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Brondolin M, Herzog D, Sultan S, Warburton F, Vigilante A, Knight RD. Migration and differentiation of muscle stem cells are coupled by RhoA signalling during regeneration. Open Biol 2023; 13:230037. [PMID: 37726092 PMCID: PMC10508982 DOI: 10.1098/rsob.230037] [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: 02/09/2023] [Accepted: 07/31/2023] [Indexed: 09/21/2023] Open
Abstract
Skeletal muscle is highly regenerative and is mediated by a population of migratory adult muscle stem cells (muSCs). Effective muscle regeneration requires a spatio-temporally regulated response of the muSC population to generate sufficient muscle progenitor cells that then differentiate at the appropriate time. The relationship between muSC migration and cell fate is poorly understood and it is not clear how forces experienced by migrating cells affect cell behaviour. We have used zebrafish to understand the relationship between muSC cell adhesion, behaviour and fate in vivo. Imaging of pax7-expressing muSCs as they respond to focal injuries in trunk muscle reveals that they migrate by protrusive-based means. By carefully characterizing their behaviour in response to injury we find that they employ an adhesion-dependent mode of migration that is regulated by the RhoA kinase ROCK. Impaired ROCK activity results in reduced expression of cell cycle genes and increased differentiation in regenerating muscle. This correlates with changes to focal adhesion dynamics and migration, revealing that ROCK inhibition alters the interaction of muSCs to their local environment. We propose that muSC migration and differentiation are coupled processes that respond to changes in force from the environment mediated by RhoA signalling.
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Affiliation(s)
- Mirco Brondolin
- Centre for Craniofacial and Regenerative Biology, King's College London, Guy's Hospital, London, London SE1 9RT, UK
| | - Dylan Herzog
- Centre for Craniofacial and Regenerative Biology, King's College London, Guy's Hospital, London, London SE1 9RT, UK
| | - Sami Sultan
- Centre for Craniofacial and Regenerative Biology, King's College London, Guy's Hospital, London, London SE1 9RT, UK
| | - Fiona Warburton
- Oral Clinical Research Unit, King's College London, London, London SE1 9RT, UK
| | | | - Robert D. Knight
- Centre for Craniofacial and Regenerative Biology, King's College London, Guy's Hospital, London, London SE1 9RT, UK
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D'Amato G, Phansalkar R, Naftaly JA, Fan X, Amir ZA, Rios Coronado PE, Cowley DO, Quinn KE, Sharma B, Caron KM, Vigilante A, Red-Horse K. Endocardium-to-coronary artery differentiation during heart development and regeneration involves sequential roles of Bmp2 and Cxcl12/Cxcr4. Dev Cell 2022; 57:2517-2532.e6. [PMID: 36347256 PMCID: PMC9833645 DOI: 10.1016/j.devcel.2022.10.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 12/02/2021] [Revised: 07/28/2022] [Accepted: 10/18/2022] [Indexed: 11/09/2022]
Abstract
Endocardial cells lining the heart lumen are coronary vessel progenitors during embryogenesis. Re-igniting this developmental process in adults could regenerate blood vessels lost during cardiac injury, but this requires additional knowledge of molecular mechanisms. Here, we use mouse genetics and scRNA-seq to identify regulators of endocardial angiogenesis and precisely assess the role of CXCL12/CXCR4 signaling. Time-specific lineage tracing demonstrated that endocardial cells differentiated into coronary endothelial cells primarily at mid-gestation. A new mouse line reporting CXCR4 activity-along with cell-specific gene deletions-demonstrated it was specifically required for artery morphogenesis rather than angiogenesis. Integrating scRNA-seq data of endocardial-derived coronary vessels from mid- and late-gestation identified a Bmp2-expressing transitioning population specific to mid-gestation. Bmp2 stimulated endocardial angiogenesis in vitro and in injured neonatal mouse hearts. Our data demonstrate how understanding the molecular mechanisms underlying endocardial angiogenesis can identify new potential therapeutic targets promoting revascularization of the injured heart.
