1
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Novosad VO. Identification of Significant RNA-Binding Proteins in the Process of CD44 Splicing Using the Boosted Beta Regression Algorithm. DOKL BIOCHEM BIOPHYS 2023; 510:99-103. [PMID: 37582871 DOI: 10.1134/s1607672923700199] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 08/17/2023]
Abstract
The expression of RNA-binding proteins and their interaction with the spliced pre-mRNA are the key factors in determining the final isoform profile. Transmembrane protein CD44 is involved in differentiation, invasion, motility, growth and survival of tumor cells, and is also a commonly accepted marker of cancer stem cells and epithelial-mesenchymal transition. However, the functions of the isoforms of this protein differ significantly. In this paper, we developed a method based on the boosted beta regression algorithm for identification of the significant RNA-binding proteins in the splicing process by modeling the isoform ratio. The application of this method to the analysis of CD44 splicing in colorectal cancer cells revealed 20 significant RNA-binding proteins. Many of them were previously shown as EMT regulators, but for the first time presented as potential CD44 splicing factors.
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Affiliation(s)
- V O Novosad
- Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Moscow, Russia.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
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2
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Bushra S, Lin YN, Joudaki A, Ito M, Ohkawara B, Ohno K, Masuda A. Neural Isoforms of Agrin Are Generated by Reduced PTBP1-RNA Interaction Network Spanning the Neuron-Specific Splicing Regions in AGRN. Int J Mol Sci 2023; 24:ijms24087420. [PMID: 37108583 PMCID: PMC10139058 DOI: 10.3390/ijms24087420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/12/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
Agrin is a heparan sulfate proteoglycan essential for the clustering of acetylcholine receptors at the neuromuscular junction. Neuron-specific isoforms of agrin are generated by alternative inclusion of three exons, called Y, Z8, and Z11 exons, although their processing mechanisms remain elusive. We found, by inspection of splicing cis-elements into the human AGRN gene, that binding sites for polypyrimidine tract binding protein 1 (PTBP1) were extensively enriched around Y and Z exons. PTBP1-silencing enhanced the coordinated inclusion of Y and Z exons in human SH-SY5Y neuronal cells, even though three constitutive exons are flanked by these alternative exons. Deletion analysis using minigenes identified five PTBP1-binding sites with remarkable splicing repression activities around Y and Z exons. Furthermore, artificial tethering experiments indicated that binding of a single PTBP1 molecule to any of these sites represses nearby Y or Z exons as well as the other distal exons. The RRM4 domain of PTBP1, which is required for looping out a target RNA segment, was likely to play a crucial role in the repression. Neuronal differentiation downregulates PTBP1 expression and promotes the coordinated inclusion of Y and Z exons. We propose that the reduction in the PTPB1-RNA network spanning these alternative exons is essential for the generation of the neuron-specific agrin isoforms.
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Affiliation(s)
- Samira Bushra
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Aichi, Japan
| | - Ying-Ni Lin
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Aichi, Japan
| | - Atefeh Joudaki
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Aichi, Japan
| | - Mikako Ito
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Aichi, Japan
| | - Bisei Ohkawara
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Aichi, Japan
| | - Kinji Ohno
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Aichi, Japan
| | - Akio Masuda
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Aichi, Japan
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3
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Mehta Z, Touma M. Post-Transcriptional Modification by Alternative Splicing and Pathogenic Splicing Variants in Cardiovascular Development and Congenital Heart Defects. Int J Mol Sci 2023; 24:ijms24021555. [PMID: 36675070 PMCID: PMC9862068 DOI: 10.3390/ijms24021555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/08/2023] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
Advancements in genomics, bioinformatics, and genome editing have uncovered new dimensions in gene regulation. Post-transcriptional modifications by the alternative splicing of mRNA transcripts are critical regulatory mechanisms of mammalian gene expression. In the heart, there is an expanding interest in elucidating the role of alternative splicing in transcriptome regulation. Substantial efforts were directed toward investigating this process in heart development and failure. However, few studies shed light on alternative splicing products and their dysregulation in congenital heart defects (CHDs). While elegant reports showed the crucial roles of RNA binding proteins (RBPs) in orchestrating splicing transitions during heart development and failure, the impact of RBPs dysregulation or genetic variation on CHDs has not been fully addressed. Herein, we review the current understanding of alternative splicing and RBPs' roles in heart development and CHDs. Wediscuss the impact of perinatal splicing transition and its dysregulation in CHDs. We further summarize the discoveries made of causal splicing variants in key transcription factors that are implicated in CHDs. An improved understanding of the roles of alternative splicing in heart development and CHDs may potentially inform novel preventive and therapeutic advancements for newborn infants with CHDs.
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Affiliation(s)
- Zubin Mehta
- Neonatal/Congenital Heart Laboratory, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Children’s Discovery and Innovation Institute, Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Stem Cell Research Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Marlin Touma
- Neonatal/Congenital Heart Laboratory, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Children’s Discovery and Innovation Institute, Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Stem Cell Research Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Correspondence:
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4
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Miao H, Wu F, Li Y, Qin C, Zhao Y, Xie M, Dai H, Yao H, Cai H, Wang Q, Song X, Li L. MALAT1 modulates alternative splicing by cooperating with the splicing factors PTBP1 and PSF. SCIENCE ADVANCES 2022; 8:eabq7289. [PMID: 36563164 PMCID: PMC9788761 DOI: 10.1126/sciadv.abq7289] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Understanding how long noncoding RNAs (lncRNAs) cooperate with splicing factors (SFs) in alternative splicing (AS) control is fundamental to human biology and disease. We show that metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), a well-documented AS-implicated lncRNA, regulates AS via two SFs, polypyrimidine tract-binding protein 1 (PTBP1) and PTB-associated SF (PSF). MALAT1 stabilizes the interaction between PTBP1 and PSF, thereby forming a functional module that affects a network of AS events. The MALAT1-stabilized PTBP1/PSF interaction occurs in multiple cellular contexts; however, the functional module, relative to MALAT1 only, has more dominant pathological significance in hepatocellular carcinoma. MALAT1 also stabilizes the PSF interaction with several heterogeneous nuclear ribonucleoparticle proteins other than PTBP1, hinting a broad role in AS control. We present a model in which MALAT1 cooperates with distinct SFs for AS regulation and pose that, relative to analyses exclusively performed for lncRNAs, a comprehensive consideration of lncRNAs and their binding partners may provide more information about their biological functions.
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Affiliation(s)
- Hui Miao
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
- Department of Platform and Technology, lncTAC Company Limited, Chengdu, Sichuan 610219, China
| | - Fan Wu
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
- Department of Platform and Technology, lncTAC Company Limited, Chengdu, Sichuan 610219, China
| | - Yu Li
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Chenyu Qin
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Yongyun Zhao
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Mingfeng Xie
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Hongyuan Dai
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Hong Yao
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
- Department of Platform and Technology, lncTAC Company Limited, Chengdu, Sichuan 610219, China
| | - Haoyang Cai
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Qianhong Wang
- The First Accredited Outpatient Department of Western General Hospital, Chengdu, Sichuan 610091, China
| | - Xu Song
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Ling Li
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
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5
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Petrić Howe M, Crerar H, Neeves J, Harley J, Tyzack GE, Klein P, Ramos A, Patani R, Luisier R. Physiological intron retaining transcripts in the cytoplasm abound during human motor neurogenesis. Genome Res 2022; 32:1808-1825. [PMID: 36180233 PMCID: PMC9712626 DOI: 10.1101/gr.276898.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 09/16/2022] [Indexed: 11/24/2022]
Abstract
Intron retention (IR) is now recognized as a dominant splicing event during motor neuron (MN) development; however, the role and regulation of intron-retaining transcripts (IRTs) localized to the cytoplasm remain particularly understudied. Here we show that IR is a physiological process that is spatiotemporally regulated during MN lineage restriction and that IRTs in the cytoplasm are detected in as many as 13% (n = 2297) of the genes expressed during this process. We identify a major class of cytoplasmic IRTs that are not associated with reduced expression of their own genes but instead show a high capacity for RNA-binding protein and miRNA occupancy. Finally, we show that ALS-causing VCP mutations lead to a selective increase in cytoplasmic abundance of this particular class of IRTs, which in turn temporally coincides with an increase in the nuclear expression level of predicted miRNA target genes. Altogether, our study identifies a previously unrecognized class of cytoplasmic intronic sequences with potential regulatory function beyond gene expression.
