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García-Ruiz S, Gustavsson EK, Zhang D, Reynolds RH, Chen Z, Fairbrother-Browne A, Gil-Martínez AL, Botia JA, Collado-Torres L, Ryten M. IntroVerse: a comprehensive database of introns across human tissues. Nucleic Acids Res 2022; 51:D167-D178. [PMID: 36399497 PMCID: PMC9825543 DOI: 10.1093/nar/gkac1056] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/21/2022] [Accepted: 10/30/2022] [Indexed: 11/19/2022] Open
Abstract
Dysregulation of RNA splicing contributes to both rare and complex diseases. RNA-sequencing data from human tissues has shown that this process can be inaccurate, resulting in the presence of novel introns detected at low frequency across samples and within an individual. To enable the full spectrum of intron use to be explored, we have developed IntroVerse, which offers an extensive catalogue on the splicing of 332,571 annotated introns and a linked set of 4,679,474 novel junctions covering 32,669 different genes. This dataset has been generated through the analysis of 17,510 human control RNA samples from 54 tissues provided by the Genotype-Tissue Expression Consortium. IntroVerse has two unique features: (i) it provides a complete catalogue of novel junctions and (ii) each novel junction has been assigned to a specific annotated intron. This unique, hierarchical structure offers multiple uses, including the identification of novel transcripts from known genes and their tissue-specific usage, and the assessment of background splicing noise for introns thought to be mis-spliced in disease states. IntroVerse provides a user-friendly web interface and is freely available at https://rytenlab.com/browser/app/introverse.
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Affiliation(s)
- Sonia García-Ruiz
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, WC1N 1EH, UK,Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
| | - Emil K Gustavsson
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, WC1N 1EH, UK,Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
| | - David Zhang
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, WC1N 1EH, UK,Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
| | - Regina H Reynolds
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, WC1N 1EH, UK,Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
| | - Zhongbo Chen
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, WC1N 1EH, UK,Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
| | - Aine Fairbrother-Browne
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, WC1N 1EH, UK,Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK,Department of Medical and Molecular Genetics, School of Basic and Medical Biosciences, King's College London, London, WC2R 2LS, UK
| | - Ana Luisa Gil-Martínez
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK,Department of Information and Communications Engineering Faculty of Informatics, Espinardo Campus, University of Murcia, Murcia, 30100, Spain
| | - Juan A Botia
- Department of Information and Communications Engineering Faculty of Informatics, Espinardo Campus, University of Murcia, Murcia, 30100, Spain
| | | | - Mina Ryten
- To whom correspondence should be addressed. Tel: +44 2081387617;
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Giaretta A. Frequency response in splicing regulation under mRNA auto-depletion control. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2022; 2022:2248-2253. [PMID: 36083926 DOI: 10.1109/embc48229.2022.9871147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Nowadays, there exists a huge literature about stochastic model of transcriptional and translational control in gene networks. However, results related to post-transcriptional regulation via splicing and its connection with transcriptional and translational regulation are almost missing in the current literature and only related to the steady state moments investigation. Nowadays, it is becoming of paramount importance the need for modeling post-transcriptional regulation via splicing especially for DNA viruses or retroviruses. However, there exists only few studies in the literature about splicing regulation and none of them investigate its behavior in the frequency domain that can unveil important features of dynamical stochastic systems that cannot be revealed by the sole steady state moment investigation. The aim of this work is to theoretically investigate a simple gene network subject to splicing regulation with negative feedback control, implemented through mRNA auto-depletion under a frequency domain perspective. This study showed the pivotal role of the burst size, enhancing the noise power spectrum, as well as the splicing conversion rates capable to increase and decrease the noise power spectrum in the pre-mRNA and mRNA, respectively, for high values of conversion rates. Importantly, it shows the capability of the mRNA autodepletion control to modulate the noise as a frequency-dependent amplifying control as a function of the negative feedback strengths.
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Ruz GA, Ashlock D, Allmendinger R, Fogel GB. Editorial: 2020 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (IEEE CIBCB 2020). Biosystems 2022; 218:104698. [PMID: 35568273 DOI: 10.1016/j.biosystems.2022.104698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Gonzalo A Ruz
- Facultad de Ingenier´ıa y Ciencias, Universidad Adolfo Ib´an˜ez Santiago, Chile; Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile.
| | - Daniel Ashlock
- Department of Mathematics and Statistics, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | | | - Gary B Fogel
- Natural Selection, Inc., 6480 Weathers Place, Suite 350, San Diego, CA 92121, USA
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