1
|
Aísa-Marín I, Rovira Q, Díaz N, Calvo-López L, Vaquerizas JM, Marfany G. Specific photoreceptor cell fate pathways are differentially altered in NR2E3-associated diseases. Neurobiol Dis 2024; 194:106463. [PMID: 38485095 DOI: 10.1016/j.nbd.2024.106463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 03/01/2024] [Accepted: 03/02/2024] [Indexed: 03/21/2024] Open
Abstract
Mutations in NR2E3, a gene encoding an orphan nuclear transcription factor, cause two retinal dystrophies with a distinct phenotype, but the precise role of NR2E3 in rod and cone transcriptional networks remains unclear. To dissect NR2E3 function, we performed scRNA-seq in the retinas of wildtype and two different Nr2e3 mouse models that show phenotypes similar to patients carrying NR2E3 mutations. Our results reveal that rod and cone populations are not homogeneous and can be separated into different sub-classes. We identify a previously unreported cone pathway that generates hybrid cones co-expressing both cone- and rod-related genes. In mutant retinas, this hybrid cone subpopulation is more abundant and includes a subpopulation of rods transitioning towards a cone cell fate. Hybrid photoreceptors with high misexpression of cone- and rod-related genes are prone to regulated necrosis. Overall, our results shed light on the role of NR2E3 in modulating photoreceptor differentiation towards cone and rod fates and explain how different mutations in NR2E3 lead to distinct visual disorders in humans.
Collapse
Affiliation(s)
- Izarbe Aísa-Marín
- Department de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona 08028, Spain; IBUB-IRSJD, Institut de Biomedicina de la Universitat de Barcelona-Institut de Recerca Sant Joan de Déu, Barcelona 08028, Spain; CIBERER, Instituto de Salud Carlos III, Barcelona 08028, Spain
| | - Quirze Rovira
- Max-Planck-Institute for Molecular Biomedicine, Münster 48149, Germany
| | - Noelia Díaz
- Max-Planck-Institute for Molecular Biomedicine, Münster 48149, Germany
| | - Laura Calvo-López
- Department de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona 08028, Spain
| | - Juan M Vaquerizas
- Max-Planck-Institute for Molecular Biomedicine, Münster 48149, Germany; MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Imperial College London, London W12 0NN, UK.; Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK.
| | - Gemma Marfany
- Department de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona 08028, Spain; IBUB-IRSJD, Institut de Biomedicina de la Universitat de Barcelona-Institut de Recerca Sant Joan de Déu, Barcelona 08028, Spain; CIBERER, Instituto de Salud Carlos III, Barcelona 08028, Spain; DBGen Ocular Genomics, Barcelona 08028, Spain.
| |
Collapse
|
2
|
Ing-Simmons E, Machnik N, Vaquerizas JM. Reply to: Revisiting the use of structural similarity index in Hi-C. Nat Genet 2023; 55:2053-2055. [PMID: 38052961 DOI: 10.1038/s41588-023-01595-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 10/25/2023] [Indexed: 12/07/2023]
Affiliation(s)
- Elizabeth Ing-Simmons
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Nick Machnik
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Juan M Vaquerizas
- MRC London Institute of Medical Sciences, London, UK.
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK.
| |
Collapse
|
3
|
Almouzni G, Vaquerizas JM. 3D genome organization and beyond! Curr Opin Struct Biol 2023; 83:102731. [PMID: 37951048 DOI: 10.1016/j.sbi.2023.102731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2023]
Affiliation(s)
- Geneviève Almouzni
- Institut Curie, CNRS, Nuclear Dynamics Unit, Equipe Labellisée Ligue Contre le Cancer, PSL Research University, Sorbonne Université, 26 Rue d'Ulm, 75005 Paris, France.
| | - Juan M Vaquerizas
- MRC London Institute of Medical Sciences, Du Cane Road, W12 0NN London, UK; Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, W12 0NN London, UK
| |
Collapse
|
4
|
Stefanova ME, Ing-Simmons E, Stefanov S, Flyamer I, Dorado Garcia H, Schöpflin R, Henssen AG, Vaquerizas JM, Mundlos S. Doxorubicin Changes the Spatial Organization of the Genome around Active Promoters. Cells 2023; 12:2001. [PMID: 37566080 PMCID: PMC10417312 DOI: 10.3390/cells12152001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 07/26/2023] [Indexed: 08/12/2023] Open
Abstract
In this study, we delve into the impact of genotoxic anticancer drug treatment on the chromatin structure of human cells, with a particular focus on the effects of doxorubicin. Using Hi-C, ChIP-seq, and RNA-seq, we explore the changes in chromatin architecture brought about by doxorubicin and ICRF193. Our results indicate that physiologically relevant doses of doxorubicin lead to a local reduction in Hi-C interactions in certain genomic regions that contain active promoters, with changes in chromatin architecture occurring independently of Top2 inhibition, cell cycle arrest, and differential gene expression. Inside the regions with decreased interactions, we detected redistribution of RAD21 around the peaks of H3K27 acetylation. Our study also revealed a common structural pattern in the regions with altered architecture, characterized by two large domains separated from each other. Additionally, doxorubicin was found to increase CTCF binding in H3K27 acetylated regions. Furthermore, we discovered that Top2-dependent chemotherapy causes changes in the distance decay of Hi-C contacts, which are driven by direct and indirect inhibitors. Our proposed model suggests that doxorubicin-induced DSBs cause cohesin redistribution, which leads to increased insulation on actively transcribed TAD boundaries. Our findings underscore the significant impact of genotoxic anticancer treatment on the chromatin structure of the human genome.
Collapse
Affiliation(s)
- Maria E. Stefanova
- Development and Disease Research Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany (S.M.)
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Elizabeth Ing-Simmons
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK; (E.I.-S.); (J.M.V.)
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Stefan Stefanov
- Berlin Institute for Molecular and Systems Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany;
- Department of Biology, Chemistry, and Pharmacology, Institute of Biochemistry, Freie Universität Berlin, 14163 Berlin, Germany
| | - Ilya Flyamer
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland;
| | - Heathcliff Dorado Garcia
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, 13125 Berlin, Germany; (H.D.G.); (A.G.H.)
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 13353 Berlin, Germany
- Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Robert Schöpflin
- Development and Disease Research Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany (S.M.)
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Anton G. Henssen
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, 13125 Berlin, Germany; (H.D.G.); (A.G.H.)
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 13353 Berlin, Germany
- Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Juan M. Vaquerizas
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK; (E.I.-S.); (J.M.V.)
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Stefan Mundlos
- Development and Disease Research Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany (S.M.)
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| |
Collapse
|
5
|
Sathyanarayanan A, Ing-Simmons E, Chen R, Jeong HW, Ozguldez HO, Fan R, Duethorn B, Kim KP, Kim YS, Stehling M, Brinkmann H, Schöler HR, Adams RH, Vaquerizas JM, Bedzhov I. Early developmental plasticity enables the induction of an intermediate extraembryonic cell state. Sci Adv 2022; 8:eabl9583. [PMID: 36332016 PMCID: PMC9635831 DOI: 10.1126/sciadv.abl9583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 09/19/2022] [Indexed: 05/23/2023]
Abstract
Two fundamental elements of pre-implantation embryogenesis are cells' intrinsic self-organization program and their developmental plasticity, which allows embryos to compensate for alterations in cell position and number; yet, these elements are still poorly understood. To be able to decipher these features, we established culture conditions that enable the two fates of blastocysts' extraembryonic lineages-the primitive endoderm and the trophectoderm-to coexist. This plasticity emerges following the mechanisms of the first lineage segregation in the mouse embryo, and it manifests as an extended potential for extraembryonic chimerism during the pre-implantation embryogenesis. Moreover, this shared state enables robust assembly into higher-order blastocyst-like structures, thus combining both the cell fate plasticity and self-organization features of the early extraembryonic lineages.
Collapse
Affiliation(s)
- Anusha Sathyanarayanan
- Embryonic Self-Organization Research Group, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149 Münster, Germany
| | - Elizabeth Ing-Simmons
- Regulatory Genomics Group, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149 Münster, Germany
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Rui Chen
- Embryonic Self-Organization Research Group, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149 Münster, Germany
| | - Hyun-Woo Jeong
- Department of Tissue Morphogenesis, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany
- Faculty of Medicine, University of Münster, Röntgenstrasse 20, 48149 Münster, Germany
| | - Hatice O. Ozguldez
- Embryonic Self-Organization Research Group, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149 Münster, Germany
| | - Rui Fan
- Embryonic Self-Organization Research Group, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149 Münster, Germany
| | - Binyamin Duethorn
- Embryonic Self-Organization Research Group, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149 Münster, Germany
| | - Kee-Pyo Kim
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149 Münster, Germany
- Department of Medical Life Sciences, College of Medicine, The Catholic University of Korea, 222 Banpo-daero Seocho-gu, Seoul 06591, Korea
| | - Yung Su Kim
- Embryonic Self-Organization Research Group, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149 Münster, Germany
| | - Martin Stehling
- Flow Cytometry Unit, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149 Münster, Germany
| | - Heike Brinkmann
- Embryonic Self-Organization Research Group, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149 Münster, Germany
| | - Hans R. Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149 Münster, Germany
| | - Ralf H. Adams
- Department of Tissue Morphogenesis, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany
- Faculty of Medicine, University of Münster, Röntgenstrasse 20, 48149 Münster, Germany
| | - Juan M. Vaquerizas
- Regulatory Genomics Group, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149 Münster, Germany
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Ivan Bedzhov
- Embryonic Self-Organization Research Group, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149 Münster, Germany
| |
Collapse
|
6
|
Baranasic D, Hörtenhuber M, Balwierz PJ, Zehnder T, Mukarram AK, Nepal C, Várnai C, Hadzhiev Y, Jimenez-Gonzalez A, Li N, Wragg J, D'Orazio FM, Relic D, Pachkov M, Díaz N, Hernández-Rodríguez B, Chen Z, Stoiber M, Dong M, Stevens I, Ross SE, Eagle A, Martin R, Obasaju O, Rastegar S, McGarvey AC, Kopp W, Chambers E, Wang D, Kim HR, Acemel RD, Naranjo S, Łapiński M, Chong V, Mathavan S, Peers B, Sauka-Spengler T, Vingron M, Carninci P, Ohler U, Lacadie SA, Burgess SM, Winata C, van Eeden F, Vaquerizas JM, Gómez-Skarmeta JL, Onichtchouk D, Brown BJ, Bogdanovic O, van Nimwegen E, Westerfield M, Wardle FC, Daub CO, Lenhard B, Müller F. Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements. Nat Genet 2022; 54:1037-1050. [PMID: 35789323 PMCID: PMC9279159 DOI: 10.1038/s41588-022-01089-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 05/03/2022] [Indexed: 12/12/2022]
Abstract
Zebrafish, a popular organism for studying embryonic development and for modeling human diseases, has so far lacked a systematic functional annotation program akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium and created a central repository to store and process zebrafish developmental functional genomic data. Our data coordination center ( https://danio-code.zfin.org ) combines a total of 1,802 sets of unpublished and re-analyzed published genomic data, which we used to improve existing annotations and show its utility in experimental design. We identified over 140,000 cis-regulatory elements throughout development, including classes with distinct features dependent on their activity in time and space. We delineated the distinct distance topology and chromatin features between regulatory elements active during zygotic genome activation and those active during organogenesis. Finally, we matched regulatory elements and epigenomic landscapes between zebrafish and mouse and predicted functional relationships between them beyond sequence similarity, thus extending the utility of zebrafish developmental genomics to mammals.
Collapse
Affiliation(s)
- Damir Baranasic
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - Matthias Hörtenhuber
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Huddinge, Sweden
| | - Piotr J Balwierz
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Tobias Zehnder
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK
- Max Planck Institute for Molecular Genetics, Department of Computational Molecular Biology, Berlin, Germany
| | - Abdul Kadir Mukarram
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Huddinge, Sweden
| | - Chirag Nepal
- Biotech Research and Innovation Centre (BRIC), Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Csilla Várnai
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Centre for Computational Biology, University of Birmingham, Birmingham, UK
| | - Yavor Hadzhiev
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Ada Jimenez-Gonzalez
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Nan Li
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Joseph Wragg
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Fabio M D'Orazio
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Dorde Relic
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Mikhail Pachkov
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Noelia Díaz
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany
- Institute of Marine Sciences, Barcelona, Spain
| | | | - Zelin Chen
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Marcus Stoiber
- Environmental Genomics & Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michaël Dong
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Huddinge, Sweden
| | - Irene Stevens
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Huddinge, Sweden
| | - Samuel E Ross
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Anne Eagle
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Ryan Martin
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Oluwapelumi Obasaju
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Sepand Rastegar
- Institute of Biological and Chemical Systems - Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Alison C McGarvey
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Wolfgang Kopp
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Emily Chambers
- Sheffield Bioinformatics Core, Sheffield Institute of Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Dennis Wang
- Sheffield Bioinformatics Core, Sheffield Institute of Translational Neuroscience, University of Sheffield, Sheffield, UK
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - Hyejeong R Kim
- Bateson Centre/Biomedical Science, University of Sheffield, Sheffield, UK
| | - Rafael D Acemel
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
- Epigenetics and Sex Development Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Silvia Naranjo
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Maciej Łapiński
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Vanessa Chong
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | | | - Bernard Peers
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA-R, SART TILMAN, University of Liège, Liège, Belgium
| | - Tatjana Sauka-Spengler
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Martin Vingron
- Max Planck Institute for Molecular Genetics, Department of Computational Molecular Biology, Berlin, Germany
| | - Piero Carninci
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Fondazione Human Technopole, Milano, Italy
| | - Uwe Ohler
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Institute of Biology, Humboldt University, Berlin, Germany
| | - Scott Allen Lacadie
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Shawn M Burgess
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Cecilia Winata
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Freek van Eeden
- Bateson Centre/Biomedical Science, University of Sheffield, Sheffield, UK
| | - Juan M Vaquerizas
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Daria Onichtchouk
- Department of Developmental Biology, Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Ben James Brown
- Environmental Genomics & Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ozren Bogdanovic
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Erik van Nimwegen
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | | | - Fiona C Wardle
- Randall Centre for Cell & Molecular Biophysics, Guy's Campus, King's College London, London, UK
| | - Carsten O Daub
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Huddinge, Sweden.
