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Morocho-Jaramillo PA, Kotlar-Goldaper I, Zakarauskas-Seth BI, Purfürst B, Filosa A, Sawamiphak S. The zebrafish heart harbors a thermogenic beige fat depot analog of human epicardial adipose tissue. Cell Rep 2024; 43:113955. [PMID: 38507414 DOI: 10.1016/j.celrep.2024.113955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 01/25/2024] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
Epicardial adipose tissue (eAT) is a metabolically active fat depot that has been associated with a wide array of cardiac homeostatic functions and cardiometabolic diseases. A full understanding of its diverse physiological and pathological roles is hindered by the dearth of animal models. Here, we show, in the heart of an ectothermic teleost, the zebrafish, the existence of a fat depot localized underneath the epicardium, originating from the epicardium and exhibiting the molecular signature of beige adipocytes. Moreover, a subset of adipocytes within this cardiac fat tissue exhibits primitive thermogenic potential. Transcriptomic profiling and cross-species analysis revealed elevated glycolytic and cardiac homeostatic gene expression with downregulated obesity and inflammatory hallmarks in the teleost eAT compared to that of lean aged humans. Our findings unveil epicardium-derived beige fat in the heart of an ectotherm considered to possess solely white adipocytes for energy storage and identify pathways that may underlie age-driven remodeling of human eAT.
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Affiliation(s)
- Paul-Andres Morocho-Jaramillo
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13125 Berlin, Germany; Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Ilan Kotlar-Goldaper
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13125 Berlin, Germany; Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Bhakti I Zakarauskas-Seth
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13125 Berlin, Germany; Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Bettina Purfürst
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Alessandro Filosa
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Suphansa Sawamiphak
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13125 Berlin, Germany.
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2
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Benedum J, Franke V, Appel LM, Walch L, Bruno M, Schneeweiss R, Gruber J, Oberndorfer H, Frank E, Strobl X, Polyansky A, Zagrovic B, Akalin A, Slade D. The SPOC proteins DIDO3 and PHF3 co-regulate gene expression and neuronal differentiation. Nat Commun 2023; 14:7912. [PMID: 38036524 PMCID: PMC10689479 DOI: 10.1038/s41467-023-43724-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 11/17/2023] [Indexed: 12/02/2023] Open
Abstract
Transcription is regulated by a multitude of activators and repressors, which bind to the RNA polymerase II (Pol II) machinery and modulate its progression. Death-inducer obliterator 3 (DIDO3) and PHD finger protein 3 (PHF3) are paralogue proteins that regulate transcription elongation by docking onto phosphorylated serine-2 in the C-terminal domain (CTD) of Pol II through their SPOC domains. Here, we show that DIDO3 and PHF3 form a complex that bridges the Pol II elongation machinery with chromatin and RNA processing factors and tethers Pol II in a phase-separated microenvironment. Their SPOC domains and C-terminal intrinsically disordered regions are critical for transcription regulation. PHF3 and DIDO exert cooperative and antagonistic effects on the expression of neuronal genes and are both essential for neuronal differentiation. In the absence of PHF3, DIDO3 is upregulated as a compensatory mechanism. In addition to shared gene targets, DIDO specifically regulates genes required for lipid metabolism. Collectively, our work reveals multiple layers of gene expression regulation by the DIDO3 and PHF3 paralogues, which have specific, co-regulatory and redundant functions in transcription.
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Affiliation(s)
- Johannes Benedum
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
- Department of Radiation Oncology, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Vedran Franke
- The Berlin Institute for Medical Systems Biology, Max Delbrück Center, Berlin, Germany
| | - Lisa-Marie Appel
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
- Department of Radiation Oncology, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Lena Walch
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
| | - Melania Bruno
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
| | - Rebecca Schneeweiss
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
| | - Juliane Gruber
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
| | - Helena Oberndorfer
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
| | - Emma Frank
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
| | - Xué Strobl
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Anton Polyansky
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Bojan Zagrovic
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Altuna Akalin
- The Berlin Institute for Medical Systems Biology, Max Delbrück Center, Berlin, Germany
| | - Dea Slade
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria.
- Department of Radiation Oncology, Medical University of Vienna, Vienna, Austria.
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria.
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3
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Schleussner N, Cauchy P, Franke V, Giefing M, Fornes O, Vankadari N, Assi SA, Costanza M, Weniger MA, Akalin A, Anagnostopoulos I, Bukur T, Casarotto MG, Damm F, Daumke O, Edginton-White B, Gebhardt JCM, Grau M, Grunwald S, Hansmann ML, Hartmann S, Huber L, Kärgel E, Lusatis S, Noerenberg D, Obier N, Pannicke U, Fischer A, Reisser A, Rosenwald A, Schwarz K, Sundararaj S, Weilemann A, Winkler W, Xu W, Lenz G, Rajewsky K, Wasserman WW, Cockerill PN, Scheidereit C, Siebert R, Küppers R, Grosschedl R, Janz M, Bonifer C, Mathas S. Transcriptional reprogramming by mutated IRF4 in lymphoma. Nat Commun 2023; 14:6947. [PMID: 37935654 PMCID: PMC10630337 DOI: 10.1038/s41467-023-41954-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 09/20/2023] [Indexed: 11/09/2023] Open
Abstract
Disease-causing mutations in genes encoding transcription factors (TFs) can affect TF interactions with their cognate DNA-binding motifs. Whether and how TF mutations impact upon the binding to TF composite elements (CE) and the interaction with other TFs is unclear. Here, we report a distinct mechanism of TF alteration in human lymphomas with perturbed B cell identity, in particular classic Hodgkin lymphoma. It is caused by a recurrent somatic missense mutation c.295 T > C (p.Cys99Arg; p.C99R) targeting the center of the DNA-binding domain of Interferon Regulatory Factor 4 (IRF4), a key TF in immune cells. IRF4-C99R fundamentally alters IRF4 DNA-binding, with loss-of-binding to canonical IRF motifs and neomorphic gain-of-binding to canonical and non-canonical IRF CEs. IRF4-C99R thoroughly modifies IRF4 function by blocking IRF4-dependent plasma cell induction, and up-regulates disease-specific genes in a non-canonical Activator Protein-1 (AP-1)-IRF-CE (AICE)-dependent manner. Our data explain how a single mutation causes a complex switch of TF specificity and gene regulation and open the perspective to specifically block the neomorphic DNA-binding activities of a mutant TF.
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Affiliation(s)
- Nikolai Schleussner
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Biology of Malignant Lymphomas, 13125, Berlin, Germany
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany
- Experimental and Clinical Research Center (ECRC), a joint cooperation between Charité and MDC, Berlin, Germany
| | - Pierre Cauchy
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- University Medical Center Freiburg, 79106, Freiburg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Vedran Franke
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center, Berlin, Germany
| | - Maciej Giefing
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, 60-479, Poland
- Institute of Human Genetics, Christian-Albrechts-University Kiel, 24105, Kiel, Germany
| | - Oriol Fornes
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Naveen Vankadari
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Salam A Assi
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Mariantonia Costanza
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Biology of Malignant Lymphomas, 13125, Berlin, Germany
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany
- Experimental and Clinical Research Center (ECRC), a joint cooperation between Charité and MDC, Berlin, Germany
| | - Marc A Weniger
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, 45122, Essen, Germany
| | - Altuna Akalin
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center, Berlin, Germany
| | - Ioannis Anagnostopoulos
- Institute of Pathology, Universität Würzburg and Comprehensive Cancer Centre Mainfranken (CCCMF), Würzburg, Germany
| | - Thomas Bukur
- TRON gGmbH - Translationale Onkologie an der Universitätsmedizin der Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Marco G Casarotto
- Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Frederik Damm
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany
| | - Oliver Daumke
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Structural Biology, 13125, Berlin, Germany
| | - Benjamin Edginton-White
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | | | - Michael Grau
- Department of Physics, University of Marburg, 35052, Marburg, Germany
- Medical Department A for Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Stephan Grunwald
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Structural Biology, 13125, Berlin, Germany
| | - Martin-Leo Hansmann
- Frankfurt Institute of Advanced Studies, Frankfurt am Main, Germany
- Institute for Pharmacology and Toxicology, Goethe University, Frankfurt am Main, Germany
| | - Sylvia Hartmann
- Dr. Senckenberg Institute of Pathology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Lionel Huber
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Eva Kärgel
- Signal Transduction in Tumor Cells, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Simone Lusatis
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Biology of Malignant Lymphomas, 13125, Berlin, Germany
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany
- Experimental and Clinical Research Center (ECRC), a joint cooperation between Charité and MDC, Berlin, Germany
| | - Daniel Noerenberg
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany
| | - Nadine Obier
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Ulrich Pannicke
- Institute for Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Anja Fischer
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89081, Ulm, Germany
| | - Anja Reisser
- Department of Physics, Institute of Biophysics, Ulm University, Ulm, Germany
| | - Andreas Rosenwald
- Institute of Pathology, Universität Würzburg and Comprehensive Cancer Centre Mainfranken (CCCMF), Würzburg, Germany
| | - Klaus Schwarz
- Institute for Transfusion Medicine, University of Ulm, Ulm, Germany
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Service Baden-Württemberg-Hessen, Ulm, Germany
| | - Srinivasan Sundararaj
- Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Andre Weilemann
- Medical Department A for Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Wiebke Winkler
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Biology of Malignant Lymphomas, 13125, Berlin, Germany
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany
- Experimental and Clinical Research Center (ECRC), a joint cooperation between Charité and MDC, Berlin, Germany
| | - Wendan Xu
- Medical Department A for Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Georg Lenz
- Medical Department A for Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Klaus Rajewsky
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Immune Regulation and Cancer, 13125, Berlin, Germany
| | - Wyeth W Wasserman
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Peter N Cockerill
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Claus Scheidereit
- Signal Transduction in Tumor Cells, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Christian-Albrechts-University Kiel, 24105, Kiel, Germany
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89081, Ulm, Germany
| | - Ralf Küppers
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, 45122, Essen, Germany
| | - Rudolf Grosschedl
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Martin Janz
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Biology of Malignant Lymphomas, 13125, Berlin, Germany
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany
- Experimental and Clinical Research Center (ECRC), a joint cooperation between Charité and MDC, Berlin, Germany
| | - Constanze Bonifer
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Stephan Mathas
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Biology of Malignant Lymphomas, 13125, Berlin, Germany.
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany.
- Experimental and Clinical Research Center (ECRC), a joint cooperation between Charité and MDC, Berlin, Germany.
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.
