoffrey Hicks
- Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, MB R3E OV9 Canada
| | - Andreas Hörlein
- Institute of Developmental Genetics, Helmholtz Zentrum München, Technische Universität München, 85764 Neuherberg, Germany
| | - Richard Houghton
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
| | | | - Danny Huylebroeck
- Department of Development and Regeneration, Faculty of Medicine, University of Leuven (KU Leuven), 3000 Leuven, Belgium
| | - Vivek Iyer
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
| | - Pieter J. de Jong
- Children’s Hospital Oakland Research Institute (CHORI), Oakland, CA 94609 USA
| | | | - Cornelia Kaloff
- Institute of Developmental Genetics, Helmholtz Zentrum München, Technische Universität München, 85764 Neuherberg, Germany
| | - Karen Kennedy
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
| | - Manousos Koutsourakis
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
| | - K. C. Kent Lloyd
- Mouse Biology Program, School of Veterinary Medicine, University of California, Davis, CA 95616 USA
| | - Susan Marschall
- Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Jeremy Mason
- The Jackson Laboratory, Bar Harbor, ME 04609 USA
| | - Colin McKerlie
- Research Institute, The Hospital for Sick Children, SickKids Foundation, Toronto, ON M5G2L3 Canada
| | - Michael P. McLeod
- The Texas A&M Institute for Genomic Medicine, College Station, TX 77843-4485 USA
| | - Harald von Melchner
- Department of Molecular Haematology, University of Frankfurt Medical School, 60590 Frankfurt am Main, Germany
| | - Mark Moore
- National Institutes of Health, Bethesda, MD 20205 USA
| | - Alejandro O. Mujica
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
- Velocigene Division, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591 USA
| | - Andras Nagy
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Joseph and Wolf Lebovic Health Complex, Toronto, ON M5G 1X5 Canada
| | - Mikhail Nefedov
- Children’s Hospital Oakland Research Institute (CHORI), Oakland, CA 94609 USA
| | - Lauryl M. Nutter
- Research Institute, The Hospital for Sick Children, SickKids Foundation, Toronto, ON M5G2L3 Canada
| | - Guillaume Pavlovic
- Institut Clinique de la Souris and Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France
| | | | - Jonathan Pollock
- Division of Basic Neuroscience and Research, National Institute of Drug Abuse (NIDA), Bethesda, MD 20892-0001 USA
| | - Ramiro Ramirez-Solis
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
| | - Derrick E. Rancourt
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB T2N 1N4 Canada
| | - Marcello Raspa
- Istituto di Biologia Cellulare, Consiglio Nazionale delle Ricerche (CNR), Monterotondo-Scalo, 00015 Rome, Italy
| | - Jacques E. Remacle
- Infectious Diseases and Public Health, European Commission, DG Research & Innovation, 1049 Brussels, Belgium
| | | | - Barry Rosen
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
| | - Nadia Rosenthal
- European Molecular Biology Laboratory (EMBL), Monterotondo, 00015 Rome, Italy
| | - Janet Rossant
- Research Institute, The Hospital for Sick Children, SickKids Foundation, Toronto, ON M5G2L3 Canada
| | - Patricia Ruiz Noppinger
- Centre for Cardiovascular Research, Department of Vertebrate Genomics, Charité, 10115 Berlin, Germany
| | - Ed Ryder
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
| | - Joel Zupicich Schick
- Institute of Developmental Genetics, Helmholtz Zentrum München, Technische Universität München, 85764 Neuherberg, Germany
| | - Frank Schnütgen
- Department of Molecular Haematology, University of Frankfurt Medical School, 60590 Frankfurt am Main, Germany
| | - Paul Schofield
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3EG UK
| | - Claudia Seisenberger
- Institute of Developmental Genetics, Helmholtz Zentrum München, Technische Universität München, 85764 Neuherberg, Germany
| | - Mohammed Selloum
- Institut Clinique de la Souris and Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France
| | - Elizabeth M. Simpson
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, Vancouver, BC V5Z 4H4 Canada
| | - William C. Skarnes
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
| | - Damian Smedley
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
- European Bioinformatics Institute (EBI), Hinxton, Cambridge, CB10 1ST UK
| | | | - A. Francis Stewart
- Biotechnology Center (BIOTEC) of the Technische Universität Dresden, 01307 Dresden, Germany
| | - Kevin Stone
- The Jackson Laboratory, Bar Harbor, ME 04609 USA
| | - Kate Swan
- Genome Canada, Ottawa, ON K2P 1P1 Canada
| | | | - Lydia Teboul
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD UK
| | | | - David Valenzuela
- Velocigene Division, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591 USA
| | - Anthony P. West
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
| | - Ken-ichi Yamamura
- Division of Developmental Genetics, Center for Animal Resources and Development, Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, 860-0811 Japan
| | - Yuko Yoshinaga
- Children’s Hospital Oakland Research Institute (CHORI), Oakland, CA 94609 USA
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, Technische Universität München, 85764 Neuherberg, Germany
- Max-Planck-Institute of Psychiatry, 80804 Munich, Germany
- Deutsches Zentrum fuer Neurodegenerative Erkrankungen e.V. (DZNE) Site Munich, 80336 Munich, Germany
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22
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van de Corput MPC, de Boer E, Knoch TA, van Cappellen WA, Quintanilla A, Ferrand L, Grosveld FG. Super-resolution imaging reveals three-dimensional folding dynamics of the β-globin locus upon gene activation. J Cell Sci 2012; 125:4630-9. [PMID: 22767512 DOI: 10.1242/jcs.108522] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The chromatin architecture is constantly changing because of cellular processes such as proliferation, differentiation and changes in the expression profile during gene activation or silencing. Unravelling the changes that occur in the chromatin structure during these processes has been a topic of interest for many years. It is known that gene activation of large gene loci is thought to occur by means of an active looping mechanism. It was also shown for the β-globin locus that the gene promoter interacts with an active chromatin hub by means of an active looping mechanism. This means that the locus changes in three-dimensional (3D) nuclear volume and chromatin shape. As a means of visualizing and measuring these dynamic changes in chromatin structure of the β-globin locus, we used a 3D DNA-FISH method in combination with 3D image acquisition to volume render fluorescent signals into 3D objects. These 3D chromatin structures were geometrically analysed, and results prior to and after gene activation were quantitatively compared. Confocal and super-resolution imaging revealed that the inactive locus occurs in several different conformations. These conformations change in shape and surface structure upon cell differentiation into a more folded and rounded structure that has a substantially smaller size and volume. These physical measurements represent the first non-biochemical evidence that, upon gene activation, an actively transcribing chromatin hub is formed by means of additional chromatin looping.