- Science for Life Laboratory, Solna, Sweden.
| | - Boris Lenhard
- MRC London Institute of Medical Sciences, London, UK.
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK.
| | - Ferenc Müller
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
| |
Collapse
|
7
|
Tsaryk R, Yucel N, Leonard EV, Diaz N, Bondareva O, Odenthal-Schnittler M, Arany Z, Vaquerizas JM, Schnittler H, Siekmann AF. Shear stress switches the association of endothelial enhancers from ETV/ETS to KLF transcription factor binding sites. Sci Rep 2022; 12:4795. [PMID: 35314737 PMCID: PMC8938417 DOI: 10.1038/s41598-022-08645-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/10/2022] [Indexed: 02/06/2023] Open
Abstract
Endothelial cells (ECs) lining blood vessels are exposed to mechanical forces, such as shear stress. These forces control many aspects of EC biology, including vascular tone, cell migration and proliferation. Despite a good understanding of the genes responding to shear stress, our insight into the transcriptional regulation of these genes is much more limited. Here, we set out to study alterations in the chromatin landscape of human umbilical vein endothelial cells (HUVEC) exposed to laminar shear stress. To do so, we performed ChIP-Seq for H3K27 acetylation, indicative of active enhancer elements and ATAC-Seq to mark regions of open chromatin in addition to RNA-Seq on HUVEC exposed to 6 h of laminar shear stress. Our results show a correlation of gained and lost enhancers with up and downregulated genes, respectively. DNA motif analysis revealed an over-representation of KLF transcription factor (TF) binding sites in gained enhancers, while lost enhancers contained more ETV/ETS motifs. We validated a subset of flow responsive enhancers using luciferase-based reporter constructs and CRISPR-Cas9 mediated genome editing. Lastly, we characterized the shear stress response in ECs of zebrafish embryos using RNA-Seq. Our results lay the groundwork for the exploration of shear stress responsive elements in controlling EC biology.
Collapse
Affiliation(s)
- Roman Tsaryk
- Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149, Münster, Germany
- Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), University of Münster, Münster, Germany
- Department of Cell and Developmental Biology and Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Nora Yucel
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Elvin V Leonard
- Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149, Münster, Germany
- Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), University of Münster, Münster, Germany
- Department of Cell and Developmental Biology and Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Noelia Diaz
- Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149, Münster, Germany
- Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), University of Münster, Münster, Germany
| | - Olga Bondareva
- Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), University of Münster, Münster, Germany
- Institute of Anatomy and Vascular Biology, Faculty of Medicine, Westfälische Wilhelms-Universität Münster, Vesaliusweg 2-4, 48149, Münster, Germany
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Philipp-Rosenthal-Str. 27, 04103, Leipzig, Germany
| | - Maria Odenthal-Schnittler
- Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149, Münster, Germany
- Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), University of Münster, Münster, Germany
- Institute of Anatomy and Vascular Biology, Faculty of Medicine, Westfälische Wilhelms-Universität Münster, Vesaliusweg 2-4, 48149, Münster, Germany
- Institute of Neuropathology, Westfälische Wilhelms-Universität Münster, Pottkamp 2, 48149, Münster, Germany
| | - Zoltan Arany
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Juan M Vaquerizas
- Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149, Münster, Germany
- Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), University of Münster, Münster, Germany
| | - Hans Schnittler
- Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149, Münster, Germany
- Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), University of Münster, Münster, Germany
- Institute of Anatomy and Vascular Biology, Faculty of Medicine, Westfälische Wilhelms-Universität Münster, Vesaliusweg 2-4, 48149, Münster, Germany
- Institute of Neuropathology, Westfälische Wilhelms-Universität Münster, Pottkamp 2, 48149, Münster, Germany
| | - Arndt F Siekmann
- Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149, Münster, Germany.
- Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), University of Münster, Münster, Germany.
- Department of Cell and Developmental Biology and Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
8
|
Duethorn B, Groll F, Rieger B, Drexler HCA, Brinkmann H, Kremer L, Stehling M, Borowski MT, Mildner K, Zeuschner D, Zernicka-Goetz M, Stemmler MP, Busch KB, Vaquerizas JM, Bedzhov I. Lima1 mediates the pluripotency control of membrane dynamics and cellular metabolism. Nat Commun 2022; 13:610. [PMID: 35105859 PMCID: PMC8807836 DOI: 10.1038/s41467-022-28139-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 01/10/2022] [Indexed: 12/13/2022] Open
Abstract
Lima1 is an extensively studied prognostic marker of malignancy and is also considered to be a tumour suppressor, but its role in a developmental context of non-transformed cells is poorly understood. Here, we characterise the expression pattern and examined the function of Lima1 in mouse embryos and pluripotent stem cell lines. We identify that Lima1 expression is controlled by the naïve pluripotency circuit and is required for the suppression of membrane blebbing, as well as for proper mitochondrial energetics in embryonic stem cells. Moreover, forcing Lima1 expression enables primed mouse and human pluripotent stem cells to be incorporated into murine pre-implantation embryos. Thus, Lima1 is a key effector molecule that mediates the pluripotency control of membrane dynamics and cellular metabolism.
Collapse
Affiliation(s)
- Binyamin Duethorn
- Embryonic Self-Organization research group, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149, Münster, Germany
| | - Fabian Groll
- Regulatory Genomics group, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149, Münster, Germany
| | - Bettina Rieger
- Institut für Integrative Zellbiologie und Physiologie, University of Münster, Schlossplatz 5, 48149, Münster, Germany
| | - Hannes C A Drexler
- Mass Spectrometry Unit, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149, Münster, Germany
| | - Heike Brinkmann
- Embryonic Self-Organization research group, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149, Münster, Germany
| | - Ludmila Kremer
- Transgenic Facility, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149, Münster, Germany
| | - Martin Stehling
- Flow Cytometry Unit, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149, Münster, Germany
| | - Marie-Theres Borowski
- Institut für Integrative Zellbiologie und Physiologie, University of Münster, Schlossplatz 5, 48149, Münster, Germany
| | - Karina Mildner
- Electron Microscopy Facility, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149, Münster, Germany
| | - Dagmar Zeuschner
- Electron Microscopy Facility, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149, Münster, Germany
| | - Magdalena Zernicka-Goetz
- Mammalian Embryo and Stem Cell Group, Department of Physiology, Development, and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3EG, UK.,Plasticity and Self-Organization Group, Division of Biology and Biological Engineering, California Institute of Technology (Caltech), Pasadena, CA, 91125, USA
| | - Marc P Stemmler
- Department of Experimental Medicine 1, Nikolaus-Fiebiger-Center for Molecular Medicine, FAU University Erlangen-Nürnberg, Erlangen, Germany
| | - Karin B Busch
- Institut für Integrative Zellbiologie und Physiologie, University of Münster, Schlossplatz 5, 48149, Münster, Germany
| | - Juan M Vaquerizas
- Regulatory Genomics group, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149, Münster, Germany.,MRC London Institute of Medical Sciences, Du Cane Road, W12 0NN, London, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Ivan Bedzhov
- Embryonic Self-Organization research group, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149, Münster, Germany.
| |
Collapse
|
9
|
Chang NC, Rovira Q, Wells JN, Feschotte C, Vaquerizas JM. Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression. Genome Res 2022; 32:1408-1423. [PMID: 34987056 PMCID: PMC9341512 DOI: 10.1101/gr.275655.121] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [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: 04/15/2021] [Accepted: 12/30/2021] [Indexed: 12/02/2022]
Abstract
There is considerable interest in understanding the effect of transposable elements (TEs) on embryonic development. Studies in humans and mice are limited by the difficulty of working with mammalian embryos and by the relative scarcity of active TEs in these organisms. The zebrafish is an outstanding model for the study of vertebrate development, and over half of its genome consists of diverse TEs. However, zebrafish TEs remain poorly characterized. Here we describe the demography and genomic distribution of zebrafish TEs and their expression throughout embryogenesis using bulk and single-cell RNA sequencing data. These results reveal a highly dynamic genomic ecosystem comprising nearly 2000 distinct TE families, which vary in copy number by four orders of magnitude and span a wide range of ages. Longer retroelements tend to be retained in intergenic regions, whereas short interspersed nuclear elements (SINEs) and DNA transposons are more frequently found nearby or within genes. Locus-specific mapping of TE expression reveals extensive TE transcription during development. Although two-thirds of TE transcripts are likely driven by nearby gene promoters, we still observe stage- and tissue-specific expression patterns in self-regulated TEs. Long terminal repeat (LTR) retroelements are most transcriptionally active immediately following zygotic genome activation, whereas DNA transposons are enriched among transcripts expressed in later stages of development. Single-cell analysis reveals several endogenous retroviruses expressed in specific somatic cell lineages. Overall, our study provides a valuable resource for using zebrafish as a model to study the impact of TEs on vertebrate development.
Collapse
|
10
|
Salewskij K, Gross-Thebing T, Ing-Simmons E, Duethorn B, Rieger B, Fan R, Chen R, Govindasamy N, Brinkmann H, Kremer L, Kuempel-Rink N, Mildner K, Zeuschner D, Stehling M, Dejosez M, Zwaka TP, Schöler HR, Busch KB, Vaquerizas JM, Bedzhov I. Ronin governs the metabolic capacity of the embryonic lineage for post-implantation development. EMBO Rep 2021; 22:e53048. [PMID: 34515391 PMCID: PMC8567215 DOI: 10.15252/embr.202153048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 12/02/2022] Open
Abstract
During implantation, the murine embryo transitions from a “quiet” into an active metabolic/proliferative state, which kick‐starts the growth and morphogenesis of the post‐implantation conceptus. Such transition is also required for embryonic stem cells to be established from mouse blastocysts, but the factors regulating this process are poorly understood. Here, we show that Ronin plays a critical role in the process by enabling active energy production, and the loss of Ronin results in the establishment of a reversible quiescent state in which naïve pluripotency is promoted. In addition, Ronin fine‐tunes the expression of genes that encode ribosomal proteins and is required for proper tissue‐scale organisation of the pluripotent lineage during the transition from blastocyst to egg cylinder stage. Thus, Ronin function is essential for governing the metabolic capacity so that it can support the pluripotent lineage’s high‐energy demands for cell proliferation and morphogenesis.
