1
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Seyres D, Gorka O, Schmidt R, Marone R, Zavolan M, Jeker LT. T helper cells exhibit a dynamic and reversible 3'-UTR landscape. RNA 2024; 30:418-434. [PMID: 38302256 PMCID: PMC10946431 DOI: 10.1261/rna.079897.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 01/16/2024] [Indexed: 02/03/2024]
Abstract
3' untranslated regions (3' UTRs) are critical elements of messenger RNAs, as they contain binding sites for RNA-binding proteins (RBPs) and microRNAs that affect various aspects of the RNA life cycle including transcript stability and cellular localization. In response to T cell receptor activation, T cells undergo massive expansion during the effector phase of the immune response and dynamically modify their 3' UTRs. Whether this serves to directly regulate the abundance of specific mRNAs or is a secondary effect of proliferation remains unclear. To study 3'-UTR dynamics in T helper cells, we investigated division-dependent alternative polyadenylation (APA). In addition, we generated 3' end UTR sequencing data from naive, activated, memory, and regulatory CD4+ T cells. 3'-UTR length changes were estimated using a nonnegative matrix factorization approach and were compared with those inferred from long-read PacBio sequencing. We found that APA events were transient and reverted after effector phase expansion. Using an orthogonal bulk RNA-seq data set, we did not find evidence of APA association with differential gene expression or transcript usage, indicating that APA has only a marginal effect on transcript abundance. 3'-UTR sequence analysis revealed conserved binding sites for T cell-relevant microRNAs and RBPs in the alternative 3' UTRs. These results indicate that poly(A) site usage could play an important role in the control of cell fate decisions and homeostasis.
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Affiliation(s)
- Denis Seyres
- Department of Biomedicine, Basel University Hospital and University of Basel, CH-4031 Basel, Switzerland
- Transplantation Immunology and Nephrology, Basel University Hospital, CH-4031 Basel, Switzerland
| | - Oliver Gorka
- Department of Biomedicine, Basel University Hospital and University of Basel, CH-4031 Basel, Switzerland
- Transplantation Immunology and Nephrology, Basel University Hospital, CH-4031 Basel, Switzerland
| | - Ralf Schmidt
- Computational and Systems Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Romina Marone
- Department of Biomedicine, Basel University Hospital and University of Basel, CH-4031 Basel, Switzerland
- Transplantation Immunology and Nephrology, Basel University Hospital, CH-4031 Basel, Switzerland
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland
- Swiss Institute of Bioinformatics, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Lukas T Jeker
- Department of Biomedicine, Basel University Hospital and University of Basel, CH-4031 Basel, Switzerland
- Transplantation Immunology and Nephrology, Basel University Hospital, CH-4031 Basel, 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. 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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3
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de Smalen LM, Börsch A, Leuchtmann AB, Gill JF, Ritz D, Zavolan M, Handschin C. Impaired age-associated mitochondrial translation is mitigated by exercise and PGC-1α. Proc Natl Acad Sci U S A 2023; 120:e2302360120. [PMID: 37639610 PMCID: PMC10483666 DOI: 10.1073/pnas.2302360120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 07/24/2023] [Indexed: 08/31/2023] Open
Abstract
Sarcopenia, the age-related loss of skeletal muscle mass and function, can dramatically impinge on quality of life and mortality. While mitochondrial dysfunction and imbalanced proteostasis are recognized as hallmarks of sarcopenia, the regulatory and functional link between these processes is underappreciated and unresolved. We therefore investigated how mitochondrial proteostasis, a crucial process that coordinates the expression of nuclear- and mitochondrial-encoded mitochondrial proteins with supercomplex formation and respiratory activity, is affected in skeletal muscle aging. Intriguingly, a robust mitochondrial translation impairment was observed in sarcopenic muscle, which is regulated by the peroxisome proliferator-activated receptor γ coactivator 1 α (PGC-1α) with the estrogen-related receptor α (ERRα). Exercise, a potent inducer of PGC-1α activity, rectifies age-related reduction in mitochondrial translation, in conjunction with quality control pathways. These results highlight the importance of mitochondrial proteostasis in muscle aging, and elucidate regulatory interactions that underlie the powerful benefits of physical activity in this context.
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Affiliation(s)
| | | | | | | | - Danilo Ritz
- Biozentrum, University of Basel, BaselCH-4056, Switzerland
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4
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Bohmann D, O'Connell M, Frendewey D, Gerber A, Hernandez N, Krämer A, Minvielle-Sebastia L, Shaw P, Wahle E, Zavolan M. Walter Keller (1938-2023): a tribute from his mentees. RNA 2023; 29:v-xiii. [PMID: 37369530 PMCID: PMC10798242 DOI: 10.1261/rna.079742.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/08/2023] [Indexed: 06/29/2023]
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5
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Moon Y, Burri D, Zavolan M. Identification of experimentally-supported poly(A) sites in single-cell RNA-seq data with SCINPAS. NAR Genom Bioinform 2023; 5:lqad079. [PMID: 37705828 PMCID: PMC10495540 DOI: 10.1093/nargab/lqad079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/15/2023] [Accepted: 08/23/2023] [Indexed: 09/15/2023] Open
Abstract
Alternative polyadenylation is a main driver of transcriptome diversity in mammals, generating transcript isoforms with different 3' ends via cleavage and polyadenylation at distinct polyadenylation (poly(A)) sites. The regulation of cell type-specific poly(A) site choice is not completely resolved, and requires quantitative poly(A) site usage data across cell types. 3' end-based single-cell RNA-seq can now be broadly used to obtain such data, enabling the identification and quantification of poly(A) sites with direct experimental support. We propose SCINPAS, a computational method to identify poly(A) sites from scRNA-seq datasets. SCINPAS modifies the read deduplication step to favor the selection of distal reads and extract those with non-templated poly(A) tails. This approach improves the resolution of poly(A) site recovery relative to standard software. SCINPAS identifies poly(A) sites in genic and non-genic regions, providing complementary information relative to other tools. The workflow is modular, and the key read deduplication step is general, enabling the use of SCINPAS in other typical analyses of single cell gene expression. Taken together, we show that SCINPAS is able to identify experimentally-supported, known and novel poly(A) sites from 3' end-based single-cell RNA sequencing data.
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Affiliation(s)
- Youngbin Moon
- Computational and Systems Biology, Biozentrum University of Basel, Spitalstrasse 41, CH-4056 Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Dominik Burri
- Computational and Systems Biology, Biozentrum University of Basel, Spitalstrasse 41, CH-4056 Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum University of Basel, Spitalstrasse 41, CH-4056 Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
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6
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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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7
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Burri D, Zavolan M. Corrigendum: Shortening of 3' UTRs in most cell types composing tumor tissues implicates alternative polyadenylation in protein metabolism. RNA 2023; 29:863. [PMID: 37192817 DOI: 10.1261/rna.079645.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
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8
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Katsantoni M, van Nimwegen E, Zavolan M. Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs. Genome Biol 2023; 24:77. [PMID: 37069586 PMCID: PMC10108518 DOI: 10.1186/s13059-023-02913-0] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 03/29/2023] [Indexed: 04/19/2023] Open
Abstract
We present RCRUNCH, an end-to-end solution to CLIP data analysis for identification of binding sites and sequence specificity of RNA-binding proteins. RCRUNCH can analyze not only reads that map uniquely to the genome but also those that map to multiple genome locations or across splice boundaries and can consider various types of background in the estimation of read enrichment. By applying RCRUNCH to the eCLIP data from the ENCODE project, we have constructed a comprehensive and homogeneous resource of in-vivo-bound RBP sequence motifs. RCRUNCH automates the reproducible analysis of CLIP data, enabling studies of post-transcriptional control of gene expression.
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Affiliation(s)
- Maria Katsantoni
- Biozentrum, University of Basel, 4056, Basel, Switzerland.
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
| | - Erik van Nimwegen
- Biozentrum, University of Basel, 4056, Basel, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Mihaela Zavolan
- Biozentrum, University of Basel, 4056, Basel, Switzerland.
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
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9
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Kaiser MS, Milan G, Ham DJ, Lin S, Oliveri F, Chojnowska K, Tintignac LA, Mittal N, Zimmerli CE, Glass DJ, Zavolan M, Rüegg MA. Dual roles of mTORC1-dependent activation of the ubiquitin-proteasome system in muscle proteostasis. Commun Biol 2022; 5:1141. [PMID: 36302954 PMCID: PMC9613904 DOI: 10.1038/s42003-022-04097-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/11/2022] [Indexed: 12/02/2022] Open
Abstract
Muscle size is controlled by the PI3K-PKB/Akt-mTORC1-FoxO pathway, which integrates signals from growth factors, energy and amino acids to activate protein synthesis and inhibit protein breakdown. While mTORC1 activity is necessary for PKB/Akt-induced muscle hypertrophy, its constant activation alone induces muscle atrophy. Here we show that this paradox is based on mTORC1 activity promoting protein breakdown through the ubiquitin-proteasome system (UPS) by simultaneously inducing ubiquitin E3 ligase expression via feedback inhibition of PKB/Akt and proteasome biogenesis via Nuclear Factor Erythroid 2-Like 1 (Nrf1). Muscle growth was restored by reactivation of PKB/Akt, but not by Nrf1 knockdown, implicating ubiquitination as the limiting step. However, both PKB/Akt activation and proteasome depletion by Nrf1 knockdown led to an immediate disruption of proteome integrity with rapid accumulation of damaged material. These data highlight the physiological importance of mTORC1-mediated PKB/Akt inhibition and point to juxtaposed roles of the UPS in atrophy and proteome integrity. Exploring the relationship between mTORC1 and the ubiquitin-proteasome system, light is shed on the paradox between mTORC1-mediated muscle hypertrophy induced by PKB/Akt and the muscle atrophy induced by mTORC1 alone.
