51
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Lin J, Zhang Y, Frankel WN, Ouyang Z. PRAS: Predicting functional targets of RNA binding proteins based on CLIP-seq peaks. PLoS Comput Biol 2019; 15:e1007227. [PMID: 31425505 PMCID: PMC6716675 DOI: 10.1371/journal.pcbi.1007227] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 08/30/2019] [Accepted: 06/28/2019] [Indexed: 11/19/2022] Open
Abstract
RNA-protein interaction plays important roles in post-transcriptional regulation. Recent advancements in cross-linking and immunoprecipitation followed by sequencing (CLIP-seq) technologies make it possible to detect the binding peaks of a given RNA binding protein (RBP) at transcriptome scale. However, it is still challenging to predict the functional consequences of RBP binding peaks. In this study, we propose the Protein-RNA Association Strength (PRAS), which integrates the intensities and positions of the binding peaks of RBPs for functional mRNA targets prediction. We illustrate the superiority of PRAS over existing approaches on predicting the functional targets of two related but divergent CELF (CUGBP, ELAV-like factor) RBPs in mouse brain and muscle. We also demonstrate the potential of PRAS for wide adoption by applying it to the enhanced CLIP-seq (eCLIP) datasets of 37 RNA decay related RBPs in two human cell lines. PRAS can be utilized to investigate any RBPs with available CLIP-seq peaks. PRAS is freely available at http://ouyanglab.jax.org/pras/.
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Affiliation(s)
- Jianan Lin
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America
- Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut, United States of America
| | - Yuping Zhang
- Department of Statistics, University of Connecticut, Storrs, Connecticut, United States of America
- Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, United States of America
- Center for Quantitative Medicine, University of Connecticut, Farmington, Connecticut, United States of America
| | - Wayne N. Frankel
- Department of Genetics and Development and Institute for Genomic Medicine, Columbia University Medical Center, New York City, New York, United States of America
| | - Zhengqing Ouyang
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America
- Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut, United States of America
- Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, United States of America
- Department of Genetics and Genome Sciences, University of Connecticut, Farmington, Connecticut, United States of America
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52
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Abstract
Most human genes have multiple sites at which RNA 3' end cleavage and polyadenylation can occur, enabling the expression of distinct transcript isoforms under different conditions. Novel methods to sequence RNA 3' ends have generated comprehensive catalogues of polyadenylation (poly(A)) sites; their analysis using innovative computational methods has revealed how poly(A) site choice is regulated by core RNA 3' end processing factors, such as cleavage factor I and cleavage and polyadenylation specificity factor, as well as by other RNA-binding proteins, particularly splicing factors. Here, we review the experimental and computational methods that have enabled the global mapping of mRNA and of long non-coding RNA 3' ends, quantification of the resulting isoforms and the discovery of regulators of alternative cleavage and polyadenylation (APA). We highlight the different types of APA-derived isoforms and their functional differences, and illustrate how APA contributes to human diseases, including cancer and haematological, immunological and neurological diseases.
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53
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Vejnar CE, Abdel Messih M, Takacs CM, Yartseva V, Oikonomou P, Christiano R, Stoeckius M, Lau S, Lee MT, Beaudoin JD, Musaev D, Darwich-Codore H, Walther TC, Tavazoie S, Cifuentes D, Giraldez AJ. Genome wide analysis of 3' UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish. Genome Res 2019; 29:1100-1114. [PMID: 31227602 PMCID: PMC6633259 DOI: 10.1101/gr.245159.118] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 06/07/2019] [Indexed: 12/16/2022]
Abstract
Posttranscriptional regulation plays a crucial role in shaping gene expression. During the maternal-to-zygotic transition (MZT), thousands of maternal transcripts are regulated. However, how different cis-elements and trans-factors are integrated to determine mRNA stability remains poorly understood. Here, we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. By using a massively parallel reporter assay, we identified cis-regulatory sequences in the 3′ UTR, including U-rich motifs that are associated with increased mRNA stability. In contrast, miR-430 target sequences, UAUUUAUU AU-rich elements (ARE), CCUC, and CUGC elements emerged as destabilizing motifs, with miR-430 and AREs causing mRNA deadenylation upon genome activation. We identified trans-factors by profiling RNA–protein interactions and found that poly(U)-binding proteins are preferentially associated with 3′ UTR sequences and stabilizing motifs. We show that this activity is antagonized by C-rich motifs and correlated with protein binding. Finally, we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.