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Affiliation(s)
- Mariëtte P C van de Corput
- Department of Cell Biology and Genetics and Center for Biomedical Genetics, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands.
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23
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Brazão TF, Demmers J, van IJcken W, Strouboulis J, Fornerod M, Romão L, Grosveld FG. A new function of ROD1 in nonsense-mediated mRNA decay. FEBS Lett 2012; 586:1101-10. [PMID: 22575643 DOI: 10.1016/j.febslet.2012.03.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Revised: 03/06/2012] [Accepted: 03/06/2012] [Indexed: 10/28/2022]
Abstract
RNA-binding proteins play a crucial role in the post-transcriptional regulation of gene expression. Polypyrimidine tract binding protein (PTB in humans) has been extensively characterized as an important splicing factor, and has additional functions in 3' end processing and translation. ROD1 is a PTB paralog containing four RRM (RNA recognition motif) domains. Here, we discover a function of ROD1 in nonsense-mediated mRNA decay (NMD). We show that ROD1 and the core NMD factor UPF1 interact and co-regulate an extensive number of target genes. Using a reporter system, we demonstrate that ROD1, similarly to UPF1 and UPF2, is required for the destabilization of a known NMD substrate. Finally, we show through RIP-seq that ROD1 and UPF1 associate with a significant number of common transcripts.
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Affiliation(s)
- T F Brazão
- Department of Cell Biology & Genetics, Erasmus MC, Rotterdam, The Netherlands.
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24
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Kolovos P, Knoch TA, Grosveld FG, Cook PR, Papantonis A. Enhancers and silencers: an integrated and simple model for their function. Epigenetics Chromatin 2012; 5:1. [PMID: 22230046 PMCID: PMC3281776 DOI: 10.1186/1756-8935-5-1] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [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: 10/22/2011] [Accepted: 01/09/2012] [Indexed: 12/27/2022] Open
Abstract
Regulatory DNA elements such as enhancers, silencers and insulators are embedded in metazoan genomes, and they control gene expression during development. Although they fulfil different roles, they share specific properties. Herein we discuss some examples and a parsimonious model for their function is proposed. All are transcription units that tether their target promoters close to, or distant from, transcriptional hot spots (or 'factories').
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Affiliation(s)
- Petros Kolovos
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
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25
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Abstract
UNLABELLED The NARWHAL software pipeline has been developed to automate the primary analysis of Illumina sequencing data. This pipeline combines a new and flexible de-multiplexing tool with open-source aligners and automated quality assessment. The entire pipeline can be run using only one simple sample-sheet for diverse sequencing applications. NARWHAL creates a sample-oriented data structure and outperforms existing tools in speed. AVAILABILITY https://trac.nbic.nl/narwhal/.
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Affiliation(s)
- R W W Brouwer
- Center for Biomics, Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands
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26
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Bezstarosti K, Ghamari A, Grosveld FG, Demmers JAA. Differential Proteomics Based on18O Labeling to Determine the Cyclin Dependent Kinase 9 Interactome. J Proteome Res 2010; 9:4464-75. [DOI: 10.1021/pr100217d] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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27
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Kepper N, Ettig R, Dickmann F, Stehr R, Grosveld FG, Wedemann G, Knoch TA. Parallel high-performance grid computing: capabilities and opportunities of a novel demanding service and business class allowing highest resource efficiency. Stud Health Technol Inform 2010; 159:264-271. [PMID: 20543448] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Especially in the life-science and the health-care sectors the huge IT requirements are imminent due to the large and complex systems to be analysed and simulated. Grid infrastructures play here a rapidly increasing role for research, diagnostics, and treatment, since they provide the necessary large-scale resources efficiently. Whereas grids were first used for huge number crunching of trivially parallelizable problems, increasingly parallel high-performance computing is required. Here, we show for the prime example of molecular dynamic simulations how the presence of large grid clusters including very fast network interconnects within grid infrastructures allows now parallel high-performance grid computing efficiently and thus combines the benefits of dedicated super-computing centres and grid infrastructures. The demands for this service class are the highest since the user group has very heterogeneous requirements: i) two to many thousands of CPUs, ii) different memory architectures, iii) huge storage capabilities, and iv) fast communication via network interconnects, are all needed in different combinations and must be considered in a highly dedicated manner to reach highest performance efficiency. Beyond, advanced and dedicated i) interaction with users, ii) the management of jobs, iii) accounting, and iv) billing, not only combines classic with parallel high-performance grid usage, but more importantly is also able to increase the efficiency of IT resource providers. Consequently, the mere "yes-we-can" becomes a huge opportunity like e.g. the life-science and health-care sectors as well as grid infrastructures by reaching higher level of resource efficiency.
