1
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Bryce-Smith S, Burri D, Gazzara MR, Herrmann CJ, Danecka W, Fitzsimmons CM, Wan YK, Zhuang F, Fansler MM, Fernández JM, Ferret M, Gonzalez-Uriarte A, Haynes S, Herdman C, Kanitz A, Katsantoni M, Marini F, McDonnel E, Nicolet B, Poon CL, Rot G, Schärfen L, Wu PJ, Yoon Y, Barash Y, Zavolan M. Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data. RNA 2023; 29:1839-1855. [PMID: 37816550 PMCID: PMC10653393 DOI: 10.1261/rna.079849.123] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 09/21/2023] [Indexed: 10/12/2023]
Abstract
The tremendous rate with which data is generated and analysis methods emerge makes it increasingly difficult to keep track of their domain of applicability, assumptions, limitations, and consequently, of the efficacy and precision with which they solve specific tasks. Therefore, there is an increasing need for benchmarks, and for the provision of infrastructure for continuous method evaluation. APAeval is an international community effort, organized by the RNA Society in 2021, to benchmark tools for the identification and quantification of the usage of alternative polyadenylation (APA) sites from short-read, bulk RNA-sequencing (RNA-seq) data. Here, we reviewed 17 tools and benchmarked eight on their ability to perform APA identification and quantification, using a comprehensive set of RNA-seq experiments comprising real, synthetic, and matched 3'-end sequencing data. To support continuous benchmarking, we have incorporated the results into the OpenEBench online platform, which allows for continuous extension of the set of methods, metrics, and challenges. We envisage that our analyses will assist researchers in selecting the appropriate tools for their studies, while the containers and reproducible workflows could easily be deployed and extended to evaluate new methods or data sets.
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Affiliation(s)
- Sam Bryce-Smith
- Department of Neuromuscular Diseases, UCL Queen Square Motor Neuron Disease Centre, UCL Queen Square Institute of Neurology, UCL, London WC1N 3BG, United Kingdom
| | - Dominik Burri
- Biozentrum, University of Basel, 4056 Basel, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Matthew R Gazzara
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Christina J Herrmann
- Biozentrum, University of Basel, 4056 Basel, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Weronika Danecka
- Institute for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3FF, United Kingdom
| | - Christina M Fitzsimmons
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Yuk Kei Wan
- Genome Institute of Singapore, Buona Vista, Singapore 138672
- Yong Loo Lin School of Medicine, National University of Singapore, Kent Ridge, Singapore 119228
| | - Farica Zhuang
- Department of Computer and Information Science, School of Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Mervin M Fansler
- Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Graduate Studies, New York, New York 10065, USA
- Cancer Biology and Genetics, Sloan-Kettering Institute, MSKCC, New York, New York 10065, USA
| | - José M Fernández
- Life Sciences Department, Barcelona Supercomputing Center, 08034 Barcelona, Spain
- Spanish National Bioinformatics Institute (INB/ELIXIR-ES), 28029 Madrid, Spain
| | - Meritxell Ferret
- Life Sciences Department, Barcelona Supercomputing Center, 08034 Barcelona, Spain
- Spanish National Bioinformatics Institute (INB/ELIXIR-ES), 28029 Madrid, Spain
| | - Asier Gonzalez-Uriarte
- Life Sciences Department, Barcelona Supercomputing Center, 08034 Barcelona, Spain
- Spanish National Bioinformatics Institute (INB/ELIXIR-ES), 28029 Madrid, Spain
| | - Samuel Haynes
- Institute for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3FF, United Kingdom
| | - Chelsea Herdman
- Department of Neurobiology, University of Utah, Salt Lake City, Utah 84132, USA
| | - Alexander Kanitz
- Biozentrum, University of Basel, 4056 Basel, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Maria Katsantoni
- Biozentrum, University of Basel, 4056 Basel, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Federico Marini
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg-University Mainz, 55118 Mainz, Germany
| | - Euan McDonnel
- Leeds Institute for Data Analytics, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9NL, United Kingdom
| | - Ben Nicolet
- Department of Hematopoiesis, Sanquin Research, Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, 1066 CX Amsterdam, The Netherlands
- Oncode Institute, 3521 AL Utrecht, The Netherlands
| | - Chi-Lam Poon
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, New York 10065, USA
| | - Gregor Rot
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Leonard Schärfen
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Pin-Jou Wu
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076 Tübingen, Germany
| | - Yoseop Yoon
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California Irvine, Irvine, California 92617, USA
| | - Yoseph Barash
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Computer and Information Science, School of Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Mihaela Zavolan
- Biozentrum, University of Basel, 4056 Basel, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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2
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Bryce-Smith S, Burri D, Gazzara MR, Herrmann CJ, Danecka W, Fitzsimmons CM, Wan YK, Zhuang F, Fansler MM, Fernández JM, Ferret M, Gonzalez-Uriarte A, Haynes S, Herdman C, Kanitz A, Katsantoni M, Marini F, McDonnel E, Nicolet B, Poon CL, Rot G, Schärfen L, Wu PJ, Yoon Y, Barash Y, Zavolan M. Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data. bioRxiv 2023:2023.06.23.546284. [PMID: 37425672 PMCID: PMC10327023 DOI: 10.1101/2023.06.23.546284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The tremendous rate with which data is generated and analysis methods emerge makes it increasingly difficult to keep track of their domain of applicability, assumptions, and limitations and consequently, of the efficacy and precision with which they solve specific tasks. Therefore, there is an increasing need for benchmarks, and for the provision of infrastructure for continuous method evaluation. APAeval is an international community effort, organized by the RNA Society in 2021, to benchmark tools for the identification and quantification of the usage of alternative polyadenylation (APA) sites from short-read, bulk RNA-sequencing (RNA-seq) data. Here, we reviewed 17 tools and benchmarked eight on their ability to perform APA identification and quantification, using a comprehensive set of RNA-seq experiments comprising real, synthetic, and matched 3'-end sequencing data. To support continuous benchmarking, we have incorporated the results into the OpenEBench online platform, which allows for seamless extension of the set of methods, metrics, and challenges. We envisage that our analyses will assist researchers in selecting the appropriate tools for their studies. Furthermore, the containers and reproducible workflows generated in the course of this project can be seamlessly deployed and extended in the future to evaluate new methods or datasets.