Collapse
Affiliation(s)
- Kirill Salewskij
- Embryonic Self-Organization Research Group, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Theresa Gross-Thebing
- Embryonic Self-Organization Research Group, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Elizabeth Ing-Simmons
- Regulatory Genomics Group, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Binyamin Duethorn
- Embryonic Self-Organization Research Group, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Bettina Rieger
- Institut für Integrative Zellbiologie und Physiologie, University of Münster, Münster, Germany
| | - Rui Fan
- Embryonic Self-Organization Research Group, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Rui Chen
- Embryonic Self-Organization Research Group, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Niraimathi Govindasamy
- Embryonic Self-Organization Research Group, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Heike Brinkmann
- Embryonic Self-Organization Research Group, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Ludmila Kremer
- Transgenic Facility, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Nannette Kuempel-Rink
- Transgenic Facility, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Karina Mildner
- Electron Microscopy Facility, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Dagmar Zeuschner
- Electron Microscopy Facility, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Martin Stehling
- Flow Cytometry Unit, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Marion Dejosez
- Department for Cell, Regenerative and Developmental Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, Huffington Foundation Center for Cell-based Research in Parkinson's Disease, New York, NY, USA
| | - Thomas P Zwaka
- Department for Cell, Regenerative and Developmental Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, Huffington Foundation Center for Cell-based Research in Parkinson's Disease, New York, NY, USA
| | - Hans R Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Karin B Busch
- Institut für Integrative Zellbiologie und Physiologie, University of Münster, Münster, Germany
| | - Juan M Vaquerizas
- Regulatory Genomics Group, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,MRC London Institute of Medical Sciences, London, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - Ivan Bedzhov
- Embryonic Self-Organization Research Group, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| |
Collapse
|
11
|
Wike CL, Guo Y, Tan M, Nakamura R, Shaw DK, Díaz N, Whittaker-Tademy AF, Durand NC, Aiden EL, Vaquerizas JM, Grunwald D, Takeda H, Cairns BR. Chromatin architecture transitions from zebrafish sperm through early embryogenesis. Genome Res 2021; 31:981-994. [PMID: 34006569 PMCID: PMC8168589 DOI: 10.1101/gr.269860.120] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 04/07/2021] [Indexed: 11/25/2022]
Abstract
Chromatin architecture mapping in 3D formats has increased our understanding of how regulatory sequences and gene expression are connected and regulated in a genome. The 3D chromatin genome shows extensive remodeling during embryonic development, and although the cleavage-stage embryos of most species lack structure before zygotic genome activation (pre-ZGA), zebrafish has been reported to have structure. Here, we aimed to determine the chromosomal architecture in paternal/sperm zebrafish gamete cells to discern whether it either resembles or informs early pre-ZGA zebrafish embryo chromatin architecture. First, we assessed the higher-order architecture through advanced low-cell in situ Hi-C. The structure of zebrafish sperm, packaged by histones, lacks topological associated domains and instead displays “hinge-like” domains of ∼150 kb that repeat every 1–2 Mbs, suggesting a condensed repeating structure resembling mitotic chromosomes. The pre-ZGA embryos lacked chromosomal structure, in contrast to prior work, and only developed structure post-ZGA. During post-ZGA, we find chromatin architecture beginning to form at small contact domains of a median length of ∼90 kb. These small contact domains are established at enhancers, including super-enhancers, and chemical inhibition of Ep300a (p300) and Crebbpa (CBP) activity, lowering histone H3K27ac, but not transcription inhibition, diminishes these contacts. Together, this study reveals hinge-like domains in histone-packaged zebrafish sperm chromatin and determines that the initial formation of high-order chromatin architecture in zebrafish embryos occurs after ZGA primarily at enhancers bearing high H3K27ac.
Collapse
Affiliation(s)
- Candice L Wike
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Yixuan Guo
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Mengyao Tan
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Ryohei Nakamura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Dana Klatt Shaw
- Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| | - Noelia Díaz
- Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany
| | - Aneasha F Whittaker-Tademy
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Neva C Durand
- The Center for Genome Architecture, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, Texas 77005, USA.,Center for Theoretical Biological Physics, Rice University, Houston, Texas 77030, USA
| | - Juan M Vaquerizas
- Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany.,MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - David Grunwald
- Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Bradley R Cairns
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| |
Collapse
|
12
|
Avgustinova A, Laudanna C, Pascual-García M, Rovira Q, Djurec M, Castellanos A, Urdiroz-Urricelqui U, Marchese D, Prats N, Van Keymeulen A, Heyn H, Vaquerizas JM, Benitah SA. Repression of endogenous retroviruses prevents antiviral immune response and is required for mammary gland development. Cell Stem Cell 2021; 28:1790-1804.e8. [PMID: 34010627 DOI: 10.1016/j.stem.2021.04.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 01/18/2021] [Accepted: 04/26/2021] [Indexed: 10/21/2022]
Abstract
The role of heterochromatin in cell fate specification during development is unclear. We demonstrate that loss of the lysine 9 of histone H3 (H3K9) methyltransferase G9a in the mammary epithelium results in de novo chromatin opening, aberrant formation of the mammary ductal tree, impaired stem cell potential, disrupted intraductal polarity, and loss of tissue function. G9a loss derepresses long terminal repeat (LTR) retroviral sequences (predominantly the ERVK family). Transcriptionally activated endogenous retroviruses generate double-stranded DNA (dsDNA) that triggers an antiviral innate immune response, and knockdown of the cytosolic dsDNA sensor Aim2 in G9a knockout (G9acKO) mammary epithelium rescues mammary ductal invasion. Mammary stem cell transplantation into immunocompromised or G9acKO-conditioned hosts shows partial dependence of the G9acKO mammary morphological defects on the inflammatory milieu of the host mammary fat pad. Thus, altering the chromatin accessibility of retroviral elements disrupts mammary gland development and stem cell activity through both cell-autonomous and non-autonomous mechanisms.
Collapse
Affiliation(s)
- Alexandra Avgustinova
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
| | - Carmelo Laudanna
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Mónica Pascual-García
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Quirze Rovira
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Magdolna Djurec
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Andres Castellanos
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Uxue Urdiroz-Urricelqui
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Domenica Marchese
- CNAG-CRG, Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Neus Prats
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | | | - Holger Heyn
- CNAG-CRG, Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Juan M Vaquerizas
- Max Planck Institute for Molecular Biomedicine, Münster, Germany; MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Salvador Aznar Benitah
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
| |
Collapse
|
13
|
D'Orazio FM, Balwierz PJ, González AJ, Guo Y, Hernández-Rodríguez B, Wheatley L, Jasiulewicz A, Hadzhiev Y, Vaquerizas JM, Cairns B, Lenhard B, Müller F. Germ cell differentiation requires Tdrd7-dependent chromatin and transcriptome reprogramming marked by germ plasm relocalization. Dev Cell 2021; 56:641-656.e5. [PMID: 33651978 PMCID: PMC7957325 DOI: 10.1016/j.devcel.2021.02.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 10/25/2020] [Accepted: 02/03/2021] [Indexed: 02/09/2023]
Abstract
In many animal models, primordial germ cell (PGC) development depends on maternally deposited germ plasm, which prevents somatic cell fate. Here, we show that PGCs respond to regulatory information from the germ plasm in two distinct phases using two distinct mechanisms in zebrafish. We demonstrate that PGCs commence zygotic genome activation together with the somatic blastocysts with no demonstrable differences in transcriptional and chromatin opening. Unexpectedly, both PGC and somatic blastocysts activate germ-cell-specific genes, which are only stabilized in PGCs by cytoplasmic germ plasm determinants. Disaggregated perinuclear relocalization of germ plasm during PGC migration is regulated by the germ plasm determinant Tdrd7 and is coupled to dramatic divergence between PGC and somatic transcriptomes. This transcriptional divergence relies on PGC-specific cis-regulatory elements characterized by promoter-proximal distribution. We show that Tdrd7-dependent reconfiguration of chromatin accessibility is required for elaboration of PGC fate but not for PGC migration. No evidence for transcriptional activation delay in zebrafish PGCs Germ-plasm-associated post-transcriptional divergence during ZGA Epigenetic reprogramming marks onset of PGC migration Epigenetic reprogramming in PGCs relies on Tdrd7, coupled to germ plasm relocalization
Collapse
Affiliation(s)
- Fabio M D'Orazio
- Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK; MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK; Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London, UK
| | - Piotr J Balwierz
- Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK; MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK; Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London, UK
| | - Ada Jimenez González
- Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Yixuan Guo
- Department of Oncological Sciences and Huntsman Cancer Institute, Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | | | - Lucy Wheatley
- Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Aleksandra Jasiulewicz
- Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Yavor Hadzhiev
- Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Juan M Vaquerizas
- MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK; Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, Muenster, Germany
| | - Bradley Cairns
- Department of Oncological Sciences and Huntsman Cancer Institute, Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Boris Lenhard
- MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK; Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London, UK.
| | - Ferenc Müller
- Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
| |
Collapse
|
14
|
Kruse K, Hug CB, Vaquerizas JM. FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data. Genome Biol 2020; 21:303. [PMID: 33334380 PMCID: PMC7745377 DOI: 10.1186/s13059-020-02215-9] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 11/30/2020] [Indexed: 01/01/2023] Open
Abstract
Chromosome conformation capture data, particularly from high-throughput approaches such as Hi-C, are typically very complex to analyse. Existing analysis tools are often single-purpose, or limited in compatibility to a small number of data formats, frequently making Hi-C analyses tedious and time-consuming. Here, we present FAN-C, an easy-to-use command-line tool and powerful Python API with a broad feature set covering matrix generation, analysis, and visualisation for C-like data ( https://github.com/vaquerizaslab/fanc ). Due to its compatibility with the most prevalent Hi-C storage formats, FAN-C can be used in combination with a large number of existing analysis tools, thus greatly simplifying Hi-C matrix analysis.
Collapse
Affiliation(s)
- Kai Kruse
- Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, 48149, Muenster, Germany
| | - Clemens B Hug
- Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, 48149, Muenster, Germany
| | - Juan M Vaquerizas
- Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, 48149, Muenster, Germany.
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK.
| |
Collapse
|
15
|
Takayama N, Murison A, Takayanagi SI, Arlidge C, Zhou S, Garcia-Prat L, Chan-Seng-Yue M, Zandi S, Gan OI, Boutzen H, Kaufmann KB, Trotman-Grant A, Schoof E, Kron K, Díaz N, Lee JJY, Medina T, De Carvalho DD, Taylor MD, Vaquerizas JM, Xie SZ, Dick JE, Lupien M. The Transition from Quiescent to Activated States in Human Hematopoietic Stem Cells Is Governed by Dynamic 3D Genome Reorganization. Cell Stem Cell 2020; 28:488-501.e10. [PMID: 33242413 DOI: 10.1016/j.stem.2020.11.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 09/17/2020] [Accepted: 11/03/2020] [Indexed: 01/06/2023]
Abstract
Lifelong blood production requires long-term hematopoietic stem cells (LT-HSCs), marked by stemness states involving quiescence and self-renewal, to transition into activated short-term HSCs (ST-HSCs) with reduced stemness. As few transcriptional changes underlie this transition, we used single-cell and bulk assay for transposase-accessible chromatin sequencing (ATAC-seq) on human HSCs and hematopoietic stem and progenitor cell (HSPC) subsets to uncover chromatin accessibility signatures, one including LT-HSCs (LT/HSPC signature) and another excluding LT-HSCs (activated HSPC [Act/HSPC] signature). These signatures inversely correlated during early hematopoietic commitment and differentiation. The Act/HSPC signature contains CCCTC-binding factor (CTCF) binding sites mediating 351 chromatin interactions engaged in ST-HSCs, but not LT-HSCs, enclosing multiple stemness pathway genes active in LT-HSCs and repressed in ST-HSCs. CTCF silencing derepressed stemness genes, restraining quiescent LT-HSCs from transitioning to activated ST-HSCs. Hence, 3D chromatin interactions centrally mediated by CTCF endow a gatekeeper function that governs the earliest fate transitions HSCs make by coordinating disparate stemness pathways linked to quiescence and self-renewal.
Collapse
Affiliation(s)
- Naoya Takayama
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Regenerative Medicine, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan
| | - Alex Murison
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Shin-Ichiro Takayanagi
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Cell Therapy Project, R&D Division, Kirin Holdings Company, Limited, Kanagawa 236-0004, Japan
| | - Christopher Arlidge
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Stanley Zhou
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Laura Garcia-Prat
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | | | - Sasan Zandi
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Olga I Gan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Héléna Boutzen
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Kerstin B Kaufmann
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Aaron Trotman-Grant
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Erwin Schoof
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Ken Kron
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Noelia Díaz
- Max Planck Institute for Molecular Biomedicine, Munster 48149, Germany
| | - John J Y Lee
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Tiago Medina
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Daniel D De Carvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Michael D Taylor
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1X8, Canada; Division of Neurosurgery, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Juan M Vaquerizas
- Max Planck Institute for Molecular Biomedicine, Munster 48149, Germany
| | - Stephanie Z Xie
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada.
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada.
| |
Collapse
|
16
|
Galan S, Machnik N, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nat Genet 2020; 52:1247-1255. [PMID: 33077914 PMCID: PMC7610641 DOI: 10.1038/s41588-020-00712-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [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: 07/23/2018] [Accepted: 09/04/2020] [Indexed: 12/11/2022]
Abstract
Dynamic changes in the three-dimensional (3D) organization of chromatin are associated with central biological processes, such as transcription, replication and development. Therefore, the comprehensive identification and quantification of these changes is fundamental to understanding of evolutionary and regulatory mechanisms. Here, we present Comparison of Hi-C Experiments using Structural Similarity (CHESS), an algorithm for the comparison of chromatin contact maps and automatic differential feature extraction. We demonstrate the robustness of CHESS to experimental variability and showcase its biological applications on (1) interspecies comparisons of syntenic regions in human and mouse models; (2) intraspecies identification of conformational changes in Zelda-depleted Drosophila embryos; (3) patient-specific aberrant chromatin conformation in a diffuse large B-cell lymphoma sample; and (4) the systematic identification of chromatin contact differences in high-resolution Capture-C data. In summary, CHESS is a computationally efficient method for the comparison and classification of changes in chromatin contact data.