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Affiliation(s)
- Gaetano D'Amato
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Ragini Phansalkar
- Department of Biology, Stanford University, Stanford, CA, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Xiaochen Fan
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Zhainib A Amir
- Department of Biology, Stanford University, Stanford, CA, USA
| | | | - Dale O Cowley
- Animal Models Core, University of North Carolina, Chapel Hill, NC, USA
| | - Kelsey E Quinn
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bikram Sharma
- Department of Biology, Ball State University, Muncie, IN, USA
| | - Kathleen M Caron
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alessandra Vigilante
- Centre for Stem Cells and Regenerative Medicine & Institute for Liver Studies, King's College London, London, UK
| | - Kristy Red-Horse
- Department of Biology, Stanford University, Stanford, CA, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford, CA, USA.
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Mitchell C, Caroff L, Solis-Lemus JA, Reyes-Aldasoro CC, Vigilante A, Warburton F, de Chaumont F, Dufour A, Dallongeville S, Olivo-Marin JC, Knight R. Cell Tracking Profiler - a user-driven analysis framework for evaluating 4D live-cell imaging data. J Cell Sci 2020; 133:jcs241422. [PMID: 33093241 PMCID: PMC7710012 DOI: 10.1242/jcs.241422] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 10/14/2020] [Indexed: 12/20/2022] Open
Abstract
Accurate measurements of cell morphology and behaviour are fundamentally important for understanding how disease, molecules and drugs affect cell function in vivo Here, by using muscle stem cell (muSC) responses to injury in zebrafish as our biological paradigm, we established a 'ground truth' for muSC behaviour. This revealed that segmentation and tracking algorithms from commonly used programs are error-prone, leading us to develop a fast semi-automated image analysis pipeline that allows user-defined parameters for segmentation and correction of cell tracking. Cell Tracking Profiler (CTP) is a package that runs two existing programs, HK Means and Phagosight within the Icy image analysis suite, to enable user-managed cell tracking from 3D time-lapse datasets to provide measures of cell shape and movement. We demonstrate how CTP can be used to reveal changes to cell behaviour of muSCs in response to manipulation of the cell cytoskeleton by small-molecule inhibitors. CTP and the associated tools we have developed for analysis of outputs thus provide a powerful framework for analysing complex cell behaviour in vivo from 4D datasets that are not amenable to straightforward analysis.
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Affiliation(s)
- Claire Mitchell
- Centre for Craniofacial and Regenerative Biology, King's College London, Guy's Hospital, London SE1 9RT, UK
| | - Lauryanne Caroff
- Centre for Craniofacial and Regenerative Biology, King's College London, Guy's Hospital, London SE1 9RT, UK
| | - Jose Alonso Solis-Lemus
- School of Mathematics, Computer Science and Engineering, City, University of London, Tait Building, Northampton Square, London EC1V 0HB, UK
| | - Constantino Carlos Reyes-Aldasoro
- School of Mathematics, Computer Science and Engineering, City, University of London, Tait Building, Northampton Square, London EC1V 0HB, UK
| | - Alessandra Vigilante
- Centre for Stem Cells and Regenerative Medicine, King's College London, Tower Wing, Guy's Hospital, London SE1 9RT, UK
| | - Fiona Warburton
- Centre for Oral, Clinical and Translational Sciences, King's College London, Guy's Hospital, London SE1 9RT, UK
| | | | - Alexandre Dufour
- Bioimage Analysis Unit, Institut Pasteur, Paris CEDEX 15, France
| | | | | | - Robert Knight
- Centre for Craniofacial and Regenerative Biology, King's College London, Guy's Hospital, London SE1 9RT, UK
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Sequeira I, Rashid M, Tomás IM, Williams MJ, Graham TA, Adams DJ, Vigilante A, Watt FM. Genomic landscape and clonal architecture of mouse oral squamous cell carcinomas dictate tumour ecology. Nat Commun 2020; 11:5671. [PMID: 33168804 PMCID: PMC7652942 DOI: 10.1038/s41467-020-19401-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 10/06/2020] [Indexed: 01/10/2023] Open
Abstract
To establish whether 4-nitroquinoline N-oxide-induced carcinogenesis mirrors the heterogeneity of human oral squamous cell carcinoma (OSCC), we have performed genomic analysis of mouse tongue lesions. The mutational signatures of human and mouse OSCC overlap extensively. Mutational burden is higher in moderate dysplasias and invasive SCCs than in hyperplasias and mild dysplasias, although mutations in p53, Notch1 and Fat1 occur in early lesions. Laminin-α3 mutations are associated with tumour invasiveness and Notch1 mutant tumours have an increased immune infiltrate. Computational modelling of clonal dynamics indicates that high genetic heterogeneity may be a feature of those mild dysplasias that are likely to progress to more aggressive tumours. These studies provide a foundation for exploring OSCC evolution, heterogeneity and progression.