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Affiliation(s)
- Sam Bryce-Smith
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Dominik Burri
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Matthew R. Gazzara
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Christina J. Herrmann
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Weronika Danecka
- Institute for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Christina M. Fitzsimmons
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Yuk Kei Wan
- Genome Institute of Singapore, Buona Vista, Singapore
- National University of Singapore, Kent Ridge, Singapore
| | - Farica Zhuang
- Department of Computer and Information Science, School of Engineering, University of Pennsylvania, Philadelphia, USA
| | - Mervin M. Fansler
- Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell GraduateStudies, New York, NY, USA
- Cancer Biology and Genetics, Sloan-Kettering Institute, MSKCC, New York, NY, USA
| | - José M. Fernández
- Barcelona Supercomputing Center, Barcelona, Spain
- Spanish National Bioinformatics Institute (INB/ELIXIR-ES)
| | - Meritxell Ferret
- Barcelona Supercomputing Center, Barcelona, Spain
- Spanish National Bioinformatics Institute (INB/ELIXIR-ES)
| | - Asier Gonzalez-Uriarte
- Barcelona Supercomputing Center, Barcelona, Spain
- Spanish National Bioinformatics Institute (INB/ELIXIR-ES)
| | - Samuel Haynes
- Institute for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | | | - Alexander Kanitz
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Maria Katsantoni
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Federico Marini
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI) - UniversityMedical Center of the Johannes Gutenberg, University Mainz, Germany
| | - Euan McDonnel
- Leeds Institute for Data Analytics, School of Molecular and Cellular Biology, University of Leeds, United Kingdom
| | - Ben Nicolet
- Department of Hematopoiesis, Sanquin Research, Landsteiner Laboratory, AmsterdamUMC, University of Amsterdam, and Oncode Institute, Amsterdam, The Netherlands
| | | | - Gregor Rot
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Institute of Molecular Life Sciences, Zurich, Switzerland
| | - Leonard Schärfen
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven CT, USA
| | - Pin-Jou Wu
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Germany
| | - Yoseop Yoon
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California Irvine, Irvine, California, USA
| | - Yoseph Barash
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
- Department of Computer and Information Science, School of Engineering, University of Pennsylvania, Philadelphia, USA
| | - Mihaela Zavolan
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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3
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Ghosh S, Ataman M, Bak M, Börsch A, Schmidt A, Buczak K, Martin G, Dimitriades B, Herrmann CJ, Kanitz A, Zavolan M. CFIm-mediated alternative polyadenylation remodels cellular signaling and miRNA biogenesis. Nucleic Acids Res 2022; 50:3096-3114. [PMID: 35234914 PMCID: PMC8989530 DOI: 10.1093/nar/gkac114] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 01/31/2022] [Accepted: 02/04/2022] [Indexed: 12/13/2022] Open
Abstract
The mammalian cleavage factor I (CFIm) has been implicated in alternative polyadenylation (APA) in a broad range of contexts, from cancers to learning deficits and parasite infections. To determine how the CFIm expression levels are translated into these diverse phenotypes, we carried out a multi-omics analysis of cell lines in which the CFIm25 (NUDT21) or CFIm68 (CPSF6) subunits were either repressed by siRNA-mediated knockdown or over-expressed from stably integrated constructs. We established that >800 genes undergo coherent APA in response to changes in CFIm levels, and they cluster in distinct functional classes related to protein metabolism. The activity of the ERK pathway traces the CFIm concentration, and explains some of the fluctuations in cell growth and metabolism that are observed upon CFIm perturbations. Furthermore, multiple transcripts encoding proteins from the miRNA pathway are targets of CFIm-dependent APA. This leads to an increased biogenesis and repressive activity of miRNAs at the same time as some 3′ UTRs become shorter and presumably less sensitive to miRNA-mediated repression. Our study provides a first systematic assessment of a core set of APA targets that respond coherently to changes in CFIm protein subunit levels (CFIm25/CFIm68). We describe the elicited signaling pathways downstream of CFIm, which improve our understanding of the key role of CFIm in integrating RNA processing with other cellular activities.
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Affiliation(s)
- Souvik Ghosh
- Computational and Systems Biology, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Meric Ataman
- Computational and Systems Biology, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.,Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Maciej Bak
- Computational and Systems Biology, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.,Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Anastasiya Börsch
- Computational and Systems Biology, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.,Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Katarzyna Buczak
- Proteomics Core Facility, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Georges Martin
- Computational and Systems Biology, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Beatrice Dimitriades
- Computational and Systems Biology, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Christina J Herrmann
- Computational and Systems Biology, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.,Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Alexander Kanitz
- Computational and Systems Biology, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.,Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.,Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
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4
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Streese L, Demougin P, Iborra P, Kanitz A, Deiseroth A, Kröpfl JM, Schmidt-Trucksäss A, Zavolan M, Hanssen H. Untargeted sequencing of circulating microRNAs in a healthy and diseased older population. Sci Rep 2022; 12:2991. [PMID: 35194110 PMCID: PMC8863825 DOI: 10.1038/s41598-022-06956-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 01/20/2022] [Indexed: 12/12/2022] Open
Abstract
We performed untargeted profiling of circulating microRNAs (miRNAs) in a well characterized cohort of older adults to verify associations of health and disease-related biomarkers with systemic miRNA expression. Differential expression analysis revealed 30 miRNAs that significantly differed between healthy active, healthy sedentary and sedentary cardiovascular risk patients. Increased expression of miRNAs miR-193b-5p, miR-122-5p, miR-885-3p, miR-193a-5p, miR-34a-5p, miR-505-3p, miR-194-5p, miR-27b-3p, miR-885-5p, miR-23b-5b, miR-365a-3p, miR-365b-3p, miR-22-5p was associated with a higher metabolic risk profile, unfavourable macro- and microvascular health, lower physical activity (PA) as well as cardiorespiratory fitness (CRF) levels. Increased expression of miR-342-3p, miR-1-3p, miR-92b-5p, miR-454-3p, miR-190a-5p and miR-375-3p was associated with a lower metabolic risk profile, favourable macro- and microvascular health as well as higher PA and CRF. Of note, the first two principal components explained as much as 20% and 11% of the data variance. miRNAs and their potential target genes appear to mediate disease- and health-related physiological and pathophysiological adaptations that need to be validated and supported by further downstream analysis in future studies. Clinical Trial Registration: ClinicalTrials.gov: NCT02796976 (https://clinicaltrials.gov/ct2/show/NCT02796976).
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Affiliation(s)
- Lukas Streese
- Department of Sport, Exercise and Health, Medical Faculty, University of Basel, Birsstrasse 320 B, 4052, Basel, Switzerland
| | - Philippe Demougin
- Transfaculty Research Platform Molecular and Cognitive Neurosciences, Life Sciences Training Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Paula Iborra
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Alexander Kanitz
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Arne Deiseroth
- Department of Sport, Exercise and Health, Medical Faculty, University of Basel, Birsstrasse 320 B, 4052, Basel, Switzerland
| | - Julia M Kröpfl
- Department of Sport, Exercise and Health, Medical Faculty, University of Basel, Birsstrasse 320 B, 4052, Basel, Switzerland
| | - Arno Schmidt-Trucksäss
- Department of Sport, Exercise and Health, Medical Faculty, University of Basel, Birsstrasse 320 B, 4052, Basel, Switzerland
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Henner Hanssen
- Department of Sport, Exercise and Health, Medical Faculty, University of Basel, Birsstrasse 320 B, 4052, Basel, Switzerland.