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Affiliation(s)
- Marija Petrić Howe
- The Francis Crick Institute, London NW1 1AT, United Kingdom
- Department of Molecular Neuroscience, UCL Institute of Neurology, London WC1N 3AR, United Kingdom
| | - Hamish Crerar
- The Francis Crick Institute, London NW1 1AT, United Kingdom
- Department of Molecular Neuroscience, UCL Institute of Neurology, London WC1N 3AR, United Kingdom
| | - Jacob Neeves
- The Francis Crick Institute, London NW1 1AT, United Kingdom
- Department of Molecular Neuroscience, UCL Institute of Neurology, London WC1N 3AR, United Kingdom
| | - Jasmine Harley
- The Francis Crick Institute, London NW1 1AT, United Kingdom
- Department of Molecular Neuroscience, UCL Institute of Neurology, London WC1N 3AR, United Kingdom
| | - Giulia E Tyzack
- The Francis Crick Institute, London NW1 1AT, United Kingdom
- Department of Molecular Neuroscience, UCL Institute of Neurology, London WC1N 3AR, United Kingdom
| | - Pierre Klein
- The Francis Crick Institute, London NW1 1AT, United Kingdom
- Research Department of Structural and Molecular Biology, University College London, London WC1E 6XA, United Kingdom
| | - Andres Ramos
- Research Department of Structural and Molecular Biology, University College London, London WC1E 6XA, United Kingdom
| | - Rickie Patani
- The Francis Crick Institute, London NW1 1AT, United Kingdom
- Department of Molecular Neuroscience, UCL Institute of Neurology, London WC1N 3AR, United Kingdom
| | - Raphaëlle Luisier
- Idiap Research Institute, Genomics and Health Informatics, CH-1920 Martigny, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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6
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Del Giudice M, Foster JG, Peirone S, Rissone A, Caizzi L, Gaudino F, Parlato C, Anselmi F, Arkell R, Guarrera S, Oliviero S, Basso G, Rajan P, Cereda M. FOXA1 regulates alternative splicing in prostate cancer. Cell Rep 2022; 40:111404. [PMID: 36170835 PMCID: PMC9532847 DOI: 10.1016/j.celrep.2022.111404] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 05/28/2022] [Accepted: 09/01/2022] [Indexed: 11/25/2022] Open
Abstract
Dysregulation of alternative splicing in prostate cancer is linked to transcriptional programs activated by AR, ERG, FOXA1, and MYC. Here, we show that FOXA1 functions as the primary orchestrator of alternative splicing dysregulation across 500 primary and metastatic prostate cancer transcriptomes. We demonstrate that FOXA1 binds to the regulatory regions of splicing-related genes, including HNRNPK and SRSF1. By controlling trans-acting factor expression, FOXA1 exploits an "exon definition" mechanism calibrating alternative splicing toward dominant isoform production. This regulation especially impacts splicing factors themselves and leads to a reduction of nonsense-mediated decay (NMD)-targeted isoforms. Inclusion of the NMD-determinant FLNA exon 30 by FOXA1-controlled oncogene SRSF1 promotes cell growth in vitro and predicts disease recurrence. Overall, we report a role for FOXA1 in rewiring the alternative splicing landscape in prostate cancer through a cascade of events from chromatin access, to splicing factor regulation, and, finally, to alternative splicing of exons influencing patient survival.
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Affiliation(s)
- Marco Del Giudice
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy; Candiolo Cancer Institute, FPO-IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy
| | - John G Foster
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Cancer Research UK Barts Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Serena Peirone
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy; Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Alberto Rissone
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy; Candiolo Cancer Institute, FPO-IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy
| | - Livia Caizzi
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy; Candiolo Cancer Institute, FPO-IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy
| | - Federica Gaudino
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy; Candiolo Cancer Institute, FPO-IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy
| | - Caterina Parlato
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy; Candiolo Cancer Institute, FPO-IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy
| | - Francesca Anselmi
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy; Department of Life Science and System Biology, Università degli Studi di Torino, via Accademia Albertina 13, 10123 Turin, Italy
| | - Rebecca Arkell
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Cancer Research UK Barts Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Simonetta Guarrera
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy; Candiolo Cancer Institute, FPO-IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy
| | - Salvatore Oliviero
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy; Department of Life Science and System Biology, Università degli Studi di Torino, via Accademia Albertina 13, 10123 Turin, Italy
| | - Giuseppe Basso
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy; Candiolo Cancer Institute, FPO-IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy
| | - Prabhakar Rajan
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Cancer Research UK Barts Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; Division of Surgery and Interventional Science, University College London, Charles Bell House, 3 Road Floor, 43-45 Foley Street, London W1W 7TS, UK; The Alan Turing Institute, British Library, 96 Euston Road, London NW1 2DB, UK; Department of Urology, Barts Health NHS Trust, the Royal London Hospital, Whitechapel Road, London E1 1BB, UK; Department of Uro-oncology, University College London NHS Foundation Trust, 47 Wimpole Street, London W1G 8SE, UK.
| | - Matteo Cereda
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy; Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy.
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7
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Saha K, Ghosh G. Cooperative engagement and subsequent selective displacement of SR proteins define the pre-mRNA 3D structural scaffold for early spliceosome assembly. Nucleic Acids Res 2022; 50:8262-8278. [PMID: 35871302 PMCID: PMC9371905 DOI: 10.1093/nar/gkac636] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/04/2022] [Accepted: 07/13/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
We recently reported that serine–arginine-rich (SR) protein-mediated pre-mRNA structural remodeling generates a pre-mRNA 3D structural scaffold that is stably recognized by the early spliceosomal components. However, the intermediate steps between the free pre-mRNA and the assembled early spliceosome are not yet characterized. By probing the early spliceosomal complexes in vitro and RNA-protein interactions in vivo, we show that the SR proteins bind the pre-mRNAs cooperatively generating a substrate that recruits U1 snRNP and U2AF65 in a splice signal-independent manner. Excess U1 snRNP selectively displaces some of the SR protein molecules from the pre-mRNA generating the substrate for splice signal-specific, sequential recognition by U1 snRNP, U2AF65 and U2AF35. Our work thus identifies a novel function of U1 snRNP in mammalian splicing substrate definition, explains the need for excess U1 snRNP compared to other U snRNPs in vivo, demonstrates how excess SR proteins could inhibit splicing, and provides a conceptual basis to examine if this mechanism of splicing substrate definition is employed by other splicing regulatory proteins.
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Affiliation(s)
- Kaushik Saha
- Department of Chemistry and Biochemistry, University of California San Diego , 9500 Gilman Drive , La Jolla , CA 92093-0375, USA
| | - Gourisankar Ghosh
- Department of Chemistry and Biochemistry, University of California San Diego , 9500 Gilman Drive , La Jolla , CA 92093-0375, USA
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8
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Chantsalnyam T, Siraj A, Tayara H, Chong KT. ncRDense: A novel computational approach for classification of non-coding RNA family by deep learning. Genomics 2021; 113:3030-3038. [PMID: 34242708 DOI: 10.1016/j.ygeno.2021.07.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 06/29/2021] [Accepted: 07/03/2021] [Indexed: 12/14/2022]
Abstract
With the rapidly growing importance of biological research, non-coding RNAs (ncRNA) attract more attention in biology and bioinformatics. They play vital roles in biological processes such as transcription and translation. Classification of ncRNAs is essential to our understanding of disease mechanisms and treatment design. Many approaches to ncRNA classification have been developed, several of which use machine learning and deep learning. In this paper, we construct a novel deep learning-based architecture, ncRDense, to effectively classify and distinguish ncRNA families. In a comparative study, our model produces comparable results with existing state-of-the-art methods. Finally, we built a freely accessible web server for the ncRDense tool, which is available at http://nsclbio.jbnu.ac.kr/tools/ncRDense/.
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Affiliation(s)
- Tuvshinbayar Chantsalnyam
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea
| | - Arslan Siraj
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea
| | - Hilal Tayara
- School of International Engineering and Science, Jeonbuk National University, Jeonju 54896, South Korea.
| | - Kil To Chong
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea; Advanced Electronics and Information Research Center, Jeonbuk National University, Jeonju 54896, South Korea.
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9
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Schieweck R, Ninkovic J, Kiebler MA. RNA-binding proteins balance brain function in health and disease. Physiol Rev 2020; 101:1309-1370. [PMID: 33000986 DOI: 10.1152/physrev.00047.2019] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Posttranscriptional gene expression including splicing, RNA transport, translation, and RNA decay provides an important regulatory layer in many if not all molecular pathways. Research in the last decades has positioned RNA-binding proteins (RBPs) right in the center of posttranscriptional gene regulation. Here, we propose interdependent networks of RBPs to regulate complex pathways within the central nervous system (CNS). These are involved in multiple aspects of neuronal development and functioning, including higher cognition. Therefore, it is not sufficient to unravel the individual contribution of a single RBP and its consequences but rather to study and understand the tight interplay between different RBPs. In this review, we summarize recent findings in the field of RBP biology and discuss the complex interplay between different RBPs. Second, we emphasize the underlying dynamics within an RBP network and how this might regulate key processes such as neurogenesis, synaptic transmission, and synaptic plasticity. Importantly, we envision that dysfunction of specific RBPs could lead to perturbation within the RBP network. This would have direct and indirect (compensatory) effects in mRNA binding and translational control leading to global changes in cellular expression programs in general and in synaptic plasticity in particular. Therefore, we focus on RBP dysfunction and how this might cause neuropsychiatric and neurodegenerative disorders. Based on recent findings, we propose that alterations in the entire regulatory RBP network might account for phenotypic dysfunctions observed in complex diseases including neurodegeneration, epilepsy, and autism spectrum disorders.