Collapse
Affiliation(s)
- Silvia Galan
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
- National Centre for Genomic Analysis, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Nick Machnik
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Kai Kruse
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Noelia Díaz
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Marc A Marti-Renom
- National Centre for Genomic Analysis, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Pompeu Fabra University, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| | - Juan M Vaquerizas
- Max Planck Institute for Molecular Biomedicine, Münster, Germany.
- Medical Research Council London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK.
| |
Collapse
|
17
|
Rhodes JDP, Feldmann A, Hernández-Rodríguez B, Díaz N, Brown JM, Fursova NA, Blackledge NP, Prathapan P, Dobrinic P, Huseyin MK, Szczurek A, Kruse K, Nasmyth KA, Buckle VJ, Vaquerizas JM, Klose RJ. Cohesin Disrupts Polycomb-Dependent Chromosome Interactions in Embryonic Stem Cells. Cell Rep 2020; 30:820-835.e10. [PMID: 31968256 PMCID: PMC6988126 DOI: 10.1016/j.celrep.2019.12.057] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 11/25/2019] [Accepted: 12/16/2019] [Indexed: 12/21/2022] Open
Abstract
How chromosome organization is related to genome function remains poorly understood. Cohesin, loop extrusion, and CCCTC-binding factor (CTCF) have been proposed to create topologically associating domains (TADs) to regulate gene expression. Here, we examine chromosome conformation in embryonic stem cells lacking cohesin and find, as in other cell types, that cohesin is required to create TADs and regulate A/B compartmentalization. However, in the absence of cohesin, we identify a series of long-range chromosomal interactions that persist. These correspond to regions of the genome occupied by the polycomb repressive system and are dependent on PRC1. Importantly, we discover that cohesin counteracts these polycomb-dependent interactions, but not interactions between super-enhancers. This disruptive activity is independent of CTCF and insulation and appears to modulate gene repression by the polycomb system. Therefore, we discover that cohesin disrupts polycomb-dependent chromosome interactions to modulate gene expression in embryonic stem cells.
Collapse
Affiliation(s)
- James D P Rhodes
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Angelika Feldmann
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | | | - Noelia Díaz
- Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, 48149 Muenster, Germany
| | - Jill M Brown
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, UK
| | - Nadezda A Fursova
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Neil P Blackledge
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Praveen Prathapan
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Paula Dobrinic
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Miles K Huseyin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Aleksander Szczurek
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Kai Kruse
- Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, 48149 Muenster, Germany
| | - Kim A Nasmyth
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Veronica J Buckle
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, UK
| | - Juan M Vaquerizas
- Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, 48149 Muenster, Germany; MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK.
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
| |
Collapse
|
18
|
Luxán G, Stewen J, Díaz N, Kato K, Maney SK, Aravamudhan A, Berkenfeld F, Nagelmann N, Drexler HC, Zeuschner D, Faber C, Schillers H, Hermann S, Wiseman J, Vaquerizas JM, Pitulescu ME, Adams RH. Endothelial EphB4 maintains vascular integrity and transport function in adult heart. eLife 2019; 8:45863. [PMID: 31782728 PMCID: PMC6884395 DOI: 10.7554/elife.45863] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 11/15/2019] [Indexed: 12/17/2022] Open
Abstract
The homeostasis of heart and other organs relies on the appropriate provision of nutrients and functional specialization of the local vasculature. Here, we have used mouse genetics, imaging and cell biology approaches to investigate how homeostasis in the adult heart is controlled by endothelial EphB4 and its ligand ephrin-B2, which are known regulators of vascular morphogenesis and arteriovenous differentiation during development. We show that inducible and endothelial cell-specific inactivation of Ephb4 in adult mice is compatible with survival, but leads to rupturing of cardiac capillaries, cardiomyocyte hypertrophy, and pathological cardiac remodeling. In contrast, EphB4 is not required for integrity and homeostasis of capillaries in skeletal muscle. Our analysis of mutant mice and cultured endothelial cells shows that EphB4 controls the function of caveolae, cell-cell adhesion under mechanical stress and lipid transport. We propose that EphB4 maintains critical functional properties of the adult cardiac vasculature and thereby prevents dilated cardiomyopathy-like defects.
Collapse
Affiliation(s)
- Guillermo Luxán
- Department of Tissue Morphogenesis, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Jonas Stewen
- Department of Tissue Morphogenesis, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Noelia Díaz
- Regulatory Genomics Laboratory, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Katsuhiro Kato
- Department of Tissue Morphogenesis, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Sathish K Maney
- Department of Tissue Morphogenesis, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Anusha Aravamudhan
- Department of Tissue Morphogenesis, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Frank Berkenfeld
- Department of Tissue Morphogenesis, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Nina Nagelmann
- Department of Clinical Radiology, University Hospital Münster, Münster, Germany
| | - Hannes Ca Drexler
- Bioanalytical Mass Spectrometry Unit, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Dagmar Zeuschner
- Electron Microscopy Unit, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Cornelius Faber
- Department of Clinical Radiology, University Hospital Münster, Münster, Germany
| | - Hermann Schillers
- Institute for Physiology II, University of Münster, Münster, Germany
| | - Sven Hermann
- European Institute for Molecular Imaging, University of Münster, Münster, Germany
| | - John Wiseman
- Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Juan M Vaquerizas
- Regulatory Genomics Laboratory, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Mara E Pitulescu
- Department of Tissue Morphogenesis, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Ralf H Adams
- Department of Tissue Morphogenesis, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Faculty of Medicine, University of Münster, Münster, Germany
| |
Collapse
|
19
|
Abstract
The three-dimensional organisation of the genome plays a crucial role in developmental gene regulation. In recent years, techniques to investigate this organisation have become more accessible to labs worldwide due to improvements in protocols and decreases in the cost of high-throughput sequencing. However, the resulting datasets are complex and can be challenging to analyse and interpret. Here, we provide a guide to visualisation approaches that can aid the interpretation of such datasets and the communication of biological results.
Collapse
Affiliation(s)
- Elizabeth Ing-Simmons
- Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, DE-48149 Muenster, Germany
| | - Juan M Vaquerizas
- Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, DE-48149 Muenster, Germany
| |
Collapse
|
20
|
Abstract
The 3D structure of chromatin in the nucleus is important for the regulation of gene expression and the correct deployment of developmental programs. The differentiation of germ cells and early embryonic development (when the zygotic genome is activated and transcription is taking place for the first time) are accompanied by dramatic changes in gene expression and the epigenetic landscape. Recent studies used Hi-C to investigate the 3D chromatin organization during these developmental transitions, uncovering remarkable remodeling of the 3D genome. Here, we highlight the changes described so far and discuss some of the implications that these findings have for our understanding of the mechanisms and functionality of 3D chromatin architecture.
Collapse
Affiliation(s)
- Clemens B Hug
- Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, 48149 Muenster, Germany
| | - Juan M Vaquerizas
- Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, 48149 Muenster, Germany. https://twitter.com/vaquerizasjm
| |
Collapse
|
21
|
Abstract
Investigating the three-dimensional architecture of chromatin offers invaluable insight into the mechanisms of gene regulation. Here, we describe a protocol for performing the chromatin conformation capture technique in situ Hi-C on staged Drosophila melanogaster embryo populations. The result is a sequencing library that allows the mapping of all chromatin interactions that occur in the nucleus in a single experiment. Embryo sorting is done manually using a fluorescent stereo microscope and a transgenic fly line containing a nuclear marker. Using this technique, embryo populations from each nuclear division cycle, and with defined cell cycle status, can be obtained with very high purity. The protocol may also be adapted to sort older embryos beyond gastrulation. Sorted embryos are used as inputs for in situ Hi-C. All experiments, including sequencing library preparation, can be completed in five days. The protocol has low input requirements and works reliably using 20 blastoderm stage embryos as input material. The end result is a sequencing library for next generation sequencing. After sequencing, the data can be processed into genome-wide chromatin interaction maps that can be analyzed using a wide range of available tools to gain information about topologically associating domain (TAD) structure, chromatin loops, and chromatin compartments during Drosophila development.
Collapse
|
22
|
Mallik M, Catinozzi M, Hug CB, Zhang L, Wagner M, Bussmann J, Bittern J, Mersmann S, Klämbt C, Drexler HCA, Huynen MA, Vaquerizas JM, Storkebaum E. Xrp1 genetically interacts with the ALS-associated FUS orthologue caz and mediates its toxicity. J Cell Biol 2018; 217:3947-3964. [PMID: 30209068 PMCID: PMC6219715 DOI: 10.1083/jcb.201802151] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 07/13/2018] [Accepted: 08/14/2018] [Indexed: 12/11/2022] Open
Abstract
Mallik et al. identify Xrp1 as a nuclear chromatin-binding protein involved in gene expression regulation that mediates phenotypes induced by loss of function of cabeza (caz), the Drosophila melanogaster orthologue of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) protein FUS. Knockdown of Xrp1 in motor neurons rescues phenotypes induced by ALS-mutant FUS. Cabeza (caz) is the single Drosophila melanogaster orthologue of the human FET proteins FUS, TAF15, and EWSR1, which have been implicated in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia. In this study, we identified Xrp1, a nuclear chromatin-binding protein, as a key modifier of caz mutant phenotypes. Xrp1 expression was strongly up-regulated in caz mutants, and Xrp1 heterozygosity rescued their motor defects and life span. Interestingly, selective neuronal Xrp1 knockdown was sufficient to rescue, and neuronal Xrp1 overexpression phenocopied caz mutant phenotypes. The caz/Xrp1 genetic interaction depended on the functionality of the AT-hook DNA-binding domain in Xrp1, and the majority of Xrp1-interacting proteins are involved in gene expression regulation. Consistently, caz mutants displayed gene expression dysregulation, which was mitigated by Xrp1 heterozygosity. Finally, Xrp1 knockdown substantially rescued the motor deficits and life span of flies expressing ALS mutant FUS in motor neurons, implicating gene expression dysregulation in ALS-FUS pathogenesis.
Collapse
Affiliation(s)
- Moushami Mallik
- Molecular Neurogenetics Laboratory, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Faculty of Medicine, University of Münster, Münster, Germany.,Department of Molecular Neurobiology, Donders Institute for Brain, Cognition and Behaviour and Radboud University, Nijmegen, Netherlands
| | - Marica Catinozzi
- Molecular Neurogenetics Laboratory, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Faculty of Medicine, University of Münster, Münster, Germany.,Department of Molecular Neurobiology, Donders Institute for Brain, Cognition and Behaviour and Radboud University, Nijmegen, Netherlands
| | - Clemens B Hug
- Regulatory Genomics, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Li Zhang
- Molecular Neurogenetics Laboratory, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Faculty of Medicine, University of Münster, Münster, Germany
| | - Marina Wagner
- Molecular Neurogenetics Laboratory, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Faculty of Medicine, University of Münster, Münster, Germany
| | - Julia Bussmann
- Molecular Neurogenetics Laboratory, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Faculty of Medicine, University of Münster, Münster, Germany
| | - Jonas Bittern
- Institute of Neuro and Behavioural Biology, University of Münster, Münster, Germany
| | - Sina Mersmann
- Molecular Neurogenetics Laboratory, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Faculty of Medicine, University of Münster, Münster, Germany
| | - Christian Klämbt
- Institute of Neuro and Behavioural Biology, University of Münster, Münster, Germany
| | - Hannes C A Drexler
- Bioanalytical Mass Spectrometry Facility, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Martijn A Huynen
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Juan M Vaquerizas
- Regulatory Genomics, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Erik Storkebaum
- Molecular Neurogenetics Laboratory, Max Planck Institute for Molecular Biomedicine, Münster, Germany .,Faculty of Medicine, University of Münster, Münster, Germany.,Department of Molecular Neurobiology, Donders Institute for Brain, Cognition and Behaviour and Radboud University, Nijmegen, Netherlands
| |
Collapse
|
23
|
Hug CB, Grimaldi AG, Kruse K, Vaquerizas JM. Chromatin Architecture Emerges during Zygotic Genome Activation Independent of Transcription. Cell 2017; 169:216-228.e19. [PMID: 28388407 DOI: 10.1016/j.cell.2017.03.024] [Citation(s) in RCA: 294] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 02/21/2017] [Accepted: 03/16/2017] [Indexed: 01/18/2023]
Abstract
Chromatin architecture is fundamental in regulating gene expression. To investigate when spatial genome organization is first established during development, we examined chromatin conformation during Drosophila embryogenesis and observed the emergence of chromatin architecture within a tight time window that coincides with the onset of transcription activation in the zygote. Prior to zygotic genome activation, the genome is mostly unstructured. Early expressed genes serve as nucleation sites for topologically associating domain (TAD) boundaries. Activation of gene expression coincides with the establishment of TADs throughout the genome and co-localization of housekeeping gene clusters, which remain stable in subsequent stages of development. However, the appearance of TAD boundaries is independent of transcription and requires the transcription factor Zelda for locus-specific TAD boundary insulation. These results offer insight into when spatial organization of the genome emerges and identify a key factor that helps trigger this architecture.