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Affiliation(s)
- Marco S Kaiser
- Biozentrum, University of Basel, Basel, Switzerland.,BIOREBA AG, Christoph Merian-Ring 7, 4153, Reinach, Switzerland
| | - Giulia Milan
- Biozentrum, University of Basel, Basel, Switzerland. .,Department of Biomedicine, University of Basel, Hebelstrasse 20, 4031, Basel, Switzerland.
| | - Daniel J Ham
- Biozentrum, University of Basel, Basel, Switzerland.
| | - Shuo Lin
- Biozentrum, University of Basel, Basel, Switzerland
| | | | - Kathrin Chojnowska
- Biozentrum, University of Basel, Basel, Switzerland.,AstraZeneca AG, Neuhofstrasse 34, 6340, Baar, Switzerland
| | - Lionel A Tintignac
- Biozentrum, University of Basel, Basel, Switzerland.,Neuromuscular Research Group, Departments of Neurology and Biomedicine, University of Basel, University Hospital Basel, Basel, Switzerland
| | | | - Christian E Zimmerli
- Biozentrum, University of Basel, Basel, Switzerland.,Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438, Frankfurt am Main, Germany
| | - David J Glass
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA.,Regeneron Pharmaceuticals, Tarrytown, NY, USA
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10
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Breda J, Banerjee A, Jayachandran R, Pieters J, Zavolan M. A novel approach to single-cell analysis reveals intrinsic differences in immune marker expression in unstimulated BALB/c and C57BL/6 macrophages. FEBS Lett 2022; 596:2630-2643. [PMID: 36001069 DOI: 10.1002/1873-3468.14478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 08/12/2022] [Accepted: 08/16/2022] [Indexed: 11/06/2022]
Abstract
The origin of functional heterogeneity among macrophages, key innate immune system components, is still debated. While mouse strains differ in their immune responses, the range of gene expression variation among their pre-stimulation macrophages is unknown. With a novel approach to scRNA-seq analysis, we reveal the gene expression variation in unstimulated macrophage populations from BALB/c and C57BL/6 mice. We show that intrinsic strain-to-strain differences are detectable before stimulation and we place the unstimulated single cells within the gene expression landscape of stimulated macrophages. C57BL/6 mice show stronger evidence of macrophage polarization than BALB/c mice, which may contribute to their relative resistance to pathogens. Our computational methods can be generally adopted to uncover biological variation between cell populations.
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Affiliation(s)
- Jeremie Breda
- Biozentrum, University of Basel, Basel, Switzerland.,Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Arka Banerjee
- Biozentrum, University of Basel, Basel, Switzerland.,Swiss Institute of Bioinformatics, Basel, Switzerland
| | | | - Jean Pieters
- Biozentrum, University of Basel, Basel, Switzerland
| | - Mihaela Zavolan
- Biozentrum, University of Basel, Basel, Switzerland.,Swiss Institute of Bioinformatics, Basel, Switzerland
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11
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Pignatti E, Altinkilic EM, Bräutigam K, Grössl M, Perren A, Zavolan M, Flück CE. Cholesterol Deprivation Drives DHEA Biosynthesis in Human Adrenals. Endocrinology 2022; 163:6588149. [PMID: 35583599 DOI: 10.1210/endocr/bqac076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Indexed: 11/19/2022]
Abstract
Adrenarche is an early event in sexual maturation in prepubertal children and corresponds to the postnatal development of the adrenocortical zona reticularis (zR). However, the molecular mechanisms that govern the onset and maturation of zR remain unknown. Using tissue laser microdissection combined with transcript quantification and immunodetection, we showed that the human zR receives low levels of cholesterol in comparison with other adrenal layers. To model this metabolic condition, we challenged adrenal cells in vitro using cholesterol deprivation. This resulted in reprogramming the steroidogenic pathway toward inactivation of 3-beta-hydroxysteroid dehydrogenase type 2 (HSD3B2), increased CYB5A expression, and increased biosynthesis of dehydroepiandrosterone (DHEA), 3 key features of zR maturation during adrenarche. Finally, we found that cholesterol deprivation leads to decreased transcriptional activity of POU3F2, which normally stimulates the expression of HSD3B2 by directly binding to its promoter. These findings demonstrate that cholesterol deprivation can account, at least in part, for the acquisition of a zR-like androgenic program in humans.
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Affiliation(s)
- Emanuele Pignatti
- Division of Pediatric Endocrinology, Diabetology and Metabolism, Department of Pediatrics, University Hospital Inselspital, University of Bern, 3010 Bern, Switzerland
- Department for BioMedical Research, University Hospital Inselspital, University of Bern, 3010 Bern, Switzerland
| | - Emre Murat Altinkilic
- Division of Pediatric Endocrinology, Diabetology and Metabolism, Department of Pediatrics, University Hospital Inselspital, University of Bern, 3010 Bern, Switzerland
- Department for BioMedical Research, University Hospital Inselspital, University of Bern , 3010 Bern, Switzerland
| | | | - Michael Grössl
- Department for BioMedical Research, University Hospital Inselspital, University of Bern , 3010 Bern, Switzerland
- Department of Nephrology and Hypertension, Inselspital, Bern University Hospital, 3010, Bern, Switzerland
| | - Aurel Perren
- Institute of Pathology, University of Bern , 3008 Bern, Switzerland
| | | | - Christa E Flück
- Division of Pediatric Endocrinology, Diabetology and Metabolism, Department of Pediatrics, University Hospital Inselspital, University of Bern, 3010 Bern, Switzerland
- Department for BioMedical Research, University Hospital Inselspital, University of Bern, 3010 Bern, Switzerland
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12
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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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13
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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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14
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Burri D, Zavolan M. Shortening of 3' UTRs in most cell types composing tumor tissues implicates alternative polyadenylation in protein metabolism. RNA 2021; 27:1459-1470. [PMID: 34521731 PMCID: PMC8594477 DOI: 10.1261/rna.078886.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/24/2021] [Indexed: 05/18/2023]
Abstract
During pre-mRNA maturation 3' end processing can occur at different polyadenylation sites in the 3' untranslated region (3' UTR) to give rise to transcript isoforms that differ in the length of their 3' UTRs. Longer 3' UTRs contain additional cis-regulatory elements that impact the fate of the transcript and/or of the resulting protein. Extensive alternative polyadenylation (APA) has been observed in cancers, but the mechanisms and roles remain elusive. In particular, it is unclear whether the APA occurs in the malignant cells or in other cell types that infiltrate the tumor. To resolve this, we developed a computational method, called SCUREL, that quantifies changes in 3' UTR length between groups of cells, including cells of the same type originating from tumor and control tissue. We used this method to study APA in human lung adenocarcinoma (LUAD). SCUREL relies solely on annotated 3' UTRs and on control systems such as T cell activation, and spermatogenesis gives qualitatively similar results at much greater sensitivity compared to the previously published scAPA method. In the LUAD samples, we find a general trend toward 3' UTR shortening not only in cancer cells compared to the cell type of origin, but also when comparing other cell types from the tumor vs. the control tissue environment. However, we also find high variability in the individual targets between patients. The findings help in understanding the extent and impact of APA in LUAD, which may support improvements in diagnosis and treatment.
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Affiliation(s)
- Dominik Burri
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, CH-4056, Switzerland SIB Swiss Institute of Bioinformatics, Basel, CH-4056, Switzerland
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, CH-4056, Switzerland SIB Swiss Institute of Bioinformatics, Basel, CH-4056, Switzerland
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15
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Abstract
BACKGROUND Nonsense-mediated mRNA decay (NMD) is a eukaryotic, translation-dependent degradation pathway that targets mRNAs with premature termination codons and also regulates the expression of some mRNAs that encode full-length proteins. Although many genes express NMD-sensitive transcripts, identifying them based on short-read sequencing data remains a challenge. RESULTS To identify and analyze endogenous targets of NMD, we apply cDNA Nanopore sequencing and short-read sequencing to human cells with varying expression levels of NMD factors. Our approach detects full-length NMD substrates that are highly unstable and increase in levels or even only appear when NMD is inhibited. Among the many new NMD-targeted isoforms that our analysis identifies, most derive from alternative exon usage. The isoform-aware analysis reveals many genes with significant changes in splicing but no significant changes in overall expression levels upon NMD knockdown. NMD-sensitive mRNAs have more exons in the 3΄UTR and, for those mRNAs with a termination codon in the last exon, the length of the 3΄UTR per se does not correlate with NMD sensitivity. Analysis of splicing signals reveals isoforms where NMD has been co-opted in the regulation of gene expression, though the main function of NMD seems to be ridding the transcriptome of isoforms resulting from spurious splicing events. CONCLUSIONS Long-read sequencing enables the identification of many novel NMD-sensitive mRNAs and reveals both known and unexpected features concerning their biogenesis and their biological role. Our data provide a highly valuable resource of human NMD transcript targets for future genomic and transcriptomic applications.
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Affiliation(s)
- Evangelos D Karousis
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Foivos Gypas
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | - Mihaela Zavolan
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Klingelbergstrasse 50-70, 4056, Basel, Switzerland
| | - Oliver Mühlemann
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland.
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16
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Ghosh S, Börsch A, Ghosh S, Zavolan M. The transcriptional landscape of a hepatoma cell line grown on scaffolds of extracellular matrix proteins. BMC Genomics 2021; 22:238. [PMID: 33823809 PMCID: PMC8025518 DOI: 10.1186/s12864-021-07532-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 03/14/2021] [Indexed: 11/10/2022] Open
Abstract
Background The behavior of cells in vivo is complex and highly dynamic, as it results from an interplay between intercellular matrix proteins with surface receptors and other microenvironmental cues. Although the effects of the cellular niche have been investigated for a number of cell types using different molecular approaches, comprehensive assessments of how the global transcriptome responds to 3D scaffolds composed of various extracellular matrix (ECM) constituents at different concentrations are still lacking. Results In this study, we explored the effects of two diverse extracellular matrix (ECM) components, Collagen I and Matrigel, on the transcriptional profile of cells in a cell culture system. Culturing Huh-7 cells on traditional cell culture plates (Control) or on the ECM components at different concentrations to modulate microenvironment properties, we have generated transcriptomics data that may be further explored to understand the differentiation and growth potential of this cell type for the development of 3D cultures. Our analysis infers transcription factors that are most responsible for the transcriptome response to the extracellular cues. Conclusion Our data indicates that the Collagen I substrate induces a robust transcriptional response in the Huh-7 cells, distinct from that induced by Matrigel. Enhanced hepatocyte markers (ALB and miR-122) reveal a potentially robust remodelling towards primary hepatocytes. Our results aid in defining the appropriate culture and transcription pathways while using hepatoma cell lines. As systems mimicking the in vivo structure and function of liver cells are still being developed, our study could potentially circumvent bottlenecks of limited availability of primary hepatocytes for preclinical studies of drug targets. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07532-2.