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Affiliation(s)
- Rico Schieweck
- Biomedical Center (BMC), Department for Cell Biology and Anatomy, Medical Faculty, Ludwig-Maximilians-University, Planegg-Martinsried, Germany
| | - Jovica Ninkovic
- Biomedical Center (BMC), Department for Cell Biology and Anatomy, Medical Faculty, Ludwig-Maximilians-University, Planegg-Martinsried, Germany
| | - Michael A Kiebler
- Biomedical Center (BMC), Department for Cell Biology and Anatomy, Medical Faculty, Ludwig-Maximilians-University, Planegg-Martinsried, Germany
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10
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Taylor K, Sobczak K. Intrinsic Regulatory Role of RNA Structural Arrangement in Alternative Splicing Control. Int J Mol Sci 2020; 21:ijms21145161. [PMID: 32708277 PMCID: PMC7404189 DOI: 10.3390/ijms21145161] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 07/17/2020] [Indexed: 12/14/2022] Open
Abstract
Alternative splicing is a highly sophisticated process, playing a significant role in posttranscriptional gene expression and underlying the diversity and complexity of organisms. Its regulation is multilayered, including an intrinsic role of RNA structural arrangement which undergoes time- and tissue-specific alterations. In this review, we describe the principles of RNA structural arrangement and briefly decipher its cis- and trans-acting cellular modulators which serve as crucial determinants of biological functionality of the RNA structure. Subsequently, we engage in a discussion about the RNA structure-mediated mechanisms of alternative splicing regulation. On one hand, the impairment of formation of optimal RNA structures may have critical consequences for the splicing outcome and further contribute to understanding the pathomechanism of severe disorders. On the other hand, the structural aspects of RNA became significant features taken into consideration in the endeavor of finding potential therapeutic treatments. Both aspects have been addressed by us emphasizing the importance of ongoing studies in both fields.
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11
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Lauria A, Peirone S, Giudice MD, Priante F, Rajan P, Caselle M, Oliviero S, Cereda M. Identification of altered biological processes in heterogeneous RNA-sequencing data by discretization of expression profiles. Nucleic Acids Res 2020; 48:1730-1747. [PMID: 31889184 PMCID: PMC7038995 DOI: 10.1093/nar/gkz1208] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/05/2019] [Accepted: 12/17/2019] [Indexed: 12/31/2022] Open
Abstract
Heterogeneity is a fundamental feature of complex phenotypes. So far, genomic screenings have profiled thousands of samples providing insights into the transcriptome of the cell. However, disentangling the heterogeneity of these transcriptomic Big Data to identify defective biological processes remains challenging. Here we present GSECA, a method exploiting the bimodal behavior of RNA-sequencing gene expression profiles to identify altered gene sets in heterogeneous patient cohorts. Using simulated and experimental RNA-sequencing data sets, we show that GSECA provides higher performances than other available algorithms in detecting truly altered biological processes in large cohorts. Applied to 5941 samples from 14 different cancer types, GSECA correctly identified the alteration of the PI3K/AKT signaling pathway driven by the somatic loss of PTEN and verified the emerging role of PTEN in modulating immune-related processes. In particular, we showed that, in prostate cancer, PTEN loss appears to establish an immunosuppressive tumor microenvironment through the activation of STAT3, and low PTEN expression levels have a detrimental impact on patient disease-free survival. GSECA is available at https://github.com/matteocereda/GSECA.
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Affiliation(s)
- Andrea Lauria
- Department of Life Science and System Biology, Università degli Studi di Torino, via Accademia Albertina 13, 10123 Turin, Italy
- IIGM - Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov.le 142, km 3.95, Candiolo (TO) 10060, Italy
| | - Serena Peirone
- IIGM - Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov.le 142, km 3.95, Candiolo (TO) 10060, Italy
- Department of Physics and INFN, Università degli Studi di Torino, via P.Giuria 1, 10125 Turin, Italy
| | - Marco Del Giudice
- IIGM - Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov.le 142, km 3.95, Candiolo (TO) 10060, Italy
- Candiolo Cancer Institute, FPO - IRCCS, Str. Prov.le 142, km 3.95, Candiolo (TO) 10060, Italy
| | - Francesca Priante
- IIGM - Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov.le 142, km 3.95, Candiolo (TO) 10060, Italy
- Candiolo Cancer Institute, FPO - IRCCS, Str. Prov.le 142, km 3.95, Candiolo (TO) 10060, Italy
| | - Prabhakar Rajan
- Centre for Cell and Molecular Biology, Barts Cancer Institute, Cancer Research UK Barts Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
- The Alan Turing Institute, British Library, 96 Euston Road, London, NW1 2DB, UK
| | - Michele Caselle
- Department of Physics and INFN, Università degli Studi di Torino, via P.Giuria 1, 10125 Turin, Italy
| | - Salvatore Oliviero
- Department of Life Science and System Biology, Università degli Studi di Torino, via Accademia Albertina 13, 10123 Turin, Italy
- IIGM - Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov.le 142, km 3.95, Candiolo (TO) 10060, Italy
| | - Matteo Cereda
- IIGM - Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov.le 142, km 3.95, Candiolo (TO) 10060, Italy
- Candiolo Cancer Institute, FPO - IRCCS, Str. Prov.le 142, km 3.95, Candiolo (TO) 10060, Italy
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12
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Abstract
High-throughput sequencing-based methods and their applications in the study of transcriptomes have revolutionized our understanding of alternative splicing. Networks of functionally coordinated and biologically important alternative splicing events continue to be discovered in an ever-increasing diversity of cell types in the context of physiologically normal and disease states. These studies have been complemented by efforts directed at defining sequence codes governing splicing and their cognate trans-acting factors, which have illuminated important combinatorial principles of regulation. Additional studies have revealed critical roles of position-dependent, multivalent protein-RNA interactions that direct splicing outcomes. Investigations of evolutionary changes in RNA binding proteins, splice variants, and associated cis elements have further shed light on the emergence, mechanisms, and functions of splicing networks. Progress in these areas has emphasized the need for a coordinated, community-based effort to systematically address the functions of individual splice variants associated with normal and disease biology.
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13
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Gohr A, Irimia M. Matt: Unix tools for alternative splicing analysis. Bioinformatics 2019; 35:130-132. [PMID: 30010778 DOI: 10.1093/bioinformatics/bty606] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 07/11/2018] [Indexed: 01/12/2023] Open
Abstract
Summary Tracking thousands of alternative splicing (AS) events genome-wide makes their downstream analysis computationally challenging and laborious. Here, we present Matt, the first UNIX command-line toolkit with focus on high-level AS analyses. With 50 commands it facilitates computational AS analyses by (i) expediting repetitive data-preparation tasks, (ii) offering routine high-level analyses, including the extraction of exon/intron features, discriminative feature detection, motif enrichment analysis, and the generation of motif RNA-maps, (iii) improving reproducibility by documenting all analysis steps and (iv) accelerating the implementation of own analysis pipelines by offering users to exploit its modular functionality. Availability and implementation matt.crg.eu under GNU LGPLv3, together with comprehensive documentation and application examples. Matt is implemented in Perl and R, invokes pdfLATEX and depends only on Perl Core modules/the R Base package simplifying its installation. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- André Gohr
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
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14
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Vázquez-Borrego MC, Fuentes-Fayos AC, Venegas-Moreno E, Rivero-Cortés E, Dios E, Moreno-Moreno P, Madrazo-Atutxa A, Remón P, Solivera J, Wildemberg LE, Kasuki L, López-Fernández JM, Gadelha MR, Gálvez-Moreno MA, Soto-Moreno A, Gahete MD, Castaño JP, Luque RM. Splicing Machinery is Dysregulated in Pituitary Neuroendocrine Tumors and is Associated with Aggressiveness Features. Cancers (Basel) 2019; 11:cancers11101439. [PMID: 31561558 PMCID: PMC6826715 DOI: 10.3390/cancers11101439] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/09/2019] [Accepted: 09/23/2019] [Indexed: 12/17/2022] Open
Abstract
Pituitary neuroendocrine tumors (PitNETs) constitute approximately 15% of all brain tumors, and most have a sporadic origin. Recent studies suggest that altered alternative splicing and, consequently, appearance of aberrant splicing variants, is a common feature of most tumor pathologies. Moreover, spliceosome is considered an attractive therapeutic target in tumor pathologies, and the inhibition of SF3B1 (e.g., using pladienolide-B) has been shown to exert antitumor effects. Therefore, we aimed to analyze the expression levels of selected splicing-machinery components in 261 PitNETs (somatotropinomas/non-functioning PitNETS/corticotropinomas/prolactinomas) and evaluated the direct effects of pladienolide-B in cell proliferation/viability/hormone secretion in human PitNETs cell cultures and pituitary cell lines (AtT-20/GH3). Results revealed a severe dysregulation of splicing-machinery components in all the PitNET subtypes compared to normal pituitaries and a unique fingerprint of splicing-machinery components that accurately discriminate between normal and tumor tissue in each PitNET subtype. Moreover, expression of specific components was associated with key clinical parameters. Interestingly, certain components were commonly dysregulated throughout all PitNET subtypes. Finally, pladienolide-B reduced cell proliferation/viability/hormone secretion in PitNET cell cultures and cell lines. Altogether, our data demonstrate a drastic dysregulation of the splicing-machinery in PitNETs that might be associated to their tumorigenesis, paving the way to explore the use of specific splicing-machinery components as novel diagnostic/prognostic and therapeutic targets in PitNETs.