Collapse
Affiliation(s)
- Clemens B Hug
- Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, 48149 Muenster, Germany
| | - Alexis G Grimaldi
- Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, 48149 Muenster, Germany
| | - Kai Kruse
- Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, 48149 Muenster, Germany
| | - Juan M Vaquerizas
- Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, 48149 Muenster, Germany.
| |
Collapse
|
24
|
Lecanda A, Nilges BS, Sharma P, Nedialkova DD, Schwarz J, Vaquerizas JM, Leidel SA. Dual randomization of oligonucleotides to reduce the bias in ribosome-profiling libraries. Methods 2016; 107:89-97. [PMID: 27450428 PMCID: PMC5024760 DOI: 10.1016/j.ymeth.2016.07.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 06/27/2016] [Accepted: 07/18/2016] [Indexed: 12/31/2022] Open
Abstract
Protein translation is at the heart of cellular metabolism and its in-depth characterization is key for many lines of research. Recently, ribosome profiling became the state-of-the-art method to quantitatively characterize translation dynamics at a transcriptome-wide level. However, the strategy of library generation affects its outcomes. Here, we present a modified ribosome-profiling protocol starting from yeast, human cells and vertebrate brain tissue. We use a DNA linker carrying four randomized positions at its 5′ end and a reverse-transcription (RT) primer with three randomized positions to reduce artifacts during library preparation. The use of seven randomized nucleotides allows to efficiently detect library-generation artifacts. We find that the effect of polymerase chain reaction (PCR) artifacts is relatively small for global analyses when sufficient input material is used. However, when input material is limiting, our strategy improves the sensitivity of gene-specific analyses. Furthermore, randomized nucleotides alleviate the skewed frequency of specific sequences at the 3′ end of ribosome-protected fragments (RPFs) likely resulting from ligase specificity. Finally, strategies that rely on dual ligation show a high degree of gene-coverage variation. Taken together, our approach helps to remedy two of the main problems associated with ribosome-profiling data. This will facilitate the analysis of translational dynamics and increase our understanding of the influence of RNA modifications on translation.
Collapse
Affiliation(s)
- Aarón Lecanda
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Von-Esmarch-Strasse 54, 48149 Muenster, Germany; Muenster Graduate School of Evolution, University of Muenster, 48149 Muenster, Germany; Cells-in-Motion Cluster of Excellence, University of Muenster, 48149 Muenster, Germany; Max Planck Research Group for Regulatory Genomics, Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, 48149 Muenster, Germany
| | - Benedikt S Nilges
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Von-Esmarch-Strasse 54, 48149 Muenster, Germany; Cells-in-Motion Cluster of Excellence, University of Muenster, 48149 Muenster, Germany
| | - Puneet Sharma
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Von-Esmarch-Strasse 54, 48149 Muenster, Germany; Cells-in-Motion Cluster of Excellence, University of Muenster, 48149 Muenster, Germany
| | - Danny D Nedialkova
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Von-Esmarch-Strasse 54, 48149 Muenster, Germany; Cells-in-Motion Cluster of Excellence, University of Muenster, 48149 Muenster, Germany
| | - Juliane Schwarz
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Von-Esmarch-Strasse 54, 48149 Muenster, Germany; Cells-in-Motion Cluster of Excellence, University of Muenster, 48149 Muenster, Germany
| | - Juan M Vaquerizas
- Muenster Graduate School of Evolution, University of Muenster, 48149 Muenster, Germany; Cells-in-Motion Cluster of Excellence, University of Muenster, 48149 Muenster, Germany; Max Planck Research Group for Regulatory Genomics, Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, 48149 Muenster, Germany
| | - Sebastian A Leidel
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Von-Esmarch-Strasse 54, 48149 Muenster, Germany; Muenster Graduate School of Evolution, University of Muenster, 48149 Muenster, Germany; Cells-in-Motion Cluster of Excellence, University of Muenster, 48149 Muenster, Germany.
| |
Collapse
|
25
|
Kruse K, Hug CB, Hernández-Rodríguez B, Vaquerizas JM. TADtool: visual parameter identification for TAD-calling algorithms. Bioinformatics 2016; 32:3190-3192. [PMID: 27318199 PMCID: PMC5048066 DOI: 10.1093/bioinformatics/btw368] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 06/06/2016] [Indexed: 11/13/2022] Open
Abstract
Summary: Eukaryotic genomes are hierarchically organized into topologically associating domains (TADs). The computational identification of these domains and their associated properties critically depends on the choice of suitable parameters of TAD-calling algorithms. To reduce the element of trial-and-error in parameter selection, we have developed TADtool: an interactive plot to find robust TAD-calling parameters with immediate visual feedback. TADtool allows the direct export of TADs called with a chosen set of parameters for two of the most common TAD calling algorithms: directionality and insulation index. It can be used as an intuitive, standalone application or as a Python package for maximum flexibility. Availability and implementation: TADtool is available as a Python package from GitHub (https://github.com/vaquerizaslab/tadtool) or can be installed directly via PyPI, the Python package index (tadtool). Contact:kai.kruse@mpi-muenster.mpg.de, jmv@mpi-muenster.mpg.de Supplementary information:Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Kai Kruse
- Max Planck Institute for Molecular Biomedicine, Münster 48149, Germany
| | - Clemens B Hug
- Max Planck Institute for Molecular Biomedicine, Münster 48149, Germany
| | | | - Juan M Vaquerizas
- Max Planck Institute for Molecular Biomedicine, Münster 48149, Germany
| |
Collapse
|
26
|
Abstract
Transcriptional regulation is one the most basic mechanisms for controlling gene expression. Over the past few years, much research has been devoted to understanding the interplay between transcription factors, histone modifications and associated enzymes required to achieve this control. However, it is becoming increasingly apparent that the three-dimensional conformation of chromatin in the interphase nucleus also plays a critical role in regulating transcription. Chromatin localisation in the nucleus is highly organised, and early studies described strong interactions between chromatin and sub-nuclear components. Single-gene studies have shed light on how chromosomal architecture affects gene expression. Lately, this has been complemented by whole-genome studies that have determined the global chromatin conformation of living cells in interphase. These studies have greatly expanded our understanding of nuclear architecture and its interplay with different physiological processes. Despite these advances, however, most of the mechanisms used to impose the three-dimensional chromatin structure remain unknown. Here, we summarise the different levels of chromatin organisation in the nucleus and discuss current efforts into characterising the mechanisms that govern it.
Collapse
|
27
|
Vaquerizas JM, Cavalli FMG, Conrad T, Akhtar A, Luscombe NM. Response to Comments on "Drosophila Dosage Compensation Involves Enhanced Pol II Recruitment to Male X-Linked Promoters". Science 2013; 340:273. [PMID: 23599465 DOI: 10.1126/science.1232874] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Ferrari et al. and Straub and Becker wrongly claim that an error in the computational analysis calls into question the conclusions of Conrad et al. All the available evidence, including the reanalyzed genomic data, show that the conclusions and the key message of the study remain unchanged: RNA polymerase II recruitment to male X-linked promoters is an important regulatory step during dosage compensation.
Collapse
Affiliation(s)
- Juan M Vaquerizas
- Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, 48149 Muenster, Germany
| | | | | | | | | |
Collapse
|
28
|
Jolma A, Yan J, Whitington T, Toivonen J, Nitta KR, Rastas P, Morgunova E, Enge M, Taipale M, Wei G, Palin K, Vaquerizas JM, Vincentelli R, Luscombe NM, Hughes TR, Lemaire P, Ukkonen E, Kivioja T, Taipale J. DNA-binding specificities of human transcription factors. Cell 2013; 152:327-39. [PMID: 23332764 DOI: 10.1016/j.cell.2012.12.009] [Citation(s) in RCA: 855] [Impact Index Per Article: 77.7] [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] [Received: 05/25/2012] [Revised: 08/18/2012] [Accepted: 12/03/2012] [Indexed: 12/23/2022]
Abstract
Although the proteins that read the gene regulatory code, transcription factors (TFs), have been largely identified, it is not well known which sequences TFs can recognize. We have analyzed the sequence-specific binding of human TFs using high-throughput SELEX and ChIP sequencing. A total of 830 binding profiles were obtained, describing 239 distinctly different binding specificities. The models represent the majority of human TFs, approximately doubling the coverage compared to existing systematic studies. Our results reveal additional specificity determinants for a large number of factors for which a partial specificity was known, including a commonly observed A- or T-rich stretch that flanks the core motifs. Global analysis of the data revealed that homodimer orientation and spacing preferences, and base-stacking interactions, have a larger role in TF-DNA binding than previously appreciated. We further describe a binding model incorporating these features that is required to understand binding of TFs to DNA.
Collapse
Affiliation(s)
- Arttu Jolma
- Science for Life Center, Department of Biosciences and Nutrition, Karolinska Institutet, 141 83 Huddinge, Sweden
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Conrad T, Cavalli FMG, Vaquerizas JM, Luscombe NM, Akhtar A. Drosophila dosage compensation involves enhanced Pol II recruitment to male X-linked promoters. Science 2012; 337:742-6. [PMID: 22821985 DOI: 10.1126/science.1221428] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [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] [Indexed: 12/31/2022]
Abstract
Through hyperacetylation of histone H4 lysine 16 (H4K16), the male-specific lethal (MSL) complex in Drosophila approximately doubles transcription from the single male X chromosome in order to match X-linked expression in females and expression from diploid autosomes. By obtaining accurate measurements of RNA polymerase II (Pol II) occupancies and short promoter-proximal RNA production, we detected a consistent, genome-scale increase in Pol II activity at the promoters of male X-linked genes. Moreover, we found that enhanced Pol II recruitment to male X-linked promoters is largely dependent on the MSL complex. These observations provide insights into how global modulation of chromatin structure by histone acetylation contributes to the precise control of Pol II function.
Collapse
Affiliation(s)
- Thomas Conrad
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg im Breisgau, Germany
| | | | | | | | | |
Collapse
|
30
|
Reimand J, Aun A, Vilo J, Vaquerizas JM, Sedman J, Luscombe NM. m:Explorer: multinomial regression models reveal positive and negative regulators of longevity in yeast quiescence. Genome Biol 2012; 13:R55. [PMID: 22720667 PMCID: PMC3446321 DOI: 10.1186/gb-2012-13-6-r55] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [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: 02/24/2012] [Accepted: 05/29/2012] [Indexed: 01/25/2023] Open
Abstract
We developed m:Explorer for identifying process-specific transcription factors (TFs) from multiple genome-wide sources, including transcriptome, DNA-binding and chromatin data. m:Explorer robustly outperforms similar techniques in finding cell cycle TFs in Saccharomyces cerevisiae. We predicted and experimentally tested regulators of quiescence (G0), a model of ageing, over a six-week time-course. We validated nine of top-12 predictions as novel G0 TFs, including Δmga2, Δcst6, Δbas1 with higher viability and G0-essential TFs Tup1, Swi3. Pathway analysis associates longevity to reduced growth, reprogrammed metabolism and cell wall remodeling. m:Explorer (http://biit.cs.ut.ee/mexplorer/) is instrumental in interrogating eukaryotic regulatory systems using heterogeneous data.
Collapse
Affiliation(s)
- Jüri Reimand
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
- University of Tartu, Institute of Computer Science, Liivi 2, Tartu 50409, Estonia
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada
| | - Anu Aun
- University of Tartu, Institute of Molecular and Cell Biology, Riia 23, Tartu 51010, Estonia
| | - Jaak Vilo
- University of Tartu, Institute of Computer Science, Liivi 2, Tartu 50409, Estonia
| | - Juan M Vaquerizas
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Juhan Sedman
- University of Tartu, Institute of Molecular and Cell Biology, Riia 23, Tartu 51010, Estonia
| | - Nicholas M Luscombe
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
- EMBL-Heidelberg Gene Expression Unit, Meyerhofstrasse 1, Heidelberg D-69117, Germany
| |
Collapse
|
31
|
Lam KC, Mühlpfordt F, Vaquerizas JM, Raja SJ, Holz H, Luscombe NM, Manke T, Akhtar A. The NSL complex regulates housekeeping genes in Drosophila. PLoS Genet 2012; 8:e1002736. [PMID: 22723752 PMCID: PMC3375229 DOI: 10.1371/journal.pgen.1002736] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [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: 10/18/2011] [Accepted: 04/13/2012] [Indexed: 11/18/2022] Open
Abstract
MOF is the major histone H4 lysine 16-specific (H4K16) acetyltransferase in mammals and Drosophila. In flies, it is involved in the regulation of X-chromosomal and autosomal genes as part of the MSL and the NSL complexes, respectively. While the function of the MSL complex as a dosage compensation regulator is fairly well understood, the role of the NSL complex in gene regulation is still poorly characterized. Here we report a comprehensive ChIP-seq analysis of four NSL complex members (NSL1, NSL3, MBD-R2, and MCRS2) throughout the Drosophila melanogaster genome. Strikingly, the majority (85.5%) of NSL-bound genes are constitutively expressed across different cell types. We find that an increased abundance of the histone modifications H4K16ac, H3K4me2, H3K4me3, and H3K9ac in gene promoter regions is characteristic of NSL-targeted genes. Furthermore, we show that these genes have a well-defined nucleosome free region and broad transcription initiation patterns. Finally, by performing ChIP-seq analyses of RNA polymerase II (Pol II) in NSL1- and NSL3-depleted cells, we demonstrate that both NSL proteins are required for efficient recruitment of Pol II to NSL target gene promoters. The observed Pol II reduction coincides with compromised binding of TBP and TFIIB to target promoters, indicating that the NSL complex is required for optimal recruitment of the pre-initiation complex on target genes. Moreover, genes that undergo the most dramatic loss of Pol II upon NSL knockdowns tend to be enriched in DNA Replication-related Element (DRE). Taken together, our findings show that the MOF-containing NSL complex acts as a major regulator of housekeeping genes in flies by modulating initiation of Pol II transcription.