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Affiliation(s)
- Souvik Ghosh
- Biozentrum, University of Basel, Basel, Switzerland.
| | - Anastasiya Börsch
- Biozentrum, University of Basel, Basel, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Mihaela Zavolan
- Biozentrum, University of Basel, Basel, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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17
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Coto-Llerena M, Tosti N, Taha-Mehlitz S, Kancherla V, Paradiso V, Gallon J, Bianco G, Garofoli A, Ghosh S, Tang F, Ercan C, Christofori GM, Matter MS, Droeser RA, Zavolan M, Soysal SD, von Flüe M, Kollmar O, Terracciano LM, Ng CKY, Piscuoglio S. Transcriptional Enhancer Factor Domain Family member 4 Exerts an Oncogenic Role in Hepatocellular Carcinoma by Hippo-Independent Regulation of Heat Shock Protein 70 Family Members. Hepatol Commun 2021; 5:661-674. [PMID: 33860124 PMCID: PMC8034568 DOI: 10.1002/hep4.1656] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/10/2020] [Accepted: 11/24/2020] [Indexed: 12/25/2022] Open
Abstract
Transcriptional enhancer factor domain family member 4 (TEAD4) is a downstream effector of the conserved Hippo signaling pathway, regulating the expression of genes involved in cell proliferation and differentiation. It is up-regulated in several cancer types and is associated with metastasis and poor prognosis. However, its role in hepatocellular carcinoma (HCC) remains largely unexplored. Using data from The Cancer Genome Atlas, we found that TEAD4 was overexpressed in HCC and was associated with aggressive HCC features and worse outcome. Overexpression of TEAD4 significantly increased proliferation and migration rates in HCC cells in vitro as well as tumor growth in vivo. Additionally, RNA sequencing analysis of TEAD4-overexpressing HCC cells demonstrated that TEAD4 overexpression was associated with the up-regulation of genes involved in epithelial-to-mesenchymal transition, proliferation, and protein-folding pathways. Among the most up-regulated genes following TEAD4 overexpression were the 70-kDa heat shock protein (HSP70) family members HSPA6 and HSPA1A. Chromatin immunoprecipitation-quantitative real-time polymerase chain reaction experiments demonstrated that TEAD4 regulates HSPA6 and HSPA1A expression by directly binding to their promoter and enhancer regions. The pharmacologic inhibition of HSP70 expression in TEAD4-overexpressing cells reduced the effect of TEAD4 on cell proliferation. Finally, by overexpressing TEAD4 in yes-associated protein (YAP)/transcriptional coactivator with PDZ binding motif (TAZ)-knockdown HCC cells, we showed that the effect of TEAD4 on cell proliferation and its regulation of HSP70 expression does not require YAP and TAZ, the main effectors of the Hippo signaling pathway. Conclusion: A novel Hippo-independent mechanism for TEAD4 promotes cell proliferation and tumor growth in HCC by directly regulating HSP70 family members.
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Affiliation(s)
- Mairene Coto-Llerena
- Institute of Medical Genetics and PathologyUniversity Hospital BaselBaselSwitzerland.,Visceral Surgery and Precision Medicine Research LaboratoryDepartment of BiomedicineUniversity of BaselBaselSwitzerland
| | - Nadia Tosti
- Institute of Medical Genetics and PathologyUniversity Hospital BaselBaselSwitzerland
| | - Stephanie Taha-Mehlitz
- Visceral Surgery and Precision Medicine Research LaboratoryDepartment of BiomedicineUniversity of BaselBaselSwitzerland.,ClarunisDepartment of Visceral SurgeryUniversity Center for Gastrointestinal and Liver DiseasesSt. Clara Hospital and University Hospital BaselBaselSwitzerland
| | - Venkatesh Kancherla
- Institute of Medical Genetics and PathologyUniversity Hospital BaselBaselSwitzerland
| | - Viola Paradiso
- Institute of Medical Genetics and PathologyUniversity Hospital BaselBaselSwitzerland
| | - John Gallon
- Visceral Surgery and Precision Medicine Research LaboratoryDepartment of BiomedicineUniversity of BaselBaselSwitzerland
| | - Gaia Bianco
- Visceral Surgery and Precision Medicine Research LaboratoryDepartment of BiomedicineUniversity of BaselBaselSwitzerland
| | - Andrea Garofoli
- Institute of Medical Genetics and PathologyUniversity Hospital BaselBaselSwitzerland
| | - Souvik Ghosh
- Computational and Systems Biology, BiozentrumUniversity of BaselBaselSwitzerland
| | - Fengyuan Tang
- Department of BiomedicineUniversity of BaselBaselSwitzerland
| | - Caner Ercan
- Institute of Medical Genetics and PathologyUniversity Hospital BaselBaselSwitzerland
| | | | - Matthias S Matter
- Institute of Medical Genetics and PathologyUniversity Hospital BaselBaselSwitzerland
| | - Raoul A Droeser
- ClarunisDepartment of Visceral SurgeryUniversity Center for Gastrointestinal and Liver DiseasesSt. Clara Hospital and University Hospital BaselBaselSwitzerland
| | - Mihaela Zavolan
- Computational and Systems Biology, BiozentrumUniversity of BaselBaselSwitzerland
| | - Savas D Soysal
- ClarunisDepartment of Visceral SurgeryUniversity Center for Gastrointestinal and Liver DiseasesSt. Clara Hospital and University Hospital BaselBaselSwitzerland
| | - Markus von Flüe
- ClarunisDepartment of Visceral SurgeryUniversity Center for Gastrointestinal and Liver DiseasesSt. Clara Hospital and University Hospital BaselBaselSwitzerland
| | - Otto Kollmar
- ClarunisDepartment of Visceral SurgeryUniversity Center for Gastrointestinal and Liver DiseasesSt. Clara Hospital and University Hospital BaselBaselSwitzerland
| | - Luigi M Terracciano
- Institute of Medical Genetics and PathologyUniversity Hospital BaselBaselSwitzerland
| | - Charlotte K Y Ng
- Department for BioMedical ResearchUniversity of BernBernSwitzerland
| | - Salvatore Piscuoglio
- Institute of Medical Genetics and PathologyUniversity Hospital BaselBaselSwitzerland.,Visceral Surgery and Precision Medicine Research LaboratoryDepartment of BiomedicineUniversity of BaselBaselSwitzerland
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18
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19
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Börsch A, Ham DJ, Mittal N, Tintignac LA, Migliavacca E, Feige JN, Rüegg MA, Zavolan M. Molecular and phenotypic analysis of rodent models reveals conserved and species-specific modulators of human sarcopenia. Commun Biol 2021; 4:194. [PMID: 33580198 PMCID: PMC7881157 DOI: 10.1038/s42003-021-01723-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 01/19/2021] [Indexed: 02/07/2023] Open
Abstract
Sarcopenia, the age-related loss of skeletal muscle mass and function, affects 5-13% of individuals aged over 60 years. While rodents are widely-used model organisms, which aspects of sarcopenia are recapitulated in different animal models is unknown. Here we generated a time series of phenotypic measurements and RNA sequencing data in mouse gastrocnemius muscle and analyzed them alongside analogous data from rats and humans. We found that rodents recapitulate mitochondrial changes observed in human sarcopenia, while inflammatory responses are conserved at pathway but not gene level. Perturbations in the extracellular matrix are shared by rats, while mice recapitulate changes in RNA processing and autophagy. We inferred transcription regulators of early and late transcriptome changes, which could be targeted therapeutically. Our study demonstrates that phenotypic measurements, such as muscle mass, are better indicators of muscle health than chronological age and should be considered when analyzing aging-related molecular data.
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Affiliation(s)
- Anastasiya Börsch
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Daniel J Ham
- Biozentrum, University of Basel, Basel, Switzerland
| | - Nitish Mittal
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Lionel A Tintignac
- Department of Biomedicine, Pharmazentrum, University of Basel, Basel, Switzerland
| | | | - Jérôme N Feige
- Nestlé Research, EPFL Innovation Park, Lausanne, Switzerland
| | | | - Mihaela Zavolan
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland.
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20
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Börsch A, Zavolan M. Transcription factor motif activity as a biomarker of muscle aging. Am J Aging Sci Res 2021; 2:19-23. [PMID: 35083472 PMCID: PMC7612261] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
In prior work, we analyzed gene expression profiles of mouse, rat and human gastrocnemius muscles to identify conserved regulators of muscle aging processes. By further comparing data obtained from different muscles we found stronger conservation of aging-related factors at the level of molecular pathways than at the level of individual genes. Here we compared the predictive power of models based on gene expression levels and those based on transcription factor motif activities for an individual's age. Although somewhat less accurate than models based on gene expression, models based on motif activities achieve good prediction of muscle age, further providing insights into aging-related molecular pathways.
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21
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Ho-Xuan H, Lehmann G, Glazar P, Gypas F, Eichner N, Heizler K, Schlitt HJ, Zavolan M, Rajewsky N, Meister G, Hackl C. Gene Expression Signatures of a Preclinical Mouse Model during Colorectal Cancer Progression under Low-Dose Metronomic Chemotherapy. Cancers (Basel) 2020; 13:E49. [PMID: 33375322 PMCID: PMC7795790 DOI: 10.3390/cancers13010049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 12/22/2022] Open
Abstract
Understanding the molecular signatures of colorectal cancer progression under chemotherapeutic treatment will be crucial for the success of future therapy improvements. Here, we used a xenograft-based mouse model to investigate, how whole transcriptome signatures change during metastatic colorectal cancer progression and how such signatures are affected by LDM chemotherapy using RNA sequencing. We characterized mRNAs as well as non-coding RNAs such as microRNAs, long non-coding RNAs and circular RNAs in colorectal-cancer bearing mice with or without LDM chemotherapy. Furthermore, we found that circZNF609 functions as oncogene, since over-expression studies lead to an increased tumor growth while specific knock down results in smaller tumors. Our data represent novel insights into the relevance of non-coding and circRNAs in colorectal cancer and provide a comprehensive resource of gene expression changes in primary tumors and metastases. In addition, we present candidate genes that could be important modulators for successful LDM chemotherapy.