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Affiliation(s)
- Inês Sequeira
- Centre for Stem Cells & Regenerative Medicine, King's College London, Guy's Hospital, Great Maze Pond, London, SE1 9RT, UK
- Institute of Dentistry, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Mamunur Rashid
- Experimental Cancer Genetics, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Inês M Tomás
- Centre for Stem Cells & Regenerative Medicine, King's College London, Guy's Hospital, Great Maze Pond, London, SE1 9RT, UK
| | - Marc J Williams
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Trevor A Graham
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - David J Adams
- Experimental Cancer Genetics, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Alessandra Vigilante
- Centre for Stem Cells & Regenerative Medicine, King's College London, Guy's Hospital, Great Maze Pond, London, SE1 9RT, UK
| | - Fiona M Watt
- Centre for Stem Cells & Regenerative Medicine, King's College London, Guy's Hospital, Great Maze Pond, London, SE1 9RT, UK.
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5
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Vigilante A, Laddach A, Moens N, Meleckyte R, Leha A, Ghahramani A, Culley OJ, Kathuria A, Hurling C, Vickers A, Wiseman E, Tewary M, Zandstra PW, Durbin R, Fraternali F, Stegle O, Birney E, Luscombe NM, Danovi D, Watt FM. Identifying Extrinsic versus Intrinsic Drivers of Variation in Cell Behavior in Human iPSC Lines from Healthy Donors. Cell Rep 2019; 26:2078-2087.e3. [PMID: 30784590 PMCID: PMC6381787 DOI: 10.1016/j.celrep.2019.01.094] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [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: 06/18/2018] [Revised: 12/11/2018] [Accepted: 01/24/2019] [Indexed: 01/08/2023] Open
Abstract
Large cohorts of human induced pluripotent stem cells (iPSCs) from healthy donors are a potentially powerful tool for investigating the relationship between genetic variants and cellular behavior. Here, we integrate high content imaging of cell shape, proliferation, and other phenotypes with gene expression and DNA sequence datasets from over 100 human iPSC lines. By applying a dimensionality reduction approach, Probabilistic Estimation of Expression Residuals (PEER), we extracted factors that captured the effects of intrinsic (genetic concordance between different cell lines from the same donor) and extrinsic (cell responses to different fibronectin concentrations) conditions. We identify genes that correlate in expression with intrinsic and extrinsic PEER factors and associate outlier cell behavior with genes containing rare deleterious non-synonymous SNVs. Our study, thus, establishes a strategy for examining the genetic basis of inter-individual variability in cell behavior.