Collapse
Affiliation(s)
- Kin Chung Lam
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Friederike Mühlpfordt
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Juan M. Vaquerizas
- EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | | | - Herbert Holz
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Nicholas M. Luscombe
- EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
- Okinawa Institute of Science and Technology, Kunigami-gun, Okinawa, Japan
| | - Thomas Manke
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Asifa Akhtar
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| |
Collapse
|
32
|
Conrad T, Cavalli FMG, Holz H, Hallacli E, Kind J, Ilik I, Vaquerizas JM, Luscombe NM, Akhtar A. The MOF chromobarrel domain controls genome-wide H4K16 acetylation and spreading of the MSL complex. Dev Cell 2012; 22:610-24. [PMID: 22421046 DOI: 10.1016/j.devcel.2011.12.016] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [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: 06/19/2011] [Revised: 11/07/2011] [Accepted: 12/16/2011] [Indexed: 12/22/2022]
Abstract
The histone H4 lysine 16 (H4K16)-specific acetyltransferase MOF is part of two distinct complexes involved in X chromosome dosage compensation and autosomal transcription regulation. Here we show that the MOF chromobarrel domain is essential for H4K16 acetylation throughout the Drosophila genome and is required for spreading of the male-specific lethal (MSL) complex on the X chromosome. The MOF chromobarrel domain directly interacts with nucleic acids and potentiates MOF's enzymatic activity after chromatin binding, making it a unique example of a chromo-like domain directly controlling acetylation activity in vivo. We also show that the Drosophila-specific N terminus of MOF has evolved to perform sex-specific functions. It modulates nucleosome binding and HAT activity and controls MSL complex assembly, thus regulating MOF function in dosage compensation. We propose that MOF has been especially tailored to achieve tight regulation of its enzymatic activity and enable its dual role on X and autosomes.
Collapse
Affiliation(s)
- Thomas Conrad
- Max-Planck-Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Vaquerizas JM, Teichmann SA, Luscombe NM. How do you find transcription factors? Computational approaches to compile and annotate repertoires of regulators for any genome. Methods Mol Biol 2012; 786:3-19. [PMID: 21938617 DOI: 10.1007/978-1-61779-292-2_1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Transcription factors (TFs) play an important role in regulating gene expression. The availability of complete genome sequences and associated functional genomic data offer excellent opportunities to understand the transcriptional regulatory system of an entire organism. To do so, however, it is essential to compile a reliable dataset of regulatory components. Here, we review computational methods and publicly accessible resources that help identify TF-coding genes in prokaryotic and eukaryotic genomes. Since the regulatory functions of most TFs remain unknown, we also discuss approaches for combining diverse genomic datasets that will help elucidate their chromosomal organisation, expression, and evolutionary conservation. These analysis methods provide a solid foundation for further investigations of the transcriptional regulatory system.
Collapse
|
34
|
Cavalli FMG, Bourgon R, Huber W, Vaquerizas JM, Luscombe NM. SpeCond: a method to detect condition-specific gene expression. Genome Biol 2011; 12:R101. [PMID: 22008066 PMCID: PMC3333772 DOI: 10.1186/gb-2011-12-10-r101] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Revised: 09/27/2011] [Accepted: 10/18/2011] [Indexed: 01/31/2023] Open
Abstract
Transcriptomic studies routinely measure expression levels across numerous conditions. These datasets allow identification of genes that are specifically expressed in a small number of conditions. However, there are currently no statistically robust methods for identifying such genes. Here we present SpeCond, a method to detect condition-specific genes that outperforms alternative approaches. We apply the method to a dataset of 32 human tissues to determine 2,673 specifically expressed genes. An implementation of SpeCond is freely available as a Bioconductor package at http://www.bioconductor.org/packages/release/bioc/html/SpeCond.html.
Collapse
Affiliation(s)
- Florence M G Cavalli
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK.
| | | | | | | | | |
Collapse
|
35
|
Raja SJ, Charapitsa I, Conrad T, Vaquerizas JM, Gebhardt P, Holz H, Kadlec J, Fraterman S, Luscombe NM, Akhtar A. The nonspecific lethal complex is a transcriptional regulator in Drosophila. Mol Cell 2010; 38:827-41. [PMID: 20620954 DOI: 10.1016/j.molcel.2010.05.021] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [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: 09/02/2009] [Revised: 01/27/2010] [Accepted: 04/06/2010] [Indexed: 01/20/2023]
Abstract
Here, we report the biochemical characterization of the nonspecific lethal (NSL) complex (NSL1, NSL2, NSL3, MCRS2, MBD-R2, and WDS) that associates with the histone acetyltransferase MOF in both Drosophila and mammals. Chromatin immunoprecipitation-Seq analysis revealed association of NSL1 and MCRS2 with the promoter regions of more than 4000 target genes, 70% of these being actively transcribed. This binding is functional, as depletion of MCRS2, MBD-R2, and NSL3 severely affects gene expression genome wide. The NSL complex members bind to their target promoters independently of MOF. However, depletion of MCRS2 affects MOF recruitment to promoters. NSL complex stability is interdependent and relies mainly on the presence of NSL1 and MCRS2. Tethering of NSL3 to a heterologous promoter leads to robust transcription activation and is sensitive to the levels of NSL1, MCRS2, and MOF. Taken together, we conclude that the NSL complex acts as a major transcriptional regulator in Drosophila.
Collapse
Affiliation(s)
- Sunil Jayaramaiah Raja
- Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Jolma A, Kivioja T, Toivonen J, Cheng L, Wei G, Enge M, Taipale M, Vaquerizas JM, Yan J, Sillanpää MJ, Bonke M, Palin K, Talukder S, Hughes TR, Luscombe NM, Ukkonen E, Taipale J. Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. Genome Res 2010; 20:861-73. [PMID: 20378718 PMCID: PMC2877582 DOI: 10.1101/gr.100552.109] [Citation(s) in RCA: 307] [Impact Index Per Article: 21.9] [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: 09/11/2009] [Accepted: 03/22/2010] [Indexed: 01/15/2023]
Abstract
The genetic code-the binding specificity of all transfer-RNAs--defines how protein primary structure is determined by DNA sequence. DNA also dictates when and where proteins are expressed, and this information is encoded in a pattern of specific sequence motifs that are recognized by transcription factors. However, the DNA-binding specificity is only known for a small fraction of the approximately 1400 human transcription factors (TFs). We describe here a high-throughput method for analyzing transcription factor binding specificity that is based on systematic evolution of ligands by exponential enrichment (SELEX) and massively parallel sequencing. The method is optimized for analysis of large numbers of TFs in parallel through the use of affinity-tagged proteins, barcoded selection oligonucleotides, and multiplexed sequencing. Data are analyzed by a new bioinformatic platform that uses the hundreds of thousands of sequencing reads obtained to control the quality of the experiments and to generate binding motifs for the TFs. The described technology allows higher throughput and identification of much longer binding profiles than current microarray-based methods. In addition, as our method is based on proteins expressed in mammalian cells, it can also be used to characterize DNA-binding preferences of full-length proteins or proteins requiring post-translational modifications. We validate the method by determining binding specificities of 14 different classes of TFs and by confirming the specificities for NFATC1 and RFX3 using ChIP-seq. Our results reveal unexpected dimeric modes of binding for several factors that were thought to preferentially bind DNA as monomers.
Collapse
Affiliation(s)
- Arttu Jolma
- Department of Molecular Medicine, National Public Health Institute (KTL) and Genome-Scale Biology Program, Institute of Biomedicine and High Throughput Center, University of Helsinki, Biomedicum, Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Teemu Kivioja
- Department of Molecular Medicine, National Public Health Institute (KTL) and Genome-Scale Biology Program, Institute of Biomedicine and High Throughput Center, University of Helsinki, Biomedicum, Helsinki, Finland
- Department of Computer Science, FI-00014 University of Helsinki, Helsinki, Finland
| | - Jarkko Toivonen
- Department of Computer Science, FI-00014 University of Helsinki, Helsinki, Finland
| | - Lu Cheng
- Department of Computer Science, FI-00014 University of Helsinki, Helsinki, Finland
| | - Gonghong Wei
- Department of Molecular Medicine, National Public Health Institute (KTL) and Genome-Scale Biology Program, Institute of Biomedicine and High Throughput Center, University of Helsinki, Biomedicum, Helsinki, Finland
| | - Martin Enge
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Mikko Taipale
- Department of Molecular Medicine, National Public Health Institute (KTL) and Genome-Scale Biology Program, Institute of Biomedicine and High Throughput Center, University of Helsinki, Biomedicum, Helsinki, Finland
| | - Juan M. Vaquerizas
- EMBL–European Bioinformatics Institute, Cambridge CB10 1SD, United Kingdom
| | - Jian Yan
- Department of Molecular Medicine, National Public Health Institute (KTL) and Genome-Scale Biology Program, Institute of Biomedicine and High Throughput Center, University of Helsinki, Biomedicum, Helsinki, Finland
| | - Mikko J. Sillanpää
- Department of Mathematics and Statistics, FI-00014 University of Helsinki, Helsinki, Finland
| | - Martin Bonke
- Department of Molecular Medicine, National Public Health Institute (KTL) and Genome-Scale Biology Program, Institute of Biomedicine and High Throughput Center, University of Helsinki, Biomedicum, Helsinki, Finland
| | - Kimmo Palin
- Department of Computer Science, FI-00014 University of Helsinki, Helsinki, Finland
| | - Shaheynoor Talukder
- Department of Molecular Genetics and Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M4T 2J4, Canada
| | - Timothy R. Hughes
- Department of Molecular Genetics and Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M4T 2J4, Canada
| | | | - Esko Ukkonen
- Department of Computer Science, FI-00014 University of Helsinki, Helsinki, Finland
| | - Jussi Taipale
- Department of Molecular Medicine, National Public Health Institute (KTL) and Genome-Scale Biology Program, Institute of Biomedicine and High Throughput Center, University of Helsinki, Biomedicum, Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
37
|
Reimand J, Vaquerizas JM, Todd AE, Vilo J, Luscombe NM. Comprehensive reanalysis of transcription factor knockout expression data in Saccharomyces cerevisiae reveals many new targets. Nucleic Acids Res 2010; 38:4768-77. [PMID: 20385592 PMCID: PMC2919724 DOI: 10.1093/nar/gkq232] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [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: 01/22/2023] Open
Abstract
Transcription factor (TF) perturbation experiments give valuable insights into gene regulation. Genome-scale evidence from microarray measurements may be used to identify regulatory interactions between TFs and targets. Recently, Hu and colleagues published a comprehensive study covering 269 TF knockout mutants for the yeast Saccharomyces cerevisiae. However, the information that can be extracted from this valuable dataset is limited by the method employed to process the microarray data. Here, we present a reanalysis of the original data using improved statistical techniques freely available from the BioConductor project. We identify over 100,000 differentially expressed genes-nine times the total reported by Hu et al. We validate the biological significance of these genes by assessing their functions, the occurrence of upstream TF-binding sites, and the prevalence of protein-protein interactions. The reanalysed dataset outperforms the original across all measures, indicating that we have uncovered a vastly expanded list of relevant targets. In summary, this work presents a high-quality reanalysis that maximizes the information contained in the Hu et al. compendium. The dataset is available from ArrayExpress (accession: E-MTAB-109) and it will be invaluable to any scientist interested in the yeast transcriptional regulatory system.