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4
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Legnini I, Emmenegger L, Zappulo A, Rybak-Wolf A, Wurmus R, Martinez AO, Jara CC, Boltengagen A, Hessler T, Mastrobuoni G, Kempa S, Zinzen R, Woehler A, Rajewsky N. Spatiotemporal, optogenetic control of gene expression in organoids. Nat Methods 2023; 20:1544-1552. [PMID: 37735569 PMCID: PMC10555836 DOI: 10.1038/s41592-023-01986-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/25/2023] [Indexed: 09/23/2023]
Abstract
Organoids derived from stem cells have become an increasingly important tool for studying human development and modeling disease. However, methods are still needed to control and study spatiotemporal patterns of gene expression in organoids. Here we combined optogenetics and gene perturbation technologies to activate or knock-down RNA of target genes in programmable spatiotemporal patterns. To illustrate the usefulness of our approach, we locally activated Sonic Hedgehog (SHH) signaling in an organoid model for human neurodevelopment. Spatial and single-cell transcriptomic analyses showed that this local induction was sufficient to generate stereotypically patterned organoids and revealed new insights into SHH's contribution to gene regulation in neurodevelopment. With this study, we propose optogenetic perturbations in combination with spatial transcriptomics as a powerful technology to reprogram and study cell fates and tissue patterning in organoids.
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Affiliation(s)
- Ivano Legnini
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany.
- Human Technopole, Milan, Italy.
| | - Lisa Emmenegger
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | - Alessandra Zappulo
- Systems Biology of Neural Tissue Differentiation, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
- Human Technopole, Milan, Italy
| | - Agnieszka Rybak-Wolf
- Organoid Platform, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | - Ricardo Wurmus
- Bioinformatics and Omics Data Science, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | - Anna Oliveras Martinez
- Systems Biology Imaging Platform, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | - Cledi Cerda Jara
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | - Anastasiya Boltengagen
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | - Talé Hessler
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | - Guido Mastrobuoni
- Proteomic and Metabolomics Platform, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | - Stefan Kempa
- Proteomic and Metabolomics Platform, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | - Robert Zinzen
- Systems Biology of Neural Tissue Differentiation, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
- Systems Biology Imaging Platform, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | - Andrew Woehler
- Systems Biology Imaging Platform, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, USA
| | - Nikolaus Rajewsky
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany.
- Charité-Universitätsmedizin, Berlin, Germany.
- German Center for Cardiovascular Research (DZHK), Berlin, Germany.
- NeuroCure Cluster of Excellence, Berlin, Germany.
- National Center for Tumor Diseases (NCT), German Cancer Consortium (DKTK), Berlin, Germany.
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5
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Ziemann M, Poulain P, Bora A. The five pillars of computational reproducibility: bioinformatics and beyond. Brief Bioinform 2023; 24:bbad375. [PMID: 37870287 PMCID: PMC10591307 DOI: 10.1093/bib/bbad375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/26/2023] [Accepted: 09/30/2023] [Indexed: 10/24/2023] Open
Abstract
Computational reproducibility is a simple premise in theory, but is difficult to achieve in practice. Building upon past efforts and proposals to maximize reproducibility and rigor in bioinformatics, we present a framework called the five pillars of reproducible computational research. These include (1) literate programming, (2) code version control and sharing, (3) compute environment control, (4) persistent data sharing and (5) documentation. These practices will ensure that computational research work can be reproduced quickly and easily, long into the future. This guide is designed for bioinformatics data analysts and bioinformaticians in training, but should be relevant to other domains of study.
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Affiliation(s)
- Mark Ziemann
- Deakin University, School of Life and Environmental Sciences, Geelong, Australia
- Burnet Institute, Melbourne, Australia
| | - Pierre Poulain
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | - Anusuiya Bora
- Deakin University, School of Life and Environmental Sciences, Geelong, Australia
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6
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Loedige I, Baranovskii A, Mendonsa S, Dantsuji S, Popitsch N, Breimann L, Zerna N, Cherepanov V, Milek M, Ameres S, Chekulaeva M. mRNA stability and m 6A are major determinants of subcellular mRNA localization in neurons. Mol Cell 2023; 83:2709-2725.e10. [PMID: 37451262 PMCID: PMC10529935 DOI: 10.1016/j.molcel.2023.06.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/04/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023]
Abstract
For cells to perform their biological functions, they need to adopt specific shapes and form functionally distinct subcellular compartments. This is achieved in part via an asymmetric distribution of mRNAs within cells. Currently, the main model of mRNA localization involves specific sequences called "zipcodes" that direct mRNAs to their proper locations. However, while thousands of mRNAs localize within cells, only a few zipcodes have been identified, suggesting that additional mechanisms contribute to localization. Here, we assess the role of mRNA stability in localization by combining the isolation of the soma and neurites of mouse primary cortical and mESC-derived neurons, SLAM-seq, m6A-RIP-seq, the perturbation of mRNA destabilization mechanisms, and the analysis of multiple mRNA localization datasets. We show that depletion of mRNA destabilization elements, such as m6A, AU-rich elements, and suboptimal codons, functions as a mechanism that mediates the localization of mRNAs associated with housekeeping functions to neurites in several types of neurons.
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Affiliation(s)
- Inga Loedige
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Artem Baranovskii
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Samantha Mendonsa
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Sayaka Dantsuji
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Niko Popitsch
- Max Perutz Labs, University of Vienna, Vienna BioCenter, 1030 Vienna, Austria
| | - Laura Breimann
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Nadja Zerna
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Vsevolod Cherepanov
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Miha Milek
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Stefan Ameres
- Max Perutz Labs, University of Vienna, Vienna BioCenter, 1030 Vienna, Austria
| | - Marina Chekulaeva
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany.
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7
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Lehle JD, McCarrey JR. Accelerating the alignment processing speed of the comprehensive end-to-end whole-genome bisulfite sequencing pipeline, wg-blimp. Biol Methods Protoc 2023; 8:bpad012. [PMID: 37431446 PMCID: PMC10329742 DOI: 10.1093/biomethods/bpad012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/12/2023] [Accepted: 06/12/2023] [Indexed: 07/12/2023] Open
Abstract
Analyzing whole-genome bisulfite and related sequencing datasets is a time-intensive process due to the complexity and size of the input raw sequencing files and lengthy read alignment step requiring correction for conversion of all unmethylated Cs to Ts genome-wide. The objective of this study was to modify the read alignment algorithm associated with the whole-genome bisulfite sequencing methylation analysis pipeline (wg-blimp) to shorten the time required to complete this phase while retaining overall read alignment accuracy. Here, we report an update to the recently published pipeline wg-blimp achieved by replacing the use of the bwa-meth aligner with the faster gemBS aligner. This improvement to the wg-blimp pipeline has led to a more than ×7 acceleration in the processing speed of samples when scaled to larger publicly available FASTQ datasets containing 80-160 million reads while maintaining nearly identical accuracy of properly mapped reads when compared with data from the previous pipeline. The modifications to the wg-blimp pipeline reported here merge the speed and accuracy of the gemBS aligner with the comprehensive analysis and data visualization assets of the wg-blimp pipeline to provide a significantly accelerated workflow that can produce high-quality data much more rapidly without compromising read accuracy at the expense of increasing RAM requirements up to 48 GB.
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Affiliation(s)
- Jake D Lehle
- Correspondence address. Department of Neurosciences, Developmental and Regenerative Biology, The University of Texas at San Antonio, 1 UTSA Circle, San Antonio, TX 78249, USA. Tel: +1 (512)-992-8144; E-mail:
| | - John R McCarrey
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San Antonio, San Antonio, TX 78249, USA
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8
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Rybak-Wolf A, Wyler E, Pentimalli TM, Legnini I, Oliveras Martinez A, Glažar P, Loewa A, Kim SJ, Kaufer BB, Woehler A, Landthaler M, Rajewsky N. Modelling viral encephalitis caused by herpes simplex virus 1 infection in cerebral organoids. Nat Microbiol 2023:10.1038/s41564-023-01405-y. [PMID: 37349587 DOI: 10.1038/s41564-023-01405-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 05/10/2023] [Indexed: 06/24/2023]
Abstract
Herpes simplex encephalitis is a life-threatening disease of the central nervous system caused by herpes simplex viruses (HSVs). Following standard of care with antiviral acyclovir treatment, most patients still experience various neurological sequelae. Here we characterize HSV-1 infection of human brain organoids by combining single-cell RNA sequencing, electrophysiology and immunostaining. We observed strong perturbations of tissue integrity, neuronal function and cellular transcriptomes. Under acyclovir treatment viral replication was stopped, but did not prevent HSV-1-driven defects such as damage of neuronal processes and neuroepithelium. Unbiased analysis of pathways deregulated upon infection revealed tumour necrosis factor activation as a potential causal factor. Combination of anti-inflammatory drugs such as necrostatin-1 or bardoxolone methyl with antiviral treatment prevented the damages caused by infection, indicating that tuning the inflammatory response in acute infection may improve current therapeutic strategies.
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Affiliation(s)
- Agnieszka Rybak-Wolf
- Organoid Platform, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.
| | - Emanuel Wyler
- Laboratory for RNA Biology, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Tancredi Massimo Pentimalli
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin School of Integrative Oncology (BSIO), Berlin, Germany
| | - Ivano Legnini
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Centre for Genomics, Functional Genomics Programme, Human Technopole, Milan, Italy
| | - Anna Oliveras Martinez
- System Biology Imaging Platform, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Petar Glažar
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Anna Loewa
- Organoid Platform, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Seung Joon Kim
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Andrew Woehler
- System Biology Imaging Platform, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, USA
| | - Markus Landthaler
- Laboratory for RNA Biology, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Institut für Biologie, Humboldt Universität zu Berlin, Berlin, Germany
| | - Nikolaus Rajewsky
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.
- Charité-Universitätsmedizin, Berlin, Germany.
- German Center for Cardiovascular Research (DZHK), Site Berlin, Berlin, Germany.
- NeuroCure Cluster of Excellence, Berlin, Germany.
- German Cancer Consortium (DKTK), Berlin, Germany.
- National Center for Tumor Diseases (NCT), Site Berlin, Berlin, Germany.
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9
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Cuadrat RRC, Kratzer A, Arnal HG, Rathgeber A, Wreczycka K, Blume A, Gündüz IB, Ebenal V, Mauno T, Osberg B, Moobed M, Hartung J, Jakobs K, Seppelt C, Meteva D, Haghikia A, Leistner D, Landmesser U, Akalin A. Cardiovascular disease biomarkers derived from circulating cell-free DNA methylation. NAR Genom Bioinform 2023; 5:lqad061. [PMID: 37388821 PMCID: PMC10304763 DOI: 10.1093/nargab/lqad061] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 05/31/2023] [Accepted: 06/07/2023] [Indexed: 07/01/2023] Open
Abstract
Acute coronary syndrome (ACS) remains a major cause of worldwide mortality. The syndrome occurs when blood flow to the heart muscle is decreased or blocked, causing muscle tissues to die or malfunction. There are three main types of ACS: Non-ST-elevation myocardial infarction, ST-elevation myocardial infarction, and unstable angina. The treatment depends on the type of ACS, and this is decided by a combination of clinical findings, such as electrocardiogram and plasma biomarkers. Circulating cell-free DNA (ccfDNA) is proposed as an additional marker for ACS since the damaged tissues can release DNA to the bloodstream. We used ccfDNA methylation profiles for differentiating between the ACS types and provided computational tools to repeat similar analysis for other diseases. We leveraged cell type specificity of DNA methylation to deconvolute the ccfDNA cell types of origin and to find methylation-based biomarkers that stratify patients. We identified hundreds of methylation markers associated with ACS types and validated them in an independent cohort. Many such markers were associated with genes involved in cardiovascular conditions and inflammation. ccfDNA methylation showed promise as a non-invasive diagnostic for acute coronary events. These methods are not limited to acute events, and may be used for chronic cardiovascular diseases as well.