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Affiliation(s)
- Alessandra Vigilante
- Centre for Stem Cells and Regenerative Medicine, King's College London, Floor 28, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Anna Laddach
- Randall Division, King's College London, New Hunts House, Great Maze Pond, London SE1 9RT, UK
| | - Nathalie Moens
- Centre for Stem Cells and Regenerative Medicine, King's College London, Floor 28, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Ruta Meleckyte
- Centre for Stem Cells and Regenerative Medicine, King's College London, Floor 28, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Andreas Leha
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Arsham Ghahramani
- Centre for Stem Cells and Regenerative Medicine, King's College London, Floor 28, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Oliver J Culley
- Centre for Stem Cells and Regenerative Medicine, King's College London, Floor 28, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Annie Kathuria
- Centre for Stem Cells and Regenerative Medicine, King's College London, Floor 28, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Chloe Hurling
- Centre for Stem Cells and Regenerative Medicine, King's College London, Floor 28, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Alice Vickers
- Centre for Stem Cells and Regenerative Medicine, King's College London, Floor 28, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Erika Wiseman
- Centre for Stem Cells and Regenerative Medicine, King's College London, Floor 28, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Mukul Tewary
- Centre for Stem Cells and Regenerative Medicine, King's College London, Floor 28, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK; School of Biomedical Engineering, The University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada; Michael Smith Laboratories, The University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4, Canada
| | - Peter W Zandstra
- School of Biomedical Engineering, The University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada; Michael Smith Laboratories, The University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4, Canada
| | - Richard Durbin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Franca Fraternali
- Randall Division, King's College London, New Hunts House, Great Maze Pond, London SE1 9RT, UK
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Nicholas M Luscombe
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Davide Danovi
- Centre for Stem Cells and Regenerative Medicine, King's College London, Floor 28, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK.
| | - Fiona M Watt
- Centre for Stem Cells and Regenerative Medicine, King's College London, Floor 28, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK.
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6
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Ambrosino L, Bostan H, di Salle P, Sangiovanni M, Vigilante A, Chiusano ML. pATsi: Paralogs and Singleton Genes from Arabidopsis thaliana. Evol Bioinform Online 2016; 12:1-7. [PMID: 26792975 PMCID: PMC4710182 DOI: 10.4137/ebo.s32536] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 10/11/2015] [Accepted: 10/17/2015] [Indexed: 11/05/2022] Open
Abstract
Arabidopsis thaliana is widely accepted as a model species in plant biology. Its genome, due to its small size and diploidy, was the first to be sequenced among plants, making this species also a reference for plant comparative genomics. Nevertheless, the evolutionary mechanisms that shaped the Arabidopsis genome are still controversial. Indeed, duplications, translocations, inversions, and gene loss events that contributed to the current organization are difficult to be traced. A reliable identification of paralogs and single-copy genes is essential to understand these mechanisms. Therefore, we implemented a dedicated pipeline to identify paralog genes and classify single-copy genes into opportune categories. PATsi, a web-accessible database, was organized to allow the straightforward access to the paralogs organized into networks and to the classification of single-copy genes. This permits to efficiently explore the gene collection of Arabidopsis for evolutionary investigations and comparative genomics.
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Affiliation(s)
- Luca Ambrosino
- Department of Agriculture, University of Naples Federico II, Portici, Italy
| | - Hamed Bostan
- Department of Agriculture, University of Naples Federico II, Portici, Italy
| | - Pasquale di Salle
- Department of Agriculture, University of Naples Federico II, Portici, Italy
| | - Mara Sangiovanni
- Department of Electrical Engineering and Information Technology, University of Naples Federico II, Naples, Italy
| | - Alessandra Vigilante
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London, UK.; The Francis Crick Institute, Lincoln's Inn Fields Laboratories, London, UK
| | - Maria L Chiusano
- Department of Agriculture, University of Naples Federico II, Portici, Italy
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Tajnik M, Vigilante A, Braun S, Hänel H, Luscombe NM, Ule J, Zarnack K, König J. Intergenic Alu exonisation facilitates the evolution of tissue-specific transcript ends. Nucleic Acids Res 2015; 43:10492-505. [PMID: 26400176 PMCID: PMC4666398 DOI: 10.1093/nar/gkv956] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Revised: 09/09/2015] [Accepted: 09/10/2015] [Indexed: 11/14/2022] Open
Abstract
The 3' untranslated regions (3' UTRs) of transcripts serve as important hubs for posttranscriptional gene expression regulation. Here, we find that the exonisation of intergenic Alu elements introduced new terminal exons and polyadenylation sites during human genome evolution. While Alu exonisation from introns has been described previously, we shed light on a novel mechanism to create alternative 3' UTRs, thereby opening opportunities for differential posttranscriptional regulation. On the mechanistic level, we show that intergenic Alu exonisation can compete both with alternative splicing and polyadenylation in the upstream gene. Notably, the Alu-derived isoforms are often expressed in a tissue-specific manner, and the Alu-derived 3' UTRs can alter mRNA stability. In summary, we demonstrate that intergenic elements can affect processing of preceding genes, and elucidate how intergenic Alu exonisation can contribute to tissue-specific posttranscriptional regulation by expanding the repertoire of 3' UTRs.