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Affiliation(s)
- Mari C Vázquez-Borrego
- Maimonides Institute of Biomedical Research of Cordoba (IMIBIC), 14004 Cordoba, Spain.
- Department of Cell Biology, Physiology and Immunology, University of Cordoba, 14004 Cordoba, Spain.
- Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain.
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004 Cordoba, Spain.
| | - Antonio C Fuentes-Fayos
- Maimonides Institute of Biomedical Research of Cordoba (IMIBIC), 14004 Cordoba, Spain.
- Department of Cell Biology, Physiology and Immunology, University of Cordoba, 14004 Cordoba, Spain.
- Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain.
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004 Cordoba, Spain.
| | - Eva Venegas-Moreno
- Metabolism and Nutrition Unit, Hospital Universitario Virgen del Rocío, Instituto de Biomedicina de Sevilla (IBIS), 41013 Sevilla, Spain.
| | - Esther Rivero-Cortés
- Maimonides Institute of Biomedical Research of Cordoba (IMIBIC), 14004 Cordoba, Spain.
- Department of Cell Biology, Physiology and Immunology, University of Cordoba, 14004 Cordoba, Spain.
- Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain.
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004 Cordoba, Spain.
| | - Elena Dios
- Metabolism and Nutrition Unit, Hospital Universitario Virgen del Rocío, Instituto de Biomedicina de Sevilla (IBIS), 41013 Sevilla, Spain.
| | - Paloma Moreno-Moreno
- Maimonides Institute of Biomedical Research of Cordoba (IMIBIC), 14004 Cordoba, Spain.
- Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain.
- Service of Endocrinology and Nutrition, Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain.
| | - Ainara Madrazo-Atutxa
- Metabolism and Nutrition Unit, Hospital Universitario Virgen del Rocío, Instituto de Biomedicina de Sevilla (IBIS), 41013 Sevilla, Spain.
| | - Pablo Remón
- Metabolism and Nutrition Unit, Hospital Universitario Virgen del Rocío, Instituto de Biomedicina de Sevilla (IBIS), 41013 Sevilla, Spain.
| | - Juan Solivera
- Maimonides Institute of Biomedical Research of Cordoba (IMIBIC), 14004 Cordoba, Spain.
- Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain.
- Service of Neurosurgery, Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain.
| | - Luiz E Wildemberg
- Neuroendocrinology Research Center/Endocrinology Division, Medical School and Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-590, Brazil.
- Neuroendocrinology Division, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro 20231-092, Brazil.
| | - Leandro Kasuki
- Neuroendocrinology Research Center/Endocrinology Division, Medical School and Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-590, Brazil.
- Neuroendocrinology Division, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro 20231-092, Brazil.
| | - Judith M López-Fernández
- Service of Endocrinology and Nutrition, Hospital Universitario de Canarias, 38320 La Laguna, Santa Cruz de Tenerife, Spain.
| | - Mônica R Gadelha
- Neuroendocrinology Research Center/Endocrinology Division, Medical School and Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-590, Brazil.
- Neuroendocrinology Division, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro 20231-092, Brazil.
| | - María A Gálvez-Moreno
- Maimonides Institute of Biomedical Research of Cordoba (IMIBIC), 14004 Cordoba, Spain.
- Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain.
- Service of Endocrinology and Nutrition, Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain.
| | - Alfonso Soto-Moreno
- Metabolism and Nutrition Unit, Hospital Universitario Virgen del Rocío, Instituto de Biomedicina de Sevilla (IBIS), 41013 Sevilla, Spain.
| | - Manuel D Gahete
- Maimonides Institute of Biomedical Research of Cordoba (IMIBIC), 14004 Cordoba, Spain.
- Department of Cell Biology, Physiology and Immunology, University of Cordoba, 14004 Cordoba, Spain.
- Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain.
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004 Cordoba, Spain.
| | - Justo P Castaño
- Maimonides Institute of Biomedical Research of Cordoba (IMIBIC), 14004 Cordoba, Spain.
- Department of Cell Biology, Physiology and Immunology, University of Cordoba, 14004 Cordoba, Spain.
- Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain.
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004 Cordoba, Spain.
| | - Raúl M Luque
- Maimonides Institute of Biomedical Research of Cordoba (IMIBIC), 14004 Cordoba, Spain.
- Department of Cell Biology, Physiology and Immunology, University of Cordoba, 14004 Cordoba, Spain.
- Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain.
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004 Cordoba, Spain.
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15
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Abstract
RNA localization mechanisms have been intensively studied and include localized protection of mRNA from degradation, diffusion-coupled local entrapment of mRNA, and directed transport of mRNAs along the cytoskeleton. While it is well understood how cells utilize these three mechanisms to organize mRNAs within the cytoplasm, a newly appreciated mechanism of RNA localization has emerged in recent years in which mRNAs phase-separate and form liquid-like droplets. mRNAs both contribute to condensation of proteins into liquid-like structures and are themselves regulated by being incorporated into membraneless organelles. This ability to condense into droplets is in many instances contributing to previously appreciated mRNA localization phenomena. Here we review how phase separation enables mRNAs to selectively and efficiently colocalize and be coregulated, allowing control of gene expression in time and space.
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Affiliation(s)
- Erin M Langdon
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;
| | - Amy S Gladfelter
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; .,Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA
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16
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Deep Splicing Code: Classifying Alternative Splicing Events Using Deep Learning. Genes (Basel) 2019; 10:genes10080587. [PMID: 31374967 PMCID: PMC6722613 DOI: 10.3390/genes10080587] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/20/2019] [Accepted: 07/30/2019] [Indexed: 12/11/2022] Open
Abstract
Alternative splicing (AS) is the process of combining different parts of the pre-mRNA to produce diverse transcripts and eventually different protein products from a single gene. In computational biology field, researchers try to understand AS behavior and regulation using computational models known as “Splicing Codes”. The final goal of these algorithms is to make an in-silico prediction of AS outcome from genomic sequence. Here, we develop a deep learning approach, called Deep Splicing Code (DSC), for categorizing the well-studied classes of AS namely alternatively skipped exons, alternative 5’ss, alternative 3’ss, and constitutively spliced exons based only on the sequence of the exon junctions. The proposed approach significantly improves the prediction and the obtained results reveal that constitutive exons have distinguishable local characteristics from alternatively spliced exons. Using the motif visualization technique, we show that the trained models learned to search for competitive alternative splice sites as well as motifs of important splicing factors with high precision. Thus, the proposed approach greatly expands the opportunities to improve alternative splicing modeling. In addition, a web-server for AS events prediction has been developed based on the proposed method.
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17
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Fontrodona N, Aubé F, Claude JB, Polvèche H, Lemaire S, Tranchevent LC, Modolo L, Mortreux F, Bourgeois CF, Auboeuf D. Interplay between coding and exonic splicing regulatory sequences. Genome Res 2019; 29:711-722. [PMID: 30962178 PMCID: PMC6499313 DOI: 10.1101/gr.241315.118] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 03/28/2019] [Indexed: 01/24/2023]
Abstract
The inclusion of exons during the splicing process depends on the binding of splicing factors to short low-complexity regulatory sequences. The relationship between exonic splicing regulatory sequences and coding sequences is still poorly understood. We demonstrate that exons that are coregulated by any given splicing factor share a similar nucleotide composition bias and preferentially code for amino acids with similar physicochemical properties because of the nonrandomness of the genetic code. Indeed, amino acids sharing similar physicochemical properties correspond to codons that have the same nucleotide composition bias. In particular, we uncover that the TRA2A and TRA2B splicing factors that bind to adenine-rich motifs promote the inclusion of adenine-rich exons coding preferentially for hydrophilic amino acids that correspond to adenine-rich codons. SRSF2 that binds guanine/cytosine-rich motifs promotes the inclusion of GC-rich exons coding preferentially for small amino acids, whereas SRSF3 that binds cytosine-rich motifs promotes the inclusion of exons coding preferentially for uncharged amino acids, like serine and threonine that can be phosphorylated. Finally, coregulated exons encoding amino acids with similar physicochemical properties correspond to specific protein features. In conclusion, the regulation of an exon by a splicing factor that relies on the affinity of this factor for specific nucleotide(s) is tightly interconnected with the exon-encoded physicochemical properties. We therefore uncover an unanticipated bidirectional interplay between the splicing regulatory process and its biological functional outcome.