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Affiliation(s)
- Hung Ho-Xuan
- Biochemistry Center Regensburg (BCR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany; (H.H.-X.); (G.L.); (N.E.); (K.H.)
| | - Gerhard Lehmann
- Biochemistry Center Regensburg (BCR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany; (H.H.-X.); (G.L.); (N.E.); (K.H.)
| | - Petar Glazar
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max-Delbruck Center for Molecular Medicine, 10115 Berlin, Germany; (P.G.); (N.R.)
| | - Foivos Gypas
- Biozentrum, University of Basel, 4056 Basel, Switzerland; (F.G.); (M.Z.)
| | - Norbert Eichner
- Biochemistry Center Regensburg (BCR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany; (H.H.-X.); (G.L.); (N.E.); (K.H.)
| | - Kevin Heizler
- Biochemistry Center Regensburg (BCR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany; (H.H.-X.); (G.L.); (N.E.); (K.H.)
| | - Hans J. Schlitt
- Department of Surgery, University Hospital Regensburg, 93053 Regensburg, Germany;
| | - Mihaela Zavolan
- Biozentrum, University of Basel, 4056 Basel, Switzerland; (F.G.); (M.Z.)
| | - Nikolaus Rajewsky
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max-Delbruck Center for Molecular Medicine, 10115 Berlin, Germany; (P.G.); (N.R.)
| | - Gunter Meister
- Biochemistry Center Regensburg (BCR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany; (H.H.-X.); (G.L.); (N.E.); (K.H.)
| | - Christina Hackl
- Department of Surgery, University Hospital Regensburg, 93053 Regensburg, Germany;
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22
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Jutzi D, Campagne S, Schmidt R, Reber S, Mechtersheimer J, Gypas F, Schweingruber C, Colombo M, von Schroetter C, Loughlin FE, Devoy A, Hedlund E, Zavolan M, Allain FHT, Ruepp MD. Aberrant interaction of FUS with the U1 snRNA provides a molecular mechanism of FUS induced amyotrophic lateral sclerosis. Nat Commun 2020; 11:6341. [PMID: 33311468 PMCID: PMC7733473 DOI: 10.1038/s41467-020-20191-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 11/13/2020] [Indexed: 12/13/2022] Open
Abstract
Mutations in the RNA-binding protein Fused in Sarcoma (FUS) cause early-onset amyotrophic lateral sclerosis (ALS). However, a detailed understanding of central RNA targets of FUS and their implications for disease remain elusive. Here, we use a unique blend of crosslinking and immunoprecipitation (CLIP) and NMR spectroscopy to identify and characterise physiological and pathological RNA targets of FUS. We find that U1 snRNA is the primary RNA target of FUS via its interaction with stem-loop 3 and provide atomic details of this RNA-mediated mode of interaction with the U1 snRNP. Furthermore, we show that ALS-associated FUS aberrantly contacts U1 snRNA at the Sm site with its zinc finger and traps snRNP biogenesis intermediates in human and murine motor neurons. Altogether, we present molecular insights into a FUS toxic gain-of-function involving direct and aberrant RNA-binding and strengthen the link between two motor neuron diseases, ALS and spinal muscular atrophy (SMA).
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Affiliation(s)
- Daniel Jutzi
- United Kingdom Dementia Research Institute Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Sébastien Campagne
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Ralf Schmidt
- Computational and Systems Biology, Biozentrum, University of Basel, CH-4056, Basel, Switzerland
| | - Stefan Reber
- United Kingdom Dementia Research Institute Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Jonas Mechtersheimer
- United Kingdom Dementia Research Institute Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Foivos Gypas
- Computational and Systems Biology, Biozentrum, University of Basel, CH-4056, Basel, Switzerland
- Friedrich Miescher Institute for Biomedical Research, CH-4058, Basel, Switzerland
| | | | - Martino Colombo
- Celgene Institute of Translational Research (CITRE), 41092, Seville, Spain
| | - Christine von Schroetter
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Fionna E Loughlin
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, CH-8093, Zürich, Switzerland
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Anny Devoy
- United Kingdom Dementia Research Institute Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Eva Hedlund
- Department of Neuroscience, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum, University of Basel, CH-4056, Basel, Switzerland
| | - Frédéric H-T Allain
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, CH-8093, Zürich, Switzerland.
| | - Marc-David Ruepp
- United Kingdom Dementia Research Institute Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, UK.
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23
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Ghosh S, Guimaraes JC, Lanzafame M, Schmidt A, Syed AP, Dimitriades B, Börsch A, Ghosh S, Mittal N, Montavon T, Correia AL, Danner J, Meister G, Terracciano LM, Pfeffer S, Piscuoglio S, Zavolan M. Prevention of dsRNA-induced interferon signaling by AGO1x is linked to breast cancer cell proliferation. EMBO J 2020; 39:e103922. [PMID: 32812257 PMCID: PMC7507497 DOI: 10.15252/embj.2019103922] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 06/27/2020] [Accepted: 07/07/2020] [Indexed: 01/05/2023] Open
Abstract
Translational readthrough, i.e., elongation of polypeptide chains beyond the stop codon, was initially reported for viral RNA, but later found also on eukaryotic transcripts, resulting in proteome diversification and protein‐level modulation. Here, we report that AGO1x, an evolutionarily conserved translational readthrough isoform of Argonaute 1, is generated in highly proliferative breast cancer cells, where it curbs accumulation of double‐stranded RNAs (dsRNAs) and consequent induction of interferon responses and apoptosis. In contrast to other mammalian Argonaute protein family members with primarily cytoplasmic functions, AGO1x exhibits nuclear localization in the vicinity of nucleoli. We identify AGO1x interaction with the polyribonucleotide nucleotidyltransferase 1 (PNPT1) and show that the depletion of this protein further augments dsRNA accumulation. Our study thus uncovers a novel function of an Argonaute protein in buffering the endogenous dsRNA‐induced interferon responses, different than the canonical function of AGO proteins in the miRNA effector pathway. As AGO1x expression is tightly linked to breast cancer cell proliferation, our study thus suggests a new direction for limiting tumor growth.
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Affiliation(s)
- Souvik Ghosh
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Joao C Guimaraes
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Manuela Lanzafame
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Afzal Pasha Syed
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Beatrice Dimitriades
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Anastasiya Börsch
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Shreemoyee Ghosh
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Nitish Mittal
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Thomas Montavon
- Architecture et Réactivité de l'ARN, Institut de biologie moléculaire et cellulaire du CNRS, Université de Strasbourg, Strasbourg, France
| | - Ana Luisa Correia
- Department of Biomedicine, University of Basel/University Hospital Basel, Basel, Switzerland
| | - Johannes Danner
- Department of Biochemistry, Department of Biology and Preclinical Medicine, University of Regensburg, Regensburg, Germany
| | - Gunter Meister
- Department of Biochemistry, Department of Biology and Preclinical Medicine, University of Regensburg, Regensburg, Germany
| | | | - Sébastien Pfeffer
- Architecture et Réactivité de l'ARN, Institut de biologie moléculaire et cellulaire du CNRS, Université de Strasbourg, Strasbourg, France
| | - Salvatore Piscuoglio
- Institute of Pathology, University Hospital Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel/University Hospital Basel, Basel, Switzerland
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
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24
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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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25
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Guimaraes JC, Mittal N, Gnann A, Jedlinski D, Riba A, Buczak K, Schmidt A, Zavolan M. A rare codon-based translational program of cell proliferation. Genome Biol 2020; 21:44. [PMID: 32102681 PMCID: PMC7045563 DOI: 10.1186/s13059-020-1943-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 01/22/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The speed of translation elongation is primarily determined by the abundance of tRNAs. Thus, the codon usage influences the rate with which individual mRNAs are translated. As the nature of tRNA pools and modifications can vary across biological conditions, codon elongation rates may also vary, leading to fluctuations in the protein production from individual mRNAs. Although it has been observed that functionally related mRNAs exhibit similar codon usage, presumably to provide an effective way to coordinate expression of multiple proteins, experimental evidence for codon-mediated translation efficiency modulation of functionally related mRNAs in specific conditions is scarce and the associated mechanisms are still debated. RESULTS Here, we reveal that mRNAs whose expression increases during cell proliferation are enriched in rare codons, poorly adapted to tRNA pools. Ribosome occupancy profiling and proteomics measurements show that upon increased cell proliferation, transcripts enriched in rare codons undergo a higher translation boost than transcripts with common codons. Re-coding of a fluorescent reporter with rare codons increased protein output by ~ 30% relative to a reporter re-coded with common codons. Although the translation capacity of proliferating cells was higher compared to resting cells, we did not find evidence for the regulation of individual tRNAs. Among the models that were proposed so far to account for codon-mediated translational regulation upon changing conditions, the one that seems most consistent with our data involves a global upregulation of ready-to-translate tRNAs, which we show can lead to a higher increase in the elongation velocity at rare codons compared to common codons. CONCLUSIONS We propose that the alleviation of translation bottlenecks in rapidly dividing cells enables preferential upregulation of pro-proliferation proteins, encoded by mRNAs that are enriched in rare codons.