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Affiliation(s)
- Charles E Vejnar
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Mario Abdel Messih
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Carter M Takacs
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA.,University of New Haven, West Haven, Connecticut 06516, USA
| | - Valeria Yartseva
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA.,Department of Neuroscience, Genentech, Incorporated, South San Francisco, California 94080, USA
| | - Panos Oikonomou
- Department of Systems Biology, Columbia University, New York, New York 10032, USA
| | - Romain Christiano
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
| | - Marlon Stoeckius
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA.,New York Genome Center, New York, New York 10013, USA
| | - Stephanie Lau
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Miler T Lee
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA.,Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Jean-Denis Beaudoin
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Damir Musaev
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Hiba Darwich-Codore
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Tobias C Walther
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA.,Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02124, USA.,Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA
| | - Saeed Tavazoie
- Department of Biochemistry and Molecular Biophysics, and Department of Systems Biology, Columbia University, New York, New York 10032, USA
| | - Daniel Cifuentes
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA.,Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA.,Yale Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut 06510, USA.,Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut 06510, USA
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54
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Makokha GN, Abe-Chayama H, Chowdhury S, Hayes CN, Tsuge M, Yoshima T, Ishida Y, Zhang Y, Uchida T, Tateno C, Akiyama R, Chayama K. Regulation of the Hepatitis B virus replication and gene expression by the multi-functional protein TARDBP. Sci Rep 2019; 9:8462. [PMID: 31186504 PMCID: PMC6560085 DOI: 10.1038/s41598-019-44934-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 12/12/2018] [Indexed: 02/06/2023] Open
Abstract
Hepatitis B virus (HBV) infects the liver and is a key risk factor for hepatocellular carcinoma. Identification of host factors that support viral replication is important to understand mechanisms of viral replication and to develop new therapeutic strategies. We identified TARDBP as a host factor that regulates HBV. Silencing or knocking out the protein in HBV infected cells severely impaired the production of viral replicative intermediates, mRNAs, proteins, and virions, whereas ectopic expression of TARDBP rescued production of these products. Mechanistically, we found that the protein binds to the HBV core promoter, as shown by chromatin precipitation as well as mutagenesis and protein-DNA interaction assays. Using LC-MS/MS analysis, we also found that TARDBP binds to a number of other proteins known to support the HBV life cycle, including NPM1, PARP1, Hsp90, HNRNPC, SFPQ, PTBP1, HNRNPK, and PUF60. Interestingly, given its key role as a regulator of RNA splicing, we found that TARDBP has an inhibitory role on pregenomic RNA splicing, which might help the virus to export its non-canonical RNAs from the nucleus without being subjected to unwanted splicing, even though mRNA nuclear export is normally closely tied to RNA splicing. Taken together, our results demonstrate that TARDBP is involved in multiple steps of HBV replication via binding to both HBV DNA and RNA. The protein's broad interactome suggests that TARDBP may function as part of a RNA-binding scaffold involved in HBV replication and that the interaction between these proteins might be a target for development of anti-HBV drugs.