Collapse
Affiliation(s)
- Jüri Reimand
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK.
| | | | | | | | | |
Collapse
|
38
|
Kind J, Vaquerizas JM, Gebhardt P, Gentzel M, Luscombe NM, Bertone P, Akhtar A. Genome-wide analysis reveals MOF as a key regulator of dosage compensation and gene expression in Drosophila. Cell 2008; 133:813-28. [PMID: 18510926 DOI: 10.1016/j.cell.2008.04.036] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2007] [Revised: 03/10/2008] [Accepted: 04/29/2008] [Indexed: 12/18/2022]
Abstract
Dosage compensation, mediated by the MSL complex, regulates X-chromosomal gene expression in Drosophila. Here we report that the histone H4 lysine 16 (H4K16) specific histone acetyltransferase MOF displays differential binding behavior depending on whether the target gene is located on the X chromosome versus the autosomes. More specifically, on the male X chromosome, where MSL1 and MSL3 are preferentially associated with the 3' end of dosage compensated genes, MOF displays a bimodal distribution binding to promoters and the 3' ends of genes. In contrast, on MSL1/MSL3 independent X-linked genes and autosomal genes in males and females, MOF binds primarily to promoters. Binding of MOF to autosomes is functional, as H4K16 acetylation and the transcription levels of a number of genes are affected upon MOF depletion. Therefore, MOF is not only involved in the onset of dosage compensation, but also acts as a regulator of gene expression in the Drosophila genome.
Collapse
Affiliation(s)
- Jop Kind
- Gene Expression Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | | | | | | | | | | |
Collapse
|
39
|
Al-Shahrour F, Minguez P, Tárraga J, Montaner D, Alloza E, Vaquerizas JM, Conde L, Blaschke C, Vera J, Dopazo J. BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments. Nucleic Acids Res 2006; 34:W472-6. [PMID: 16845052 PMCID: PMC1538844 DOI: 10.1093/nar/gkl172] [Citation(s) in RCA: 216] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
We present a new version of Babelomics, a complete suite of web tools for functional analysis of genome-scale experiments, with new and improved tools. New functionally relevant terms have been included such as CisRed motifs or bioentities obtained by text-mining procedures. An improved indexing has considerably speeded up several of the modules. An improved version of the FatiScan method for studying the coordinate behaviour of groups of functionally related genes is presented, along with a similar tool, the Gene Set Enrichment Analysis. Babelomics is now more oriented to test systems biology inspired hypotheses. Babelomics can be found at .
Collapse
Affiliation(s)
- Fátima Al-Shahrour
- Bioinformatics Department, Centro de Investigación Príncipe Felipe (CIPF)Autopista del Saler 16, E-46013, Valencia, Spain
| | - Pablo Minguez
- Bioinformatics Department, Centro de Investigación Príncipe Felipe (CIPF)Autopista del Saler 16, E-46013, Valencia, Spain
| | - Joaquín Tárraga
- Bioinformatics Department, Centro de Investigación Príncipe Felipe (CIPF)Autopista del Saler 16, E-46013, Valencia, Spain
- Functional Genomics Node, INBCIPF, Autopista del Saler 16, E-46013, Valencia, Spain
| | - David Montaner
- Bioinformatics Department, Centro de Investigación Príncipe Felipe (CIPF)Autopista del Saler 16, E-46013, Valencia, Spain
- Functional Genomics Node, INBCIPF, Autopista del Saler 16, E-46013, Valencia, Spain
| | - Eva Alloza
- Bioinformatics Department, Centro de Investigación Príncipe Felipe (CIPF)Autopista del Saler 16, E-46013, Valencia, Spain
| | - Juan M. Vaquerizas
- Bioinformatics Department, Centro de Investigación Príncipe Felipe (CIPF)Autopista del Saler 16, E-46013, Valencia, Spain
| | - Lucía Conde
- Bioinformatics Department, Centro de Investigación Príncipe Felipe (CIPF)Autopista del Saler 16, E-46013, Valencia, Spain
| | | | - Javier Vera
- INB—BSC, Jordi Girona 29Edifici Nexus II, E-08034 Barcelona, Spain
| | - Joaquín Dopazo
- Bioinformatics Department, Centro de Investigación Príncipe Felipe (CIPF)Autopista del Saler 16, E-46013, Valencia, Spain
- Functional Genomics Node, INBCIPF, Autopista del Saler 16, E-46013, Valencia, Spain
- To whom correspondence should be addressed. Tel: +34 963289680; Fax: +34 963289701;
| |
Collapse
|
40
|
Conde L, Vaquerizas JM, Dopazo H, Arbiza L, Reumers J, Rousseau F, Schymkowitz J, Dopazo J. PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes. Nucleic Acids Res 2006; 34:W621-5. [PMID: 16845085 PMCID: PMC1538854 DOI: 10.1093/nar/gkl071] [Citation(s) in RCA: 177] [Impact Index Per Article: 9.8] [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] [Indexed: 12/02/2022] Open
Abstract
We have developed a web tool, PupaSuite, for the selection of single nucleotide polymorphisms (SNPs) with potential phenotypic effect, specifically oriented to help in the design of large-scale genotyping projects. PupaSuite uses a collection of data on SNPs from heterogeneous sources and a large number of pre-calculated predictions to offer a flexible and intuitive interface for selecting an optimal set of SNPs. It improves the functionality of PupaSNP and PupasView programs and implements new facilities such as the analysis of user's data to derive haplotypes with functional information. A new estimator of putative effect of polymorphisms has been included that uses evolutionary information. Also SNPeffect database predictions have been included. The PupaSuite web interface is accessible through and through .
Collapse
Affiliation(s)
- Lucía Conde
- Department of Bioinformatics, Centro de Investigación Príncipe Felipe (CIPF)Valencia, 46013, Spain
| | - Juan M. Vaquerizas
- Department of Bioinformatics, Centro de Investigación Príncipe Felipe (CIPF)Valencia, 46013, Spain
| | - Hernán Dopazo
- Department of Bioinformatics, Centro de Investigación Príncipe Felipe (CIPF)Valencia, 46013, Spain
| | - Leonardo Arbiza
- Department of Bioinformatics, Centro de Investigación Príncipe Felipe (CIPF)Valencia, 46013, Spain
| | - Joke Reumers
- Switch laboratory, Flanders Interuniversity Institute for Biotechnology. (VIB), Vrije Universiteit BrusselPleinlaan 2, 1050 Brussels, Belgium
| | - Frederic Rousseau
- Switch laboratory, Flanders Interuniversity Institute for Biotechnology. (VIB), Vrije Universiteit BrusselPleinlaan 2, 1050 Brussels, Belgium
| | - Joost Schymkowitz
- Switch laboratory, Flanders Interuniversity Institute for Biotechnology. (VIB), Vrije Universiteit BrusselPleinlaan 2, 1050 Brussels, Belgium
| | - Joaquín Dopazo
- Department of Bioinformatics, Centro de Investigación Príncipe Felipe (CIPF)Valencia, 46013, Spain
- Functional Genomics Node, INBCIPF Valencia 46013, Spain
- To whom correspondence should be addressed. Tel: +34 963289680; Fax: +34 963289701;
| |
Collapse
|
41
|
Montaner D, Tárraga J, Huerta-Cepas J, Burguet J, Vaquerizas JM, Conde L, Minguez P, Vera J, Mukherjee S, Valls J, Pujana MAG, Alloza E, Herrero J, Al-Shahrour F, Dopazo J. Next station in microarray data analysis: GEPAS. Nucleic Acids Res 2006; 34:W486-91. [PMID: 16845056 PMCID: PMC1538867 DOI: 10.1093/nar/gkl197] [Citation(s) in RCA: 93] [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: 02/14/2006] [Revised: 03/21/2006] [Accepted: 03/21/2006] [Indexed: 11/15/2022] Open
Abstract
The Gene Expression Profile Analysis Suite (GEPAS) has been running for more than four years. During this time it has evolved to keep pace with the new interests and trends in the still changing world of microarray data analysis. GEPAS has been designed to provide an intuitive although powerful web-based interface that offers diverse analysis options from the early step of preprocessing (normalization of Affymetrix and two-colour microarray experiments and other preprocessing options), to the final step of the functional annotation of the experiment (using Gene Ontology, pathways, PubMed abstracts etc.), and include different possibilities for clustering, gene selection, class prediction and array-comparative genomic hybridization management. GEPAS is extensively used by researchers of many countries and its records indicate an average usage rate of 400 experiments per day. The web-based pipeline for microarray gene expression data, GEPAS, is available at http://www.gepas.org.
Collapse
Affiliation(s)
- David Montaner
- Bioinformatics Department, Centro de Investigación Príncipe Felipe (CIPF)Autopista del Saler 16, E46013, Valencia, Spain
- Functional Genomics Node, INBCIPF, Autopista del Saler 16, E46013, Valencia, Spain
| | - Joaquín Tárraga
- Bioinformatics Department, Centro de Investigación Príncipe Felipe (CIPF)Autopista del Saler 16, E46013, Valencia, Spain
- Functional Genomics Node, INBCIPF, Autopista del Saler 16, E46013, Valencia, Spain
| | - Jaime Huerta-Cepas
- Bioinformatics Department, Centro de Investigación Príncipe Felipe (CIPF)Autopista del Saler 16, E46013, Valencia, Spain
- Functional Genomics Node, INBCIPF, Autopista del Saler 16, E46013, Valencia, Spain
| | - Jordi Burguet
- Bioinformatics Department, Centro de Investigación Príncipe Felipe (CIPF)Autopista del Saler 16, E46013, Valencia, Spain
| | - Juan M. Vaquerizas
- Bioinformatics Department, Centro de Investigación Príncipe Felipe (CIPF)Autopista del Saler 16, E46013, Valencia, Spain
| | - Lucía Conde
- Bioinformatics Department, Centro de Investigación Príncipe Felipe (CIPF)Autopista del Saler 16, E46013, Valencia, Spain
| | - Pablo Minguez
- Bioinformatics Department, Centro de Investigación Príncipe Felipe (CIPF)Autopista del Saler 16, E46013, Valencia, Spain
| | - Javier Vera
- INB—BSCJordi Girona 29, Edifici Nexus II, E-08034 Barcelona, Spain
| | - Sach Mukherjee
- Pattern Analysis and Machine Learning Group, Department of Engineering Science University of OxfordOxford OX1 2JD, UK
| | - Joan Valls
- Translational Research Laboratory, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge, L'Hospitalet08907 Barcelona, Spain
| | - Miguel A. G. Pujana
- Translational Research Laboratory, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge, L'Hospitalet08907 Barcelona, Spain
| | - Eva Alloza
- Bioinformatics Department, Centro de Investigación Príncipe Felipe (CIPF)Autopista del Saler 16, E46013, Valencia, Spain
| | | | - Fátima Al-Shahrour
- Bioinformatics Department, Centro de Investigación Príncipe Felipe (CIPF)Autopista del Saler 16, E46013, Valencia, Spain
| | - Joaquín Dopazo
- Bioinformatics Department, Centro de Investigación Príncipe Felipe (CIPF)Autopista del Saler 16, E46013, Valencia, Spain
- Functional Genomics Node, INBCIPF, Autopista del Saler 16, E46013, Valencia, Spain
| |
Collapse
|
42
|
Conde L, Vaquerizas JM, Ferrer-Costa C, de la Cruz X, Orozco M, Dopazo J. PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes. Nucleic Acids Res 2005; 33:W501-5. [PMID: 15980522 PMCID: PMC1165690 DOI: 10.1093/nar/gki476] [Citation(s) in RCA: 197] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We have developed a web tool, PupasView, for the selection of single nucleotide polymorphisms (SNPs) with potential phenotypic effect. PupasView constitutes an interactive environment in which functional information and population frequency data can be used as sequential filters over linkage disequilibrium parameters to obtain a final list of SNPs optimal for genotyping purposes. PupasView is the first resource that integrates phenotypic effects caused by SNPs at both the translational and the transcriptional level. PupasView retrieves SNPs that could affect conserved regions that the cellular machinery uses for the correct processing of genes (intron/exon boundaries or exonic splicing enhancers), predicted transcription factor binding sites and changes in amino acids in the proteins for which a putative pathological effect is calculated. The program uses the mapping of SNPs in the genome provided by Ensembl. PupasView will be of much help in studies of multifactorial disorders, where the use of functional SNPs will increase the sensitivity of the identification of the genes responsible for the disease. The PupasView web interface is accessible through http://pupasview.ochoa.fib.es and through http://www.pupasnp.org.