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Affiliation(s)
| | | | | | - Anja C Rathgeber
- Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Katarzyna Wreczycka
- Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany
| | - Alexander Blume
- Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany
| | - Irem B Gündüz
- Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany
| | - Veronika Ebenal
- Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany
| | - Tiina Mauno
- Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany
| | - Brendan Osberg
- Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany
| | - Minoo Moobed
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Cardiology, Campus Benjamin Franklin, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany
| | - Johannes Hartung
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Cardiology, Campus Benjamin Franklin, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany
| | - Kai Jakobs
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Cardiology, Campus Benjamin Franklin, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany
| | - Claudio Seppelt
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Cardiology, Campus Benjamin Franklin, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany
- Universitätsklinikum Frankfurt am Main, Medizinische Klinik 3, Klinik für Kardiologie und Angiologie, Germany
| | - Denitsa Meteva
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Cardiology, Campus Benjamin Franklin, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany
| | - Arash Haghikia
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Cardiology, Campus Benjamin Franklin, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - David M Leistner
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Cardiology, Campus Benjamin Franklin, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany
- Universitätsklinikum Frankfurt am Main, Medizinische Klinik 3, Klinik für Kardiologie und Angiologie, Germany
| | - Ulf Landmesser
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Cardiology, Campus Benjamin Franklin, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Altuna Akalin
- To whom correspondence should be addressed. Tel: +49 30 94 060 42 71; Fax: +49 30 94 060 49 341;
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10
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Massively parallel identification of mRNA localization elements in primary cortical neurons. Nat Neurosci 2023; 26:394-405. [PMID: 36646877 PMCID: PMC9991926 DOI: 10.1038/s41593-022-01243-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 12/01/2022] [Indexed: 01/18/2023]
Abstract
Cells adopt highly polarized shapes and form distinct subcellular compartments in many cases due to the localization of many mRNAs to specific areas, where they are translated into proteins with local functions. This mRNA localization is mediated by specific cis-regulatory elements in mRNAs, commonly called 'zipcodes'. Although there are hundreds of localized mRNAs, only a few zipcodes have been characterized. Here we describe a novel neuronal zipcode identification protocol (N-zip) that can identify zipcodes across hundreds of 3' untranslated regions. This approach combines a method of separating the principal subcellular compartments of neurons-cell bodies and neurites-with a massively parallel reporter assay. N-zip identifies the let-7 binding site and (AU)n motif as de novo zipcodes in mouse primary cortical neurons. Our analysis also provides, to our knowledge, the first demonstration of an miRNA affecting mRNA localization and suggests a strategy for detecting many more zipcodes.
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11
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A multimorphic mutation in IRF4 causes human autosomal dominant combined immunodeficiency. Sci Immunol 2023; 8:eade7953. [PMID: 36662884 PMCID: PMC10825898 DOI: 10.1126/sciimmunol.ade7953] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 12/22/2022] [Indexed: 01/22/2023]
Abstract
Interferon regulatory factor 4 (IRF4) is a transcription factor (TF) and key regulator of immune cell development and function. We report a recurrent heterozygous mutation in IRF4, p.T95R, causing an autosomal dominant combined immunodeficiency (CID) in seven patients from six unrelated families. The patients exhibited profound susceptibility to opportunistic infections, notably Pneumocystis jirovecii, and presented with agammaglobulinemia. Patients' B cells showed impaired maturation, decreased immunoglobulin isotype switching, and defective plasma cell differentiation, whereas their T cells contained reduced TH17 and TFH populations and exhibited decreased cytokine production. A knock-in mouse model of heterozygous T95R showed a severe defect in antibody production both at the steady state and after immunization with different types of antigens, consistent with the CID observed in these patients. The IRF4T95R variant maps to the TF's DNA binding domain, alters its canonical DNA binding specificities, and results in a simultaneous multimorphic combination of loss, gain, and new functions for IRF4. IRF4T95R behaved as a gain-of-function hypermorph by binding to DNA with higher affinity than IRF4WT. Despite this increased affinity for DNA, the transcriptional activity on IRF4 canonical genes was reduced, showcasing a hypomorphic activity of IRF4T95R. Simultaneously, IRF4T95R functions as a neomorph by binding to noncanonical DNA sites to alter the gene expression profile, including the transcription of genes exclusively induced by IRF4T95R but not by IRF4WT. This previously undescribed multimorphic IRF4 pathophysiology disrupts normal lymphocyte biology, causing human disease.
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12
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Appel LM, Franke V, Benedum J, Grishkovskaya I, Strobl X, Polyansky A, Ammann G, Platzer S, Neudolt A, Wunder A, Walch L, Kaiser S, Zagrovic B, Djinovic-Carugo K, Akalin A, Slade D. The SPOC domain is a phosphoserine binding module that bridges transcription machinery with co- and post-transcriptional regulators. Nat Commun 2023; 14:166. [PMID: 36631525 PMCID: PMC9834408 DOI: 10.1038/s41467-023-35853-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 01/05/2023] [Indexed: 01/13/2023] Open
Abstract
The heptad repeats of the C-terminal domain (CTD) of RNA polymerase II (Pol II) are extensively modified throughout the transcription cycle. The CTD coordinates RNA synthesis and processing by recruiting transcription regulators as well as RNA capping, splicing and 3'end processing factors. The SPOC domain of PHF3 was recently identified as a CTD reader domain specifically binding to phosphorylated serine-2 residues in adjacent CTD repeats. Here, we establish the SPOC domains of the human proteins DIDO, SHARP (also known as SPEN) and RBM15 as phosphoserine binding modules that can act as CTD readers but also recognize other phosphorylated binding partners. We report the crystal structure of SHARP SPOC in complex with CTD and identify the molecular determinants for its specific binding to phosphorylated serine-5. PHF3 and DIDO SPOC domains preferentially interact with the Pol II elongation complex, while RBM15 and SHARP SPOC domains engage with writers and readers of m6A, the most abundant RNA modification. RBM15 positively regulates m6A levels and mRNA stability in a SPOC-dependent manner, while SHARP SPOC is essential for its localization to inactive X-chromosomes. Our findings suggest that the SPOC domain is a major interface between the transcription machinery and regulators of transcription and co-transcriptional processes.
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Affiliation(s)
- Lisa-Marie Appel
- Department of Radiation Oncology, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - Vedran Franke
- The Berlin Institute for Medical Systems Biology, Max Delbrück Center, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Johannes Benedum
- Department of Radiation Oncology, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Dr. Bohr-Gasse 9, 1030, Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, 1030, Vienna, Austria
| | - Irina Grishkovskaya
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Xué Strobl
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Dr. Bohr-Gasse 9, 1030, Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, 1030, Vienna, Austria
| | - Anton Polyansky
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Gregor Ammann
- Department of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt, Germany
| | - Sebastian Platzer
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - Andrea Neudolt
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - Anna Wunder
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - Lena Walch
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - Stefanie Kaiser
- Department of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt, Germany
| | - Bojan Zagrovic
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Kristina Djinovic-Carugo
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter, Campus Vienna Biocenter 5, 1030, Vienna, Austria
- Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecčna Pot 113, 1000, Ljubljana, Slovenia
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs, CS 90181, 38042, Grenoble, Cedex 9, France
| | - Altuna Akalin
- The Berlin Institute for Medical Systems Biology, Max Delbrück Center, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Dea Slade
- Department of Radiation Oncology, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria.
- Comprehensive Cancer Center, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria.
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Dr. Bohr-Gasse 9, 1030, Vienna, Austria.
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13
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Schumann VF, de Castro Cuadrat RR, Wyler E, Wurmus R, Deter A, Quedenau C, Dohmen J, Faxel M, Borodina T, Blume A, Freimuth J, Meixner M, Grau JH, Liere K, Hackenbeck T, Zietzschmann F, Gnirss R, Böckelmann U, Uyar B, Franke V, Barke N, Altmüller J, Rajewsky N, Landthaler M, Akalin A. SARS-CoV-2 infection dynamics revealed by wastewater sequencing analysis and deconvolution. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 853:158931. [PMID: 36228784 PMCID: PMC9549760 DOI: 10.1016/j.scitotenv.2022.158931] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/27/2022] [Accepted: 09/18/2022] [Indexed: 06/16/2023]
Abstract
The use of RNA sequencing from wastewater samples is a valuable way for estimating infection dynamics and circulating lineages of SARS-CoV-2. This approach is independent from testing individuals and can therefore become the key tool to monitor this and potentially other viruses. However, it is equally important to develop easily accessible and scalable tools which can highlight critical changes in infection rates and dynamics over time across different locations given sequencing data from wastewater. Here, we provide an analysis of lineage dynamics in Berlin and New York City using wastewater sequencing and present PiGx SARS-CoV-2, a highly reproducible computational analysis pipeline with comprehensive reports. This end-to-end pipeline includes all steps from raw data to shareable reports, additional taxonomic analysis, deconvolution and geospatial time series analyses. Using simulated datasets (in silico generated and spiked-in samples) we could demonstrate the accuracy of our pipeline calculating proportions of Variants of Concern (VOC) from environmental as well as pre-mixed samples (spiked-in). By applying our pipeline on a dataset of wastewater samples from Berlin between February 2021 and January 2022, we could reconstruct the emergence of B.1.1.7(alpha) in February/March 2021 and the replacement dynamics from B.1.617.2 (delta) to BA.1 and BA.2 (omicron) during the winter of 2021/2022. Using data from very-short-reads generated in an industrial scale setting, we could see even higher accuracy in our deconvolution. Lastly, using a targeted sequencing dataset from New York City (receptor-binding-domain (RBD) only), we could reproduce the results recovering the proportions of the so-called cryptic lineages shown in the original study. Overall our study provides an in-depth analysis reconstructing virus lineage dynamics from wastewater. While applying our tool on a wide range of different datasets (from different types of wastewater sample locations and sequenced with different methods), we show that PiGx SARS-CoV-2 can be used to identify new mutations and detect any emerging new lineages in a highly automated and scalable way. Our approach can support efforts to establish continuous monitoring and early-warning projects for detecting SARS-CoV-2 or any other pathogen.