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Affiliation(s)
- Nick Kepper
- Biophysical Genomics, Dept. Cell Biology & Genetics, Erasmus MC, GE Rotterdam, The Netherlands
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28
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Kepper N, Schmitt E, Lesnussa M, Weiland Y, Eussen HB, Grosveld FG, Hausmann M, Knoch TA. Visualization, analysis, and design of COMBO-FISH probes in the grid-based GLOBE 3D genome platform. Stud Health Technol Inform 2010; 159:171-180. [PMID: 20543436] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The genome architecture in cell nuclei plays an important role in modern microscopy for the monitoring of medical diagnosis and therapy since changes of function and dynamics of genes are interlinked with changing geometrical parameters. The planning of corresponding diagnostic experiments and their imaging is a complex and often interactive IT intensive challenge and thus makes high-performance grids a necessity. To detect genetic changes we recently developed a new form of fluorescence in situ hybridization (FISH) - COMBinatorial Oligonucleotide FISH (COMBO-FISH) - which labels small nucleotide sequences clustering at a desired genomic location. To achieve a unique hybridization spot other side clusters have to be excluded. Therefore, we have designed an interactive pipeline using the grid-based GLOBE 3D Genome Viewer and Platform to design and display different labelling variants of candidate probe sets. Thus, we have created a grid-based virtual "paper" tool for easy interactive calculation, analysis, management, and representation for COMBO-FISH probe design with many an advantage: Since all the calculations and analysis run in a grid, one can instantly and with great visual ease locate duplications of gene subsequences to guide the elimination of side clustering sequences during the probe design process, as well as get at least an impression of the 3D architectural embedding of the respective chromosome region, which is of major importance to estimate the hybridization probe dynamics. Beyond, even several people at different locations could work on the same process in a team wise manner. Consequently, we present how a complex interactive process can profit from grid infrastructure technology using our unique GLOBE 3D Genome Platform gateway towards a real interactive curative diagnosis planning and therapy monitoring.
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Affiliation(s)
- Nick Kepper
- Biophysical Genomics, Dept. Cell Biology & Genetics, Erasmus MC, Dr. Molewaterplein, Rotterdam, The Netherlands
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29
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Estrada K, Abuseiris A, Grosveld FG, Uitterlinden AG, Knoch TA, Rivadeneira F. GRIMP: a web- and grid-based tool for high-speed analysis of large-scale genome-wide association using imputed data. ACTA ACUST UNITED AC 2009; 25:2750-2. [PMID: 19700477 PMCID: PMC2759548 DOI: 10.1093/bioinformatics/btp497] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The current fast growth of genome-wide association studies (GWAS) combined with now common computationally expensive imputation requires the online access of large user groups to high-performance computing resources capable of analyzing rapidly and efficiently millions of genetic markers for ten thousands of individuals. Here, we present a web-based interface--called GRIMP--to run publicly available genetic software for extremely large GWAS on scalable super-computing grid infrastructures. This is of major importance for the enlargement of GWAS with the availability of whole-genome sequence data from the 1000 Genomes Project and for future whole-population efforts.
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Affiliation(s)
- Karol Estrada
- Department of Internal Medicine, Erasmus MC, Dr. Molewaterplein 50, 3015GE Rotterdam, The Netherlands
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Knoch TA, Göker M, Lohner R, Abuseiris A, Grosveld FG. Fine-structured multi-scaling long-range correlations in completely sequenced genomes--features, origin, and classification. Eur Biophys J 2009; 38:757-79. [PMID: 19533117 PMCID: PMC2701493 DOI: 10.1007/s00249-009-0489-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Revised: 05/05/2009] [Accepted: 05/13/2009] [Indexed: 11/26/2022]
Abstract
The sequential organization of genomes, i.e. the relations between distant base pairs and regions within sequences, and its connection to the three-dimensional organization of genomes is still a largely unresolved problem. Long-range power-law correlations were found using correlation analysis on almost the entire observable scale of 132 completely sequenced chromosomes of 0.5 × 106 to 3.0 × 107 bp from Archaea, Bacteria, Arabidopsis thaliana, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster, and Homo sapiens. The local correlation coefficients show a species-specific multi-scaling behaviour: close to random correlations on the scale of a few base pairs, a first maximum from 40 to 3,400 bp (for Arabidopsis thaliana and Drosophila melanogaster divided in two submaxima), and often a region of one or more second maxima from 105 to 3 × 105 bp. Within this multi-scaling behaviour, an additional fine-structure is present and attributable to codon usage in all except the human sequences, where it is related to nucleosomal binding. Computer-generated random sequences assuming a block organization of genomes, the codon usage, and nucleosomal binding explain these results. Mutation by sequence reshuffling destroyed all correlations. Thus, the stability of correlations seems to be evolutionarily tightly controlled and connected to the spatial genome organization, especially on large scales. In summary, genomes show a complex sequential organization related closely to their three-dimensional organization.
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MESH Headings
- Algorithms
- Animals
- Arabidopsis/genetics
- Chromosomes/chemistry
- Chromosomes/genetics
- Chromosomes/ultrastructure
- Chromosomes, Fungal/chemistry
- Chromosomes, Fungal/genetics
- Chromosomes, Fungal/ultrastructure
- Chromosomes, Human/chemistry
- Chromosomes, Human/genetics
- Chromosomes, Human/ultrastructure
- Chromosomes, Plant/chemistry
- Chromosomes, Plant/genetics
- Chromosomes, Plant/ultrastructure
- Codon/chemistry
- Computer Simulation
- DNA/chemistry
- Drosophila melanogaster/genetics
- Genome
- Humans
- Models, Genetic
- Mutation
- Nucleosomes/chemistry
- Saccharomyces cerevisiae/genetics
- Schizosaccharomyces/genetics
- Sequence Analysis, DNA
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Affiliation(s)
- Tobias A Knoch
- Biophysical Genomics, Cell Biology and Genetics, Erasmus Medical Center, Rotterdam, The Netherlands.