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Affiliation(s)
- Joao C Guimaraes
- Computational and Systems Biology, Biozentrum University of Basel, Klingelbergstrasse 50-70, 4056, Basel, Switzerland.
| | - Nitish Mittal
- Computational and Systems Biology, Biozentrum University of Basel, Klingelbergstrasse 50-70, 4056, Basel, Switzerland
| | - Alexandra Gnann
- Computational and Systems Biology, Biozentrum University of Basel, Klingelbergstrasse 50-70, 4056, Basel, Switzerland
- Department of Biomedicine, University of Basel/University Hospital Basel, Hebelstrasse 20, 4031, Basel, Switzerland
| | - Dominik Jedlinski
- Computational and Systems Biology, Biozentrum University of Basel, Klingelbergstrasse 50-70, 4056, Basel, Switzerland
| | - Andrea Riba
- Computational and Systems Biology, Biozentrum University of Basel, Klingelbergstrasse 50-70, 4056, Basel, Switzerland
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch CEDEX, France
| | - Katarzyna Buczak
- Proteomics Core Facility, Biozentrum University of Basel, Klingelbergstrasse 50-70, 4056, Basel, Switzerland
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum University of Basel, Klingelbergstrasse 50-70, 4056, Basel, Switzerland
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum University of Basel, Klingelbergstrasse 50-70, 4056, Basel, Switzerland.
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26
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Gruber AJ, Zavolan M. Reply to 'A different perspective on alternative cleavage and polyadenylation'. Nat Rev Genet 2019; 21:63-64. [PMID: 31745294 DOI: 10.1038/s41576-019-0199-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Andreas J Gruber
- Oxford Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland.
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27
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Păunescu V, Zavolan M, Oprea T. In memoriam: Francisc Schneider (1933‐2017). J Cell Mol Med 2019. [PMCID: PMC6433889 DOI: 10.1111/jcmm.14173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
This is the obituary for Francisc Schneider, who introduced clinical physiology in Romania and mentored generations of scientists.
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Affiliation(s)
| | | | - Tudor Oprea
- Department of Internal Medicine UNM School of Medicine Albuquerque New Mexico
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28
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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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29
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Gruber AJ, Gypas F, Riba A, Schmidt R, Zavolan M. Terminal exon characterization with TECtool reveals an abundance of cell-specific isoforms. Nat Methods 2018; 15:832-836. [PMID: 30202060 PMCID: PMC7611301 DOI: 10.1038/s41592-018-0114-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [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: 11/06/2017] [Accepted: 07/10/2018] [Indexed: 11/23/2022]
Abstract
Sequencing of RNA 3' ends has uncovered numerous sites that do not correspond to the termination sites of known transcripts. Through their 3' untranslated regions, protein-coding RNAs interact with RNA-binding proteins and microRNAs, which regulate many properties, including RNA stability and subcellular localization. We developed the terminal exon characterization (TEC) tool ( http://tectool.unibas.ch ), which can be used with RNA-sequencing data from any species for which a genome annotation that includes sites of RNA cleavage and polyadenylation is available. We discovered hundreds of previously unknown isoforms and cell-type-specific terminal exons in human cells. Ribosome profiling data revealed that many of these isoforms were translated. By applying TECtool to single-cell sequencing data, we found that the newly identified isoforms were expressed in subpopulations of cells. Thus, TECtool enables the identification of previously unknown isoforms in well-studied cell systems and in rare cell types.
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Affiliation(s)
- Andreas J Gruber
- Oxford Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Foivos Gypas
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Andrea Riba
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Ralf Schmidt
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland.
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30
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Essig K, Kronbeck N, Guimaraes JC, Lohs C, Schlundt A, Hoffmann A, Behrens G, Brenner S, Kowalska J, Lopez-Rodriguez C, Jemielity J, Holtmann H, Reiche K, Hackermüller J, Sattler M, Zavolan M, Heissmeyer V. Roquin targets mRNAs in a 3'-UTR-specific manner by different modes of regulation. Nat Commun 2018; 9:3810. [PMID: 30232334 PMCID: PMC6145892 DOI: 10.1038/s41467-018-06184-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 08/14/2018] [Indexed: 12/12/2022] Open
Abstract
The RNA-binding proteins Roquin-1 and Roquin-2 redundantly control gene expression and cell-fate decisions. Here, we show that Roquin not only interacts with stem–loop structures, but also with a linear sequence element present in about half of its targets. Comprehensive analysis of a minimal response element of the Nfkbid 3′-UTR shows that six stem–loop structures cooperate to exert robust and profound post-transcriptional regulation. Only binding of multiple Roquin proteins to several stem–loops exerts full repression, which redundantly involved deadenylation and decapping, but also translational inhibition. Globally, most Roquin targets are regulated by mRNA decay, whereas a small subset, including the Nfat5 mRNA, with more binding sites in their 3′-UTRs, are also subject to translational inhibition. These findings provide insights into how the robustness and magnitude of Roquin-mediated regulation is encoded in complex cis-elements. Roquin targets are known to contain two types of sequence-structure motifs, the constitutive and the alternative decay elements (CDE and ADE). Here, the authors describe a linear Roquin binding element (LBE) also involved in target recognition, and show that Roquin binding affects the translation of a subset of targeted mRNAs.
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Affiliation(s)
- Katharina Essig
- Institute for Immunology at the Biomedical Center, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
| | - Nina Kronbeck
- Institute for Immunology at the Biomedical Center, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
| | - Joao C Guimaraes
- Computational and Systems Biology, Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Claudia Lohs
- Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, 81377, München, Germany
| | - Andreas Schlundt
- Institute of Structural Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany.,Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, 85748, Garching, Germany
| | - Anne Hoffmann
- Young Investigators Group Bioinformatics and Transcriptomics, Department Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.,Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center of Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107, Leipzig, Germany
| | - Gesine Behrens
- Institute for Immunology at the Biomedical Center, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
| | - Sven Brenner
- Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, 81377, München, Germany
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089, Warsaw, Poland
| | - Cristina Lopez-Rodriguez
- Immunology Unit, Department of Experimental and Health Sciences, Pompeu Fabra University, 08003, Barcelona, Spain
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, 02-097, Warsaw, Poland
| | - Helmut Holtmann
- Institute of Biochemistry, Hannover Medical School, 30623, Hannover, Germany
| | - Kristin Reiche
- Young Investigators Group Bioinformatics and Transcriptomics, Department Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.,Bioinformatics Unit, Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology-IZI, Leipzig, Germany
| | - Jörg Hackermüller
- Young Investigators Group Bioinformatics and Transcriptomics, Department Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany.,Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, 85748, Garching, Germany
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum, University of Basel, 4056, Basel, Switzerland.
| | - Vigo Heissmeyer
- Institute for Immunology at the Biomedical Center, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany. .,Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, 81377, München, Germany.
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31
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Zavolan M, Gerber AP. Mirroring the multifaceted role of
RNA
and its partners in gene expression. FEBS Lett 2018; 592:2825-2827. [DOI: 10.1002/1873-3468.13230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
| | - André P. Gerber
- Faculty of Health and Medical Sciences Department of Microbial Sciences School of Biosciences and Medicine University of Surrey Guildford UK
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32
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Rzepiela AJ, Ghosh S, Breda J, Vina-Vilaseca A, Syed AP, Gruber AJ, Eschbach K, Beisel C, van Nimwegen E, Zavolan M. Single-cell mRNA profiling reveals the hierarchical response of miRNA targets to miRNA induction. Mol Syst Biol 2018; 14:e8266. [PMID: 30150282 PMCID: PMC6110312 DOI: 10.15252/msb.20188266] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 07/31/2018] [Accepted: 08/03/2018] [Indexed: 12/14/2022] Open
Abstract
miRNAs are small RNAs that regulate gene expression post-transcriptionally. By repressing the translation and promoting the degradation of target mRNAs, miRNAs may reduce the cell-to-cell variability in protein expression, induce correlations between target expression levels, and provide a layer through which targets can influence each other's expression as "competing RNAs" (ceRNAs). However, experimental evidence for these behaviors is limited. Combining mathematical modeling with RNA sequencing of individual human embryonic kidney cells in which the expression of two distinct miRNAs was induced over a wide range, we have inferred parameters describing the response of hundreds of miRNA targets to miRNA induction. Individual targets have widely different response dynamics, and only a small proportion of predicted targets exhibit high sensitivity to miRNA induction. Our data reveal for the first time the response parameters of the entire network of endogenous miRNA targets to miRNA induction, demonstrating that miRNAs correlate target expression and at the same time increase the variability in expression of individual targets across cells. The approach is generalizable to other miRNAs and post-transcriptional regulators to improve the understanding of gene expression dynamics in individual cell types.
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Affiliation(s)
- Andrzej J Rzepiela
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Souvik Ghosh
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Jeremie Breda
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Arnau Vina-Vilaseca
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Afzal P Syed
- 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
| | - Katja Eschbach
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Erik van Nimwegen
- 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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33
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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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34
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Essig K, Hu D, Guimaraes JC, Alterauge D, Edelmann S, Raj T, Kranich J, Behrens G, Heiseke A, Floess S, Klein J, Maiser A, Marschall S, Hrabĕ de Angelis M, Leonhardt H, Calkhoven CF, Noessner E, Brocker T, Huehn J, Krug AB, Zavolan M, Baumjohann D, Heissmeyer V. Roquin Suppresses the PI3K-mTOR Signaling Pathway to Inhibit T Helper Cell Differentiation and Conversion of Treg to Tfr Cells. Immunity 2017; 47:1067-1082.e12. [PMID: 29246441 DOI: 10.1016/j.immuni.2017.11.008] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 07/20/2017] [Accepted: 11/06/2017] [Indexed: 12/14/2022]
Abstract
Roquin proteins preclude spontaneous T cell activation and aberrant differentiation of T follicular helper (Tfh) or T helper 17 (Th17) cells. Here we showed that deletion of Roquin-encoding alleles specifically in regulatory T (Treg) cells also caused the activation of conventional T cells. Roquin-deficient Treg cells downregulated CD25, acquired a follicular Treg (Tfr) cell phenotype, and suppressed germinal center reactions but could not protect from colitis. Roquin inhibited the PI3K-mTOR signaling pathway by upregulation of Pten through interfering with miR-17∼92 binding to an overlapping cis-element in the Pten 3' UTR, and downregulated the Foxo1-specific E3 ubiquitin ligase Itch. Loss of Roquin enhanced Akt-mTOR signaling and protein synthesis, whereas inhibition of PI3K or mTOR in Roquin-deficient T cells corrected enhanced Tfh and Th17 or reduced iTreg cell differentiation. Thereby, Roquin-mediated control of PI3K-mTOR signaling prevents autoimmunity by restraining activation and differentiation of conventional T cells and specialization of Treg cells.