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Affiliation(s)
- Vic-Fabienne Schumann
- Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany
| | - Rafael Ricardo de Castro Cuadrat
- Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany
| | - Emanuel Wyler
- RNA Biology and Posttranscriptional Regulation, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany
| | - Ricardo Wurmus
- Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany
| | - Aylina Deter
- RNA Biology and Posttranscriptional Regulation, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany
| | - Claudia Quedenau
- Genomics Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany
| | - Jan Dohmen
- Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany
| | - Miriam Faxel
- Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany
| | - Tatiana Borodina
- Genomics Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany
| | - Alexander Blume
- Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany
| | - Jonas Freimuth
- Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany
| | | | | | | | | | | | | | | | - Bora Uyar
- Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany
| | - Vedran Franke
- Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany
| | - Niclas Barke
- RNA Biology and Posttranscriptional Regulation, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany
| | - Janine Altmüller
- Genomics Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany
| | - Nikolaus Rajewsky
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany.
| | - Markus Landthaler
- RNA Biology and Posttranscriptional Regulation, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany.
| | - Altuna Akalin
- Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany.
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14
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Kim H, Sim M, Park N, Kwon K, Kim J, Kim J. msPIPE: a pipeline for the analysis and visualization of whole-genome bisulfite sequencing data. BMC Bioinformatics 2022; 23:383. [PMID: 36123620 PMCID: PMC9487059 DOI: 10.1186/s12859-022-04925-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 09/13/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA methylation is an important epigenetic modification that is known to regulate gene expression. Whole-genome bisulfite sequencing (WGBS) is a powerful method for studying cytosine methylation in a whole genome. However, it is difficult to obtain methylation profiles using the WGBS raw reads and is necessary to be proficient in all types of bioinformatic tools for the study of DNA methylation. In addition, recent end-to-end pipelines for DNA methylation analyses are not sufficient for addressing those difficulties. RESULTS Here we present msPIPE, a pipeline for DNA methylation analyses with WGBS data seamlessly connecting all the required tasks ranging from data pre-processing to multiple downstream DNA methylation analyses. The msPIPE can generate various methylation profiles to analyze methylation patterns in the given sample, including statistical summaries and methylation levels. Also, the methylation levels in the functional regions of a genome are computed with proper annotation. The results of methylation profiles, hypomethylation, and differential methylation analysis are plotted in publication-quality figures. The msPIPE can be easily and conveniently used with a Docker image, which includes all dependent packages and software related to DNA methylation analyses. CONCLUSION msPIPE is a new end-to-end pipeline designed for methylation calling, profiling, and various types of downstream DNA methylation analyses, leading to the creation of publication-quality figures. msPIPE allows researchers to process and analyze the WGBS data in an easy and convenient way. It is available at https://github.com/jkimlab/msPIPE and https://hub.docker.com/r/jkimlab/mspipe .
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Affiliation(s)
- Heesun Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Mikang Sim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Nayoung Park
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Kisang Kwon
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Junyoung Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Jaebum Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea.
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15
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Sztanka-Toth TR, Jens M, Karaiskos N, Rajewsky N. Spacemake: processing and analysis of large-scale spatial transcriptomics data. Gigascience 2022; 11:6646447. [PMID: 35852420 PMCID: PMC9295369 DOI: 10.1093/gigascience/giac064] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/10/2022] [Accepted: 05/31/2022] [Indexed: 01/24/2023] Open
Abstract
Background Spatial sequencing methods increasingly gain popularity within RNA biology studies. State-of-the-art techniques quantify messenger RNA expression levels from tissue sections and at the same time register information about the original locations of the molecules in the tissue. The resulting data sets are processed and analyzed by accompanying software that, however, is incompatible across inputs from different technologies. Findings Here, we present spacemake, a modular, robust, and scalable spatial transcriptomics pipeline built in Snakemake and Python. Spacemake is designed to handle all major spatial transcriptomics data sets and can be readily configured for other technologies. It can process and analyze several samples in parallel, even if they stem from different experimental methods. Spacemake's unified framework enables reproducible data processing from raw sequencing data to automatically generated downstream analysis reports. Spacemake is built with a modular design and offers additional functionality such as sample merging, saturation analysis, and analysis of long reads as separate modules. Moreover, spacemake employs novoSpaRc to integrate spatial and single-cell transcriptomics data, resulting in increased gene counts for the spatial data set. Spacemake is open source and extendable, and it can be seamlessly integrated with existing computational workflows.
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Affiliation(s)
- Tamas Ryszard Sztanka-Toth
- Systems Biology of Gene Regulatory Elements, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), 10115 Berlin, Germany.,Humboldt-Universität zu Berlin, Institut für Biologie, 10099 Berlin, Germany
| | - Marvin Jens
- Systems Biology of Gene Regulatory Elements, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), 10115 Berlin, Germany
| | - Nikos Karaiskos
- Systems Biology of Gene Regulatory Elements, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), 10115 Berlin, Germany
| | - Nikolaus Rajewsky
- Systems Biology of Gene Regulatory Elements, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), 10115 Berlin, Germany.,Humboldt-Universität zu Berlin, Institut für Biologie, 10099 Berlin, Germany.,DZHK (German Center for Cardiovascular Research), Partner Site Berlin, 10117 Berlin, Germany.,Department of Pediatric Oncology, Universitätsmedizin Charité, 13353 Berlin, Germany
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16
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SUMOylation of the chromodomain factor MRG-1 in C. elegans affects chromatin-regulatory dynamics. Biotechniques 2022; 73:5-17. [PMID: 35698829 DOI: 10.2144/btn-2021-0075] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Epigenetic mechanisms control chromatin accessibility and gene expression to ensure proper cell fate specification. Histone proteins are integral chromatin components, and their modification promotes gene expression regulation. Specific proteins recognize modified histones such as the chromodomain protein MRG-1. MRG-1 is the Caenorhabditis elegans ortholog of mammalian MRG15, which is involved in DNA repair. MRG-1 binds methylated histone H3 and is important for germline maturation and safeguarding. To elucidate interacting proteins that modulate MRG-1 activity, we performed in-depth protein-protein interaction analysis using immunoprecipitations coupled with mass spectrometry. We detected strong association with the Small ubiquitin-like modifier SUMO, and found that MRG-1 is post-translationally modified by SUMO. SUMOylation affects chromatin-binding dynamics of MRG-1, suggesting an epigenetic regulation pathway, which may be conserved.
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Gunturkun MH, Flashner E, Wang T, Mulligan MK, Williams RW, Prins P, Chen H. GeneCup: mining PubMed and GWAS catalog for gene-keyword relationships. G3 (BETHESDA, MD.) 2022; 12:jkac059. [PMID: 35285473 PMCID: PMC9073678 DOI: 10.1093/g3journal/jkac059] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/04/2022] [Indexed: 11/13/2022]
Abstract
Interpreting and integrating results from omics studies typically requires a comprehensive and time consuming survey of extant literature. GeneCup is a literature mining web service that retrieves sentences containing user-provided gene symbols and keywords from PubMed abstracts. The keywords are organized into an ontology and can be extended to include results from human genome-wide association studies. We provide a drug addiction keyword ontology that contains over 300 keywords as an example. The literature search is conducted by querying the PubMed server using a programming interface, which is followed by retrieving abstracts from a local copy of the PubMed archive. The main results presented to the user are sentences where gene symbol and keywords co-occur. These sentences are presented through an interactive graphical interface or as tables. All results are linked to the original abstract in PubMed. In addition, a convolutional neural network is employed to distinguish sentences describing systemic stress from those describing cellular stress. The automated and comprehensive search strategy provided by GeneCup facilitates the integration of new discoveries from omic studies with existing literature. GeneCup is free and open source software. The source code of GeneCup and the link to a running instance is available at https://github.com/hakangunturkun/GeneCup.
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Affiliation(s)
- Mustafa H Gunturkun
- Department of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Science, Memphis, TN 38103, USA
| | - Efraim Flashner
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science, Memphis, TN 38103, USA
| | - Tengfei Wang
- Department of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Science, Memphis, TN 38103, USA
| | - Megan K Mulligan
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science, Memphis, TN 38103, USA
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science, Memphis, TN 38103, USA
| | - Pjotr Prins
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science, Memphis, TN 38103, USA
| | - Hao Chen
- Department of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Science, Memphis, TN 38103, USA
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18
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GEMmaker: process massive RNA-seq datasets on heterogeneous computational infrastructure. BMC Bioinformatics 2022; 23:156. [PMID: 35501696 PMCID: PMC9063052 DOI: 10.1186/s12859-022-04629-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 03/07/2022] [Indexed: 11/17/2022] Open
Abstract
Background Quantification of gene expression from RNA-seq data is a prerequisite for transcriptome analysis such as differential gene expression analysis and gene co-expression network construction. Individual RNA-seq experiments are larger and combining multiple experiments from sequence repositories can result in datasets with thousands of samples. Processing hundreds to thousands of RNA-seq data can result in challenges related to data management, access to sufficient computational resources, navigation of high-performance computing (HPC) systems, installation of required software dependencies, and reproducibility. Processing of larger and deeper RNA-seq experiments will become more common as sequencing technology matures. Results GEMmaker, is a nf-core compliant, Nextflow workflow, that quantifies gene expression from small to massive RNA-seq datasets. GEMmaker ensures results are highly reproducible through the use of versioned containerized software that can be executed on a single workstation, institutional compute cluster, Kubernetes platform or the cloud. GEMmaker supports popular alignment and quantification tools providing results in raw and normalized formats. GEMmaker is unique in that it can scale to process thousands of local or remote stored samples without exceeding available data storage. Conclusions Workflows that quantify gene expression are not new, and many already address issues of portability, reusability, and scale in terms of access to CPUs. GEMmaker provides these benefits and adds the ability to scale despite low data storage infrastructure. This allows users to process hundreds to thousands of RNA-seq samples even when data storage resources are limited. GEMmaker is freely available and fully documented with step-by-step setup and execution instructions. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04629-7.
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19
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Gong T, Borgard H, Zhang Z, Chen S, Gao Z, Deng Y. Analysis and Performance Assessment of the Whole Genome Bisulfite Sequencing Data Workflow: Currently Available Tools and a Practical Guide to Advance DNA Methylation Studies. SMALL METHODS 2022; 6:e2101251. [PMID: 35064762 PMCID: PMC8963483 DOI: 10.1002/smtd.202101251] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/30/2021] [Indexed: 05/09/2023]
Abstract
DNA methylation is associated with transcriptional repression, genomic imprinting, stem cell differentiation, embryonic development, and inflammation. Aberrant DNA methylation can indicate disease states, including cancer and neurological disorders. Therefore, the prevalence and location of 5-methylcytosine in the human genome is a topic of interest. Whole-genome bisulfite sequencing (WGBS) is a high-throughput method for analyzing DNA methylation. This technique involves library preparation, alignment, and quality control. Advancements in epigenetic technology have led to an increase in DNA methylation studies. This review compares the detailed experimental methodology of WGBS using accessible and up-to-date analysis tools. Practical codes for WGBS data processing are included as a general guide to assist progress in DNA methylation studies through a comprehensive case study.