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Affiliation(s)
- Grace Naswa Makokha
- Department of Gastroenterology and Metabolism, Institute of Biomedical and Health Science, Hiroshima, Japan
- Liver Research Project Center, Hiroshima, Japan
| | - Hiromi Abe-Chayama
- Department of Gastroenterology and Metabolism, Institute of Biomedical and Health Science, Hiroshima, Japan
- Liver Research Project Center, Hiroshima, Japan
- Center for Medical Specialist Graduate Education and Research, Hiroshima, Japan
| | - Sajeda Chowdhury
- Department of Gastroenterology and Metabolism, Institute of Biomedical and Health Science, Hiroshima, Japan
- Liver Research Project Center, Hiroshima, Japan
| | - C Nelson Hayes
- Department of Gastroenterology and Metabolism, Institute of Biomedical and Health Science, Hiroshima, Japan
- Liver Research Project Center, Hiroshima, Japan
| | - Masataka Tsuge
- Department of Gastroenterology and Metabolism, Institute of Biomedical and Health Science, Hiroshima, Japan
- Liver Research Project Center, Hiroshima, Japan
- Natural Science Center for Basic Research and Development, Hiroshima, Japan
| | - Tadahiko Yoshima
- Liver Research Project Center, Hiroshima, Japan
- Laboratory for Digestive Diseases, RIKEN Center for Integrative Medical Sciences Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima-shi, 734-8551, Japan
| | - Yuji Ishida
- PhoenixBio Co., Ltd., 3-4-1 Kagamiyama, Higashihiroshima, 739-0046, Japan
| | - Yizhou Zhang
- Department of Gastroenterology and Metabolism, Institute of Biomedical and Health Science, Hiroshima, Japan
- Liver Research Project Center, Hiroshima, Japan
| | - Takuro Uchida
- Department of Gastroenterology and Metabolism, Institute of Biomedical and Health Science, Hiroshima, Japan
- Liver Research Project Center, Hiroshima, Japan
| | - Chise Tateno
- PhoenixBio Co., Ltd., 3-4-1 Kagamiyama, Higashihiroshima, 739-0046, Japan
| | - Rie Akiyama
- Department of Gastroenterology and Metabolism, Institute of Biomedical and Health Science, Hiroshima, Japan
- Liver Research Project Center, Hiroshima, Japan
| | - Kazuaki Chayama
- Department of Gastroenterology and Metabolism, Institute of Biomedical and Health Science, Hiroshima, Japan.
- Liver Research Project Center, Hiroshima, Japan.
- Laboratory for Digestive Diseases, RIKEN Center for Integrative Medical Sciences Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima-shi, 734-8551, Japan.
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55
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Modic M, Grosch M, Rot G, Schirge S, Lepko T, Yamazaki T, Lee FCY, Rusha E, Shaposhnikov D, Palo M, Merl-Pham J, Cacchiarelli D, Rogelj B, Hauck SM, von Mering C, Meissner A, Lickert H, Hirose T, Ule J, Drukker M. Cross-Regulation between TDP-43 and Paraspeckles Promotes Pluripotency-Differentiation Transition. Mol Cell 2019; 74:951-965.e13. [PMID: 31047794 PMCID: PMC6561722 DOI: 10.1016/j.molcel.2019.03.041] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 02/12/2019] [Accepted: 03/28/2019] [Indexed: 01/22/2023]
Abstract
RNA-binding proteins (RBPs) and long non-coding RNAs (lncRNAs) are key regulators of gene expression, but their joint functions in coordinating cell fate decisions are poorly understood. Here we show that the expression and activity of the RBP TDP-43 and the long isoform of the lncRNA Neat1, the scaffold of the nuclear compartment "paraspeckles," are reciprocal in pluripotent and differentiated cells because of their cross-regulation. In pluripotent cells, TDP-43 represses the formation of paraspeckles by enhancing the polyadenylated short isoform of Neat1. TDP-43 also promotes pluripotency by regulating alternative polyadenylation of transcripts encoding pluripotency factors, including Sox2, which partially protects its 3' UTR from miR-21-mediated degradation. Conversely, paraspeckles sequester TDP-43 and other RBPs from mRNAs and promote exit from pluripotency and embryonic patterning in the mouse. We demonstrate that cross-regulation between TDP-43 and Neat1 is essential for their efficient regulation of a broad network of genes and, therefore, of pluripotency and differentiation.