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Gontan C, Güttler T, Engelen E, Demmers J, Fornerod M, Grosveld FG, Tibboel D, Görlich D, Poot RA, Rottier RJ. Exportin 4 mediates a novel nuclear import pathway for Sox family transcription factors. Dev Biol 2009. [PMID: 19349578 DOI: 10.1016/j.ydbio.2008.05.306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
SRY and other Sox-type transcription factors are important developmental regulators with various implications in human disease. In this study, we identified Exp4 (exportin 4) as an interaction partner of Sox2 in mouse embryonic stem cells and neural progenitors. We show that, besides its established function in nuclear export, Exp4 acts as a bona fide nuclear import receptor for Sox2 and SRY. Thus, Exp4 is an example of a nuclear transport receptor carrying distinct cargoes into different directions. In contrast to a published study, we observed that the import activity of Imp-alpha (importin-a) isoforms toward Sox2 is negligible. Instead, we found that Imp9 and the Imp-beta/7 heterodimer mediate nuclear import of Sox2 in parallel to Exp4. Import signals for the three pathways overlap and include conserved residues in the Sox2 high-mobility group (HMG) box domain that are also critical for DNA binding. This suggests that nuclear import of Sox proteins is facilitated by several parallel import pathways.
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Affiliation(s)
- Cristina Gontan
- Department of Pediatric Surgery, Erasmus Medical Center, Rotterdam, Netherlands
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33
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Gontan C, Güttler T, Engelen E, Demmers J, Fornerod M, Grosveld FG, Tibboel D, Görlich D, Poot RA, Rottier RJ. Exportin 4 mediates a novel nuclear import pathway for Sox family transcription factors. ACTA ACUST UNITED AC 2009; 185:27-34. [PMID: 19349578 PMCID: PMC2700522 DOI: 10.1083/jcb.200810106] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
SRY and other Sox-type transcription factors are important developmental regulators with various implications in human disease. In this study, we identified Exp4 (exportin 4) as an interaction partner of Sox2 in mouse embryonic stem cells and neural progenitors. We show that, besides its established function in nuclear export, Exp4 acts as a bona fide nuclear import receptor for Sox2 and SRY. Thus, Exp4 is an example of a nuclear transport receptor carrying distinct cargoes into different directions. In contrast to a published study, we observed that the import activity of Imp-α (importin-a) isoforms toward Sox2 is negligible. Instead, we found that Imp9 and the Imp-β/7 heterodimer mediate nuclear import of Sox2 in parallel to Exp4. Import signals for the three pathways overlap and include conserved residues in the Sox2 high-mobility group (HMG) box domain that are also critical for DNA binding. This suggests that nuclear import of Sox proteins is facilitated by several parallel import pathways.
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Affiliation(s)
- Cristina Gontan
- Department of Pediatric Surgery, Erasmus Medical Center, Rotterdam, Netherlands
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34
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Knoch TA, Baumgärtner V, de Zeeuw LV, Grosveld FG, Egger K. e-Human Grid Ecology - understanding and approaching the inverse tragedy of the commons in the e-Grid society. Stud Health Technol Inform 2009; 147:269-276. [PMID: 19593066] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
With ever-new technologies emerging also the amount of information to be stored and processed is growing exponentially and is believed to be always at the limit. In contrast, however, huge resources are available in the IT sector alike e.g. the renewable energy sector, which are often even not at all used. This under-usage bares any rational especially in the IT sector where e.g. virtualisation and grid approaches could be fast implemented due to the great technical and fast turnover opportunities. Here, we describe this obvious paradox for the first time as the Inverse Tragedy of the Commons, in contrast to the Classical Tragedy of the Commons where resources are overexploited. From this perspective the grid IT sector attempting to share resources for better efficiency, reveals two challenges leading to the heart of the paradox: i) From a macro perspective all grid infrastructures involve not only mere technical solutions but also dominantly all of the autopoietic social sub-systems ranging from religion to policy. ii) On the micro level the individual players and their psychology and risk behaviour are of major importance for acting within the macro autopoietic framework. Thus, the challenges of grid implementation are similar to those of e.g. climate protection. This is well described by the classic Human Ecology triangle and our extension to a rectangle: invironment-individual-society-environment. Extension of this classical interdisciplinary field of basic and applied research to an e-Human Grid Ecology rational, allows the Inverse Tragedy of the Commons of the grid sector to be understood and approached better and implies obvious guidelines in the day-to-day management for grid and other (networked) resources, which is of importance for many fields with similar paradoxes as in (e-)society.
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Affiliation(s)
- Tobias A Knoch
- Biophysical Genomics & Erasmus Computing Grid, Erasmus MC, Rotterdam, The Netherlands.
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Knoch TA, Lesnussa M, Kepper N, Eussen HB, Grosveld FG. The GLOBE 3D Genome Platform - towards a novel system-biological paper tool to integrate the huge complexity of genome organization and function. Stud Health Technol Inform 2009; 147:105-116. [PMID: 19593049] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Genomes are tremendous co-evolutionary holistic systems for molecular storage, processing and fabrication of information. Their system-biological complexity remains, however, still largely mysterious, despite immense sequencing achievements and huge advances in the understanding of the general sequential, three-dimensional and regulatory organization. Here, we present the GLOBE 3D Genome Platform a completely novel grid based virtual "paper" tool and in fact the first system-biological genome browser integrating the holistic complexity of genomes in a single easy comprehensible platform: Based on a detailed study of biophysical and IT requirements, every architectural level from sequence to morphology of one or several genomes can be approached in a real and in a symbolic representation simultaneously and navigated by continuous scale-free zooming within a unique three-dimensional OpenGL and grid driven environment. In principle an unlimited number of multi-dimensional data sets can be visualized, customized in terms of arrangement, shape, colour, and texture etc. as well as accessed and annotated individually or in groups using internal or external data bases/facilities. Any information can be searched and correlated by importing or calculating simple relations in real-time using grid resources. A general correlation and application platform for more complex correlative analysis and a front-end for system-biological simulations both using again the huge capabilities of grid infrastructures is currently under development. Hence, the GLOBE 3D Genome Platform is an example of a grid based approach towards a virtual desktop for genomic work combining the three fundamental distributed resources: i) visual data representation, ii) data access and management, and iii) data analysis and creation. Thus, the GLOBE 3D Genome Platform is the novel system-biology oriented information system urgently needed to access, present, annotate, and to simulate the holistic genome complexity in a unique gateway towards a real understanding, educative presentation and curative manipulation planning of this tremendous evolutionary information grail - genomes.