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Affiliation(s)
- Ting Gong
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu HI 96813, USA
| | - Heather Borgard
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu HI 96813, USA
| | - Zao Zhang
- Department of Medicine, The Queen’s Medical Center, Honolulu HI 96813, USA
| | - Shaoqiu Chen
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu HI 96813, USA
| | - Zitong Gao
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu HI 96813, USA
| | - Youping Deng
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu HI 96813, USA
- Correspondence: Youping Deng,
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20
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Hüther P, Hagmann J, Nunn A, Kakoulidou I, Pisupati R, Langenberger D, Weigel D, Johannes F, Schultheiss SJ, Becker C. MethylScore, a pipeline for accurate and context-aware identification of differentially methylated regions from population-scale plant whole-genome bisulfite sequencing data. QUANTITATIVE PLANT BIOLOGY 2022; 3:e19. [PMID: 37077980 PMCID: PMC10095865 DOI: 10.1017/qpb.2022.14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 07/14/2022] [Accepted: 07/15/2022] [Indexed: 05/03/2023]
Abstract
Whole-genome bisulfite sequencing (WGBS) is the standard method for profiling DNA methylation at single-nucleotide resolution. Different tools have been developed to extract differentially methylated regions (DMRs), often built upon assumptions from mammalian data. Here, we present MethylScore, a pipeline to analyse WGBS data and to account for the substantially more complex and variable nature of plant DNA methylation. MethylScore uses an unsupervised machine learning approach to segment the genome by classification into states of high and low methylation. It processes data from genomic alignments to DMR output and is designed to be usable by novice and expert users alike. We show how MethylScore can identify DMRs from hundreds of samples and how its data-driven approach can stratify associated samples without prior information. We identify DMRs in the A. thaliana 1,001 Genomes dataset to unveil known and unknown genotype-epigenotype associations .
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Affiliation(s)
- Patrick Hüther
- Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030 Vienna, Austria
- LMU Biocenter, Faculty of Biology, Ludwig-Maximilians-University Munich, 82152 Martinsried, Germany
| | | | - Adam Nunn
- ecSeq Bioinformatics GmbH, 04103 Leipzig, Germany
- Department of Computer Science, Leipzig University, 04107 Leipzig, Germany
| | - Ioanna Kakoulidou
- Department of Plant Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Rahul Pisupati
- Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030 Vienna, Austria
| | | | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
| | - Frank Johannes
- Department of Plant Sciences, Technical University of Munich, 85354 Freising, Germany
- Institute for Advanced Study, Technical University of Munich, 85748 Garching, Germany
| | | | - Claude Becker
- Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030 Vienna, Austria
- LMU Biocenter, Faculty of Biology, Ludwig-Maximilians-University Munich, 82152 Martinsried, Germany
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21
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Arora D, Park JE, Lim D, Choi BH, Cho IC, Srikanth K, Kim J, Park W. Comparative methylation and RNA-seq expression analysis in CpG context to identify genes involved in Backfat vs. Liver diversification in Nanchukmacdon Pig. BMC Genomics 2021; 22:801. [PMID: 34743693 PMCID: PMC8573883 DOI: 10.1186/s12864-021-08123-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 10/25/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND DNA methylation and demethylation at CpG islands is one of the main regulatory factors that allow cells to respond to different stimuli. These regulatory mechanisms help in developing tissue without affecting the genomic composition or undergoing selection. Liver and backfat play important roles in regulating lipid metabolism and control various pathways involved in reproductive performance, meat quality, and immunity. Genes inside these tissue store a plethora of information and an understanding of these genes is required to enhance tissue characteristics in the future generation. RESULTS A total of 16 CpG islands were identified, and they were involved in differentially methylation regions (DMRs) as well as differentially expressed genes (DEGs) of liver and backfat tissue samples. The genes C7orf50, ACTB and MLC1 in backfat and TNNT3, SIX2, SDK1, CLSTN3, LTBP4, CFAP74, SLC22A23, FOXC1, GMDS, GSC, GATA4, SEMA5A and HOXA5 in the liver, were categorized as differentially-methylated. Subsequently, Motif analysis for DMRs was performed to understand the role of the methylated motif for tissue-specific differentiation. Gene ontology studies revealed association with collagen fibril organization, the Bone Morphogenetic Proteins (BMP) signaling pathway in backfat and cholesterol biosynthesis, bile acid and bile salt transport, and immunity-related pathways in methylated genes expressed in the liver. CONCLUSIONS In this study, to understand the role of genes in the differentiation process, we have performed whole-genome bisulfite sequencing (WGBS) and RNA-seq analysis of Nanchukmacdon pigs. Methylation and motif analysis reveals the critical role of CpG islands and transcriptional factors binding site (TFBS) in guiding the differential patterns. Our findings could help in understanding how methylation of certain genes plays an important role and can be used as biomarkers to study tissue specific characteristics.
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Affiliation(s)
- Devender Arora
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, 55365, Wanju, Republic of Korea
| | - Jong-Eun Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, 55365, Wanju, Republic of Korea
| | - Dajeong Lim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, 55365, Wanju, Republic of Korea
| | - Bong-Hwan Choi
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, 55365, Wanju, Republic of Korea
| | - In-Cheol Cho
- Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, 63242, Jeju, Korea
| | - Krishnamoorthy Srikanth
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, 55365, Wanju, Republic of Korea
- Department of Animal Science, Cornell University, NY, 14853, Ithaca, USA
| | - Jaebum Kim
- Department of Biomedical Science and Engineering, Konkuk University, 05029, Seoul, Republic of Korea
| | - Woncheoul Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, 55365, Wanju, Republic of Korea.
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22
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Appel LM, Franke V, Bruno M, Grishkovskaya I, Kasiliauskaite A, Kaufmann T, Schoeberl UE, Puchinger MG, Kostrhon S, Ebenwaldner C, Sebesta M, Beltzung E, Mechtler K, Lin G, Vlasova A, Leeb M, Pavri R, Stark A, Akalin A, Stefl R, Bernecky C, Djinovic-Carugo K, Slade D. PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. Nat Commun 2021; 12:6078. [PMID: 34667177 PMCID: PMC8526623 DOI: 10.1038/s41467-021-26360-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 09/29/2021] [Indexed: 12/16/2022] Open
Abstract
The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) is a regulatory hub for transcription and RNA processing. Here, we identify PHD-finger protein 3 (PHF3) as a regulator of transcription and mRNA stability that docks onto Pol II CTD through its SPOC domain. We characterize SPOC as a CTD reader domain that preferentially binds two phosphorylated Serine-2 marks in adjacent CTD repeats. PHF3 drives liquid-liquid phase separation of phosphorylated Pol II, colocalizes with Pol II clusters and tracks with Pol II across the length of genes. PHF3 knock-out or SPOC deletion in human cells results in increased Pol II stalling, reduced elongation rate and an increase in mRNA stability, with marked derepression of neuronal genes. Key neuronal genes are aberrantly expressed in Phf3 knock-out mouse embryonic stem cells, resulting in impaired neuronal differentiation. Our data suggest that PHF3 acts as a prominent effector of neuronal gene regulation by bridging transcription with mRNA decay.
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Affiliation(s)
- Lisa-Marie Appel
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Vedran Franke
- The Berlin Institute for Medical Systems Biology, Max Delbrück Center, Berlin, Germany
| | - Melania Bruno
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Irina Grishkovskaya
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Aiste Kasiliauskaite
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Tanja Kaufmann
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Ursula E Schoeberl
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Martin G Puchinger
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Sebastian Kostrhon
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Carmen Ebenwaldner
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Marek Sebesta
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Etienne Beltzung
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, Vienna Biocenter (VBC), Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Gen Lin
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, Vienna Biocenter (VBC), Vienna, Austria
| | - Anna Vlasova
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, Vienna Biocenter (VBC), Vienna, Austria
| | - Martin Leeb
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Rushad Pavri
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, Vienna Biocenter (VBC), Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, Vienna Biocenter (VBC), Vienna, Austria
| | - Altuna Akalin
- The Berlin Institute for Medical Systems Biology, Max Delbrück Center, Berlin, Germany
| | - Richard Stefl
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Carrie Bernecky
- Institute of Science and Technology Austria (IST Austria), Am Campus 1, Klosterneuburg, Austria
| | - Kristina Djinovic-Carugo
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
- Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Dea Slade
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria.
- Department of Radiation Oncology, Medical University of Vienna, Vienna, Austria.
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria.
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23
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Ma L, Peterson EA, Shin IJ, Muesse J, Marino K, Steliga MA, Johann DJ. NPARS-A Novel Approach to Address Accuracy and Reproducibility in Genomic Data Science. Front Big Data 2021; 4:725095. [PMID: 34647017 PMCID: PMC8503682 DOI: 10.3389/fdata.2021.725095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/07/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Accuracy and reproducibility are vital in science and presents a significant challenge in the emerging discipline of data science, especially when the data are scientifically complex and massive in size. Further complicating matters, in the field of genomic-based science high-throughput sequencing technologies generate considerable amounts of data that needs to be stored, manipulated, and analyzed using a plethora of software tools. Researchers are rarely able to reproduce published genomic studies. Results: Presented is a novel approach which facilitates accuracy and reproducibility for large genomic research data sets. All data needed is loaded into a portable local database, which serves as an interface for well-known software frameworks. These include python-based Jupyter Notebooks and the use of RStudio projects and R markdown. All software is encapsulated using Docker containers and managed by Git, simplifying software configuration management. Conclusion: Accuracy and reproducibility in science is of a paramount importance. For the biomedical sciences, advances in high throughput technologies, molecular biology and quantitative methods are providing unprecedented insights into disease mechanisms. With these insights come the associated challenge of scientific data that is complex and massive in size. This makes collaboration, verification, validation, and reproducibility of findings difficult. To address these challenges the NGS post-pipeline accuracy and reproducibility system (NPARS) was developed. NPARS is a robust software infrastructure and methodology that can encapsulate data, code, and reporting for large genomic studies. This paper demonstrates the successful use of NPARS on large and complex genomic data sets across different computational platforms.