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Affiliation(s)
- Nicolas Fontrodona
- Université Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Fabien Aubé
- Université Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Jean-Baptiste Claude
- Université Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Hélène Polvèche
- Université Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Sébastien Lemaire
- Université Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Léon-Charles Tranchevent
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health (LIH), L-1445 Strassen, Luxembourg
| | - Laurent Modolo
- LBMC Biocomputing Center, CNRS UMR 5239, INSERM U1210, F-69007, Lyon, France
| | - Franck Mortreux
- Université Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Cyril F Bourgeois
- Université Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Didier Auboeuf
- Université Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
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18
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Yee BA, Pratt GA, Graveley BR, Van Nostrand EL, Yeo GW. RBP-Maps enables robust generation of splicing regulatory maps. RNA (NEW YORK, N.Y.) 2019; 25:193-204. [PMID: 30413564 PMCID: PMC6348990 DOI: 10.1261/rna.069237.118] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 11/01/2018] [Indexed: 05/22/2023]
Abstract
Alternative splicing of pre-messenger RNA transcripts enables the generation of multiple protein isoforms from the same gene locus, providing a major source of protein diversity in mammalian genomes. RNA binding proteins (RBPs) bind to RNA to control splice site choice and define which exons are included in the resulting mature RNA transcript. However, depending on where the RBPs bind relative to splice sites, they can activate or repress splice site usage. To explore this position-specific regulation, in vivo binding sites identified by methods such as cross-linking and immunoprecipitation (CLIP) are integrated with alternative splicing events identified by RNA-seq or microarray. Merging these data sets enables the generation of a "splicing map," where CLIP signal relative to a merged meta-exon provides a simple summary of the position-specific effect of binding on splicing regulation. Here, we provide RBP-Maps, a software tool to simplify generation of these maps and enable researchers to rapidly query regulatory patterns of an RBP of interest. Further, we discuss various alternative approaches to generate such splicing maps, focusing on how decisions in construction (such as the use of peak versus read density, or whole-reads versus only single-nucleotide candidate crosslink positions) can affect the interpretation of these maps using example eCLIP data from the 150 RBPs profiled by the ENCODE consortium.
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Affiliation(s)
- Brian A Yee
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA
- Institute for Genomic Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - Gabriel A Pratt
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA
- Institute for Genomic Medicine, University of California at San Diego, La Jolla, California 92093, USA
- Bioinformatics and Systems Biology Graduate Program, University of California at San Diego, La Jolla, California 92093, USA
| | - Brenton R Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, Connecticut 06030, USA
| | - Eric L Van Nostrand
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA
- Institute for Genomic Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA
- Institute for Genomic Medicine, University of California at San Diego, La Jolla, California 92093, USA
- Bioinformatics and Systems Biology Graduate Program, University of California at San Diego, La Jolla, California 92093, USA
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19
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Alvelos MI, Juan-Mateu J, Colli ML, Turatsinze JV, Eizirik DL. When one becomes many-Alternative splicing in β-cell function and failure. Diabetes Obes Metab 2018; 20 Suppl 2:77-87. [PMID: 30230174 PMCID: PMC6148369 DOI: 10.1111/dom.13388] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 05/22/2018] [Accepted: 05/30/2018] [Indexed: 12/20/2022]
Abstract
Pancreatic β-cell dysfunction and death are determinant events in type 1 diabetes (T1D), but the molecular mechanisms behind β-cell fate remain poorly understood. Alternative splicing is a post-transcriptional mechanism by which a single gene generates different mRNA and protein isoforms, expanding the transcriptome complexity and enhancing protein diversity. Neuron-specific and certain serine/arginine-rich RNA binding proteins (RBP) are enriched in β-cells, playing crucial roles in the regulation of insulin secretion and β-cell survival. Moreover, alternative exon networks, regulated by inflammation or diabetes susceptibility genes, control key pathways and processes for the correct function and survival of β-cells. The challenge ahead of us is to understand the precise role of alternative splicing regulators and splice variants on β-cell function, dysfunction and death and develop tools to modulate it.
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Affiliation(s)
- Maria Inês Alvelos
- ULB Center for Diabetes Research and Welbio, Medical Faculty, Université Libre de Bruxelles (ULB), Route de Lennik, 808 – CP618, B-1070 Brussels, Belgium
| | - Jonàs Juan-Mateu
- ULB Center for Diabetes Research and Welbio, Medical Faculty, Université Libre de Bruxelles (ULB), Route de Lennik, 808 – CP618, B-1070 Brussels, Belgium
| | - Maikel Luis Colli
- ULB Center for Diabetes Research and Welbio, Medical Faculty, Université Libre de Bruxelles (ULB), Route de Lennik, 808 – CP618, B-1070 Brussels, Belgium
| | - Jean-Valéry Turatsinze
- ULB Center for Diabetes Research and Welbio, Medical Faculty, Université Libre de Bruxelles (ULB), Route de Lennik, 808 – CP618, B-1070 Brussels, Belgium
| | - Décio L. Eizirik
- ULB Center for Diabetes Research and Welbio, Medical Faculty, Université Libre de Bruxelles (ULB), Route de Lennik, 808 – CP618, B-1070 Brussels, Belgium
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20
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Attig J, Agostini F, Gooding C, Chakrabarti AM, Singh A, Haberman N, Zagalak JA, Emmett W, Smith CWJ, Luscombe NM, Ule J. Heteromeric RNP Assembly at LINEs Controls Lineage-Specific RNA Processing. Cell 2018; 174:1067-1081.e17. [PMID: 30078707 PMCID: PMC6108849 DOI: 10.1016/j.cell.2018.07.001] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 04/23/2018] [Accepted: 07/01/2018] [Indexed: 12/30/2022]
Abstract
Long mammalian introns make it challenging for the RNA processing machinery to identify exons accurately. We find that LINE-derived sequences (LINEs) contribute to this selection by recruiting dozens of RNA-binding proteins (RBPs) to introns. This includes MATR3, which promotes binding of PTBP1 to multivalent binding sites within LINEs. Both RBPs repress splicing and 3' end processing within and around LINEs. Notably, repressive RBPs preferentially bind to evolutionarily young LINEs, which are located far from exons. These RBPs insulate the LINEs and the surrounding intronic regions from RNA processing. Upon evolutionary divergence, changes in RNA motifs within LINEs lead to gradual loss of their insulation. Hence, older LINEs are located closer to exons, are a common source of tissue-specific exons, and increasingly bind to RBPs that enhance RNA processing. Thus, LINEs are hubs for the assembly of repressive RBPs and also contribute to the evolution of new, lineage-specific transcripts in mammals. VIDEO ABSTRACT.
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Affiliation(s)
- Jan Attig
- The Francis Crick Institute, Midland Road 1, Kings Cross, London NW1 1AT, UK; Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK.
| | - Federico Agostini
- The Francis Crick Institute, Midland Road 1, Kings Cross, London NW1 1AT, UK
| | - Clare Gooding
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Anob M Chakrabarti
- The Francis Crick Institute, Midland Road 1, Kings Cross, London NW1 1AT, UK; Department of Genetics, Environment and Evolution, UCL Genetics Institute, Gower Street, London WC1E 6BT, UK
| | - Aarti Singh
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; Department of Comparative Biomedical Sciences, The Royal Veterinary College, Royal College Street, London NW1 0TU, UK
| | - Nejc Haberman
- The Francis Crick Institute, Midland Road 1, Kings Cross, London NW1 1AT, UK; Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Julian A Zagalak
- The Francis Crick Institute, Midland Road 1, Kings Cross, London NW1 1AT, UK; Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Warren Emmett
- The Francis Crick Institute, Midland Road 1, Kings Cross, London NW1 1AT, UK; Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; Department of Genetics, Environment and Evolution, UCL Genetics Institute, Gower Street, London WC1E 6BT, UK
| | - Christopher W J Smith
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Nicholas M Luscombe
- The Francis Crick Institute, Midland Road 1, Kings Cross, London NW1 1AT, UK; Department of Genetics, Environment and Evolution, UCL Genetics Institute, Gower Street, London WC1E 6BT, UK; Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Jernej Ule
- The Francis Crick Institute, Midland Road 1, Kings Cross, London NW1 1AT, UK; Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK.
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21
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Chakrabarti AM, Haberman N, Praznik A, Luscombe NM, Ule J. Data Science Issues in Studying Protein–RNA Interactions with CLIP Technologies. Annu Rev Biomed Data Sci 2018; 1:235-261. [PMID: 37123514 PMCID: PMC7614488 DOI: 10.1146/annurev-biodatasci-080917-013525] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An interplay of experimental and computational methods is required to achieve a comprehensive understanding of protein–RNA interactions. UV crosslinking and immunoprecipitation (CLIP) identifies endogenous interactions by sequencing RNA fragments that copurify with a selected RNA-binding protein under stringent conditions. Here we focus on approaches for the analysis of the resulting data and appraise the methods for peak calling, visualization, analysis, and computational modeling of protein–RNA binding sites. We advocate that the sensitivity and specificity of data be assessed in combination for computational quality control. Moreover, we demonstrate the value of analyzing sequence motif enrichment in peaks assigned from CLIP data and of visualizing RNA maps, which examine the positional distribution of peaks around regulated landmarks in transcripts. We use these to assess how variations in CLIP data quality and in different peak calling methods affect the insights into regulatory mechanisms. We conclude by discussing future opportunities for the computational analysis of protein–RNA interaction experiments.