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Affiliation(s)
- Miha Modic
- Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; The Francis Crick Institute, London NW1 1AT, UK; Department for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Markus Grosch
- Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Gregor Rot
- Institute of Molecular Life Sciences of the University of Zurich and Swiss Institute of Bioinformatics, 8057 Zurich, Switzerland
| | - Silvia Schirge
- Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Tjasa Lepko
- Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Tomohiro Yamazaki
- Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Flora C Y Lee
- The Francis Crick Institute, London NW1 1AT, UK; Department for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Ejona Rusha
- Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Dmitry Shaposhnikov
- Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Michael Palo
- The Francis Crick Institute, London NW1 1AT, UK; Department for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Juliane Merl-Pham
- Research Unit Protein Science, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 80939 Munich, Germany
| | - Davide Cacchiarelli
- Broad Institute of Harvard University/MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Telethon Institute of Genetics and Medicine (TIGEM), NA 80078 Pozzuoli, Italy
| | - Boris Rogelj
- Department of Biotechnology, Jožef Stefan Institute, 1000 Ljubljana, Slovenia; Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia; Biomedical Research Institute BRIS, 1000 Ljubljana, Slovenia
| | - Stefanie M Hauck
- Research Unit Protein Science, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 80939 Munich, Germany
| | - Christian von Mering
- Institute of Molecular Life Sciences of the University of Zurich and Swiss Institute of Bioinformatics, 8057 Zurich, Switzerland
| | - Alexander Meissner
- Broad Institute of Harvard University/MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Heiko Lickert
- Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Tetsuro Hirose
- Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Jernej Ule
- The Francis Crick Institute, London NW1 1AT, UK; Department for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK.
| | - Micha Drukker
- Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Comprehensive Pneumology Center (CPC-M), Ludwig-Maximilians-Universität München, Asklepios Fachkliniken München-Gauting und Helmholtz Zentrum München, Max-Lebsche-Platz 31, 81377 Munich, Germany.
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56
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Viphakone N, Sudbery I, Griffith L, Heath CG, Sims D, Wilson SA. Co-transcriptional Loading of RNA Export Factors Shapes the Human Transcriptome. Mol Cell 2019; 75:310-323.e8. [PMID: 31104896 PMCID: PMC6675937 DOI: 10.1016/j.molcel.2019.04.034] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 02/25/2019] [Accepted: 04/29/2019] [Indexed: 11/29/2022]
Abstract
During gene expression, RNA export factors are mainly known for driving nucleo-cytoplasmic transport. While early studies suggested that the exon junction complex (EJC) provides a binding platform for them, subsequent work proposed that they are only recruited by the cap binding complex to the 5′ end of RNAs, as part of TREX. Using iCLIP, we show that the export receptor Nxf1 and two TREX subunits, Alyref and Chtop, are recruited to the whole mRNA co-transcriptionally via splicing but before 3′ end processing. Consequently, Alyref alters splicing decisions and Chtop regulates alternative polyadenylation. Alyref is recruited to the 5′ end of RNAs by CBC, and our data reveal subsequent binding to RNAs near EJCs. We demonstrate that eIF4A3 stimulates Alyref deposition not only on spliced RNAs close to EJC sites but also on single-exon transcripts. Our study reveals mechanistic insights into the co-transcriptional recruitment of mRNA export factors and how this shapes the human transcriptome. 5′ cap binding complex CBC acts as a transient landing pad for Alyref Alyref is deposited upstream of the exon-exon junction next to the EJC Alyref can be deposited on introns and regulate splicing Chtop is mainly deposited on 3′ UTRs and influences poly(A) site choices
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Affiliation(s)
- Nicolas Viphakone
- Sheffield Institute For Nucleic Acids (SInFoNiA) and Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK.
| | - Ian Sudbery
- Sheffield Institute For Nucleic Acids (SInFoNiA) and Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Llywelyn Griffith
- Sheffield Institute For Nucleic Acids (SInFoNiA) and Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Catherine G Heath
- Sheffield Institute For Nucleic Acids (SInFoNiA) and Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - David Sims
- MRC Computational Genomics Analysis and Training Programme (CGAT), MRC Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DS UK
| | - Stuart A Wilson
- Sheffield Institute For Nucleic Acids (SInFoNiA) and Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK.