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Affiliation(s)
- Tobias A Knoch
- Department of Cell Biology & Genetics, Erasmus MC, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands.
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Jhunjhunwala S, van Zelm MC, Peak MM, Cutchin S, Riblet R, van Dongen JJ, Grosveld FG, Knoch TA, Murre C. The 3D structure of the immunoglobulin heavy-chain locus: implications for long-range genomic interactions. Cell 2008; 133:265-79. [PMID: 18423198 PMCID: PMC2771211 DOI: 10.1016/j.cell.2008.03.024] [Citation(s) in RCA: 224] [Impact Index Per Article: 14.0] [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: 05/27/2007] [Revised: 01/04/2008] [Accepted: 03/16/2008] [Indexed: 12/23/2022]
Abstract
The immunoglobulin heavy-chain (Igh) locus is organized into distinct regions that contain multiple variable (V(H)), diversity (D(H)), joining (J(H)) and constant (C(H)) coding elements. How the Igh locus is structured in 3D space is unknown. To probe the topography of the Igh locus, spatial distance distributions were determined between 12 genomic markers that span the entire Igh locus. Comparison of the distance distributions to computer simulations of alternative chromatin arrangements predicted that the Igh locus is organized into compartments containing clusters of loops separated by linkers. Trilateration and triple-point angle measurements indicated the mean relative 3D positions of the V(H), D(H), J(H), and C(H) elements, showed compartmentalization and striking conformational changes involving V(H) and D(H)-J(H) elements during early B cell development. In pro-B cells, the entire repertoire of V(H) regions (2 Mbp) appeared to have merged and juxtaposed to the D(H) elements, mechanistically permitting long-range genomic interactions to occur with relatively high frequency.
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Affiliation(s)
- Suchit Jhunjhunwala
- Division of Biological Sciences, 0377, University of California, San Diego, La Jolla, CA 92093, USA
| | - Menno C. van Zelm
- Division of Biological Sciences, 0377, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mandy M. Peak
- Division of Biological Sciences, 0377, University of California, San Diego, La Jolla, CA 92093, USA
| | - Steve Cutchin
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92037, USA
| | - Roy Riblet
- Torrey Pines Institute for Molecular Studies, San Diego, CA 92121, USA
| | - Jacques J.M. van Dongen
- Department of Immunology, Erasmus MC, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
| | - Frank G. Grosveld
- Departments of Biophysical Genomics, Cell Biology and Genetics, Erasmus MC, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
| | - Tobias A. Knoch
- Departments of Biophysical Genomics, Cell Biology and Genetics, Erasmus MC, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
- Ruperto-Carola University Heidelberg, Kirchhoff Institute for Physics, Department of Biophysical Genomics, Im Neuenheimfer Feld 280, 69120 Heidelberg, Germany
| | - Cornelis Murre
- Division of Biological Sciences, 0377, University of California, San Diego, La Jolla, CA 92093, USA
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Papachatzopoulou A, Kaimakis P, Pourfarzad F, Menounos PG, Evangelakou P, Kollia P, Grosveld FG, Patrinos GP. Increased gamma-globin gene expression in beta-thalassemia intermedia patients correlates with a mutation in 3'HS1. Am J Hematol 2007; 82:1005-9. [PMID: 17654503 DOI: 10.1002/ajh.20979] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [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] [Indexed: 11/08/2022]
Abstract
We report a novel set of genetic markers in the DNaseI hypersensitive sites comprising the human beta-globin locus chromatin hub (CH), namely HS-111 and 3'HS1. The HS-111 (-21 G>A) and 3'HS1 (+179 C>T) transitions form CH haplotypes, which occur at different frequencies in beta-thalassemia intermedia and major patients and normal (nonthalassemic) individuals. We also show that the 3'HS1 (+179 C>T) variation results in a GATA-1 binding site and correlates with increased fetal hemoglobin production in beta-thalassemia intermedia patients. In contrast, the HS-111 (+126 G>A) transition, found in three normal chromosomes, is simply a rare polymorphism. We conclude that the CH haplotypes are useful genetic determinants for beta-thalassemia major and intermedia patients, while the 3'HS1 (+179 C>T) mutation may have functional consequences in gamma-globin genes expression.
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38
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Asselin-Labat ML, Sutherland KD, Barker H, Thomas R, Shackleton M, Forrest NC, Hartley L, Robb L, Grosveld FG, van der Wees J, Lindeman GJ, Visvader JE. Gata-3 is an essential regulator of mammary-gland morphogenesis and luminal-cell differentiation. Nat Cell Biol 2006; 9:201-9. [PMID: 17187062 DOI: 10.1038/ncb1530] [Citation(s) in RCA: 629] [Impact Index Per Article: 34.9] [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: 11/16/2006] [Accepted: 12/12/2006] [Indexed: 12/16/2022]
Abstract
The transcription factor Gata-3 is a defining marker of the 'luminal' subtypes of breast cancer. To gain insight into the role of Gata-3 in breast epithelial development and oncogenesis, we have explored its normal function within the mammary gland by conditionally deleting Gata-3 at different stages of development. We report that Gata-3 has essential roles in the morphogenesis of the mammary gland in both the embryo and adult. Through the discovery of a novel marker (beta3-integrin) of luminal progenitor cells and their purification, we demonstrate that Gata-3 deficiency leads to an expansion of luminal progenitors and a concomitant block in differentiation. Remarkably, introduction of Gata-3 into a stem cell-enriched population induced maturation along the alveolar luminal lineage. These studies provide evidence for the existence of an epithelial hierarchy within the mammary gland and establish Gata-3 as a critical regulator of luminal differentiation.