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5
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Rehm HL, Page AJ, Smith L, Adams JB, Alterovitz G, Babb LJ, Barkley MP, Baudis M, Beauvais MJ, Beck T, Beckmann JS, Beltran S, Bernick D, Bernier A, Bonfield JK, Boughtwood TF, Bourque G, Bowers SR, Brookes AJ, Brudno M, Brush MH, Bujold D, Burdett T, Buske OJ, Cabili MN, Cameron DL, Carroll RJ, Casas-Silva E, Chakravarty D, Chaudhari BP, Chen SH, Cherry JM, Chung J, Cline M, Clissold HL, Cook-Deegan RM, Courtot M, Cunningham F, Cupak M, Davies RM, Denisko D, Doerr MJ, Dolman LI, Dove ES, Dursi LJ, Dyke SO, Eddy JA, Eilbeck K, Ellrott KP, Fairley S, Fakhro KA, Firth HV, Fitzsimons MS, Fiume M, Flicek P, Fore IM, Freeberg MA, Freimuth RR, Fromont LA, Fuerth J, Gaff CL, Gan W, Ghanaim EM, Glazer D, Green RC, Griffith M, Griffith OL, Grossman RL, Groza T, Guidry Auvil JM, Guigó R, Gupta D, Haendel MA, Hamosh A, Hansen DP, Hart RK, Hartley DM, Haussler D, Hendricks-Sturrup RM, Ho CW, Hobb AE, Hoffman MM, Hofmann OM, Holub P, Hsu JS, Hubaux JP, Hunt SE, Husami A, Jacobsen JO, Jamuar SS, Janes EL, Jeanson F, Jené A, Johns AL, Joly Y, Jones SJ, Kanitz A, Kato K, Keane TM, Kekesi-Lafrance K, Kelleher J, Kerry G, Khor SS, Knoppers BM, Konopko MA, Kosaki K, Kuba M, Lawson J, Leinonen R, Li S, Lin MF, Linden M, Liu X, Liyanage IU, Lopez J, Lucassen AM, Lukowski M, Mann AL, Marshall J, Mattioni M, Metke-Jimenez A, Middleton A, Milne RJ, Molnár-Gábor F, Mulder N, Munoz-Torres MC, Nag R, Nakagawa H, Nasir J, Navarro A, Nelson TH, Niewielska A, Nisselle A, Niu J, Nyrönen TH, O’Connor BD, Oesterle S, Ogishima S, Ota Wang V, Paglione LA, Palumbo E, Parkinson HE, Philippakis AA, Pizarro AD, Prlic A, Rambla J, Rendon A, Rider RA, Robinson PN, Rodarmer KW, Rodriguez LL, Rubin AF, Rueda M, Rushton GA, Ryan RS, Saunders GI, Schuilenburg H, Schwede T, Scollen S, Senf A, Sheffield NC, Skantharajah N, Smith AV, Sofia HJ, Spalding D, Spurdle AB, Stark Z, Stein LD, Suematsu M, Tan P, Tedds JA, Thomson AA, Thorogood A, Tickle TL, Tokunaga K, Törnroos J, Torrents D, Upchurch S, Valencia A, Guimera RV, Vamathevan J, Varma S, Vears DF, Viner C, Voisin C, Wagner AH, Wallace SE, Walsh BP, Williams MS, Winkler EC, Wold BJ, Wood GM, Woolley JP, Yamasaki C, Yates AD, Yung CK, Zass LJ, Zaytseva K, Zhang J, Goodhand P, North K, Birney E. GA4GH: International policies and standards for data sharing across genomic research and healthcare. Cell Genom 2021; 1:100029. [PMID: 35072136 PMCID: PMC8774288 DOI: 10.1016/j.xgen.2021.100029] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits.
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Affiliation(s)
- Heidi L. Rehm
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Angela J.H. Page
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Global Alliance for Genomics and Health, Toronto, ON, Canada
| | - Lindsay Smith
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Jeremy B. Adams
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Gil Alterovitz
- Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | | | - Michael Baudis
- University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Michael J.S. Beauvais
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- McGill University, Montreal, QC, Canada
| | - Tim Beck
- University of Leicester, Leicester, UK
| | | | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Universitat de Barcelona, Barcelona, Spain
| | - David Bernick
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Tiffany F. Boughtwood
- Australian Genomics, Parkville, VIC, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
| | - Guillaume Bourque
- McGill University, Montreal, QC, Canada
- Canadian Center for Computational Genomics, Montreal, QC, Canada
| | | | | | - Michael Brudno
- Canadian Center for Computational Genomics, Montreal, QC, Canada
- University of Toronto, Toronto, ON, Canada
- University Health Network, Toronto, ON, Canada
- Vector Institute, Toronto, ON, Canada
- Canadian Distributed Infrastructure for Genomics (CanDIG), Toronto, ON, Canada
| | | | - David Bujold
- McGill University, Montreal, QC, Canada
- Canadian Center for Computational Genomics, Montreal, QC, Canada
- Canadian Distributed Infrastructure for Genomics (CanDIG), Toronto, ON, Canada
| | - Tony Burdett
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | - Daniel L. Cameron
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | | | | | | | - Bimal P. Chaudhari
- Nationwide Children’s Hospital, Columbus, OH, USA
- The Ohio State University, Columbus, OH, USA
| | - Shu Hui Chen
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Justina Chung
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Melissa Cline
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | | | | | - Mélanie Courtot
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | | | | | | | | | - L. Jonathan Dursi
- University Health Network, Toronto, ON, Canada
- Canadian Distributed Infrastructure for Genomics (CanDIG), Toronto, ON, Canada
| | | | | | | | | | - Susan Fairley
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Khalid A. Fakhro
- Sidra Medicine, Doha, Qatar
- Weill Cornell Medicine - Qatar, Doha, Qatar
| | - Helen V. Firth
- Wellcome Sanger Institute, Hinxton, UK
- Addenbrooke’s Hospital, Cambridge, UK
| | | | | | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Ian M. Fore
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mallory A. Freeberg
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | - Lauren A. Fromont
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Clara L. Gaff
- Australian Genomics, Parkville, VIC, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Weiniu Gan
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Elena M. Ghanaim
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - David Glazer
- Verily Life Sciences, South San Francisco, CA, USA
| | - Robert C. Green
- Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Malachi Griffith
- Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Obi L. Griffith
- Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | | | | | | | - Roderic Guigó
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Dipayan Gupta
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | - Ada Hamosh
- Johns Hopkins University, Baltimore, MD, USA
| | - David P. Hansen
- Australian Genomics, Parkville, VIC, Australia
- The Australian e-Health Research Centre, CSIRO, Herston, QLD, Australia
| | - Reece K. Hart
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Invitae, San Francisco, CA, USA
- MyOme, Inc, San Bruno, CA, USA
| | | | - David Haussler
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, University of California, Santa Cruz, CA, USA
| | | | | | | | - Michael M. Hoffman
- University of Toronto, Toronto, ON, Canada
- University Health Network, Toronto, ON, Canada
- Vector Institute, Toronto, ON, Canada
| | - Oliver M. Hofmann
- University of Toronto, Toronto, ON, Canada
- University of Melbourne, Melbourne, VIC, Australia
| | - Petr Holub
- BBMRI-ERIC, Graz, Austria
- Masaryk University, Brno, Czech Republic
| | | | | | - Sarah E. Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Ammar Husami
- Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | | | - Saumya S. Jamuar
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Republic of Singapore
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore, Republic of Singapore
| | - Elizabeth L. Janes
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- University of Waterloo, Waterloo, ON, Canada
| | | | - Aina Jené
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Amber L. Johns
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Yann Joly
- McGill University, Montreal, QC, Canada
| | - Steven J.M. Jones
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Alexander Kanitz
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- University of Basel, Basel, Switzerland
| | | | - Thomas M. Keane
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- University of Nottingham, Nottingham, UK
| | - Kristina Kekesi-Lafrance
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- McGill University, Montreal, QC, Canada
| | | | - Giselle Kerry
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Seik-Soon Khor
- National Center for Global Health and Medicine Hospital, Tokyo, Japan
- University of Tokyo, Tokyo, Japan
| | | | | | | | | | | | - Rasko Leinonen
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Stephanie Li
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Global Alliance for Genomics and Health, Toronto, ON, Canada
| | | | - Mikael Linden
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | | | - Isuru Udara Liyanage
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | | | - Alice L. Mann
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Wellcome Sanger Institute, Hinxton, UK
| | | | | | | | - Anna Middleton
- Wellcome Connecting Science, Hinxton, UK
- University of Cambridge, Cambridge, UK
| | - Richard J. Milne
- Wellcome Connecting Science, Hinxton, UK
- University of Cambridge, Cambridge, UK
| | | | - Nicola Mulder
- H3ABioNet, Computational Biology Division, IDM, Faculty of Health Sciences, Cape Town, South Africa
| | | | - Rishi Nag