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Affiliation(s)
- Katharina Essig
- Institute for Immunology, Biomedical Center, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Desheng Hu
- Institute for Immunology, Biomedical Center, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany.
| | - Joao C Guimaraes
- Computational and Systems Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Dominik Alterauge
- Institute for Immunology, Biomedical Center, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Stephanie Edelmann
- Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, 81377 München, Germany
| | - Timsse Raj
- Institute for Immunology, Biomedical Center, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Jan Kranich
- Institute for Immunology, Biomedical Center, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Gesine Behrens
- Institute for Immunology, Biomedical Center, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Alexander Heiseke
- Institute for Immunology, Biomedical Center, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Stefan Floess
- Experimental Immunology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Juliane Klein
- Institute for Immunology, Biomedical Center, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Andreas Maiser
- Center for Integrated Protein Science, Department of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Susan Marschall
- German Center for Diabetes Research (DZD), 85764 Neuherberg, German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Chair of Experimental Genetics, School of Life Science Weihenstephan, Technische Universität München, Freising 85353, Germany
| | - Martin Hrabĕ de Angelis
- German Center for Diabetes Research (DZD), 85764 Neuherberg, German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Chair of Experimental Genetics, School of Life Science Weihenstephan, Technische Universität München, Freising 85353, Germany
| | - Heinrich Leonhardt
- Center for Integrated Protein Science, Department of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Cornelis F Calkhoven
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9700 AD Groningen, the Netherlands
| | - Elfriede Noessner
- Immunoanalytics Core Facility, Helmholtz Zentrum München, 81377 München, Germany
| | - Thomas Brocker
- Institute for Immunology, Biomedical Center, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Jochen Huehn
- Experimental Immunology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Anne B Krug
- Institute for Immunology, Biomedical Center, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Dirk Baumjohann
- Institute for Immunology, Biomedical Center, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Vigo Heissmeyer
- Institute for Immunology, Biomedical Center, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany; Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, 81377 München, Germany.
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35
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Zavolan M, Graveley BR. RNAs: dynamic and mutable. Genome Biol 2017; 18:226. [PMID: 29187228 PMCID: PMC5708131 DOI: 10.1186/s13059-017-1361-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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36
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Abstract
Studies in the last decade have revealed a complex and dynamic variety of pre-mRNA cleavage and polyadenylation reactions. mRNAs with long 3' untranslated regions (UTRs) are generated in differentiated cells whereas proliferating cells preferentially express transcripts with short 3'UTRs. We describe the A-seq protocol, now at its second version, which was developed to map polyadenylation sites genome-wide and study the regulation of pre-mRNA 3' end processing. Also this current protocol takes advantage of the polyadenylate (poly(A)) tails that are added during the biogenesis of most mammalian mRNAs to enrich for fully processed mRNAs. A DNA adaptor with deoxyuracil at its fourth position allows the precise processing of mRNA 3' end fragments for sequencing. Not including the cell culture and the overnight ligations, the protocol requires about 8 h hands-on time. Along with it, an easy-to-use software package for the analysis of the derived sequencing data is provided. A-seq2 and the associated analysis software provide an efficient and reliable solution to the mapping of pre-mRNA 3' ends in a wide range of conditions, from 106 or fewer cells.
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Affiliation(s)
- Georges Martin
- Computational and Systems Biology, Biozentrum, University of Basel
| | - Ralf Schmidt
- Computational and Systems Biology, Biozentrum, University of Basel
| | - Andreas J Gruber
- Computational and Systems Biology, Biozentrum, University of Basel
| | - Souvik Ghosh
- Computational and Systems Biology, Biozentrum, University of Basel
| | - Walter Keller
- Computational and Systems Biology, Biozentrum, University of Basel
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum, University of Basel; Swiss Institute of Bioinformatics, Biozentrum, University of Basel;
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37
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Omidi S, Zavolan M, Pachkov M, Breda J, Berger S, van Nimwegen E. Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors. PLoS Comput Biol 2017; 13:e1005176. [PMID: 28753602 PMCID: PMC5550003 DOI: 10.1371/journal.pcbi.1005176] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 08/09/2017] [Accepted: 06/02/2017] [Indexed: 11/17/2022] Open
Abstract
Gene regulatory networks are ultimately encoded by the sequence-specific binding of (TFs) to short DNA segments. Although it is customary to represent the binding specificity of a TF by a position-specific weight matrix (PSWM), which assumes each position within a site contributes independently to the overall binding affinity, evidence has been accumulating that there can be significant dependencies between positions. Unfortunately, methodological challenges have so far hindered the development of a practical and generally-accepted extension of the PSWM model. On the one hand, simple models that only consider dependencies between nearest-neighbor positions are easy to use in practice, but fail to account for the distal dependencies that are observed in the data. On the other hand, models that allow for arbitrary dependencies are prone to overfitting, requiring regularization schemes that are difficult to use in practice for non-experts. Here we present a new regulatory motif model, called dinucleotide weight tensor (DWT), that incorporates arbitrary pairwise dependencies between positions in binding sites, rigorously from first principles, and free from tunable parameters. We demonstrate the power of the method on a large set of ChIP-seq data-sets, showing that DWTs outperform both PSWMs and motif models that only incorporate nearest-neighbor dependencies. We also demonstrate that DWTs outperform two previously proposed methods. Finally, we show that DWTs inferred from ChIP-seq data also outperform PSWMs on HT-SELEX data for the same TF, suggesting that DWTs capture inherent biophysical properties of the interactions between the DNA binding domains of TFs and their binding sites. We make a suite of DWT tools available at dwt.unibas.ch, that allow users to automatically perform ‘motif finding’, i.e. the inference of DWT motifs from a set of sequences, binding site prediction with DWTs, and visualization of DWT ‘dilogo’ motifs. Gene regulatory networks are ultimately encoded in constellations of short binding sites in the DNA and RNA that are recognized by regulatory factors such as transcription factors (TFs). For several decades, computational analysis of regulatory networks has relied on a model of TF sequence-specificity, the position-specific weight-matrix (PSWM), that assumes different positions in a binding site contribute independently to the total binding energy of the TF. However, in recent years evidence has been accumulating that, at least for some TFs, this assumption does not hold. Here we present a new model for the sequence-specificity of TFs, the dinucleotide weight tensor (DWT), that takes arbitrary dependencies between positions in binding sites into account and show that it consistently outperforms PSWMs on high-throughput datasets on TF binding. Moreover, in contrast to previous approaches, DWTs are directly derived from first principles within a Bayesian framework, and contain no tunable parameters. This allows them to be easily applied in practice and we make a suite of tools available for computational analysis with DWTs.
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Affiliation(s)
- Saeed Omidi
- Biozentrum, University of Basel, Basel, Switzerland.,Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Mihaela Zavolan
- Biozentrum, University of Basel, Basel, Switzerland.,Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Mikhail Pachkov
- Biozentrum, University of Basel, Basel, Switzerland.,Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Jeremie Breda
- Biozentrum, University of Basel, Basel, Switzerland.,Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Severin Berger
- Biozentrum, University of Basel, Basel, Switzerland.,Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Erik van Nimwegen
- Biozentrum, University of Basel, Basel, Switzerland.,Swiss Institute of Bioinformatics, Basel, Switzerland
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38
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Dimitrova Y, Gruber AJ, Mittal N, Ghosh S, Dimitriades B, Mathow D, Grandy WA, Christofori G, Zavolan M. TFAP2A is a component of the ZEB1/2 network that regulates TGFB1-induced epithelial to mesenchymal transition. Biol Direct 2017; 12:8. [PMID: 28412966 PMCID: PMC5392957 DOI: 10.1186/s13062-017-0180-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 03/22/2017] [Indexed: 01/28/2023] Open
Abstract
Background The transition between epithelial and mesenchymal phenotypes (EMT) occurs in a variety of contexts. It is critical for mammalian development and it is also involved in tumor initiation and progression. Master transcription factor (TF) regulators of this process are conserved between mouse and human. Methods From a computational analysis of a variety of high-throughput sequencing data sets we initially inferred that TFAP2A is connected to the core EMT network in both species. We then analysed publicly available human breast cancer data for TFAP2A expression and also studied the expression (by mRNA sequencing), activity (by monitoring the expression of its predicted targets), and binding (by electrophoretic mobility shift assay and chromatin immunoprecipitation) of this factor in a mouse mammary gland EMT model system (NMuMG) cell line. Results We found that upon induction of EMT, the activity of TFAP2A, reflected in the expression level of its predicted targets, is up-regulated in a variety of systems, both murine and human, while TFAP2A’s expression is increased in more “stem-like” cancers. We provide strong evidence for the direct interaction between the TFAP2A TF and the ZEB2 promoter and we demonstrate that this interaction affects ZEB2 expression. Overexpression of TFAP2A from an exogenous construct perturbs EMT, however, in a manner similar to the downregulation of endogenous TFAP2A that takes place during EMT. Conclusions Our study reveals that TFAP2A is a conserved component of the core network that regulates EMT, acting as a repressor of many genes, including ZEB2. Reviewers This article has been reviewed by Dr. Martijn Huynen and Dr. Nicola Aceto. Electronic supplementary material The online version of this article (doi:10.1186/s13062-017-0180-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yoana Dimitrova
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056, Basel, Switzerland
| | - Andreas J Gruber
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056, Basel, Switzerland
| | - Nitish Mittal
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056, Basel, Switzerland
| | - Souvik Ghosh
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056, Basel, Switzerland
| | - Beatrice Dimitriades
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056, Basel, Switzerland
| | - Daniel Mathow
- Department of Cellular and Molecular Pathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - William Aaron Grandy
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056, Basel, Switzerland
| | - Gerhard Christofori
- Department of Biomedicine, University of Basel, Mattenstrasse 28, CH-4058, Basel, Switzerland
| | - Mihaela Zavolan
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056, Basel, Switzerland.