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57
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Kamieniarz-Gdula K, Gdula MR, Panser K, Nojima T, Monks J, Wiśniewski JR, Riepsaame J, Brockdorff N, Pauli A, Proudfoot NJ. Selective Roles of Vertebrate PCF11 in Premature and Full-Length Transcript Termination. Mol Cell 2019; 74:158-172.e9. [PMID: 30819644 PMCID: PMC6458999 DOI: 10.1016/j.molcel.2019.01.027] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 12/07/2018] [Accepted: 01/17/2019] [Indexed: 12/02/2022]
Abstract
The pervasive nature of RNA polymerase II (Pol II) transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation (CPA) factor PCF11, which directly binds to the Pol II C-terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11-mediated termination is essential for vertebrate development. A range of genomic analyses, including mNET-seq, 3′ mRNA-seq, chromatin RNA-seq, and ChIP-seq, reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome-wide. PCF11 binds preferentially between closely spaced genes, where it prevents transcriptional interference and consequent gene downregulation. Notably, PCF11 is sub-stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto-regulatory mechanism involving premature termination of its own transcript and are important for normal development. Both in human cell culture and during zebrafish development, PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Human PCF11 enhances transcription termination and 3′ end processing, genome-wide PCF11 is substoichiometric to CPA complex due to autoregulation of its transcription PCF11 stimulates expression of closely spaced genes but attenuates other genes PCF11-mediated functions are conserved in vertebrates and essential in development
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Affiliation(s)
- Kinga Kamieniarz-Gdula
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
| | - Michal R Gdula
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Karin Panser
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Takayuki Nojima
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Joan Monks
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Jacek R Wiśniewski
- Biochemical Proteomics Group, Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Joey Riepsaame
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Neil Brockdorff
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Andrea Pauli
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria.
| | - Nick J Proudfoot
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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58
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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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59
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Krchňáková Z, Thakur PK, Krausová M, Bieberstein N, Haberman N, Müller-McNicoll M, Staněk D. Splicing of long non-coding RNAs primarily depends on polypyrimidine tract and 5' splice-site sequences due to weak interactions with SR proteins. Nucleic Acids Res 2019; 47:911-928. [PMID: 30445574 PMCID: PMC6344860 DOI: 10.1093/nar/gky1147] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 10/26/2018] [Accepted: 10/30/2018] [Indexed: 12/20/2022] Open
Abstract
Many nascent long non-coding RNAs (lncRNAs) undergo the same maturation steps as pre-mRNAs of protein-coding genes (PCGs), but they are often poorly spliced. To identify the underlying mechanisms for this phenomenon, we searched for putative splicing inhibitory sequences using the ncRNA-a2 as a model. Genome-wide analyses of intergenic lncRNAs (lincRNAs) revealed that lincRNA splicing efficiency positively correlates with 5'ss strength while no such correlation was identified for PCGs. In addition, efficiently spliced lincRNAs have higher thymidine content in the polypyrimidine tract (PPT) compared to efficiently spliced PCGs. Using model lincRNAs, we provide experimental evidence that strengthening the 5'ss and increasing the T content in PPT significantly enhances lincRNA splicing. We further showed that lincRNA exons contain less putative binding sites for SR proteins. To map binding of SR proteins to lincRNAs, we performed iCLIP with SRSF2, SRSF5 and SRSF6 and analyzed eCLIP data for SRSF1, SRSF7 and SRSF9. All examined SR proteins bind lincRNA exons to a much lower extent than expression-matched PCGs. We propose that lincRNAs lack the cooperative interaction network that enhances splicing, which renders their splicing outcome more dependent on the optimality of splice sites.