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Affiliation(s)
- Anob M. Chakrabarti
- The Francis Crick Institute, London NW1 1AT, United Kingdom
- Department of Genetics, Environment and Evolution, UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Nejc Haberman
- The Francis Crick Institute, London NW1 1AT, United Kingdom
- Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, London WC1E 6BT, United Kingdom
| | - Arne Praznik
- The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Nicholas M. Luscombe
- The Francis Crick Institute, London NW1 1AT, United Kingdom
- Department of Genetics, Environment and Evolution, UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
- Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0412, Japan
| | - Jernej Ule
- The Francis Crick Institute, London NW1 1AT, United Kingdom
- Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, London WC1E 6BT, United Kingdom
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22
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Dominguez D, Freese P, Alexis MS, Su A, Hochman M, Palden T, Bazile C, Lambert NJ, Van Nostrand EL, Pratt GA, Yeo GW, Graveley BR, Burge CB. Sequence, Structure, and Context Preferences of Human RNA Binding Proteins. Mol Cell 2018; 70:854-867.e9. [PMID: 29883606 PMCID: PMC6062212 DOI: 10.1016/j.molcel.2018.05.001] [Citation(s) in RCA: 298] [Impact Index Per Article: 49.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 03/20/2018] [Accepted: 05/01/2018] [Indexed: 01/03/2023]
Abstract
RNA binding proteins (RBPs) orchestrate the production, processing, and function of mRNAs. Here, we present the affinity landscapes of 78 human RBPs using an unbiased assay that determines the sequence, structure, and context preferences of these proteins in vitro by deep sequencing of bound RNAs. These data enable construction of "RNA maps" of RBP activity without requiring crosslinking-based assays. We found an unexpectedly low diversity of RNA motifs, implying frequent convergence of binding specificity toward a relatively small set of RNA motifs, many with low compositional complexity. Offsetting this trend, however, we observed extensive preferences for contextual features distinct from short linear RNA motifs, including spaced "bipartite" motifs, biased flanking nucleotide composition, and bias away from or toward RNA structure. Our results emphasize the importance of contextual features in RNA recognition, which likely enable targeting of distinct subsets of transcripts by different RBPs that recognize the same linear motif.
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Affiliation(s)
| | - Peter Freese
- Program in Computational and Systems Biology, MIT, Cambridge, MA, USA
| | - Maria S Alexis
- Program in Computational and Systems Biology, MIT, Cambridge, MA, USA
| | - Amanda Su
- Department of Biology, MIT, Cambridge, MA, USA
| | | | | | | | | | - Eric L Van Nostrand
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Gabriel A Pratt
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA; Bioinformatics and Systems Biology Graduate Program, University of California at San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore; Molecular Engineering Laboratory, A(∗)STAR, Singapore, Singapore
| | - Brenton R Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health, Farmington, CT, USA
| | - Christopher B Burge
- Department of Biology, MIT, Cambridge, MA, USA; Department of Biological Engineering, MIT, Cambridge, MA, USA.
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23
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Agostini F, Ule J, Zagalak JA. No way out: when RNA elements promote nuclear retention. EMBO J 2018; 37:embj.201899123. [PMID: 29487065 DOI: 10.15252/embj.201899123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
| | - Jernej Ule
- The Francis Crick Institute, London, UK.,Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Julian A Zagalak
- The Francis Crick Institute, London, UK.,Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
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24
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Rot G, Wang Z, Huppertz I, Modic M, Lenče T, Hallegger M, Haberman N, Curk T, von Mering C, Ule J. High-Resolution RNA Maps Suggest Common Principles of Splicing and Polyadenylation Regulation by TDP-43. Cell Rep 2018; 19:1056-1067. [PMID: 28467899 PMCID: PMC5437728 DOI: 10.1016/j.celrep.2017.04.028] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 03/06/2017] [Accepted: 04/06/2017] [Indexed: 11/05/2022] Open
Abstract
Many RNA-binding proteins (RBPs) regulate both alternative exons and poly(A) site selection. To understand their regulatory principles, we developed expressRNA, a web platform encompassing computational tools for integration of iCLIP and RNA motif analyses with RNA-seq and 3′ mRNA sequencing. This reveals at nucleotide resolution the “RNA maps” describing how the RNA binding positions of RBPs relate to their regulatory functions. We use this approach to examine how TDP-43, an RBP involved in several neurodegenerative diseases, binds around its regulated poly(A) sites. Binding close to the poly(A) site generally represses, whereas binding further downstream enhances use of the site, which is similar to TDP-43 binding around regulated exons. Our RNAmotifs2 software also identifies sequence motifs that cluster together with the binding motifs of TDP-43. We conclude that TDP-43 directly regulates diverse types of pre-mRNA processing according to common position-dependent principles. TDP-43 regulates competing poly(A) sites in a highly position-dependent manner expressRNA is a new platform for analysis of alternative polyadenylation and splicing RNAmotifs2 is a cluster motif analysis platform integrated with expressRNA Regulation of pre-mRNA processing might follow common position-dependent principles
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Affiliation(s)
- Gregor Rot
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, Winterthurerstrasse 190, 8057 Zurich, Switzerland; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| | - Zhen Wang
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Institut de Biologie de l'ENS (IBENS), 46 rue d'Ulm, Paris 75005, France
| | - Ina Huppertz
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Miha Modic
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Institute of Stem Cell Research, Helmholtz Center Munich, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
| | - Tina Lenče
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany
| | - Martina Hallegger
- UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Nejc Haberman
- UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Tomaž Curk
- Faculty of Computer and Information Science, University of Ljubljana, Večna pot 113, 1001 Ljubljana, Slovenia
| | - Christian von Mering
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Jernej Ule
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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25
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Brillen AL, Schöneweis K, Walotka L, Hartmann L, Müller L, Ptok J, Kaisers W, Poschmann G, Stühler K, Buratti E, Theiss S, Schaal H. Succession of splicing regulatory elements determines cryptic 5΄ss functionality. Nucleic Acids Res 2017; 45:4202-4216. [PMID: 28039323 PMCID: PMC5397162 DOI: 10.1093/nar/gkw1317] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 12/19/2016] [Indexed: 12/25/2022] Open
Abstract
A critical step in exon definition is the recognition of a proper splice donor (5΄ss) by the 5’ end of U1 snRNA. In the selection of appropriate 5΄ss, cis-acting splicing regulatory elements (SREs) are indispensable. As a model for 5΄ss recognition, we investigated cryptic 5΄ss selection within the human fibrinogen Bβ-chain gene (FGB) exon 7, where we identified several exonic SREs that simultaneously acted on up- and downstream cryptic 5΄ss. In the FGB exon 7 model system, 5΄ss selection iteratively proceeded along an alternating sequence of U1 snRNA binding sites and interleaved SREs which in principle supported different 3’ exon ends. Like in a relay race, SREs either suppressed a potential 5΄ss and passed the splicing baton on or splicing actually occurred. From RNA-Seq data, we systematically selected 19 genes containing exons with silent U1 snRNA binding sites competing with nearby highly used 5΄ss. Extensive SRE analysis by different algorithms found authentic 5΄ss significantly more supported by SREs than silent U1 snRNA binding sites, indicating that our concept may permit generalization to a model for 5΄ss selection and 3’ exon end definition.
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Affiliation(s)
- Anna-Lena Brillen
- Institute for Virology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Katrin Schöneweis
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Lara Walotka
- Institute for Virology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Linda Hartmann
- Institute for Virology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Lisa Müller
- Institute for Virology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Johannes Ptok
- Institute for Virology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Wolfgang Kaisers
- Department of Anesthesiology, University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Gereon Poschmann
- Molecular Proteomics Laboratory, BMFZ, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Kai Stühler
- Molecular Proteomics Laboratory, BMFZ, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany.,Institute for Molecular Medicine, University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Area Science Park, 34149 Trieste, Italy
| | - Stephan Theiss
- Institute of Clinical Neuroscience and Medical Psychology, Heinrich-Heine-University Düsseldorf, 40225
| | - Heiner Schaal
- Institute for Virology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
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26
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Aghamirzaie D, Collakova E, Li S, Grene R. CoSpliceNet: a framework for co-splicing network inference from transcriptomics data. BMC Genomics 2016; 17:845. [PMID: 27793091 PMCID: PMC5086072 DOI: 10.1186/s12864-016-3172-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 10/18/2016] [Indexed: 11/10/2022] Open
Abstract
Background Alternative splicing has been proposed to increase transcript diversity and protein plasticity in eukaryotic organisms, but the extent to which this is the case is currently unclear, especially with regard to the diversification of molecular function. Eukaryotic splicing involves complex interactions of splicing factors and their targets. Inference of co-splicing networks capturing these types of interactions is important for understanding this crucial, highly regulated post-transcriptional process at the systems level. Results First, several transcript and protein attributes, including coding potential of transcripts and differences in functional domains of proteins, were compared between splice variants and protein isoforms to assess transcript and protein diversity in a biological system. Alternative splicing was shown to increase transcript and function-related protein diversity in developing Arabidopsis embryos. Second, CoSpliceNet, which integrates co-expression and motif discovery at splicing regulatory regions to infer co-splicing networks, was developed. CoSpliceNet was applied to temporal RNA sequencing data to identify candidate regulators of splicing events and predict RNA-binding motifs, some of which are supported by prior experimental evidence. Analysis of inferred splicing factor targets revealed an unexpected role for the unfolded protein response in embryo development. Conclusions The methods presented here can be used in any biological system to assess transcript diversity and protein plasticity and to predict candidate regulators, their targets, and RNA-binding motifs for splicing factors. CoSpliceNet is freely available at http://delasa.github.io/co-spliceNet/. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3172-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Delasa Aghamirzaie
- Genetics, Bioinformatics and Computational Biology, Virginia Tech, Blacksburg, VA, 24061, USA.