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Affiliation(s)
- Li Ma
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States
- Department of Information Science, University of Arkansas at Little Rock, Little Rock, AR, United States
| | - Erich A. Peterson
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Ik Jae Shin
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Jason Muesse
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Katy Marino
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Matthew A. Steliga
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Donald J. Johann
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States
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24
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Froehlich JJ, Uyar B, Herzog M, Theil K, Glažar P, Akalin A, Rajewsky N. Parallel genetics of regulatory sequences using scalable genome editing in vivo. Cell Rep 2021; 35:108988. [PMID: 33852857 DOI: 10.1016/j.celrep.2021.108988] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 01/13/2021] [Accepted: 03/23/2021] [Indexed: 12/27/2022] Open
Abstract
How regulatory sequences control gene expression is fundamental for explaining phenotypes in health and disease. Regulatory elements must ultimately be understood within their genomic environment and development- or tissue-specific contexts. Because this is technically challenging, few regulatory elements have been characterized in vivo. Here, we use inducible Cas9 and multiplexed guide RNAs to create hundreds of mutations in enhancers/promoters and 3' UTRs of 16 genes in C. elegans. Our software crispr-DART analyzes indel mutations in targeted DNA sequencing. We quantify the impact of mutations on expression and fitness by targeted RNA sequencing and DNA sampling. When applying our approach to the lin-41 3' UTR, generating hundreds of mutants, we find that the two adjacent binding sites for the miRNA let-7 can regulate lin-41 expression independently of each other. Finally, we map regulatory genotypes to phenotypic traits for several genes. Our approach enables parallel analysis of regulatory sequences directly in animals.
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Affiliation(s)
- Jonathan J Froehlich
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Bora Uyar
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Margareta Herzog
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Kathrin Theil
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Petar Glažar
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Altuna Akalin
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Nikolaus Rajewsky
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany.
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25
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Arora D, Srikanth K, Lee J, Lee D, Park N, Wy S, Kim H, Park JE, Chai HH, Lim D, Cho IC, Kim J, Park W. Integration of multi-omics approaches for functional characterization of muscle related selective sweep genes in Nanchukmacdon. Sci Rep 2021; 11:7219. [PMID: 33785872 PMCID: PMC8009959 DOI: 10.1038/s41598-021-86683-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/12/2021] [Indexed: 02/01/2023] Open
Abstract
Pig as a food source serves daily dietary demand to a wide population around the world. Preference of meat depends on various factors with muscle play the central role. In this regards, selective breeding abled us to develop "Nanchukmacdon" a pig breeds with an enhanced variety of meat and high fertility rate. To identify genomic regions under selection we performed whole-genome resequencing, transcriptome, and whole-genome bisulfite sequencing from Nanchukmacdon muscles samples and used published data for three other breeds such as Landrace, Duroc, Jeju native pig and analyzed the functional characterization of candidate genes. In this study, we present a comprehensive approach to identify candidate genes by using multi-omics approaches. We performed two different methods XP-EHH, XP-CLR to identify traces of artificial selection for traits of economic importance. Moreover, RNAseq analysis was done to identify differentially expressed genes in the crossed breed population. Several genes (UGT8, ZGRF1, NDUFA10, EBF3, ELN, UBE2L6, NCALD, MELK, SERP2, GDPD5, and FHL2) were identified as selective sweep and differentially expressed in muscles related pathways. Furthermore, nucleotide diversity analysis revealed low genetic diversity in Nanchukmacdon for identified genes in comparison to related breeds and whole-genome bisulfite sequencing data shows the critical role of DNA methylation pattern in identified genes that leads to enhanced variety of meat. This work demonstrates a way to identify the molecular signature and lays a foundation for future genomic enabled pig breeding.
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Affiliation(s)
- Devender Arora
- grid.484502.f0000 0004 5935 1171Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365 Republic of Korea
| | - Krishnamoorthy Srikanth
- grid.484502.f0000 0004 5935 1171Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365 Republic of Korea ,grid.5386.8000000041936877XDepartment of Animal Science, Cornell University, Ithaca, NY 14853 USA
| | - Jongin Lee
- grid.258676.80000 0004 0532 8339Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Daehwan Lee
- grid.258676.80000 0004 0532 8339Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Nayoung Park
- grid.258676.80000 0004 0532 8339Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Suyeon Wy
- grid.258676.80000 0004 0532 8339Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Hyeonji Kim
- grid.258676.80000 0004 0532 8339Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Jong-Eun Park
- grid.484502.f0000 0004 5935 1171Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365 Republic of Korea
| | - Han-Ha Chai
- grid.484502.f0000 0004 5935 1171Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365 Republic of Korea
| | - Dajeong Lim
- grid.484502.f0000 0004 5935 1171Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365 Republic of Korea
| | - In-Cheol Cho
- grid.484502.f0000 0004 5935 1171Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, Jeju, 63242 Korea
| | - Jaebum Kim
- grid.258676.80000 0004 0532 8339Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Woncheoul Park
- grid.484502.f0000 0004 5935 1171Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365 Republic of Korea
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26
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Delgado-Benito V, Berruezo-Llacuna M, Altwasser R, Winkler W, Sundaravinayagam D, Balasubramanian S, Caganova M, Graf R, Rahjouei A, Henke MT, Driesner M, Keller L, Prigione A, Janz M, Akalin A, Di Virgilio M. PDGFA-associated protein 1 protects mature B lymphocytes from stress-induced cell death and promotes antibody gene diversification. J Exp Med 2021; 217:151913. [PMID: 32609329 PMCID: PMC7537392 DOI: 10.1084/jem.20200137] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 04/20/2020] [Accepted: 05/19/2020] [Indexed: 12/13/2022] Open
Abstract
The establishment of protective humoral immunity is dependent on the ability of mature B cells to undergo antibody gene diversification while adjusting to the physiological stressors induced by activation with the antigen. Mature B cells diversify their antibody genes by class switch recombination (CSR) and somatic hypermutation (SHM), which are both dependent on efficient induction of activation-induced cytidine deaminase (AID). Here, we identified PDGFA-associated protein 1 (Pdap1) as an essential regulator of cellular homeostasis in mature B cells. Pdap1 deficiency leads to sustained expression of the integrated stress response (ISR) effector activating transcription factor 4 (Atf4) and induction of the ISR transcriptional program, increased cell death, and defective AID expression. As a consequence, loss of Pdap1 reduces germinal center B cell formation and impairs CSR and SHM. Thus, Pdap1 protects mature B cells against chronic ISR activation and ensures efficient antibody diversification by promoting their survival and optimal function.
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Affiliation(s)
- Verónica Delgado-Benito
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Maria Berruezo-Llacuna
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Robert Altwasser
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Bioinformatics and Omics Data Science Technology Platform, Berlin Institute of Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Wiebke Winkler
- Laboratory of Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Laboratory of Biology of Malignant Lymphomas, Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité, University Medicine, Berlin, Germany
| | - Devakumar Sundaravinayagam
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Sandhya Balasubramanian
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Marieta Caganova
- Laboratory of Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Robin Graf
- Laboratory of Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Ali Rahjouei
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Marie-Thérèse Henke
- Laboratory of Mitochondria and Cell Fate Reprogramming, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Madlen Driesner
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Lisa Keller
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Alessandro Prigione
- Laboratory of Mitochondria and Cell Fate Reprogramming, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Department of General Pediatrics, Neonatology and Pediatric Cardiology, University Children's Hospital, Heinrich Heine University, Düsseldorf, Germany
| | - Martin Janz
- Laboratory of Biology of Malignant Lymphomas, Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité, University Medicine, Berlin, Germany
| | - Altuna Akalin
- Bioinformatics and Omics Data Science Technology Platform, Berlin Institute of Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Michela Di Virgilio
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Charité-Universitätsmedizin Berlin, Berlin, Germany
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27
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Miko H, Qiu Y, Gaertner B, Sander M, Ohler U. Inferring time series chromatin states for promoter-enhancer pairs based on Hi-C data. BMC Genomics 2021; 22:84. [PMID: 33509077 PMCID: PMC7841892 DOI: 10.1186/s12864-021-07373-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 01/07/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Co-localized combinations of histone modifications ("chromatin states") have been shown to correlate with promoter and enhancer activity. Changes in chromatin states over multiple time points ("chromatin state trajectories") have previously been analyzed at promoter and enhancers separately. With the advent of time series Hi-C data it is now possible to connect promoters and enhancers and to analyze chromatin state trajectories at promoter-enhancer pairs. RESULTS We present TimelessFlex, a framework for investigating chromatin state trajectories at promoters and enhancers and at promoter-enhancer pairs based on Hi-C information. TimelessFlex extends our previous approach Timeless, a Bayesian network for clustering multiple histone modification data sets at promoter and enhancer feature regions. We utilize time series ATAC-seq data measuring open chromatin to define promoters and enhancer candidates. We developed an expectation-maximization algorithm to assign promoters and enhancers to each other based on Hi-C interactions and jointly cluster their feature regions into paired chromatin state trajectories. We find jointly clustered promoter-enhancer pairs showing the same activation patterns on both sides but with a stronger trend at the enhancer side. While the promoter side remains accessible across the time series, the enhancer side becomes dynamically more open towards the gene activation time point. Promoter cluster patterns show strong correlations with gene expression signals, whereas Hi-C signals get only slightly stronger towards activation. The code of the framework is available at https://github.com/henriettemiko/TimelessFlex . CONCLUSIONS TimelessFlex clusters time series histone modifications at promoter-enhancer pairs based on Hi-C and it can identify distinct chromatin states at promoter and enhancer feature regions and their changes over time.
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Affiliation(s)
- Henriette Miko
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
- Department of Computer Science, Humboldt-Universität zu Berlin, 10117, Berlin, Germany
| | - Yunjiang Qiu
- Ludwig Institute for Cancer Research, La Jolla, CA, 92093, USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Bjoern Gaertner
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Pediatrics, Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Maike Sander
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Pediatrics, Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Uwe Ohler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany.
- Department of Computer Science, Humboldt-Universität zu Berlin, 10117, Berlin, Germany.
- Department of Biology, Humboldt-Universität zu Berlin, 10117, Berlin, Germany.
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28
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Reiter T, Brooks† PT, Irber† L, Joslin† SEK, Reid† CM, Scott† C, Brown CT, Pierce-Ward NT. Streamlining data-intensive biology with workflow systems. Gigascience 2021; 10:giaa140. [PMID: 33438730 PMCID: PMC8631065 DOI: 10.1093/gigascience/giaa140] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 11/06/2020] [Accepted: 11/13/2020] [Indexed: 11/14/2022] Open
Abstract
As the scale of biological data generation has increased, the bottleneck of research has shifted from data generation to analysis. Researchers commonly need to build computational workflows that include multiple analytic tools and require incremental development as experimental insights demand tool and parameter modifications. These workflows can produce hundreds to thousands of intermediate files and results that must be integrated for biological insight. Data-centric workflow systems that internally manage computational resources, software, and conditional execution of analysis steps are reshaping the landscape of biological data analysis and empowering researchers to conduct reproducible analyses at scale. Adoption of these tools can facilitate and expedite robust data analysis, but knowledge of these techniques is still lacking. Here, we provide a series of strategies for leveraging workflow systems with structured project, data, and resource management to streamline large-scale biological analysis. We present these practices in the context of high-throughput sequencing data analysis, but the principles are broadly applicable to biologists working beyond this field.