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39
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Gumienny R, Jedlinski DJ, Schmidt A, Gypas F, Martin G, Vina-Vilaseca A, Zavolan M. High-throughput identification of C/D box snoRNA targets with CLIP and RiboMeth-seq. Nucleic Acids Res 2017; 45:2341-2353. [PMID: 28031372 PMCID: PMC5389715 DOI: 10.1093/nar/gkw1321] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [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: 09/02/2016] [Revised: 12/08/2016] [Accepted: 12/19/2016] [Indexed: 01/02/2023] Open
Abstract
High-throughput sequencing has greatly facilitated the discovery of long and short non-coding RNAs (ncRNAs), which frequently guide ribonucleoprotein complexes to RNA targets, to modulate their metabolism and expression. However, for many ncRNAs, the targets remain to be discovered. In this study, we developed computational methods to map C/D box snoRNA target sites using data from core small nucleolar ribonucleoprotein crosslinking and immunoprecipitation and from transcriptome-wide mapping of 2΄-O-ribose methylation sites. We thereby assigned the snoRNA guide to a known methylation site in the 18S rRNA, we uncovered a novel partially methylated site in the 28S ribosomal RNA, and we captured a site in the 28S rRNA in interaction with multiple snoRNAs. Although we also captured mRNAs in interaction with snoRNAs, we did not detect 2΄-O-methylation of these targets. Our study provides an integrated approach to the comprehensive characterization of 2΄-O-methylation targets of snoRNAs in species beyond those in which these interactions have been traditionally studied and contributes to the rapidly developing field of 'epitranscriptomics'.
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MESH Headings
- Algorithms
- Base Sequence
- Cross-Linking Reagents/chemistry
- Databases, Genetic
- High-Throughput Nucleotide Sequencing/methods
- Immunoprecipitation
- Methylation
- Protein Binding
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 18S/metabolism
- RNA, Ribosomal, 28S/genetics
- RNA, Ribosomal, 28S/metabolism
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- Ribonucleoproteins, Small Nucleolar/genetics
- Ribonucleoproteins, Small Nucleolar/metabolism
- Ribose/metabolism
- Software
- Transcriptome
- RNA, Guide, CRISPR-Cas Systems
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Affiliation(s)
- Rafal Gumienny
- Computational and Systems Biology, Biozentrum, University of Basel, Switzerland
- Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Switzerland
| | | | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum, University of Basel, Switzerland
| | - Foivos Gypas
- Computational and Systems Biology, Biozentrum, University of Basel, Switzerland
- Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Switzerland
| | - Georges Martin
- Computational and Systems Biology, Biozentrum, University of Basel, Switzerland
| | - Arnau Vina-Vilaseca
- Computational and Systems Biology, Biozentrum, University of Basel, Switzerland
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum, University of Basel, Switzerland
- Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Switzerland
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40
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Riba A, Emmenlauer M, Chen A, Sigoillot F, Cong F, Dehio C, Jenkins J, Zavolan M. Explicit Modeling of siRNA-Dependent On- and Off-Target Repression Improves the Interpretation of Screening Results. Cell Syst 2017; 4:182-193.e4. [PMID: 28215525 DOI: 10.1016/j.cels.2017.01.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 12/09/2016] [Accepted: 01/13/2017] [Indexed: 12/31/2022]
Abstract
RNAi is broadly used to map gene regulatory networks, but the identification of genes that are responsible for the observed phenotypes is challenging, as small interfering RNAs (siRNAs) simultaneously downregulate the intended on targets and many partially complementary off targets. Additionally, the scarcity of publicly available control datasets hinders the development and comparative evaluation of computational methods for analyzing the data. Here, we introduce PheLiM (https://github.com/andreariba/PheLiM), a method that uses predictions of siRNA on- and off-target downregulation to infer gene-specific contributions to phenotypes. To assess the performance of PheLiM, we carried out siRNA- and CRISPR/Cas9-based genome-wide screening of two well-characterized pathways, bone morphogenetic protein (BMP) and nuclear factor κB (NF-κB), and we reanalyzed publicly available siRNA screens. We demonstrate that PheLiM has the overall highest accuracy and most reproducible results compared to other available methods. PheLiM can accommodate various methods for predicting siRNA off targets and is broadly applicable to the identification of genes underlying complex phenotypes.
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Affiliation(s)
- Andrea Riba
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Mario Emmenlauer
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Amy Chen
- Developmental & Molecular Pathways, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Frederic Sigoillot
- Developmental & Molecular Pathways, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Feng Cong
- Developmental & Molecular Pathways, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Christoph Dehio
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Jeremy Jenkins
- Developmental & Molecular Pathways, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Mihaela Zavolan
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland.
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41
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Abstract
Background Ribosomes are highly conserved molecular machines whose core composition has traditionally been regarded as invariant. However, recent studies have reported intriguing differences in the expression of some ribosomal proteins (RPs) across tissues and highly specific effects on the translation of individual mRNAs. Results To determine whether RPs are more generally linked to cell identity, we analyze the heterogeneity of RP expression in a large set of human tissues, primary cells, and tumors. We find that about a quarter of human RPs exhibit tissue-specific expression and that primary hematopoietic cells display the most complex patterns of RP expression, likely shaped by context-restricted transcriptional regulators. Strikingly, we uncover patterns of dysregulated expression of individual RPs across cancer types that arise through copy number variations and are predictive for disease progression. Conclusions Our study reveals an unanticipated plasticity of RP expression across normal and malignant human cell types and provides a foundation for future characterization of cellular behaviors that are orchestrated by specific RPs. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1104-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joao C Guimaraes
- Computational and Systems Biology, Biozentrum, University of Basel, 4056, Basel, Switzerland.
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum, University of Basel, 4056, Basel, Switzerland.
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42
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Ustianenko D, Pasulka J, Feketova Z, Bednarik L, Zigackova D, Fortova A, Zavolan M, Vanacova S. TUT-DIS3L2 is a mammalian surveillance pathway for aberrant structured non-coding RNAs. EMBO J 2016; 35:2179-2191. [PMID: 27647875 PMCID: PMC5069555 DOI: 10.15252/embj.201694857] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 08/19/2016] [Indexed: 11/19/2022] Open
Abstract
Uridylation of various cellular RNA species at the 3′ end has been generally linked to RNA degradation. In mammals, uridylated pre‐let‐7 miRNAs and mRNAs are targeted by the 3′ to 5′ exoribonuclease DIS3L2. Mutations in DIS3L2 have been associated with Perlman syndrome and with Wilms tumor susceptibility. Using in vivo cross‐linking and immunoprecipitation (CLIP) method, we discovered the DIS3L2‐dependent cytoplasmic uridylome of human cells. We found a broad spectrum of uridylated RNAs including rRNAs, snRNAs, snoRNAs, tRNAs, vault, 7SL, Y RNAs, mRNAs, lncRNAs, and transcripts from pseudogenes. The unifying features of most of these identified RNAs are aberrant processing and the presence of stable secondary structures. Most importantly, we demonstrate that uridylation mediates DIS3L2 degradation of short RNA polymerase II‐derived RNAs. Our findings establish the role of DIS3L2 and oligouridylation as the cytoplasmic quality control for highly structured ncRNAs.
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Affiliation(s)
- Dmytro Ustianenko
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Josef Pasulka
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Zuzana Feketova
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Lukas Bednarik
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Dagmar Zigackova
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Andrea Fortova
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Mihaela Zavolan
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Stepanka Vanacova
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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43
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Gruber AJ, Schmidt R, Gruber AR, Martin G, Ghosh S, Belmadani M, Keller W, Zavolan M. A comprehensive analysis of 3' end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation. Genome Res 2016; 26:1145-59. [PMID: 27382025 PMCID: PMC4971764 DOI: 10.1101/gr.202432.115] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 05/31/2016] [Indexed: 12/22/2022]
Abstract
Alternative polyadenylation (APA) is a general mechanism of transcript diversification in mammals, which has been recently linked to proliferative states and cancer. Different 3′ untranslated region (3′ UTR) isoforms interact with different RNA-binding proteins (RBPs), which modify the stability, translation, and subcellular localization of the corresponding transcripts. Although the heterogeneity of pre-mRNA 3′ end processing has been established with high-throughput approaches, the mechanisms that underlie systematic changes in 3′ UTR lengths remain to be characterized. Through a uniform analysis of a large number of 3′ end sequencing data sets, we have uncovered 18 signals, six of which are novel, whose positioning with respect to pre-mRNA cleavage sites indicates a role in pre-mRNA 3′ end processing in both mouse and human. With 3′ end sequencing we have demonstrated that the heterogeneous ribonucleoprotein C (HNRNPC), which binds the poly(U) motif whose frequency also peaks in the vicinity of polyadenylation (poly(A)) sites, has a genome-wide effect on poly(A) site usage. HNRNPC-regulated 3′ UTRs are enriched in ELAV-like RBP 1 (ELAVL1) binding sites and include those of the CD47 gene, which participate in the recently discovered mechanism of 3′ UTR–dependent protein localization (UDPL). Our study thus establishes an up-to-date, high-confidence catalog of 3′ end processing sites and poly(A) signals, and it uncovers an important role of HNRNPC in regulating 3′ end processing. It further suggests that U-rich elements mediate interactions with multiple RBPs that regulate different stages in a transcript's life cycle.