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Affiliation(s)
- Marie-Liesse Asselin-Labat
- VBCRC Laboratory, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3050, Australia
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Kurek D, Garinis GA, van Doorninck JH, van der Wees J, Grosveld FG. Transcriptome and phenotypic analysis reveals Gata3-dependent signalling pathways in murine hair follicles. Development 2006; 134:261-72. [PMID: 17151017 DOI: 10.1242/dev.02721] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The transcription factor Gata3 is crucially involved in epidermis and hair follicle differentiation. Yet, little is known about how Gata3 co-ordinates stem cell lineage determination in skin, what pathways are involved and how Gata3 differentially regulates distinct cell populations within the hair follicle. Here, we describe a conditional Gata3-/- mouse (K14-Gata3-/-) in which Gata3 is specifically deleted in epidermis and hair follicles. K14-Gata3-/- mice show aberrant postnatal growth and development, delayed hair growth and maintenance, abnormal hair follicle organization and irregular pigmentation. After the first hair cycle, the germinative layer surrounding the dermal papilla was not restored; instead, proliferation was pronounced in basal epidermal cells. Transcriptome analysis of laser-dissected K14-Gata3-/- hair follicles revealed mitosis, epithelial differentiation and the Notch, Wnt and BMP signaling pathways to be significantly overrepresented. Elucidation of these pathways at the RNA and protein levels and physiologic endpoints suggests that Gata3 integrates diverse signaling networks to regulate the balance between hair follicle and epidermal cell fates.
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Affiliation(s)
- Dorota Kurek
- Department of Cell Biology, Erasmus Medical Center, P.O. Box 1738, 3000 DR Rotterdam, The Netherlands
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Patrinos GP, de Krom M, de Boer E, Langeveld A, Imam AMA, Strouboulis J, de Laat W, Grosveld FG. Multiple interactions between regulatory regions are required to stabilize an active chromatin hub. Genes Dev 2004; 18:1495-509. [PMID: 15198986 PMCID: PMC423198 DOI: 10.1101/gad.289704] [Citation(s) in RCA: 147] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2003] [Accepted: 04/20/2004] [Indexed: 11/25/2022]
Abstract
The human beta-globin locus control region (LCR) is required for the maintenance of an open chromatin configuration of the locus. It interacts with the genes and the hypersensitive regions flanking the locus to form an active chromatin hub (ACH) transcribing the genes. Proper developmental control of globin genes is largely determined by gene proximal regulatory sequences. Here, we provide the first functional evidence of the role of the most active sites of the LCR and the promoter of the beta-globin gene in the maintenance of the ACH. When the human beta-globin gene promoter is deleted in the context of a full LCR, the ACH is maintained with the beta-globin gene remaining in proximity. Additional deletion of hypersensitive site HS3 or HS2 of the LCR shows that HS3, but not HS2, in combination with the beta-globin promoter is crucial for the maintenance of the ACH at the definitive stage. We conclude that multiple interactions between the LCR and the beta-globin gene are required to maintain the appropriate spatial configuration in vivo.
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Affiliation(s)
- George P Patrinos
- Erasmus University Medical Center, Faculty of Medicine and Health Sciences, MGC Department of Cell Biology and Genetics, Rotterdam, 3000 DR, The Netherlands
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van der Wees J, van Looij MAJ, de Ruiter MM, Elias H, van der Burg H, Liem SS, Kurek D, Engel JD, Karis A, van Zanten BGA, de Zeeuw CI, Grosveld FG, van Doorninck JH. Hearing loss following Gata3 haploinsufficiency is caused by cochlear disorder. Neurobiol Dis 2004; 16:169-78. [PMID: 15207274 DOI: 10.1016/j.nbd.2004.02.004] [Citation(s) in RCA: 60] [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: 09/18/2003] [Revised: 01/30/2004] [Accepted: 02/13/2004] [Indexed: 11/21/2022] Open
Abstract
Patients with HDR syndrome suffer from hypoparathyroidism, deafness, and renal dysplasia due to a heterozygous deletion of the transcription factor GATA3. Since GATA3 is prominently expressed in both the inner ear and different parts of the auditory nervous system, it is not clear whether the deafness in HDR patients is caused by peripheral and/or central deficits. Therefore, we have created and examined heterozygous Gata3 knockout mice. Auditory brainstem response (ABR) thresholds of alert heterozygous Gata3 mice, analyzed from 1 to 19 months of age, showed a hearing loss of 30 dB compared to wild-type littermates. Neither physiological nor morphological abnormalities were found in the brainstem, cerebral cortex, the outer or the middle ear. In contrast, cochleae of heterozygous Gata3 mice showed significant progressive morphological degeneration starting with the outer hair cells (OHCs) at the apex and ultimately affecting all hair cells and supporting cells in the entire cochlea. Together, these findings indicate that hearing loss following Gata3 haploinsufficiency is peripheral in origin and that this defect is detectable from early postnatal development and maintains through adulthood.