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Hidewaki Nakagawa
- Japan Agency for Medical Research & Development (AMED), Tokyo, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Arcadi Navarro
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- Barcelonaβeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona, Spain
| | | | - Ania Niewielska
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Amy Nisselle
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
- Human Genetics Society of Australasia Education, Ethics & Social Issues Committee, Alexandria, NSW, Australia
| | - Jeffrey Niu
- University Health Network, Toronto, ON, Canada
| | - Tommi H. Nyrönen
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | | | - Sabine Oesterle
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Vivian Ota Wang
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Emilio Palumbo
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Helen E. Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | | | - Jordi Rambla
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Renee A. Rider
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Peter N. Robinson
- The Jackson Laboratory, Farmington, CT, USA
- University of Connecticut, Farmington, CT, USA
| | - Kurt W. Rodarmer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | - Alan F. Rubin
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Manuel Rueda
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | | | | | - Helen Schuilenburg
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Torsten Schwede
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- University of Basel, Basel, Switzerland
| | | | | | | | - Neerjah Skantharajah
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Heidi J. Sofia
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dylan Spalding
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | | | - Zornitza Stark
- Australian Genomics, Parkville, VIC, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Lincoln D. Stein
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | | | - Patrick Tan
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Republic of Singapore
- Precision Health Research Singapore, Singapore, Republic of Singapore
- Genome Institute of Singapore, Singapore, Republic of Singapore
| | | | - Alastair A. Thomson
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Adrian Thorogood
- McGill University, Montreal, QC, Canada
- University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | | | - Katsushi Tokunaga
- University of Tokyo, Tokyo, Japan
- National Center for Global Health and Medicine, Tokyo, Japan
| | - Juha Törnroos
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | - David Torrents
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- Barcelona Supercomputing Center, Barcelona, Spain
| | - Sean Upchurch
- California Institute of Technology, Pasadena, CA, USA
| | - Alfonso Valencia
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- Barcelona Supercomputing Center, Barcelona, Spain
| | | | - Jessica Vamathevan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Susheel Varma
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- Health Data Research UK, London, UK
| | - Danya F. Vears
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
- Human Genetics Society of Australasia Education, Ethics & Social Issues Committee, Alexandria, NSW, Australia
- Melbourne Law School, University of Melbourne, Parkville, VIC, Australia
| | - Coby Viner
- University of Toronto, Toronto, ON, Canada
- University Health Network, Toronto, ON, Canada
| | | | - Alex H. Wagner
- Nationwide Children’s Hospital, Columbus, OH, USA
- The Ohio State University, Columbus, OH, USA
| | | | | | | | - Eva C. Winkler
- Section of Translational Medical Ethics, University Hospital Heidelberg, Heidelberg, Germany
| | | | | | | | | | - Andrew D. Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Christina K. Yung
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Indoc Research, Toronto, ON, Canada
| | - Lyndon J. Zass
- H3ABioNet, Computational Biology Division, IDM, Faculty of Health Sciences, Cape Town, South Africa
| | - Ksenia Zaytseva
- McGill University, Montreal, QC, Canada
- Canadian Centre for Computational Genomics, Montreal, QC, Canada
| | - Junjun Zhang
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Peter Goodhand
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Kathryn North
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Toronto, Toronto, ON, Canada
- University of Melbourne, Melbourne, VIC, Australia
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- European Molecular Biology Laboratory, Heidelberg, Germany
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6
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Wang Y, Soneson C, Malinowska AL, Laski A, Ghosh S, Kanitz A, Gebert LFR, Robinson MD, Hall J. MiR-CLIP reveals iso-miR selective regulation in the miR-124 targetome. Nucleic Acids Res 2021; 49:25-37. [PMID: 33300035 PMCID: PMC7797034 DOI: 10.1093/nar/gkaa1117] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 10/04/2020] [Accepted: 12/07/2020] [Indexed: 12/15/2022] Open
Abstract
Many microRNAs regulate gene expression via atypical mechanisms, which are difficult to discern using native cross-linking methods. To ascertain the scope of non-canonical miRNA targeting, methods are needed that identify all targets of a given miRNA. We designed a new class of miR-CLIP probe, whereby psoralen is conjugated to the 3p arm of a pre-microRNA to capture targetomes of miR-124 and miR-132 in HEK293T cells. Processing of pre-miR-124 yields miR-124 and a 5′-extended isoform, iso-miR-124. Using miR-CLIP, we identified overlapping targetomes from both isoforms. From a set of 16 targets, 13 were differently inhibited at mRNA/protein levels by the isoforms. Moreover, delivery of pre-miR-124 into cells repressed these targets more strongly than individual treatments with miR-124 and iso-miR-124, suggesting that isomirs from one pre-miRNA may function synergistically. By mining the miR-CLIP targetome, we identified nine G-bulged target-sites that are regulated at the protein level by miR-124 but not isomiR-124. Using structural data, we propose a model involving AGO2 helix-7 that suggests why only miR-124 can engage these sites. In summary, access to the miR-124 targetome via miR-CLIP revealed for the first time how heterogeneous processing of miRNAs combined with non-canonical targeting mechanisms expand the regulatory range of a miRNA.
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Affiliation(s)
- Yuluan Wang
- Institute of Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Charlotte Soneson
- Department of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, 8057, Zurich, Switzerland
| | - Anna L Malinowska
- Institute of Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Artur Laski
- Institute of Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Souvik Ghosh
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | | | - Luca F R Gebert
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Mark D Robinson
- Department of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, 8057, Zurich, Switzerland
| | - Jonathan Hall
- Institute of Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
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7
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Mölder F, Jablonski KP, Letcher B, Hall MB, Tomkins-Tinch CH, Sochat V, Forster J, Lee S, Twardziok SO, Kanitz A, Wilm A, Holtgrewe M, Rahmann S, Nahnsen S, Köster J. Sustainable data analysis with Snakemake. F1000Res 2021; 10:33. [PMID: 34035898 PMCID: PMC8114187 DOI: 10.12688/f1000research.29032.2] [Citation(s) in RCA: 406] [Impact Index Per Article: 135.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/08/2021] [Indexed: 01/22/2023] Open
Abstract
Data analysis often entails a multitude of heterogeneous steps, from the application of various command line tools to the usage of scripting languages like R or Python for the generation of plots and tables. It is widely recognized that data analyses should ideally be conducted in a reproducible way. Reproducibility enables technical validation and regeneration of results on the original or even new data. However, reproducibility alone is by no means sufficient to deliver an analysis that is of lasting impact (i.e., sustainable) for the field, or even just one research group. We postulate that it is equally important to ensure adaptability and transparency. The former describes the ability to modify the analysis to answer extended or slightly different research questions. The latter describes the ability to understand the analysis in order to judge whether it is not only technically, but methodologically valid. Here, we analyze the properties needed for a data analysis to become reproducible, adaptable, and transparent. We show how the popular workflow management system Snakemake can be used to guarantee this, and how it enables an ergonomic, combined, unified representation of all steps involved in data analysis, ranging from raw data processing, to quality control and fine-grained, interactive exploration and plotting of final results.