| | - Eva Collakova
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Song Li
- Genetics, Bioinformatics and Computational Biology, Virginia Tech, Blacksburg, VA, 24061, USA.,Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Ruth Grene
- Genetics, Bioinformatics and Computational Biology, Virginia Tech, Blacksburg, VA, 24061, USA.,Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, 24061, USA
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27
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mCarts: Genome-Wide Prediction of Clustered Sequence Motifs as Binding Sites for RNA-Binding Proteins. Methods Mol Biol 2016; 1421:215-26. [PMID: 26965268 DOI: 10.1007/978-1-4939-3591-8_17] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
RNA-binding proteins (RBPs) are critical components of post-transcriptional gene expression regulation. However, their binding sites have until recently been difficult to determine due to the apparent low specificity of RBPs for their target transcripts and the lack of high-throughput assays for analyzing binding sites genome wide. Here we present a bioinformatics method for predicting RBP binding motif sites on a genome-wide scale that leverages motif conservation, RNA secondary structure, and the tendency of RBP binding sites to cluster together. A probabilistic model is learned from bona fide binding sites determined by CLIP and applied genome wide to generate high specificity binding site predictions.
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28
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Introduction to Bioinformatics Resources for Post-transcriptional Regulation of Gene Expression. Methods Mol Biol 2016; 1358:3-28. [PMID: 26463374 DOI: 10.1007/978-1-4939-3067-8_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Untranslated regions (UTRs) and, to a lesser extent, coding sequences of mRNAs are involved in defining the fate of the mature transcripts through the modulation of three primary control processes, mRNA localization, degradation and translation; the action of trans-factors such as RNA-binding proteins (RBPs) and noncoding RNAs (ncRNAs) combined with the presence of defined sequence and structural cis-elements ultimately determines translation levels. Identifying functional regions in UTRs and uncovering post-transcriptional regulators acting upon these regions is thus of paramount importance to understand the spectrum of regulatory possibilities for any given mRNA. This tasks can now be approached computationally, to reduce the space of testable hypotheses and to drive experimental validation.This chapter focuses on presenting databases and tools allowing to study the various aspects of post-transcriptional regulation, including motif search (sequence and secondary structure), prediction of regulatory networks (e.g., RBP and ncRNA binding sites), profiling of the mRNAs translational state, and other aspects of this level of gene expression regulation. Two analysis pipelines are also presented as practical examples of how the described tools could be integrated and effectively employed.
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29
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Rivers C, Idris J, Scott H, Rogers M, Lee YB, Gaunt J, Phylactou L, Curk T, Campbell C, Ule J, Norman M, Uney JB. iCLIP identifies novel roles for SAFB1 in regulating RNA processing and neuronal function. BMC Biol 2015; 13:111. [PMID: 26694817 PMCID: PMC4689037 DOI: 10.1186/s12915-015-0220-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 12/10/2015] [Indexed: 01/07/2023] Open
Abstract
Background SAFB1 is a RNA binding protein implicated in the regulation of multiple cellular processes such as the regulation of transcription, stress response, DNA repair and RNA processing. To gain further insight into SAFB1 function we used iCLIP and mapped its interaction with RNA on a genome wide level. Results iCLIP analysis found SAFB1 binding was enriched, specifically in exons, ncRNAs, 3’ and 5’ untranslated regions. SAFB1 was found to recognise a purine-rich GAAGA motif with the highest frequency and it is therefore likely to bind core AGA, GAA, or AAG motifs. Confirmatory RT-PCR experiments showed that the expression of coding and non-coding genes with SAFB1 cross-link sites was altered by SAFB1 knockdown. For example, we found that the isoform-specific expression of neural cell adhesion molecule (NCAM1) and ASTN2 was influenced by SAFB1 and that the processing of miR-19a from the miR-17-92 cluster was regulated by SAFB1. These data suggest SAFB1 may influence alternative splicing and, using an NCAM1 minigene, we showed that SAFB1 knockdown altered the expression of two of the three NCAM1 alternative spliced isoforms. However, when the AGA, GAA, and AAG motifs were mutated, SAFB1 knockdown no longer mediated a decrease in the NCAM1 9–10 alternative spliced form. To further investigate the association of SAFB1 with splicing we used exon array analysis and found SAFB1 knockdown mediated the statistically significant up- and downregulation of alternative exons. Further analysis using RNAmotifs to investigate the frequency of association between the motif pairs (AGA followed by AGA, GAA or AAG) and alternative spliced exons found there was a highly significant correlation with downregulated exons. Together, our data suggest SAFB1 will play an important physiological role in the central nervous system regulating synaptic function. We found that SAFB1 regulates dendritic spine density in hippocampal neurons and hence provide empirical evidence supporting this conclusion. Conclusions iCLIP showed that SAFB1 has previously uncharacterised specific RNA binding properties that help coordinate the isoform-specific expression of coding and non-coding genes. These genes regulate splicing, axonal and synaptic function, and are associated with neuropsychiatric disease, suggesting that SAFB1 is an important regulator of key neuronal processes. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0220-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Caroline Rivers
- Regenerative Medicine Laboratories, School of Clinical Sciences, Cellular & Molecular Medicine, Medical Sciences Building, University Walk, University of Bristol, Bristol, BS8 1TD, UK.
| | - Jalilah Idris
- Regenerative Medicine Laboratories, School of Clinical Sciences, Cellular & Molecular Medicine, Medical Sciences Building, University Walk, University of Bristol, Bristol, BS8 1TD, UK. .,Institute of Medical Sciences & Technology, University of Kuala Lumpur, Kuala Lumpur, 43000, Malaysia.
| | - Helen Scott
- Regenerative Medicine Laboratories, School of Clinical Sciences, Cellular & Molecular Medicine, Medical Sciences Building, University Walk, University of Bristol, Bristol, BS8 1TD, UK.
| | - Mark Rogers
- Intelligent Systems Laboratory, Department of Engineering & Mathematics, Merchant Venturers Building, University of Bristol, Bristol, BS8 1UB, UK.
| | - Youn-Bok Lee
- MRC Centre for Neurodegeneration Research, King's College London, Institute of Psychiatry, London, UK.
| | - Jessica Gaunt
- Regenerative Medicine Laboratories, School of Clinical Sciences, Cellular & Molecular Medicine, Medical Sciences Building, University Walk, University of Bristol, Bristol, BS8 1TD, UK.
| | - Leonidas Phylactou
- Faculty of Computer and Information Science, University of Ljubljana, Trzaska cesta 25, SI-1001, Ljubljana, Slovenia.
| | - Tomaz Curk
- The Cyprus Institute of Neurology & Genetics, PO Box 23462, 1683, Nicosia, Cyprus.
| | - Colin Campbell
- Institute of Medical Sciences & Technology, University of Kuala Lumpur, Kuala Lumpur, 43000, Malaysia.
| | - Jernej Ule
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK.
| | - Michael Norman
- Regenerative Medicine Laboratories, School of Clinical Sciences, Cellular & Molecular Medicine, Medical Sciences Building, University Walk, University of Bristol, Bristol, BS8 1TD, UK.
| | - James B Uney
- Regenerative Medicine Laboratories, School of Clinical Sciences, Cellular & Molecular Medicine, Medical Sciences Building, University Walk, University of Bristol, Bristol, BS8 1TD, UK.
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30
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Raj B, Blencowe B. Alternative Splicing in the Mammalian Nervous System: Recent Insights into Mechanisms and Functional Roles. Neuron 2015; 87:14-27. [DOI: 10.1016/j.neuron.2015.05.004] [Citation(s) in RCA: 328] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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31
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Coelho MB, Attig J, Bellora N, König J, Hallegger M, Kayikci M, Eyras E, Ule J, Smith CWJ. Nuclear matrix protein Matrin3 regulates alternative splicing and forms overlapping regulatory networks with PTB. EMBO J 2015; 34:653-68. [PMID: 25599992 PMCID: PMC4365034 DOI: 10.15252/embj.201489852] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Matrin3 is an RNA- and DNA-binding nuclear matrix protein found to be associated with neural and muscular degenerative diseases. A number of possible functions of Matrin3 have been suggested, but no widespread role in RNA metabolism has yet been clearly demonstrated. We identified Matrin3 by its interaction with the second RRM domain of the splicing regulator PTB. Using a combination of RNAi knockdown, transcriptome profiling and iCLIP, we find that Matrin3 is a regulator of hundreds of alternative splicing events, principally acting as a splicing repressor with only a small proportion of targeted events being co-regulated by PTB. In contrast to other splicing regulators, Matrin3 binds to an extended region within repressed exons and flanking introns with no sharply defined peaks. The identification of this clear molecular function of Matrin3 should help to clarify the molecular pathology of ALS and other diseases caused by mutations of Matrin3.