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Affiliation(s)
- Andreas J Gruber
- Computational and Systems Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Ralf Schmidt
- Computational and Systems Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Andreas R Gruber
- Computational and Systems Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Georges Martin
- Computational and Systems Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Souvik Ghosh
- Computational and Systems Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Manuel Belmadani
- Computational and Systems Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Walter Keller
- Computational and Systems Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland
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44
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Jorjani H, Kehr S, Jedlinski DJ, Gumienny R, Hertel J, Stadler PF, Zavolan M, Gruber AR. An updated human snoRNAome. Nucleic Acids Res 2016; 44:5068-82. [PMID: 27174936 PMCID: PMC4914119 DOI: 10.1093/nar/gkw386] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [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: 11/13/2015] [Accepted: 04/23/2016] [Indexed: 12/18/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) are a class of non-coding RNAs that guide the post-transcriptional processing of other non-coding RNAs (mostly ribosomal RNAs), but have also been implicated in processes ranging from microRNA-dependent gene silencing to alternative splicing. In order to construct an up-to-date catalog of human snoRNAs we have combined data from various databases, de novo prediction and extensive literature review. In total, we list more than 750 curated genomic loci that give rise to snoRNA and snoRNA-like genes. Utilizing small RNA-seq data from the ENCODE project, our study characterizes the plasticity of snoRNA expression identifying both constitutively as well as cell type specific expressed snoRNAs. Especially, the comparison of malignant to non-malignant tissues and cell types shows a dramatic perturbation of the snoRNA expression profile. Finally, we developed a high-throughput variant of the reverse-transcriptase-based method for identifying 2'-O-methyl modifications in RNAs termed RimSeq. Using the data from this and other high-throughput protocols together with previously reported modification sites and state-of-the-art target prediction methods we re-estimate the snoRNA target RNA interaction network. Our current results assign a reliable modification site to 83% of the canonical snoRNAs, leaving only 76 snoRNA sequences as orphan.
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Affiliation(s)
- Hadi Jorjani
- Computational and Systems Biology, Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel CH-4056, Switzerland
| | - Stephanie Kehr
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, D-04107 Leipzig, Germany
| | - Dominik J Jedlinski
- Computational and Systems Biology, Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel CH-4056, Switzerland
| | - Rafal Gumienny
- Computational and Systems Biology, Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel CH-4056, Switzerland
| | - Jana Hertel
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, D-04107 Leipzig, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, D-04107 Leipzig, Germany Max Planck Institute for Mathematics in the Sciences, D-04103 Leipzig, Germany RNomics Group, Fraunhofer Institute for Cell Therapy and Immunology, D-04103 Leipzig, Germany Department of Theoretical Chemistry, University of Vienna, A-1090 Vienna, Austria Santa Fe Institute, NM-87501Santa Fe, USA
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel CH-4056, Switzerland
| | - Andreas R Gruber
- Computational and Systems Biology, Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel CH-4056, Switzerland
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Breda J, Rzepiela AJ, Gumienny R, van Nimwegen E, Zavolan M. Corrigendum to "Quantifying the strength of miRNA-target interactions" [Methods (2015) 90-99]. Methods 2016; 104:204-205. [PMID: 27372217 DOI: 10.1016/j.ymeth.2015.12.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Jeremie Breda
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Klingelbergstrasse 50-70, 4056 Basel, Switzerland
| | - Andrzej J Rzepiela
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Klingelbergstrasse 50-70, 4056 Basel, Switzerland
| | - Rafal Gumienny
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Klingelbergstrasse 50-70, 4056 Basel, Switzerland
| | - Erik van Nimwegen
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Klingelbergstrasse 50-70, 4056 Basel, Switzerland
| | - Mihaela Zavolan
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Klingelbergstrasse 50-70, 4056 Basel, Switzerland.
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Gumienny R, Zavolan M. Accurate transcriptome-wide prediction of microRNA targets and small interfering RNA off-targets with MIRZA-G. Nucleic Acids Res 2015; 43:9095. [PMID: 26365243 PMCID: PMC4605328 DOI: 10.1093/nar/gkv924] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Breda J, Rzepiela AJ, Gumienny R, van Nimwegen E, Zavolan M. Quantifying the strength of miRNA–target interactions. Methods 2015; 85:90-99. [DOI: 10.1016/j.ymeth.2015.04.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 04/09/2015] [Accepted: 04/10/2015] [Indexed: 01/01/2023] Open
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Subasic D, Brümmer A, Wu Y, Pinto SM, Imig J, Keller M, Jovanovic M, Lightfoot HL, Nasso S, Goetze S, Brunner E, Hall J, Aebersold R, Zavolan M, Hengartner MO. Cooperative target mRNA destabilization and translation inhibition by miR-58 microRNA family in C. elegans. Genome Res 2015; 25:1680-91. [PMID: 26232411 PMCID: PMC4617964 DOI: 10.1101/gr.183160.114] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 07/27/2015] [Indexed: 12/19/2022]
Abstract
In animals, microRNAs frequently form families with related sequences. The functional relevance of miRNA families and the relative contribution of family members to target repression have remained, however, largely unexplored. Here, we used the Caenorhabditis elegans miR-58 miRNA family, composed primarily of the four highly abundant members miR-58.1, miR-80, miR-81, and miR-82, as a model to investigate the redundancy of miRNA family members and their impact on target expression in an in vivo setting. We found that miR-58 family members repress largely overlapping sets of targets in a predominantly additive fashion. Progressive deletions of miR-58 family members lead to cumulative up-regulation of target protein and RNA levels. Phenotypic defects could only be observed in the family quadruple mutant, which also showed the strongest change in target protein levels. Interestingly, although the seed sequences of miR-80 and miR-58.1 differ in a single nucleotide, predicted canonical miR-80 targets were efficiently up-regulated in the mir-58.1 single mutant, indicating functional redundancy of distinct members of this miRNA family. At the aggregate level, target binding leads mainly to mRNA degradation, although we also observed some degree of translational inhibition, particularly in the single miR-58 family mutants. These results provide a framework for understanding how miRNA family members interact to regulate target mRNAs.
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Affiliation(s)
- Deni Subasic
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland; Molecular Life Sciences PhD Program, Swiss Federal Institute of Technology and University of Zurich, 8057 Zurich, Switzerland
| | - Anneke Brümmer
- Biozentrum, University of Basel, 4056 Basel, Switzerland; Department of Integrative Biology and Physiology, University of California, Los Angeles, California 90095, USA
| | - Yibo Wu
- Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
| | - Sérgio Morgado Pinto
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland; Graduate Program in Areas of Basic and Applied Biology (GABBA), University of Porto, 4099-002 Porto, Portugal
| | - Jochen Imig
- Institute of Pharmaceutical Chemistry, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
| | - Martin Keller
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland; Molecular Life Sciences PhD Program, Swiss Federal Institute of Technology and University of Zurich, 8057 Zurich, Switzerland
| | - Marko Jovanovic
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Helen Louise Lightfoot
- Institute of Pharmaceutical Chemistry, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
| | - Sara Nasso
- Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
| | - Sandra Goetze
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland; Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
| | - Erich Brunner
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Jonathan Hall
- Institute of Pharmaceutical Chemistry, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland; Faculty of Science, University of Zurich, 8057 Zurich, Switzerland
| | | | - Michael O Hengartner
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
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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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50
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Tattikota SG, Rathjen T, Hausser J, Khedkar A, Kabra UD, Pandey V, Sury M, Wessels HH, Mollet IG, Eliasson L, Selbach M, Zinzen RP, Zavolan M, Kadener S, Tschöp MH, Jastroch M, Friedländer MR, Poy MN. miR-184 Regulates Pancreatic β-Cell Function According to Glucose Metabolism. J Biol Chem 2015; 290:20284-94. [PMID: 26152724 DOI: 10.1074/jbc.m115.658625] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Indexed: 02/03/2023] Open
Abstract
In response to fasting or hyperglycemia, the pancreatic β-cell alters its output of secreted insulin; however, the pathways governing this adaptive response are not entirely established. Although the precise role of microRNAs (miRNAs) is also unclear, a recurring theme emphasizes their function in cellular stress responses. We recently showed that miR-184, an abundant miRNA in the β-cell, regulates compensatory proliferation and secretion during insulin resistance. Consistent with previous studies showing miR-184 suppresses insulin release, expression of this miRNA was increased in islets after fasting, demonstrating an active role in the β-cell as glucose levels lower and the insulin demand ceases. Additionally, miR-184 was negatively regulated upon the administration of a sucrose-rich diet in Drosophila, demonstrating strong conservation of this pathway through evolution. Furthermore, miR-184 and its target Argonaute2 remained inversely correlated as concentrations of extracellular glucose increased, underlining a functional relationship between this miRNA and its targets. Lastly, restoration of Argonaute2 in the presence of miR-184 rescued suppression of miR-375-targeted genes, suggesting these genes act in a coordinated manner during changes in the metabolic context. Together, these results highlight the adaptive role of miR-184 according to glucose metabolism and suggest the regulatory role of this miRNA in energy homeostasis is highly conserved.
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Affiliation(s)
- Sudhir G Tattikota
- From the Max Delbrueck Center for Molecular Medicine, 13125 Berlin, Germany
| | - Thomas Rathjen
- From the Max Delbrueck Center for Molecular Medicine, 13125 Berlin, Germany
| | - Jean Hausser
- Computational and Systems Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Aditya Khedkar
- From the Max Delbrueck Center for Molecular Medicine, 13125 Berlin, Germany
| | - Uma D Kabra
- Institute for Diabetes and Obesity, Helmholtz Centre for Health and Environment and Division of Metabolic Diseases, Technical University Munich, 85748 Munich, Germany
| | - Varun Pandey
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Matthias Sury
- From the Max Delbrueck Center for Molecular Medicine, 13125 Berlin, Germany
| | | | - Inês G Mollet
- Islet cell exocytosis, Lund University Diabetes Center, CRC 91-11, Jan Waldenströms gata 35, 20502 Malmö, Sweden, and
| | - Lena Eliasson
- Islet cell exocytosis, Lund University Diabetes Center, CRC 91-11, Jan Waldenströms gata 35, 20502 Malmö, Sweden, and
| | - Matthias Selbach
- From the Max Delbrueck Center for Molecular Medicine, 13125 Berlin, Germany
| | - Robert P Zinzen
- From the Max Delbrueck Center for Molecular Medicine, 13125 Berlin, Germany
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Sebastian Kadener
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Matthias H Tschöp
- Institute for Diabetes and Obesity, Helmholtz Centre for Health and Environment and Division of Metabolic Diseases, Technical University Munich, 85748 Munich, Germany
| | - Martin Jastroch
- Institute for Diabetes and Obesity, Helmholtz Centre for Health and Environment and Division of Metabolic Diseases, Technical University Munich, 85748 Munich, Germany
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 17121 Stockholm, Sweden
| | - Matthew N Poy
- From the Max Delbrueck Center for Molecular Medicine, 13125 Berlin, Germany,
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