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Affiliation(s)
- Felix Mölder
- Algorithms for reproducible bioinformatics, Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Kim Philipp Jablonski
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,Swiss Institute of Bioinformatics (SIB), Basel, Switzerland
| | | | | | - Christopher H Tomkins-Tinch
- Broad Institute of MIT and Harvard, Cambridge, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, USA
| | - Vanessa Sochat
- Stanford University Research Computing Center, Stanford University, Stanford, USA
| | - Jan Forster
- Algorithms for reproducible bioinformatics, Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Soohyun Lee
- Biomedical Informatics, Harvard Medical School, Harvard University, Boston, USA
| | - Sven O Twardziok
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Center for Digital Health, Berlin, Germany
| | - Alexander Kanitz
- Biozentrum, University of Basel, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics / ELIXIR Switzerland, Lausanne, Switzerland
| | | | - Manuel Holtgrewe
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Center for Digital Health, Berlin, Germany.,CUBI - Core Unit Bioinformatics, Berlin Institute of Health, Berlin, Germany
| | - Sven Rahmann
- Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Sven Nahnsen
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
| | - Johannes Köster
- Algorithms for reproducible bioinformatics, Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Medical Oncology, Harvard Medical School, Harvard University, Boston, USA
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8
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Mölder F, Jablonski KP, Letcher B, Hall MB, Tomkins-Tinch CH, Sochat V, Forster J, Lee S, Twardziok SO, Kanitz A, Wilm A, Holtgrewe M, Rahmann S, Nahnsen S, Köster J. Sustainable data analysis with Snakemake. F1000Res 2021; 10:33. [PMID: 34035898 DOI: 10.12688/f1000research.29032.1] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/07/2021] [Indexed: 01/22/2023] Open
Abstract
Data analysis often entails a multitude of heterogeneous steps, from the application of various command line tools to the usage of scripting languages like R or Python for the generation of plots and tables. It is widely recognized that data analyses should ideally be conducted in a reproducible way. Reproducibility enables technical validation and regeneration of results on the original or even new data. However, reproducibility alone is by no means sufficient to deliver an analysis that is of lasting impact (i.e., sustainable) for the field, or even just one research group. We postulate that it is equally important to ensure adaptability and transparency. The former describes the ability to modify the analysis to answer extended or slightly different research questions. The latter describes the ability to understand the analysis in order to judge whether it is not only technically, but methodologically valid. Here, we analyze the properties needed for a data analysis to become reproducible, adaptable, and transparent. We show how the popular workflow management system Snakemake can be used to guarantee this, and how it enables an ergonomic, combined, unified representation of all steps involved in data analysis, ranging from raw data processing, to quality control and fine-grained, interactive exploration and plotting of final results.
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Affiliation(s)
- Felix Mölder
- Algorithms for reproducible bioinformatics, Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Kim Philipp Jablonski
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,Swiss Institute of Bioinformatics (SIB), Basel, Switzerland
| | | | | | - Christopher H Tomkins-Tinch
- Broad Institute of MIT and Harvard, Cambridge, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, USA
| | - Vanessa Sochat
- Stanford University Research Computing Center, Stanford University, Stanford, USA
| | - Jan Forster
- Algorithms for reproducible bioinformatics, Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Soohyun Lee
- Biomedical Informatics, Harvard Medical School, Harvard University, Boston, USA
| | - Sven O Twardziok
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Center for Digital Health, Berlin, Germany
| | - Alexander Kanitz
- Biozentrum, University of Basel, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics / ELIXIR Switzerland, Lausanne, Switzerland
| | | | - Manuel Holtgrewe
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Center for Digital Health, Berlin, Germany.,CUBI - Core Unit Bioinformatics, Berlin Institute of Health, Berlin, Germany
| | - Sven Rahmann
- Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Sven Nahnsen
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
| | - Johannes Köster
- Algorithms for reproducible bioinformatics, Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Medical Oncology, Harvard Medical School, Harvard University, Boston, USA
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9
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Herrmann CJ, Schmidt R, Kanitz A, Artimo P, Gruber AJ, Zavolan M. PolyASite 2.0: a consolidated atlas of polyadenylation sites from 3' end sequencing. Nucleic Acids Res 2020; 48:D174-D179. [PMID: 31617559 PMCID: PMC7145510 DOI: 10.1093/nar/gkz918] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/26/2019] [Accepted: 10/14/2019] [Indexed: 12/31/2022] Open
Abstract
Generated by 3′ end cleavage and polyadenylation at alternative polyadenylation (poly(A)) sites, alternative terminal exons account for much of the variation between human transcript isoforms. More than a dozen protocols have been developed so far for capturing and sequencing RNA 3′ ends from a variety of cell types and species. In previous studies, we have used these data to uncover novel regulatory signals and cell type-specific isoforms. Here we present an update of the PolyASite (https://polyasite.unibas.ch) resource of poly(A) sites, constructed from publicly available human, mouse and worm 3′ end sequencing datasets by enforcing uniform quality measures, including the flagging of putative internal priming sites. Through integrated processing of all data, we identified and clustered sites that are closely spaced and share polyadenylation signals, as these are likely the result of stochastic variations in processing. For each cluster, we identified the representative - most frequently processed - site and estimated the relative use in the transcriptome across all samples. We have established a modern web portal for efficient finding, exploration and export of data. Database generation is fully automated, greatly facilitating incorporation of new datasets and the updating of underlying genome resources.
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Affiliation(s)
| | - Ralf Schmidt
- Biozentrum, University of Basel, Basel, Switzerland
| | | | - Panu Artimo
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Andreas J Gruber
- Oxford Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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10
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Kanitz A, Kalus MR, Gurevich EL, Ostendorf A, Barcikowski S, Amans D. Review on experimental and theoretical investigations of the early stage, femtoseconds to microseconds processes during laser ablation in liquid-phase for the synthesis of colloidal nanoparticles. ACTA ACUST UNITED AC 2019. [DOI: 10.1088/1361-6595/ab3dbe] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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11
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Iadevaia V, Wouters MD, Kanitz A, Matia-González AM, Laing EE, Gerber AP. Tandem RNA isolation reveals functional rearrangement of RNA-binding proteins on CDKN1B/p27Kip1 3'UTRs in cisplatin treated cells. RNA Biol 2019; 17:33-46. [PMID: 31522610 PMCID: PMC6948961 DOI: 10.1080/15476286.2019.1662268] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Post-transcriptional control of gene expression is mediated via RNA-binding proteins (RBPs) that interact with mRNAs in a combinatorial fashion. While recent global RNA interactome capture experiments expanded the repertoire of cellular RBPs quiet dramatically, little is known about the assembly of RBPs on particular mRNAs; and how these associations change and control the fate of the mRNA in drug-treatment conditions. Here we introduce a novel biochemical approach, termed tobramycin-based tandem RNA isolation procedure (tobTRIP), to quantify proteins associated with the 3ʹUTRs of cyclin-dependent kinase inhibitor 1B (CDKN1B/p27Kip1) mRNAs in vivo. P27Kip1 plays an important role in mediating a cell’s response to cisplatin (CP), a widely used chemotherapeutic cancer drug that induces DNA damage and cell cycle arrest. We found that p27Kip1 mRNA is stabilized upon CP treatment of HEK293 cells through elements in its 3ʹUTR. Applying tobTRIP, we further compared the associated proteins in CP and non-treated cells, and identified more than 50 interacting RBPs, many functionally related and evoking a coordinated response. Knock-downs of several of the identified RBPs in HEK293 cells confirmed their involvement in CP-induced p27 mRNA regulation; while knock-down of the KH-type splicing regulatory protein (KHSRP) further enhanced the sensitivity of MCF7 adenocarcinoma cancer cells to CP treatment. Our results highlight the benefit of specific in vivo mRNA-protein interactome capture to reveal post-transcriptional regulatory networks implicated in cellular drug response and adaptation.