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Affiliation(s)
- Taylor Reiter
- Department of Population Health and Reproduction, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Phillip T Brooks†
- Department of Population Health and Reproduction, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Luiz Irber†
- Department of Population Health and Reproduction, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Shannon E K Joslin†
- Department of Animal Science, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Charles M Reid†
- Department of Population Health and Reproduction, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Camille Scott†
- Department of Population Health and Reproduction, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - C Titus Brown
- Department of Population Health and Reproduction, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - N Tessa Pierce-Ward
- Department of Population Health and Reproduction, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
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29
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Wesolowski R, Kowenz-Leutz E, Zimmermann K, Dörr D, Hofstätter M, Slany RK, Mildner A, Leutz A. Myeloid transformation by MLL- ENL depends strictly on C/EBP. Life Sci Alliance 2021; 4:e202000709. [PMID: 33144337 PMCID: PMC7652399 DOI: 10.26508/lsa.202000709] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 12/02/2022] Open
Abstract
Chromosomal rearrangements of the mixed-lineage leukemia gene MLL1 are the hallmark of infant acute leukemia. The granulocyte-macrophage progenitor state forms the epigenetic basis for myelomonocytic leukemia stemness and transformation by MLL-type oncoproteins. Previously, it was shown that the establishment of murine myelomonocytic MLL-ENL transformation, but not its maintenance, depends on the transcription factor C/EBPα, suggesting an epigenetic hit-and-run mechanism of MLL-driven oncogenesis. Here, we demonstrate that compound deletion of Cebpa/Cebpb almost entirely abrogated the growth and survival of MLL-ENL-transformed cells. Rare, slow-growing, and apoptosis-prone MLL-ENL-transformed escapees were recovered from compound Cebpa/Cebpb deletions. The escapees were uniformly characterized by high expression of the resident Cebpe gene, suggesting inferior functional compensation of C/EBPα/C/EBPβ deficiency by C/EBPε. Complementation was augmented by ectopic C/EBPβ expression and downstream activation of IGF1 that enhanced growth. Cebpe gene inactivation was accomplished only in the presence of complementing C/EBPβ, but not in its absence, confirming the Cebpe dependency of the Cebpa/Cebpb double knockouts. Our data show that MLL-transformed myeloid cells are dependent on C/EBPs during the initiation and maintenance of transformation.
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Affiliation(s)
| | | | | | - Dorothea Dörr
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | | | - Robert K Slany
- Department of Genetics, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | | | - Achim Leutz
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Institute of Biology, Humboldt University of Berlin, Berlin, Germany
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30
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Kim M, Franke V, Brandt B, Lowenstein ED, Schöwel V, Spuler S, Akalin A, Birchmeier C. Single-nucleus transcriptomics reveals functional compartmentalization in syncytial skeletal muscle cells. Nat Commun 2020; 11:6375. [PMID: 33311457 PMCID: PMC7732842 DOI: 10.1038/s41467-020-20064-9] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 11/09/2020] [Indexed: 11/25/2022] Open
Abstract
Syncytial skeletal muscle cells contain hundreds of nuclei in a shared cytoplasm. We investigated nuclear heterogeneity and transcriptional dynamics in the uninjured and regenerating muscle using single-nucleus RNA-sequencing (snRNAseq) of isolated nuclei from muscle fibers. This revealed distinct nuclear subtypes unrelated to fiber type diversity, previously unknown subtypes as well as the expected ones at the neuromuscular and myotendinous junctions. In fibers of the Mdx dystrophy mouse model, distinct subtypes emerged, among them nuclei expressing a repair signature that were also abundant in the muscle of dystrophy patients, and a nuclear population associated with necrotic fibers. Finally, modifications of our approach revealed the compartmentalization in the rare and specialized muscle spindle. Our data identifies nuclear compartments of the myofiber and defines a molecular roadmap for their functional analyses; the data can be freely explored on the MyoExplorer server ( https://shiny.mdc-berlin.de/MyoExplorer/ ).
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Affiliation(s)
- Minchul Kim
- Developmental Biology/Signal Transduction, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Vedran Franke
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Bettina Brandt
- Developmental Biology/Signal Transduction, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Elijah D Lowenstein
- Developmental Biology/Signal Transduction, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Verena Schöwel
- Muscle Research Unit, Experimental and Clinical Research Center, Charité Universitätsmedizin Berlin and Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Simone Spuler
- Muscle Research Unit, Experimental and Clinical Research Center, Charité Universitätsmedizin Berlin and Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Altuna Akalin
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, Berlin, Germany.
| | - Carmen Birchmeier
- Developmental Biology/Signal Transduction, Max Delbrueck Center for Molecular Medicine, Berlin, Germany.
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31
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Uyar B, Palmer D, Kowald A, Murua Escobar H, Barrantes I, Möller S, Akalin A, Fuellen G. Single-cell analyses of aging, inflammation and senescence. Ageing Res Rev 2020; 64:101156. [PMID: 32949770 PMCID: PMC7493798 DOI: 10.1016/j.arr.2020.101156] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 02/09/2023]
Abstract
Single-cell gene expression (transcriptomics) data are becoming robust and abundant, and are increasingly used to track organisms along their life-course. This allows investigation into how aging affects cellular transcriptomes, and how changes in transcriptomes may underlie aging, including chronic inflammation (inflammaging), immunosenescence and cellular senescence. We compiled and tabulated aging-related single-cell datasets published to date, collected and discussed relevant findings, and inspected some of these datasets ourselves. We specifically note insights that cannot (or not easily) be based on bulk data. For example, in some datasets, the fraction of cells expressing p16 (CDKN2A), one of the most prominent markers of cellular senescence, was reported to increase, in addition to its upregulated mean expression over all cells. Moreover, we found evidence for inflammatory processes in most datasets, some of these driven by specific cells of the immune system. Further, single-cell data are specifically useful to investigate whether transcriptional heterogeneity (also called noise or variability) increases with age, and many (but not all) studies in our review report an increase in such heterogeneity. Finally, we demonstrate some stability of marker gene expression patterns across closely similar studies and suggest that single-cell experiments may hold the key to provide detailed insights whenever interventions (countering aging, inflammation, senescence, disease, etc.) are affecting cells depending on cell type.
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Affiliation(s)
- Bora Uyar
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Daniel Palmer
- Rostock University Medical Center, Institute for Biostatistics and Informatics in Medicine and Aging Research, Rostock, Germany
| | - Axel Kowald
- Rostock University Medical Center, Institute for Biostatistics and Informatics in Medicine and Aging Research, Rostock, Germany
| | - Hugo Murua Escobar
- Rostock University Medical Center, Department of Hematology, Oncology and Palliative Medicine, Department of Medicine III, Rostock, Germany
| | - Israel Barrantes
- Rostock University Medical Center, Institute for Biostatistics and Informatics in Medicine and Aging Research, Rostock, Germany
| | - Steffen Möller
- Rostock University Medical Center, Institute for Biostatistics and Informatics in Medicine and Aging Research, Rostock, Germany
| | - Altuna Akalin
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Georg Fuellen
- Rostock University Medical Center, Institute for Biostatistics and Informatics in Medicine and Aging Research, Rostock, Germany.
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32
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Bedő J, Di Stefano L, Papenfuss AT. Unifying package managers, workflow engines, and containers: Computational reproducibility with BioNix. Gigascience 2020; 9:giaa121. [PMID: 33205815 PMCID: PMC7672450 DOI: 10.1093/gigascience/giaa121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 04/10/2020] [Indexed: 01/22/2023] Open
Abstract
MOTIVATION A challenge for computational biologists is to make our analyses reproducible-i.e. to rerun, combine, and share, with the assurance that equivalent runs will generate identical results. Current best practice aims at this using a combination of package managers, workflow engines, and containers. RESULTS We present BioNix, a lightweight library built on the Nix deployment system. BioNix manages software dependencies, computational environments, and workflow stages together using a single abstraction: pure functions. This lets users specify workflows in a clean, uniform way, with strong reproducibility guarantees. AVAILABILITY AND IMPLEMENTATION BioNix is implemented in the Nix expression language and is released on GitHub under the 3-clause BSD license: https://github.com/PapenfussLab/bionix (biotools:BioNix) (BioNix, RRID:SCR_017662).
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Affiliation(s)
- Justin Bedő
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Pde., Parkville, VIC 3052, Australia
- School of Computing and Information Systems, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Leon Di Stefano
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Pde., Parkville, VIC 3052, Australia
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, 615 N. Wolfe Street, Baltimore, Maryland, U.S.A
| | - Anthony T Papenfuss
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Pde., Parkville, VIC 3052, Australia
- Peter MacCallum Cancer Centre, 305 Grattan St., Melbourne, VIC 3000, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3010, Australia
- School of Mathematics and Statistics, University of Melbourne, Melbourne, VIC 3010, Australia
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33
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Bonnay F, Veloso A, Steinmann V, Köcher T, Abdusselamoglu MD, Bajaj S, Rivelles E, Landskron L, Esterbauer H, Zinzen RP, Knoblich JA. Oxidative Metabolism Drives Immortalization of Neural Stem Cells during Tumorigenesis. Cell 2020; 182:1490-1507.e19. [PMID: 32916131 DOI: 10.1016/j.cell.2020.07.039] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 06/24/2020] [Accepted: 07/28/2020] [Indexed: 01/04/2023]
Abstract
Metabolic reprogramming is a key feature of many cancers, but how and when it contributes to tumorigenesis remains unclear. Here we demonstrate that metabolic reprogramming induced by mitochondrial fusion can be rate-limiting for immortalization of tumor-initiating cells (TICs) and trigger their irreversible dedication to tumorigenesis. Using single-cell transcriptomics, we find that Drosophila brain tumors contain a rapidly dividing stem cell population defined by upregulation of oxidative phosphorylation (OxPhos). We combine targeted metabolomics and in vivo genetic screening to demonstrate that OxPhos is required for tumor cell immortalization but dispensable in neural stem cells (NSCs) giving rise to tumors. Employing an in vivo NADH/NAD+ sensor, we show that NSCs precisely increase OxPhos during immortalization. Blocking OxPhos or mitochondrial fusion stalls TICs in quiescence and prevents tumorigenesis through impaired NAD+ regeneration. Our work establishes a unique connection between cellular metabolism and immortalization of tumor-initiating cells.