Collapse
Affiliation(s)
- Lucía Conde
- Bioinformatics Unit, Centro Nacional de Investigaciones Oncológicas (CNIO)Madrid 28029, Spain
| | - Juan M. Vaquerizas
- Bioinformatics Unit, Centro Nacional de Investigaciones Oncológicas (CNIO)Madrid 28029, Spain
| | - Carles Ferrer-Costa
- Molecular Modelling and Bioinformatics Unit, Institut de Recerca BiomèdicaBarcelona 08028, Spain
| | - Xavier de la Cruz
- Molecular Modelling and Bioinformatics Unit, Institut de Recerca BiomèdicaBarcelona 08028, Spain
- Institució Catalana per la Recerca i Estudis Avançats (ICREA)08018 Barcelona, Spain
| | - Modesto Orozco
- Molecular Modelling and Bioinformatics Unit, Institut de Recerca BiomèdicaBarcelona 08028, Spain
- Structure and Modelling Node INB, Parc Científic de BarcelonaBarcelona 08028, Spain
- Departament de Bioquímica i Biología Molecular Facultat de Química, Universitat de BarcelonaBarcelona 08028, Spain
| | - Joaquín Dopazo
- Bioinformatics Unit, Centro Nacional de Investigaciones Oncológicas (CNIO)Madrid 28029, Spain
- Functional Genomics Node, National Institute of Bioinformatics (INB)CIPF Valencia 46013, Spain
- To whom correspondence should be addressed.
| |
Collapse
|
43
|
Al-Shahrour F, Minguez P, Vaquerizas JM, Conde L, Dopazo J. BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments. Nucleic Acids Res 2005; 33:W460-4. [PMID: 15980512 PMCID: PMC1160217 DOI: 10.1093/nar/gki456] [Citation(s) in RCA: 192] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present Babelomics, a complete suite of web tools for the functional analysis of groups of genes in high-throughput experiments, which includes the use of information on Gene Ontology terms, interpro motifs, KEGG pathways, Swiss-Prot keywords, analysis of predicted transcription factor binding sites, chromosomal positions and presence in tissues with determined histological characteristics, through five integrated modules: FatiGO (fast assignment and transference of information), FatiWise, transcription factor association test, GenomeGO and tissues mining tool, respectively. Additionally, another module, FatiScan, provides a new procedure that integrates biological information in combination with experimental results in order to find groups of genes with modest but coordinate significant differential behaviour. FatiScan is highly sensitive and is capable of finding significant asymmetries in the distribution of genes of common function across a list of ordered genes even if these asymmetries were not extreme. The strong multiple-testing nature of the contrasts made by the tools is taken into account. All the tools are integrated in the gene expression analysis package GEPAS. Babelomics is the natural evolution of our tool FatiGO (which analysed almost 22 000 experiments during the last year) to include more sources on information and new modes of using it. Babelomics can be found at .
Collapse
Affiliation(s)
- Fátima Al-Shahrour
- Bioinformatics Unit, Centro Nacional de Investigaciones Oncológicas (CNIO)Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Pablo Minguez
- Bioinformatics Unit, Centro Nacional de Investigaciones Oncológicas (CNIO)Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Juan M. Vaquerizas
- Bioinformatics Unit, Centro Nacional de Investigaciones Oncológicas (CNIO)Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Lucía Conde
- Bioinformatics Unit, Centro Nacional de Investigaciones Oncológicas (CNIO)Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Joaquín Dopazo
- Bioinformatics Unit, Centro Nacional de Investigaciones Oncológicas (CNIO)Melchor Fernández Almagro 3, 28029, Madrid, Spain
- Functional Genomics Node, INB, Centro de Investigación Príncipe FelipeAutopista del Saler 16, E46013, Valencia, Spain
- To whom correspondence should be addressed. Tel: +34 96 3289680; Fax: +34 96 3289701;
| |
Collapse
|
44
|
Vaquerizas JM, Conde L, Yankilevich P, Cabezón A, Minguez P, Díaz-Uriarte R, Al-Shahrour F, Herrero J, Dopazo J. GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data. Nucleic Acids Res 2005; 33:W616-20. [PMID: 15980548 PMCID: PMC1160260 DOI: 10.1093/nar/gki500] [Citation(s) in RCA: 80] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2005] [Revised: 04/09/2005] [Accepted: 05/03/2005] [Indexed: 02/02/2023] Open
Abstract
The Gene Expression Profile Analysis Suite, GEPAS, has been running for more than three years. With >76,000 experiments analysed during the last year and a daily average of almost 300 analyses, GEPAS can be considered a well-established and widely used platform for gene expression microarray data analysis. GEPAS is oriented to the analysis of whole series of experiments. Its design and development have been driven by the demands of the biomedical community, probably the most active collective in the field of microarray users. Although clustering methods have obviously been implemented in GEPAS, our interest has focused more on methods for finding genes differentially expressed among distinct classes of experiments or correlated to diverse clinical outcomes, as well as on building predictors. There is also a great interest in CGH-arrays which fostered the development of the corresponding tool in GEPAS: InSilicoCGH. Much effort has been invested in GEPAS for developing and implementing efficient methods for functional annotation of experiments in the proper statistical framework. Thus, the popular FatiGO has expanded to a suite of programs for functional annotation of experiments, including information on transcription factor binding sites, chromosomal location and tissues. The web-based pipeline for microarray gene expression data, GEPAS, is available at http://www.gepas.org.
Collapse
Affiliation(s)
- Juan M. Vaquerizas
- Bioinformatics Unit, Centro Nacional de Investigaciones Oncológicas (CNIO)Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Lucía Conde
- Bioinformatics Unit, Centro Nacional de Investigaciones Oncológicas (CNIO)Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Patricio Yankilevich
- Bioinformatics Unit, Centro Nacional de Investigaciones Oncológicas (CNIO)Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Amaya Cabezón
- Bioinformatics Unit, Centro Nacional de Investigaciones Oncológicas (CNIO)Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Pablo Minguez
- Bioinformatics Unit, Centro Nacional de Investigaciones Oncológicas (CNIO)Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Ramón Díaz-Uriarte
- Bioinformatics Unit, Centro Nacional de Investigaciones Oncológicas (CNIO)Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Fátima Al-Shahrour
- Bioinformatics Unit, Centro Nacional de Investigaciones Oncológicas (CNIO)Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Javier Herrero
- Bioinformatics Unit, Centro Nacional de Investigaciones Oncológicas (CNIO)Melchor Fernández Almagro 3, 28029 Madrid, Spain
- Ensembl Team, EMBL-EBIHinxton, Cambridge, UK
| | - Joaquín Dopazo
- Bioinformatics Unit, Centro Nacional de Investigaciones Oncológicas (CNIO)Melchor Fernández Almagro 3, 28029 Madrid, Spain
- Functional Genomics Node, INB, Centro de Investigación Príncipe FelipeAutopista del Saler 16, 46013 Valencia, Spain
| |
Collapse
|
45
|
Abstract
MOTIVATION Small interfering RNA (siRNA) is widely used in functional genomics to silence genes by decreasing their expression to study the resulting phenotypes. The possibility of performing large-scale functional assays by gene silencing accentuates the necessity of a software capable of the high-throughput design of highly specific siRNA. The main objective sought was the design of a large number of siRNAs with appropriate thermodynamic properties and, especially, high specificity. Since all the available procedures require, to some extent, manual processing of the results to guarantee specific results, specificity constitutes to date, the major obstacle to the complete automation of all the steps necessary for the selection of optimal candidate siRNAs. RESULT Here, we present a program that for the first time completely automates the search for siRNAs. In SiDE, the most complete set of rules for the selection of siRNA candidates (including G+C content, nucleotides at determined positions, thermodynamic properties, propensity to form internal hairpins, etc.) is implemented and moreover, specificity is achieved by a conceptually new method. After selecting possible siRNA candidates with the optimal functional properties, putative unspecific matches, which can cause cross-hybridization, are checked in databases containing a unique entry for each gene. These truly non-redundant databases are constructed from the genome annotations (Ensembl). Also intron/exon boundaries, presence of polymorphisms (single nucleotide polymorphisms) specificity for either gene or transcript, and other features can be selected to be considered in the design of siRNAs. AVAILABILITY The program is available as a web server at http://side.bioinfo.cnio.es. The program was written under the GPL license. CONTACT jdopazo@cnio.es.
Collapse
Affiliation(s)
- Javier Santoyo
- Bioinformatics Unit, Centro Nacional de Investigaciones Oncológicas (CNIO) and Functional Genomics Node, INB, Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | | | | |
Collapse
|
46
|
Conde L, Vaquerizas JM, Santoyo J, Al-Shahrour F, Ruiz-Llorente S, Robledo M, Dopazo J. PupaSNP Finder: a web tool for finding SNPs with putative effect at transcriptional level. Nucleic Acids Res 2004; 32:W242-8. [PMID: 15215388 PMCID: PMC441576 DOI: 10.1093/nar/gkh438] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.5] [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: 11/12/2022] Open
Abstract
We have developed a web tool, PupaSNP Finder (PupaSNP for short), for high-throughput searching for single nucleotide polymorphisms (SNPs) with potential phenotypic effect. PupaSNP takes as its input lists of genes (or generates them from chromosomal coordinates) and retrieves SNPs that could affect the conserved regions that the cellular machinery uses for the correct processing of genes (intron/exon boundaries or exonic splicing enhancers), predicted transcription factor binding sites (TFBS) and changes in amino acids in the proteins. The program uses the mapping of SNPs in the genome provided by Ensembl. Additionally, user-defined SNPs (not yet mapped in the genome) can be easily provided to the program. Also, additional functional information from Gene Ontology, OMIM and homologies in other model organisms is provided. In contrast to other programs already available, which focus only on SNPs with possible effect in the protein, PupaSNP includes SNPs with possible transcriptional effect. PupaSNP will be of significant help in studies of multifactorial disorders, where the use of functional SNPs will increase the sensitivity of identification of the genes responsible for the disease. The PupaSNP web interface is accessible through http://pupasnp.bioinfo.cnio.es.
Collapse
Affiliation(s)
- Lucía Conde
- Bioinformatics Unit, Centro Nacional de Investigaciones Oncológicas, Madrid, Spain
| | | | | | | | | | | | | |
Collapse
|
47
|
Abstract
SUMMARY We present a web server for Diagnosis and Normalization of MicroArray Data (DNMAD). DNMAD includes several common data transformations such as spatial and global robust local regression or multiple slide normalization, and allows for detecting several kinds of errors that result from the manipulation and the image analysis of the arrays. This tool offers a user-friendly interface, and is completely integrated within the Gene Expression Pattern Analysis Suite (GEPAS). AVAILABILITY The tool is accessible on-line at http://dnmad.bioinfo.cnio.es.
Collapse
Affiliation(s)
- Juan M Vaquerizas
- Bioinformatics Unit, CNIO, Spanish National Cancer Centre, Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | | | | |
Collapse
|
48
|
Herrero J, Vaquerizas JM, Al-Shahrour F, Conde L, Mateos A, Díaz-Uriarte JSR, Dopazo J. New challenges in gene expression data analysis and the extended GEPAS. Nucleic Acids Res 2004; 32:W485-91. [PMID: 15215434 PMCID: PMC441559 DOI: 10.1093/nar/gkh421] [Citation(s) in RCA: 39] [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] [Received: 02/13/2004] [Revised: 04/07/2004] [Accepted: 04/07/2004] [Indexed: 01/30/2023] Open
Abstract
Since the first papers published in the late nineties, including, for the first time, a comprehensive analysis of microarray data, the number of questions that have been addressed through this technique have both increased and diversified. Initially, interest focussed on genes coexpressing across sets of experimental conditions, implying, essentially, the use of clustering techniques. Recently, however, interest has focussed more on finding genes differentially expressed among distinct classes of experiments, or correlated to diverse clinical outcomes, as well as in building predictors. In addition to this, the availability of accurate genomic data and the recent implementation of CGH arrays has made mapping expression and genomic data on the chromosomes possible. There is also a clear demand for methods that allow the automatic transfer of biological information to the results of microarray experiments. Different initiatives, such as the Gene Ontology (GO) consortium, pathways databases, protein functional motifs, etc., provide curated annotations for genes. Whereas many resources on the web focus mainly on clustering methods, GEPAS has evolved to cope with the aforementioned new challenges that have recently arisen in the field of microarray data analysis. The web-based pipeline for microarray gene expression data, GEPAS, is available at http://gepas.bioinfo.cnio.es.
Collapse
Affiliation(s)
- Javier Herrero
- Bioinformatics Unit, Biotechnology Programme, Centro Nacional de Investigaciones Oncológicas, Melchor Fernández Almagro, 3, E-28029 Madrid, Spain
| | | | | | | | | | | | | |
Collapse
|
49
|
Herrero J, Al-Shahrour F, Díaz-Uriarte R, Mateos A, Vaquerizas JM, Santoyo J, Dopazo J. GEPAS: A web-based resource for microarray gene expression data analysis. Nucleic Acids Res 2003; 31:3461-7. [PMID: 12824345 PMCID: PMC168997 DOI: 10.1093/nar/gkg591] [Citation(s) in RCA: 142] [Impact Index Per Article: 6.8] [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 present a web-based pipeline for microarray gene expression profile analysis, GEPAS, which stands for Gene Expression Profile Analysis Suite (http://gepas.bioinfo.cnio.es). GEPAS is composed of different interconnected modules which include tools for data pre-processing, two-conditions comparison, unsupervised and supervised clustering (which include some of the most popular methods as well as home made algorithms) and several tests for differential gene expression among different classes, continuous variables or survival analysis. A multiple purpose tool for data mining, based on Gene Ontology, is also linked to the tools, which constitutes a very convenient way of analysing clustering results. On-line tutorials are available from our main web server (http://bioinfo.cnio.es).
Collapse
Affiliation(s)
- Javier Herrero
- Bioinformatics Unit, Centro Nacional de Investigaciones Oncológicas, c/Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | | | | | | | | | | | | |
Collapse
|