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Affiliation(s)
- Valentina Iadevaia
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK
| | - Maikel D Wouters
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK
| | | | - Ana M Matia-González
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK
| | - Emma E Laing
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK
| | - André P Gerber
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK
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12
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Letzel A, Reich S, Dos Santos Rolo T, Kanitz A, Hoppius J, Rack A, Olbinado MP, Ostendorf A, Gökce B, Plech A, Barcikowski S. Time and Mechanism of Nanoparticle Functionalization by Macromolecular Ligands during Pulsed Laser Ablation in Liquids. Langmuir 2019; 35:3038-3047. [PMID: 30646687 DOI: 10.1021/acs.langmuir.8b01585] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Laser ablation of gold in liquids with nanosecond laser pulses in aqueous solutions of inorganic electrolytes and macromolecular ligands for gold nanoparticle size quenching is probed inside the laser-induced cavitation bubble by in situ X-ray multicontrast imaging with a Hartmann mask (XHI). It is found that (i) the in situ size quenching power of sodium chloride (NaCl) in comparison to the ablation in pure water can be observed by the scattering contrast from XHI already inside the cavitation bubble, while (ii) for polyvinylpyrrolidone (PVP) as a macromolecular model ligand an in situ size quenching cannot be observed. Complementary ex situ characterization confirms the overall size quenching ability of both additive types NaCl and PVP. The macromolecular ligand as well as its monomer N-vinylpyrrolidone (NVP) are mainly effective for growth quenching of larger nanoparticles on later time scales, leading to the conclusion of an alternative interaction mechanism with ablated nanoparticles compared to the electrolyte NaCl, probably outside of the cavitation bubble, in the surrounding liquid phase. While monomer and polymer have similar effects on the particle properties, with the polymer being slightly more efficient, only the polymer is effective against hydrodynamic aggregation.
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Affiliation(s)
- Alexander Letzel
- Department of Technical Chemistry I and Center for Nanointegration Duisburg-Essen (CENIDE) , University of Duisburg-Essen , Universitätsstraße 7 , 45141 Essen , Germany
| | - Stefan Reich
- Institute for Photon Science and Synchrotron Radiation , Karlsruhe Institute of Technology (KIT) , Hermann-von-Helmholtz-Platz 1 , 76344 Eggenstein-Leopoldshafen , Germany
| | - Tomy Dos Santos Rolo
- Institute for Photon Science and Synchrotron Radiation , Karlsruhe Institute of Technology (KIT) , Hermann-von-Helmholtz-Platz 1 , 76344 Eggenstein-Leopoldshafen , Germany
- Department of Electrical and Electronic Engineering , Southern University of Science and Technology , 518055 Shenzen , China
| | - Alexander Kanitz
- Applied Laser Technologies , Ruhr-University Bochum , Universitätsstraße 150 , 44801 Bochum , Germany
| | - Jan Hoppius
- Applied Laser Technologies , Ruhr-University Bochum , Universitätsstraße 150 , 44801 Bochum , Germany
| | - Alexander Rack
- ESRF - The European Synchrotron Radiation Facility , 30843 Grenoble , France
| | - Margie P Olbinado
- ESRF - The European Synchrotron Radiation Facility , 30843 Grenoble , France
| | - Andreas Ostendorf
- Applied Laser Technologies , Ruhr-University Bochum , Universitätsstraße 150 , 44801 Bochum , Germany
| | - Bilal Gökce
- Department of Technical Chemistry I and Center for Nanointegration Duisburg-Essen (CENIDE) , University of Duisburg-Essen , Universitätsstraße 7 , 45141 Essen , Germany
| | - Anton Plech
- Institute for Photon Science and Synchrotron Radiation , Karlsruhe Institute of Technology (KIT) , Hermann-von-Helmholtz-Platz 1 , 76344 Eggenstein-Leopoldshafen , Germany
| | - Stephan Barcikowski
- Department of Technical Chemistry I and Center for Nanointegration Duisburg-Essen (CENIDE) , University of Duisburg-Essen , Universitätsstraße 7 , 45141 Essen , Germany
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Abstract
BACKGROUND Along with the reorganization of epigenetic and transcriptional networks, somatic cell reprogramming brings about numerous changes at the level of RNA processing. These include the expression of specific transcript isoforms and 3' untranslated regions. A number of studies have uncovered RNA processing factors that modulate the efficiency of the reprogramming process. However, a comprehensive evaluation of the involvement of RNA processing factors in the reprogramming of somatic mammalian cells is lacking. RESULTS Here, we used data from a large number of studies carried out in three mammalian species, mouse, chimpanzee and human, to uncover consistent changes in gene expression upon reprogramming of somatic cells. We found that a core set of nine splicing factors have consistent changes across the majority of data sets in all three species. Most striking among these are ESRP1 and ESRP2, which accelerate and enhance the efficiency of somatic cell reprogramming by promoting isoform expression changes associated with mesenchymal-to-epithelial transition. We further identify genes and processes in which splicing changes are observed in both human and mouse. CONCLUSIONS Our results provide a general resource for gene expression and splicing changes that take place during somatic cell reprogramming. Furthermore, they support the concept that splicing factors with evolutionarily conserved, cell type-specific expression can modulate the efficiency of the process by reinforcing intermediate states resembling the cell types in which these factors are normally expressed.
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Affiliation(s)
- Alexander Kanitz
- Biozentrum, University of Basel, Basel, Switzerland
- RNA Regulatory Networks, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Afzal Pasha Syed
- Biozentrum, University of Basel, Basel, Switzerland
- RNA Regulatory Networks, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Keisuke Kaji
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Mihaela Zavolan
- Biozentrum, University of Basel, Basel, Switzerland
- RNA Regulatory Networks, Swiss Institute of Bioinformatics, Lausanne, Switzerland
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14
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Zavolan M, Kanitz A. RNA splicing and its connection with other regulatory layers in somatic cell reprogramming. Curr Opin Cell Biol 2017; 52:8-13. [PMID: 29275148 DOI: 10.1016/j.ceb.2017.12.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 12/05/2017] [Accepted: 12/11/2017] [Indexed: 01/30/2023]
Abstract
Understanding how cell identity is established and maintained is one of the most exciting challenges of molecular biology today. Recent work has added a conserved layer of RNA splicing and other post-transcriptional regulatory processes to the transcriptional and epigenetic networks already known to cooperate in the establishment and maintenance of cell identity. Here we summarize these findings, highlighting specifically the multitude of splicing factors that can modulate the efficiency of somatic cell reprogramming. Distinct patterns of gene expression dynamics of these factors during reprogramming suggest that further improvements in efficiency could be obtained through optimal timing of overexpression or knockdown of individual regulators.