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Affiliation(s)
- Miguel B Coelho
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Jan Attig
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK MRC-Laboratory of Molecular Biology, Cambridge, UK
| | - Nicolás Bellora
- Computational Genomics, Universitat Pompeu Fabra, Barcelona, Spain Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain INIBIOMA CONICET-UNComahue, Bariloche, Argentina
| | - Julian König
- MRC-Laboratory of Molecular Biology, Cambridge, UK
| | - Martina Hallegger
- Department of Biochemistry, University of Cambridge, Cambridge, UK Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | | | - Eduardo Eyras
- Computational Genomics, Universitat Pompeu Fabra, Barcelona, Spain Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Jernej Ule
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
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32
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Reyes-Herrera PH, Ficarra E. Computational Methods for CLIP-seq Data Processing. Bioinform Biol Insights 2014; 8:199-207. [PMID: 25336930 PMCID: PMC4196881 DOI: 10.4137/bbi.s16803] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Revised: 07/29/2014] [Accepted: 08/01/2014] [Indexed: 12/25/2022] Open
Abstract
RNA-binding proteins (RBPs) are at the core of post-transcriptional regulation and thus of gene expression control at the RNA level. One of the principal challenges in the field of gene expression regulation is to understand RBPs mechanism of action. As a result of recent evolution of experimental techniques, it is now possible to obtain the RNA regions recognized by RBPs on a transcriptome-wide scale. In fact, CLIP-seq protocols use the joint action of CLIP, crosslinking immunoprecipitation, and high-throughput sequencing to recover the transcriptome-wide set of interaction regions for a particular protein. Nevertheless, computational methods are necessary to process CLIP-seq experimental data and are a key to advancement in the understanding of gene regulatory mechanisms. Considering the importance of computational methods in this area, we present a review of the current status of computational approaches used and proposed for CLIP-seq data.
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Affiliation(s)
- Paula H Reyes-Herrera
- Facultad de Ingeniería Electrónica y Biomédica, Universidad Antonio Nariño, Bogotá, Colombia
| | - Elisa Ficarra
- Department of Control and Computer Engineering, Politecnico di Torino, TO, Italy
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33
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Erkelenz S, Theiss S, Otte M, Widera M, Peter JO, Schaal H. Genomic HEXploring allows landscaping of novel potential splicing regulatory elements. Nucleic Acids Res 2014; 42:10681-97. [PMID: 25147205 PMCID: PMC4176321 DOI: 10.1093/nar/gku736] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Effective splice site selection is critically controlled by flanking splicing regulatory elements (SREs) that can enhance or repress splice site use. Although several computational algorithms currently identify a multitude of potential SRE motifs, their predictive power with respect to mutation effects is limited. Following a RESCUE-type approach, we defined a hexamer-based ‘HEXplorer score’ as average Z-score of all six hexamers overlapping with a given nucleotide in an arbitrary genomic sequence. Plotted along genomic regions, HEXplorer score profiles varied slowly in the vicinity of splice sites. They reflected the respective splice enhancing and silencing properties of splice site neighborhoods beyond the identification of single dedicated SRE motifs. In particular, HEXplorer score differences between mutant and reference sequences faithfully represented exonic mutation effects on splice site usage. Using the HIV-1 pre-mRNA as a model system highly dependent on SREs, we found an excellent correlation in 29 mutations between splicing activity and HEXplorer score. We successfully predicted and confirmed five novel SREs and optimized mutations inactivating a known silencer. The HEXplorer score allowed landscaping of splicing regulatory regions, provided a quantitative measure of mutation effects on splice enhancing and silencing properties and permitted calculation of the mutationally most effective nucleotide.
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Affiliation(s)
- Steffen Erkelenz
- Institute for Virology, Heinrich-Heine-University Duesseldorf, Duesseldorf, Germany
| | - Stephan Theiss
- Institute of Clinical Neuroscience and Medical Psychology, Heinrich-Heine-University Duesseldorf, Duesseldorf, Germany
| | - Marianne Otte
- Institute of Evolutionary Genetics, Heinrich-Heine-University Duesseldorf, Duesseldorf, Germany
| | - Marek Widera
- Institute for Virology, Heinrich-Heine-University Duesseldorf, Duesseldorf, Germany
| | - Jan Otto Peter
- Institute for Virology, Heinrich-Heine-University Duesseldorf, Duesseldorf, Germany
| | - Heiner Schaal
- Institute for Virology, Heinrich-Heine-University Duesseldorf, Duesseldorf, Germany
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Mickleburgh I, Kafasla P, Cherny D, Llorian M, Curry S, Jackson RJ, Smith CWJ. The organization of RNA contacts by PTB for regulation of FAS splicing. Nucleic Acids Res 2014; 42:8605-20. [PMID: 24957602 PMCID: PMC4117754 DOI: 10.1093/nar/gku519] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Post-transcriptional steps of gene expression are regulated by RNA binding proteins. Major progress has been made in characterizing RNA-protein interactions, from high resolution structures to transcriptome-wide profiling. Due to the inherent technical challenges, less attention has been paid to the way in which proteins with multiple RNA binding domains engage with target RNAs. We have investigated how the four RNA recognition motif (RRM) domains of Polypyrimidine tract binding (PTB) protein, a major splicing regulator, interact with FAS pre-mRNA under conditions in which PTB represses FAS exon 6 splicing. A combination of tethered hydroxyl radical probing, targeted inactivation of individual RRMs and single molecule analyses revealed an unequal division of labour between the four RRMs of PTB. RNA binding by RRM4 is the most important for function despite the low intrinsic binding specificity and the complete lack of effect of disrupting individual RRM4 contact points on the RNA. The ordered RRM3-4 di-domain packing provides an extended binding surface for RNA interacting at RRM4, via basic residues in the preceding linker. Our results illustrate how multiple alternative low-specificity binding configurations of RRM4 are consistent with repressor function as long as the overall ribonucleoprotein architecture provided by appropriate di-domain packing is maintained.
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Affiliation(s)
- Ian Mickleburgh
- Department of Biochemistry, University of Cambridge, Downing Site, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Panagiota Kafasla
- Department of Biochemistry, University of Cambridge, Downing Site, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Dmitry Cherny
- Department of Biochemistry, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK
| | - Miriam Llorian
- Department of Biochemistry, University of Cambridge, Downing Site, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Stephen Curry
- Division of Cell and Molecular Biology, Imperial College, Exhibition Road, London SW7 2AZ, UK
| | - Richard J Jackson
- Department of Biochemistry, University of Cambridge, Downing Site, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Christopher W J Smith
- Department of Biochemistry, University of Cambridge, Downing Site, Tennis Court Road, Cambridge, CB2 1QW, UK
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Paz I, Kosti I, Ares M, Cline M, Mandel-Gutfreund Y. RBPmap: a web server for mapping binding sites of RNA-binding proteins. Nucleic Acids Res 2014; 42:W361-7. [PMID: 24829458 PMCID: PMC4086114 DOI: 10.1093/nar/gku406] [Citation(s) in RCA: 353] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Regulation of gene expression is executed in many cases by RNA-binding proteins
(RBPs) that bind to mRNAs as well as to non-coding RNAs. RBPs recognize their
RNA target via specific binding sites on the RNA. Predicting the binding sites
of RBPs is known to be a major challenge. We present a new webserver, RBPmap,
freely accessible through the website http://rbpmap.technion.ac.il/ for accurate prediction and
mapping of RBP binding sites. RBPmap has been developed specifically for mapping
RBPs in human, mouse and Drosophila melanogaster genomes,
though it supports other organisms too. RBPmap enables the users to select
motifs from a large database of experimentally defined motifs. In addition,
users can provide any motif of interest, given as either a consensus or a PSSM.
The algorithm for mapping the motifs is based on a Weighted-Rank approach, which
considers the clustering propensity of the binding sites and the overall
tendency of regulatory regions to be conserved. In addition, RBPmap incorporates
a position-specific background model, designed uniquely for different genomic
regions, such as splice sites, 5’ and 3’ UTRs, non-coding RNA
and intergenic regions. RBPmap was tested on high-throughput RNA-binding
experiments and was proved to be highly accurate.
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Affiliation(s)
- Inbal Paz
- Department of Biology, Technion - Israel Institute of Technology, Technion City, Haifa 32000, Israel
| | - Idit Kosti
- Department of Biology, Technion - Israel Institute of Technology, Technion City, Haifa 32000, Israel
| | - Manuel Ares
- Department of Molecular, Cellular and Developmental Biology, UCSC, Santa Cruz, CA, USA
| | - Melissa Cline
- Center for Biomolecular Science & Engineering, UCSC, Santa Cruz, CA, USA
| | - Yael Mandel-Gutfreund
- Department of Biology, Technion - Israel Institute of Technology, Technion City, Haifa 32000, Israel
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