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Affiliation(s)
- Jacqueline van der Wees
- Department of Cell Biology, Erasmus Medical Center, P.O. Box 1738, 3000 DR Rotterdam, The Netherlands
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Abstract
Since the first description of in situ hybridization in 1969 the technique has advanced to allow sensitive detection of DNA and mRNA molecules at the cellular and subcellular levels. In particular fluorescence in situ hybridization (FISH) has become a frequently used tool in basic and applied biomedical research since detection is sensitive and allows discrimination of multiple targets in the same sample. By using RNA-FISH we have been able to detect primary transcripts of the human embryonic, fetal, and adult globins in erythroid cells to study the competitive transcription mechanism or variegated expression patterns of the human beta-globin locus. We have correlated such expression patterns with other parameters such as cell type, cell cycle, replication, and stage of differentiation by simultaneous detection of, e.g., incorporated BrdUTPs, proteins (e.g., cyclins A and E, PCNA, histones), and globin (primary) transcripts and/or locus integration sites. Thus a combination of FISH and immunofluorescence methods allow the visualization of different processes taking place in the nucleus relative to each other in terms of three-dimensional space and structure and time (development, cell cycle).
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Affiliation(s)
- M P van de Corput
- Department of Cell Biology and Genetics, Faculty of Medicine and Health Sciences, Erasmus University, Dr. Molewaterplein 50, Rotterdam, 3015 GE, The Netherlands
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Imam AM, Patrinos GP, de Krom M, Bottardi S, Janssens RJ, Katsantoni E, Wai AW, Sherratt DJ, Grosveld FG. Modification of human beta-globin locus PAC clones by homologous recombination in Escherichia coli. Nucleic Acids Res 2000; 28:E65. [PMID: 10871388 PMCID: PMC102750 DOI: 10.1093/nar/28.12.e65] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We report here modifications of human beta-globin PAC clones by homologous recombination in Escherichia coli DH10B, utilising a plasmid temperature sensitive for replication, the recA gene and a wild-type copy of the rpsL gene which allows for an efficient selection for plasmid loss in this host. High frequencies of recombination are observed even with very small lengths of homology and the method has general utility for introducing insertions, deletions and point mutations. No rearrangements were detected with the exception of one highly repetitive genomic sequence when either the E.COLI: RecA- or the lambdoid phage encoded RecT and RecE-dependent recombination systems were used.
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Affiliation(s)
- A M Imam
- Erasmus University Rotterdam, CBG and MGC-Department of Cell Biology, PO Box 1738, 3000 DR Rotterdam, The Netherlands.
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Kleinjan DA, Dekker S, Guy JA, Grosveld FG. Cloning and sequencing of the CRABP-I locus from chicken and pufferfish: analysis of the promoter regions in transgenic mice. Transgenic Res 1998; 7:85-94. [PMID: 9608736 DOI: 10.1023/a:1008864224100] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Retinoic acid (RA), a derivative of vitamin A, is an important molecule for development and homeostasis of vertebrate organisms. The intracellular retinoic acid binding protein CRABP-I has a high affinity for RA, and is thought to be involved in the mechanism of RA signalling. CRABP-I is well conserved in evolution and shows a specific expression pattern during development, but mice made deficient for the protein by gene targeting appear normal. However, the high degree of homology with CRABP-I from other species indicates that the protein has been subject to strong selective conservation, indicative of an important biological function. In this paper we have compared the conservation in the expression pattern of the mouse, chicken and pufferfish CRABP-I genes to substantiate this argument further. First we cloned and sequenced genes and promoter regions of the CRABP-I genes from chicken and the Japanese pufferfish, Fugu rubripes. Sequence comparison with the mouse gene did not show any large blocks of homology in the promoter regions. Nevertheless, the promoter of the chicken gene directed expression to a subset of the tissues that show expression with the promoter from the mouse gene. The pattern observed with the pufferfish promoter is even more restricted, essentially to rhombomere 4 only, indicating that this region may be functionally the most important for CRABP-I expression in the developing embryo.
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Affiliation(s)
- D A Kleinjan
- Department of Cell Biology and Genetics, Erasmus University Rotterdam, The Netherlands
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46
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van Leeuwen FW, de Kleijn DP, van den Hurk HH, Neubauer A, Sonnemans MA, Sluijs JA, Köycü S, Ramdjielal RD, Salehi A, Martens GJ, Grosveld FG, Peter J, Burbach H, Hol EM. Frameshift mutants of beta amyloid precursor protein and ubiquitin-B in Alzheimer's and Down patients. Science 1998; 279:242-7. [PMID: 9422699 DOI: 10.1126/science.279.5348.242] [Citation(s) in RCA: 452] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The cerebral cortex of Alzheimer's and Down syndrome patients is characterized by the presence of protein deposits in neurofibrillary tangles, neuritic plaques, and neuropil threads. These structures were shown to contain forms of beta amyloid precursor protein and ubiquitin-B that are aberrant (+1 proteins) in the carboxyl terminus. The +1 proteins were not found in young control patients, whereas the presence of ubiquitin-B+1 in elderly control patients may indicate early stages of neurodegeneration. The two species of +1 proteins displayed cellular colocalization, suggesting a common origin, operating at the transcriptional level or by posttranscriptional editing of RNA. This type of transcript mutation is likely an important factor in the widely occurring nonfamilial early- and late-onset forms of Alzheimer's disease.
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Affiliation(s)
- F W van Leeuwen
- Graduate School for Neurosciences Amsterdam, Netherlands Institute for Brain Research, 1105 AZ Amsterdam, The Netherlands.