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Affiliation(s)
- Mihaela Zavolan
- RNA Regulatory Networks, Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland; Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland.
| | - Alexander Kanitz
- RNA Regulatory Networks, Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland; Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
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15
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Kanitz A, Hoppius JS, del Mar Sanz M, Maicas M, Ostendorf A, Gurevich EL. Synthesis of Magnetic Nanoparticles by Ultrashort Pulsed Laser Ablation of Iron in Different Liquids. Chemphyschem 2017; 18:1155-1164. [DOI: 10.1002/cphc.201601252] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 02/06/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Alexander Kanitz
- Applied Laser Technologies, Ruhr-Universität Bochum; Universitätsstr.150 44801 Bochum Germany
| | - Jan S. Hoppius
- Applied Laser Technologies, Ruhr-Universität Bochum; Universitätsstr.150 44801 Bochum Germany
| | - María del Mar Sanz
- Instituto de Sistemas Optoelectrónicos y Microstecnología (ISOM), E.T.S.I.T-U.P.M.; Avda. Complutense 30 28004 Madrid Spain
| | - Marco Maicas
- Instituto de Sistemas Optoelectrónicos y Microstecnología (ISOM), E.T.S.I.T-U.P.M.; Avda. Complutense 30 28004 Madrid Spain
| | - Andreas Ostendorf
- Applied Laser Technologies, Ruhr-Universität Bochum; Universitätsstr.150 44801 Bochum Germany
| | - Evgeny L. Gurevich
- Applied Laser Technologies, Ruhr-Universität Bochum; Universitätsstr.150 44801 Bochum Germany
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16
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Kanitz A, Gypas F, Gruber AJ, Gruber AR, Martin G, Zavolan M. Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data. Genome Biol 2015. [PMID: 26201343 PMCID: PMC4511015 DOI: 10.1186/s13059-015-0702-5] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Background Understanding the regulation of gene expression, including transcription start site usage, alternative splicing, and polyadenylation, requires accurate quantification of expression levels down to the level of individual transcript isoforms. To comparatively evaluate the accuracy of the many methods that have been proposed for estimating transcript isoform abundance from RNA sequencing data, we have used both synthetic data as well as an independent experimental method for quantifying the abundance of transcript ends at the genome-wide level. Results We found that many tools have good accuracy and yield better estimates of gene-level expression compared to commonly used count-based approaches, but they vary widely in memory and runtime requirements. Nucleotide composition and intron/exon structure have comparatively little influence on the accuracy of expression estimates, which correlates most strongly with transcript/gene expression levels. To facilitate the reproduction and further extension of our study, we provide datasets, source code, and an online analysis tool on a companion website, where developers can upload expression estimates obtained with their own tool to compare them to those inferred by the methods assessed here. Conclusions As many methods for quantifying isoform abundance with comparable accuracy are available, a user’s choice will likely be determined by factors such as the memory and runtime requirements, as well as the availability of methods for downstream analyses. Sequencing-based methods to quantify the abundance of specific transcript regions could complement validation schemes based on synthetic data and quantitative PCR in future or ongoing assessments of RNA-seq analysis methods. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0702-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexander Kanitz
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland.
| | - Foivos Gypas
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland.
| | - Andreas J Gruber
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland.
| | - Andreas R Gruber
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland.
| | - Georges Martin
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland.
| | - Mihaela Zavolan
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland.
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17
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Imig J, Kanitz A, Gerber AP. RNA regulons and the RNA-protein interaction network. Biomol Concepts 2014; 3:403-14. [PMID: 25436546 DOI: 10.1515/bmc-2012-0016] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 05/28/2012] [Indexed: 11/15/2022] Open
Abstract
Abstract The development of genome-wide analysis tools has prompted global investigation of the gene expression program, revealing highly coordinated control mechanisms that ensure proper spatiotemporal activity of a cell's macromolecular components. With respect to the regulation of RNA transcripts, the concept of RNA regulons, which - by analogy with DNA regulons in bacteria - refers to the coordinated control of functionally related RNA molecules, has emerged as a unifying theory that describes the logic of regulatory RNA-protein interactions in eukaryotes. Hundreds of RNA-binding proteins and small non-coding RNAs, such as microRNAs, bind to distinct elements in target RNAs, thereby exerting specific and concerted control over posttranscriptional events. In this review, we discuss recent reports committed to systematically explore the RNA-protein interaction network and outline some of the principles and recurring features of RNA regulons: the coordination of functionally related mRNAs through RNA-binding proteins or non-coding RNAs, the modular structure of its components, and the dynamic rewiring of RNA-protein interactions upon exposure to internal or external stimuli. We also summarize evidence for robust combinatorial control of mRNAs, which could determine the ultimate fate of each mRNA molecule in a cell. Finally, the compilation and integration of global protein-RNA interaction data has yielded first insights into network structures and provided the hypothesis that RNA regulons may, in part, constitute noise 'buffers' to handle stochasticity in cellular transcription.
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18
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Alberton C, Pinto S, Cadore E, Tartaruga M, Kanitz A, Antunes A, Finatto P, Kruel L. Oxygen Uptake, Muscle Activity and Ground Reaction Force during Water Aerobic Exercises. Int J Sports Med 2014; 35:1161-9. [DOI: 10.1055/s-0034-1383597] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- C. Alberton
- School of Physical Education, Federal University of Pelotas, Pelotas, Brazil
| | - S. Pinto
- School of Physical Education, Federal University of Pelotas, Pelotas, Brazil
| | - E. Cadore
- School of Physical Education, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - M. Tartaruga
- School of Physical Education, Midwest State University of Parana, Guarapuava, Brazil
| | - A. Kanitz
- School of Physical Education, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - A. Antunes
- School of Physical Education, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - P. Finatto
- School of Physical Education, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - L. Kruel
- School of Physical Education, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
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19
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Kanitz A, Imig J, Dziunycz PJ, Primorac A, Galgano A, Hofbauer GFL, Gerber AP, Detmar M. The expression levels of microRNA-361-5p and its target VEGFA are inversely correlated in human cutaneous squamous cell carcinoma. PLoS One 2012; 7:e49568. [PMID: 23166713 PMCID: PMC3498195 DOI: 10.1371/journal.pone.0049568] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 10/12/2012] [Indexed: 12/21/2022] Open
Abstract
Vascular endothelial growth factor A (VEGFA) plays a key role in the angiogenesis of human skin. Elevated levels of VEGFA are associated with several pathological conditions, including chronic inflammatory skin diseases and several types of skin cancer. In particular, squamous cell carcinoma (SCC) of the skin, the second most common skin cancer in the general population, is characterized by invasive growth, pronounced angiogenesis and elevated levels of VEGFA. The processing, turnover and production of VEGFA are extensively regulated at the post-transcriptional level, both by RNA-binding proteins and microRNAs (miRNAs). In the present study, we identified a new miRNA recognition element in a downstream conserved region of the VEGFA 3'-UTR. We confirmed the repressive effect of miR-361-5p on this element in vitro, identifying the first target for this miRNA. Importantly, we found that miR-361-5p levels are inversely correlated with VEGFA expression in SCC and in healthy skin, indicating that miR-361-5p could play a role in cancers.
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Affiliation(s)
- Alexander Kanitz
- Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
| | - Jochen Imig
- Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
| | - Piotr J. Dziunycz
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
| | - Adriana Primorac
- Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
| | - Alessia Galgano
- Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
| | | | - André P. Gerber
- Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
- * E-mail: (APG); (MD)
| | - Michael Detmar
- Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
- * E-mail: (APG); (MD)
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20
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Abstract
Some of the classical paradigms of gene regulation have been challenged by global-scale analysis of eukaryotic transcriptional and post-transcriptional gene regulation (PTGR), made possible by the development of genomics and proteomics tools. Post-transcriptional events in particular are increasingly being recognized as important sources of gene regulation. The hundreds of regulatory RNA-binding proteins that exist in eukaryotes may regulate dozens to hundreds of functionally related RNA targets. Likewise, the expression of considerable fractions of many eukaryotic genomes is affected by hundreds of non-coding RNAs, e.g., microRNAs. These findings suggest an enormous regulatory potential for PTGR that may affect virtually every message in a cell. All gene regulatory systems are composed of simple network circuits that coordinate the transfer of regulatory signals to a target gene/message.