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Affiliation(s)
- Mojca Tajnik
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy
| | - Alessandra Vigilante
- UCL Genetics Institute, Department of Genetics, Evolution & Environment, University College London, Gower Street, London WC1E 6BT, UK Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Simon Braun
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128 Mainz, Germany
| | - Heike Hänel
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128 Mainz, Germany
| | - Nicholas M Luscombe
- UCL Genetics Institute, Department of Genetics, Evolution & Environment, University College London, Gower Street, London WC1E 6BT, UK Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK Okinawa Institute of Science & Technology, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Jernej Ule
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Kathi Zarnack
- Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Str. 15, 60438 Frankfurt, Germany
| | - Julian König
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128 Mainz, Germany Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
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Sugimoto Y, Vigilante A, Darbo E, Zirra A, Militti C, D’Ambrogio A, Luscombe NM, Ule J. hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1. Nature 2015; 519:491-4. [PMID: 25799984 PMCID: PMC4376666 DOI: 10.1038/nature14280] [Citation(s) in RCA: 211] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Accepted: 02/02/2015] [Indexed: 02/02/2023]
Abstract
The structure of messenger RNA is important for post-transcriptional regulation, mainly because it affects binding of trans-acting factors. However, little is known about the in vivo structure of full-length mRNAs. Here we present hiCLIP, a biochemical technique for transcriptome-wide identification of RNA secondary structures interacting with RNA-binding proteins (RBPs). Using this technique to investigate RNA structures bound by Staufen 1 (STAU1) in human cells, we uncover a dominance of intra-molecular RNA duplexes, a depletion of duplexes from coding regions of highly translated mRNAs, an unexpected prevalence of long-range duplexes in 3' untranslated regions (UTRs), and a decreased incidence of single nucleotide polymorphisms in duplex-forming regions. We also discover a duplex spanning 858 nucleotides in the 3' UTR of the X-box binding protein 1 (XBP1) mRNA that regulates its cytoplasmic splicing and stability. Our study reveals the fundamental role of mRNA secondary structures in gene expression and introduces hiCLIP as a widely applicable method for discovering new, especially long-range, RNA duplexes.
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Affiliation(s)
- Yoichiro Sugimoto
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Alessandra Vigilante
- Cancer Research UK London Research Institute, 44 Lincoln’s Inn Fields, London WC2A 3LY, UK
- UCL Genetics Institute, Department of Genetics, Evolution & Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Elodie Darbo
- Cancer Research UK London Research Institute, 44 Lincoln’s Inn Fields, London WC2A 3LY, UK
| | - Alexandra Zirra
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Cristina Militti
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Andrea D’Ambrogio
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Nicholas M Luscombe
- Cancer Research UK London Research Institute, 44 Lincoln’s Inn Fields, London WC2A 3LY, UK
- UCL Genetics Institute, Department of Genetics, Evolution & Environment, University College London, Gower Street, London WC1E 6BT, UK
- Okinawa Institute of Science & Technology, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Jernej Ule
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
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9
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Cofrancesco E, Vigilante A, Revoltella R. A turbidimetric assay method for studying antibody-induced lysis of hapten-coated erythrocytes. Ric Clin Lab 1976; 6:11-20. [PMID: 1019542 DOI: 10.1007/bf02949081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A method is described, based on the application of trubidimetry for study of antibody-mediated complement-dependent lysis of hapten-coated erythrocytes. The procedure is simple, reliable and sensitive. Time-rate studies over the entire range of interaction between the reactants are possible, with a minimal consumption of materials and time. The method also gives the possibility of adding substances to the reaction mixture, even at high concentrations, without introducing errors by multiple handling and washing.
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