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Affiliation(s)
- François Bonnay
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), 1030 Vienna, Austria
| | - Ana Veloso
- Systems Biology of Neurogenesis, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Victoria Steinmann
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), 1030 Vienna, Austria
| | - Thomas Köcher
- Vienna Biocenter Core Facilities (VBCF), 1030 Vienna, Austria
| | | | - Sunanjay Bajaj
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), 1030 Vienna, Austria
| | - Elisa Rivelles
- Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Lisa Landskron
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), 1030 Vienna, Austria
| | - Harald Esterbauer
- Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Robert P Zinzen
- Systems Biology of Neurogenesis, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Juergen A Knoblich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), 1030 Vienna, Austria.
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34
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von Kügelgen N, Chekulaeva M. Conservation of a core neurite transcriptome across neuronal types and species. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1590. [PMID: 32059075 DOI: 10.1002/wrna.1590] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/20/2020] [Accepted: 01/23/2020] [Indexed: 12/23/2022]
Abstract
The intracellular localization of mRNAs allows neurons to control gene expression in neurite extensions (axons and dendrites) and respond rapidly to local stimuli. This plays an important role in diverse processes including neuronal growth and synaptic plasticity, which in turn serves as a foundation for learning and memory. Recent high-throughput analyses have revealed that neurites contain hundreds to thousands of mRNAs, but an analysis comparing the transcriptomes derived from these studies has been lacking. Here we analyze 20 datasets pertaining to neuronal mRNA localization across species and neuronal types and identify a conserved set of mRNAs that had robustly localized to neurites in a high number of the studies. The set includes mRNAs encoding for ribosomal proteins and other components of the translation machinery, mitochondrial proteins, cytoskeletal components, and proteins associated with neurite formation. Our combinatorial analysis provides a unique resource for future hypothesis-driven research. This article is categorized under: RNA Export and Localization > RNA Localization RNA Evolution and Genomics > Computational Analyses of RNA RNA Methods > RNA Analyses in Cells.
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Affiliation(s)
- Nicolai von Kügelgen
- Non-coding RNAs and Mechanisms of Cytoplasmic Gene Regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Marina Chekulaeva
- Non-coding RNAs and Mechanisms of Cytoplasmic Gene Regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
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Müthel S, Uyar B, He M, Krause A, Vitrinel B, Bulut S, Vasiljevic D, Marchal I, Kempa S, Akalin A, Tursun B. The conserved histone chaperone LIN-53 is required for normal lifespan and maintenance of muscle integrity in Caenorhabditis elegans. Aging Cell 2019; 18:e13012. [PMID: 31397537 PMCID: PMC6826145 DOI: 10.1111/acel.13012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/27/2019] [Accepted: 07/02/2019] [Indexed: 12/27/2022] Open
Abstract
Whether extension of lifespan provides an extended time without health deteriorations is an important issue for human aging. However, to which degree lifespan and aspects of healthspan regulation might be linked is not well understood. Chromatin factors could be involved in linking both aging aspects, as epigenetic mechanisms bridge regulation of different biological processes. The epigenetic factor LIN‐53 (RBBP4/7) associates with different chromatin‐regulating complexes to safeguard cell identities in Caenorhabditis elegans as well as mammals, and has a role in preventing memory loss and premature aging in humans. We show that LIN‐53 interacts with the nucleosome remodeling and deacetylase (NuRD) complex in C. elegans muscles to ensure functional muscles during postembryonic development and in adults. While mutants for other NuRD members show a normal lifespan, animals lacking LIN‐53 die early because LIN‐53 depletion affects also the histone deacetylase complex Sin3, which is required for a normal lifespan. To determine why lin‐53 and sin‐3 mutants die early, we performed transcriptome and metabolomic analysis revealing that levels of the disaccharide trehalose are significantly decreased in both mutants. As trehalose is required for normal lifespan in C. elegans, lin‐53 and sin‐3 mutants could be rescued by either feeding with trehalose or increasing trehalose levels via the insulin/IGF1 signaling pathway. Overall, our findings suggest that LIN‐53 is required for maintaining lifespan and muscle integrity through discrete chromatin regulatory mechanisms. Since both LIN‐53 and its mammalian homologs safeguard cell identities, it is conceivable that its implication in lifespan regulation is also evolutionarily conserved.
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Affiliation(s)
- Stefanie Müthel
- Berlin Institute of Medical Systems Biology Berlin Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association Berlin Germany
| | - Bora Uyar
- Berlin Institute of Medical Systems Biology Berlin Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association Berlin Germany
| | - Mei He
- Berlin Institute of Medical Systems Biology Berlin Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association Berlin Germany
| | - Anne Krause
- Berlin Institute of Medical Systems Biology Berlin Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association Berlin Germany
| | - Burcu Vitrinel
- Berlin Institute of Medical Systems Biology Berlin Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association Berlin Germany
| | - Selman Bulut
- Berlin Institute of Medical Systems Biology Berlin Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association Berlin Germany
| | - Djordje Vasiljevic
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association Berlin Germany
| | - Iris Marchal
- Berlin Institute of Medical Systems Biology Berlin Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association Berlin Germany
| | - Stefan Kempa
- Berlin Institute of Medical Systems Biology Berlin Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association Berlin Germany
| | - Altuna Akalin
- Berlin Institute of Medical Systems Biology Berlin Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association Berlin Germany
| | - Baris Tursun
- Berlin Institute of Medical Systems Biology Berlin Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association Berlin Germany
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Wyler E, Franke V, Menegatti J, Kocks C, Boltengagen A, Praktiknjo S, Walch-Rückheim B, Bosse J, Rajewsky N, Grässer F, Akalin A, Landthaler M. Single-cell RNA-sequencing of herpes simplex virus 1-infected cells connects NRF2 activation to an antiviral program. Nat Commun 2019; 10:4878. [PMID: 31653857 PMCID: PMC6814756 DOI: 10.1038/s41467-019-12894-z] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 09/26/2019] [Indexed: 01/10/2023] Open
Abstract
Herpesvirus infection initiates a range of perturbations in the host cell, which remain poorly understood at the level of individual cells. Here, we quantify the transcriptome of single human primary fibroblasts during the first hours of lytic infection with HSV-1. By applying a generalizable analysis scheme, we define a precise temporal order of early viral gene expression and propose a set-wise emergence of viral genes. We identify host cell genes and pathways relevant for infection by combining three different computational approaches: gene and pathway overdispersion analysis, prediction of cell-state transition probabilities, as well as future cell states. One transcriptional program, which correlates with increased resistance to infection, implicates the transcription factor NRF2. Consequently, Bardoxolone methyl and Sulforaphane, two known NRF2 agonists, impair virus production, suggesting that NRF2 activation restricts viral infection. Our study provides insights into early stages of HSV-1 infection and serves as a general blueprint for the investigation of heterogeneous cell states in virus infection.
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Affiliation(s)
- Emanuel Wyler
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Vedran Franke
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Jennifer Menegatti
- Institute of Virology, Saarland University Medical School, Kirrbergerstrasse Haus, 4766421, Homburg/Saar, Germany
| | - Christine Kocks
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Anastasiya Boltengagen
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Samantha Praktiknjo
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Barbara Walch-Rückheim
- Institute of Virology and Center of Human und Molecular Biology, Saarland University, Saarbrücken, Germany
| | - Jens Bosse
- Heinrich Pette Institute (HPI), Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Nikolaus Rajewsky
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Friedrich Grässer
- Institute of Virology, Saarland University Medical School, Kirrbergerstrasse Haus, 4766421, Homburg/Saar, Germany
| | - Altuna Akalin
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125, Berlin, Germany.
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125, Berlin, Germany.
- IRI Life Sciences, Institute für Biologie, Humboldt Universität zu Berlin, Philippstraße 13, 10115, Berlin, Germany.
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Genome-wide analysis of RNA and protein localization and local translation in mESC-derived neurons. Methods 2019; 162-163:31-41. [PMID: 30742998 DOI: 10.1016/j.ymeth.2019.02.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/01/2019] [Accepted: 02/05/2019] [Indexed: 01/18/2023] Open
Abstract
The subcellular localization and translation of mRNAs are fundamental biological processes. In neurons, they underlie cell growth and synaptic plasticity, which serves as a foundation of learning and memory. Multiple approaches have been developed to separate neurons on subcellular compartments - cell bodies (soma) and cell extensions (axons and dendrites) - for further biochemical analyses. Here we describe neurite/soma separation approach in combination with RNA sequencing and proteomic analyses to identify localized and locally translated RNAs and proteins. This approach allows quantification of around 7000 of local proteins and the entire local transcriptome. It provides a powerful tool for investigation of the mechanisms underlying RNA localization and local translation in neurons.
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Wurmus R, Uyar B, Osberg B, Franke V, Gosdschan A, Wreczycka K, Ronen J, Akalin A. PiGx: reproducible genomics analysis pipelines with GNU Guix. Gigascience 2018; 7:5114263. [PMID: 30277498 PMCID: PMC6275446 DOI: 10.1093/gigascience/giy123] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 07/27/2018] [Accepted: 09/24/2018] [Indexed: 11/25/2022] Open
Abstract
In bioinformatics, as well as other computationally intensive research fields, there is a need for workflows that can reliably produce consistent output, from known sources, independent of the software environment or configuration settings of the machine on which they are executed. Indeed, this is essential for controlled comparison between different observations and for the wider dissemination of workflows. However, providing this type of reproducibility and traceability is often complicated by the need to accommodate the myriad dependencies included in a larger body of software, each of which generally comes in various versions. Moreover, in many fields (bioinformatics being a prime example), these versions are subject to continual change due to rapidly evolving technologies, further complicating problems related to reproducibility. Here, we propose a principled approach for building analysis pipelines and managing their dependencies with GNU Guix. As a case study to demonstrate the utility of our approach, we present a set of highly reproducible pipelines called PiGx for the analysis of RNA sequencing, chromatin immunoprecipitation sequencing, bisulfite-treated DNA sequencing, and single-cell resolution RNA sequencing. All pipelines process raw experimental data and generate reports containing publication-ready plots and figures, with interactive report elements and standard observables. Users may install these highly reproducible packages and apply them to their own datasets without any special computational expertise beyond the use of the command line. We hope such a toolkit will provide immediate benefit to laboratory workers wishing to process their own datasets or bioinformaticians seeking to automate all, or parts of, their analyses. In the long term, we hope our approach to reproducibility will serve as a blueprint for reproducible workflows in other areas. Our pipelines, along with their corresponding documentation and sample reports, are available at http://bioinformatics.mdc-berlin.de/pigx.
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Affiliation(s)
- Ricardo Wurmus
- Bioinformatics Platform, The Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Bora Uyar
- Bioinformatics Platform, The Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Brendan Osberg
- Bioinformatics Platform, The Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Vedran Franke
- Bioinformatics Platform, The Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Alexander Gosdschan
- Bioinformatics Platform, The Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Katarzyna Wreczycka
- Bioinformatics Platform, The Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Jonathan Ronen
- Bioinformatics Platform, The Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Altuna Akalin
- Bioinformatics Platform, The Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
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