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Affiliation(s)
| | - André P Gerber
- Institute of Pharmaceutical Sciences, ETH Zurich, Switzerland
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21
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Galgano A, Forrer M, Jaskiewicz L, Kanitz A, Zavolan M, Gerber AP. Comparative analysis of mRNA targets for human PUF-family proteins suggests extensive interaction with the miRNA regulatory system. PLoS One 2008; 3:e3164. [PMID: 18776931 PMCID: PMC2522278 DOI: 10.1371/journal.pone.0003164] [Citation(s) in RCA: 212] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2008] [Accepted: 08/18/2008] [Indexed: 12/03/2022] Open
Abstract
Genome-wide identification of mRNAs regulated by RNA-binding proteins is crucial to uncover post-transcriptional gene regulatory systems. The conserved PUF family RNA-binding proteins repress gene expression post-transcriptionally by binding to sequence elements in 3′-UTRs of mRNAs. Despite their well-studied implications for development and neurogenesis in metazoa, the mammalian PUF family members are only poorly characterized and mRNA targets are largely unknown. We have systematically identified the mRNAs associated with the two human PUF proteins, PUM1 and PUM2, by the recovery of endogenously formed ribonucleoprotein complexes and the analysis of associated RNAs with DNA microarrays. A largely overlapping set comprised of hundreds of mRNAs were reproducibly associated with the paralogous PUM proteins, many of them encoding functionally related proteins. A characteristic PUF-binding motif was highly enriched among PUM bound messages and validated with RNA pull-down experiments. Moreover, PUF motifs as well as surrounding sequences exhibit higher conservation in PUM bound messages as opposed to transcripts that were not found to be associated, suggesting that PUM function may be modulated by other factors that bind conserved elements. Strikingly, we found that PUF motifs are enriched around predicted miRNA binding sites and that high-confidence miRNA binding sites are significantly enriched in the 3′-UTRs of experimentally determined PUM1 and PUM2 targets, strongly suggesting an interaction of human PUM proteins with the miRNA regulatory system. Our work suggests extensive connections between the RBP and miRNA post-transcriptional regulatory systems and provides a framework for deciphering the molecular mechanism by which PUF proteins regulate their target mRNAs.
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Affiliation(s)
- Alessia Galgano
- Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
| | - Michael Forrer
- Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
| | | | - Alexander Kanitz
- Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
| | | | - André P. Gerber
- Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
- * E-mail:
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22
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Korndörfer IP, Kanitz A, Danzer J, Zimmer M, Loessner MJ, Skerra A. Structural analysis of the L-alanoyl-D-glutamate endopeptidase domain of Listeria bacteriophage endolysin Ply500 reveals a new member of the LAS peptidase family. Acta Crystallogr D Biol Crystallogr 2008; 64:644-50. [PMID: 18560152 DOI: 10.1107/s0907444908007890] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2008] [Accepted: 03/23/2008] [Indexed: 11/10/2022]
Abstract
Similar to many other bacterial cell-wall-hydrolyzing enzymes, the Listeria bacteriophage A500 endopeptidase Ply500 has a modular architecture consisting of an enzymatically active domain (EAD) linked to a cell-wall-binding domain (CBD) in a single polypeptide chain. The crystal structure of the EAD of Ply500 has been solved at 1.8 A resolution. The shape of the enzyme resembles a sofa chair: one alpha-helix and three antiparallel beta-strands form the seat, which is supported by two more alpha-helices, while another alpha-helix together with the following loop give rise to the backrest. A sulfate anion bound to the active site, which harbours a catalytic Zn2+ ion, indicates mechanistic details of the peptidase reaction, which involves a tetrahedral transition state. Despite very low sequence similarity, a clear structural relationship was detected to the peptidases VanX, DDC, MSH and MepA, which belong to the so-called 'LAS' family. Their gross functional similarity is supported by a common bound Zn2+ ion and a highly conserved set of coordinating residues (His80, Asp87 and His133) as well as other side chains (Arg50, Gln55, Ser78 and Asp130) in the active site. Considering the high sequence similarity to the EAD of the Listeria phage endopeptidase Ply118, both enzymes can thus be assigned to the LAS family. The same is the case for the L,D-endopeptidase CwlK from Bacillus subtilis, which shows both functional and amino-acid sequence similarity. The fact that the CBD of Ply500 is closely homologous to the CBD of the Listeria phage N-acetylmuramoyl-L-alanine amidase PlyPSA, which exhibits a totally different EAD, illustrates the modular composition and functional variability of this class of enzymes and opens interesting possibilities for protein engineering.
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Affiliation(s)
- Ingo P Korndörfer
- Lehrstuhl für Biologische Chemie, Technische Universität München, An der Saatzucht 5, D-85350 Freising, Germany.
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Markusic DM, Kanitz A, Oude-Elferink RPJ, Seppen J. Preferential gene transfer of lentiviral vectors to liver-derived cells, using a hepatitis B peptide displayed on GP64. Hum Gene Ther 2007; 18:673-9. [PMID: 17630838 DOI: 10.1089/hum.2007.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
One of the problems that limit the efficiency of viral gene therapy is the lack of specificity of viral particle binding. The development of techniques to target viral particles to specific cell types is therefore important. Because GP64 can efficiently pseudotype lentiviral vectors, we investigated the possibility of using GP64 for lentiviral vector particle targeting. A peptide derived from the hepatitis B virus (HBV) PreS1 protein, with known affinity for an unidentified receptor expressed on hepatocytes, was inserted at amino acid position 278 of the GP64 protein (PreS1-GP64). The GP64 and PreS1-GP64 proteins were expressed and incorporated into lentiviral particles at comparable levels. Flow cytometry measurements confirmed surface display of the PreS1 peptide. The highest titers of PreS1-GP64-pseudotyped lentiviral vectors were observed on liver-derived cell lines. Gene transfer of PreS1-GP64 lentiviral vectors was inhibited by coincubation with an antibody directed against the PreS1 peptide. These data suggest that the PreS1 peptide is involved in viral attachment to the cell surface. The insertion of targeting peptides into the GP64 envelope protein represents a potential approach for the targeting of lentiviral vectors to specific cell types.
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Markusic D, van Til N, Kanitz A, Hiralall J, Oude-Elferink R, Seppen J. 465. Pseudotyping Lentiviral Vectors with a Modified GP64 Envelope Proteins Redirects Gene Transfer In Vitro and In Vivo. Mol Ther 2006. [DOI: 10.1016/j.ymthe.2006.08.534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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26
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Stöel M, Staudigel J, Steuber F, Simmerer J, Wittmann G, Kanitz A, Klausmann H, Rogler W, Roth W, Schumann J, Winnacker A. Charge injection barrier modification in organic LEDs. Phys Chem Chem Phys 1999. [DOI: 10.1039/a808595a] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Kanitz A. Schlusswort zu meiner Polemik mit E. Weinland in der „Zeitschrift für Biologie“. Pflugers Arch 1903. [DOI: 10.1007/bf01663096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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