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Longo L, Bygrave A, Grosveld FG, Pandolfi PP. The chromosome make-up of mouse embryonic stem cells is predictive of somatic and germ cell chimaerism. Transgenic Res 1997; 6:321-8. [PMID: 9322369 DOI: 10.1023/a:1018418914106] [Citation(s) in RCA: 136] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Mouse pluripotent embryonic stem (ES) cells, once reintroduced into a mouse blastocyst, can contribute to the formation of all tissues, including the germline, of an organism referred to as a chimaeric. However, the reasons why this contribution often appears erratic are poorly understood. We have tested the notion that the chromosome make-up may be important in contributing both to somatic cell chimaerism and to germ line transmission. We found that the percentage of chimaerism of ES cell-embryo chimaeras, the absolute number of chimaeras and the ratio of chimaeras to total pups born all correlate closely with the percentage of euploid metaphases in the ES cell clones injected into the murine blastocyst. The majority of the ES cell clones that we tested, which were obtained from different gene targeting knockout experiments and harboured 50 to 100% euploid metaphases, did transmit to the germline; in contrast, none of the ES cell clones with more than 50% of chromosomally abnormal metaphases transmitted to the germline. Euploid ES cell clones cultured in vitro for more than 20 passages rapidly became severely aneuploid, and again this correlated closely with the percentage of chimaerism and with the number of ES cell-embryo chimaeras obtained per number of blastocysts injected. At the same time, the ability of these clones to contribute to the germline was lost when the proportion of euploid cells dropped below 50%. This study suggests that aneuploidy, rather than 'loss of totipotency', in ES cells, is the major cause of failure in obtaining contributions to all tissues of the adult chimaera, including the germline. Because euploidy is predictive of germline transmission, karyotype analysis is crucial and time/cost saving in any gene-targeting experiment.
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Affiliation(s)
- L Longo
- Department of Haematology, Royal Postgraduate Medical School, London, UK
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Elefanty AG, Antoniou M, Custodio N, Carmo-Fonseca M, Grosveld FG. GATA transcription factors associate with a novel class of nuclear bodies in erythroblasts and megakaryocytes. EMBO J 1996; 15:319-33. [PMID: 8617207 PMCID: PMC449947] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The nuclear distribution of GATA transcription factors in murine haemopoietic cells was examined by indirect immunofluorescence. Specific bright foci of GATA-1 fluorescence were observed in erythroleukaemia cells and primary murine erythroblasts and megakaryocytes, in addition to diffuse nucleoplasmic localization. These foci, which were preferentially found adjacent to nucleoli or at the nuclear periphery, did not represent sites of active transcription or binding of GATA-1 to consensus sites in the beta-globin loci. Immunoelectron microscopy demonstrated the presence of intensely labelled structures likely to represent the GATA-1 foci seen by immunofluorescence. The GATA-1 nuclear bodies differed from previously described nuclear structures and there was no co-localization with nuclear antigens involved in RNA processing or other ubiquitous (Spl, c-Jun and TBP) or haemopoietic (NF-E2) transcription factors. Interestingly, GATA-2 and GATA-3 proteins also localized to the same nuclear bodies in cell lines co-expressing GATA-1 and -2 or GATA-1 and -3 gene products. This pattern of distribution is, thus far, unique to the GATA transcription factors and suggests a protein-protein interaction with other components of the nuclear bodies via the GATA zinc finger domain.
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Zhou XY, Morreau H, Rottier R, Davis D, Bonten E, Gillemans N, Wenger D, Grosveld FG, Doherty P, Suzuki K, Grosveld GC, d'Azzo A. Mouse model for the lysosomal disorder galactosialidosis and correction of the phenotype with overexpressing erythroid precursor cells. Genes Dev 1995; 9:2623-34. [PMID: 7590240 DOI: 10.1101/gad.9.21.2623] [Citation(s) in RCA: 96] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The lysosomal storage disorder galactosialidosis results from a primary deficiency of the protective protein/cathepsin A (PPCA), which in turn affects the activities of beta-galactosidase and neuraminidase. Mice homozygous for a null mutation at the PPCA locus present with signs of the disease shortly after birth and develop a phenotype closely resembling human patients with galactosialidosis. Most of their tissues show characteristic vacuolation of specific cells, attributable to lysosomal storage. Excessive excretion of sialyloligosaccharides in urine is diagnostic of the disease. Affected mice progressively deteriorate as a consequence of severe organ dysfunction, especially of the kidney. The deficient phenotype can be corrected by transplanting null mutants with bone marrow from a transgenic line overexpressing human PPCA in erythroid precursor cells. The transgenic bone marrow gives a more efficient and complete correction of the visceral organs than normal bone marrow. Our data demonstrate the usefulness of this animal model, very similar to the human disease, for experimenting therapeutic strategies aimed to deliver the functional protein or gene to affected organs. Furthermore, they suggest the feasibility of gene therapy for galactosialidosis and other disorders, using bone marrow cells engineered to overexpress and secrete the correcting lysosomal protein.
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Affiliation(s)
- X Y Zhou
- Department of Genetics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
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Pandolfi PP, Roth ME, Karis A, Leonard MW, Dzierzak E, Grosveld FG, Engel JD, Lindenbaum MH. Targeted disruption of the GATA3 gene causes severe abnormalities in the nervous system and in fetal liver haematopoiesis. Nat Genet 1995; 11:40-4. [PMID: 7550312 DOI: 10.1038/ng0995-40] [Citation(s) in RCA: 485] [Impact Index Per Article: 16.7] [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] [Indexed: 01/25/2023]
Abstract
GATA-3 is one member of a growing family of related transcription factors which share a strongly conserved expression pattern in all vertebrate organisms. In order to elucidate GATA-3 function using a direct genetic approach, we have disrupted the murine gene by homologous recombination in embryonic stem cells. Mice heterozygous for the GATA3 mutation are fertile and appear in all respects to be normal, whereas homozygous mutant embryos die between days 11 and 12 postcoitum (p.c.) and display massive internal bleeding, marked growth retardation, severe deformities of the brain and spinal cord, and gross aberrations in fetal liver haematopoiesis.
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Affiliation(s)
- P P Pandolfi
- Dept. of Haematology, Royal Postgraduate Medical School, Hammersmith Hospital, London, UK
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