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Affiliation(s)
- Zuzana Krchňáková
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Prasoon Kumar Thakur
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Michaela Krausová
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Nicole Bieberstein
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Nejc Haberman
- Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London W12 0NN, UK
| | | | - David Staněk
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
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Premature polyadenylation-mediated loss of stathmin-2 is a hallmark of TDP-43-dependent neurodegeneration. Nat Neurosci 2019; 22:180-190. [PMID: 30643298 PMCID: PMC6348009 DOI: 10.1038/s41593-018-0293-z] [Citation(s) in RCA: 307] [Impact Index Per Article: 61.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 11/13/2018] [Indexed: 12/11/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are associated with loss of nuclear TDP-43. Here we identify that TDP-43 regulates expression of the neuronal growth-associated factor stathmin-2. Lowered TDP-43 levels, which reduce its binding to sites within the first intron of stathmin-2 pre-mRNA, uncover a cryptic polyadenylation site whose utilization produces a truncated, non-functional mRNA. Reduced stathmin-2 expression is found in neurons trans-differentiated from patient fibroblasts expressing an ALS-causing TDP-43 mutation, in motor cortex and spinal motor neurons from sporadic ALS patients and familial ALS patients with expansion in C9orf72, and in induced pluripotent stem cell (iPSC)-derived motor neurons depleted of TDP-43. Remarkably, while reduction in TDP-43 is shown to inhibit axonal regeneration of iPSC-derived motor neurons, rescue of stathmin-2 expression restores axonal regenerative capacity. Thus, premature polyadenylation-mediated reduction in stathmin-2 is a hallmark of ALS/FTD that functionally links reduced nuclear TDP-43 function to enhanced neuronal vulnerability.
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View from an mRNP: The Roles of SR Proteins in Assembly, Maturation and Turnover. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1203:83-112. [PMID: 31811631 DOI: 10.1007/978-3-030-31434-7_3] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Serine- and arginine-rich proteins (SR proteins) are a family of multitasking RNA-binding proteins (RBPs) that are key determinants of messenger ribonucleoprotein (mRNP) formation, identity and fate. Apart from their essential functions in pre-mRNA splicing, SR proteins display additional pre- and post-splicing activities and connect nuclear and cytoplasmic gene expression machineries. Through changes in their post-translational modifications (PTMs) and their subcellular localization, they provide functional specificity and adjustability to mRNPs. Transcriptome-wide UV crosslinking and immunoprecipitation (CLIP-Seq) studies revealed that individual SR proteins are present in distinct mRNPs and act in specific pairs to regulate different gene expression programmes. Adopting an mRNP-centric viewpoint, we discuss the roles of SR proteins in the assembly, maturation, quality control and turnover of mRNPs and describe the mechanisms by which they integrate external signals, coordinate their multiple tasks and couple subsequent mRNA processing steps.
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Distinct multilevel misregulations of Parkin and PINK1 revealed in cell and animal models of TDP-43 proteinopathy. Cell Death Dis 2018; 9:953. [PMID: 30237395 PMCID: PMC6148241 DOI: 10.1038/s41419-018-1022-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 08/07/2018] [Accepted: 09/03/2018] [Indexed: 12/13/2022]
Abstract
Parkin and PINK1 play an important role in mitochondrial quality control, whose malfunction may also be involved in the pathogenesis of amyotrophic lateral sclerosis (ALS). Excessive TDP-43 accumulation is a pathological hallmark of ALS and is associated with Parkin protein reduction in spinal cord neurons from sporadic ALS patients. In this study, we reveal that Parkin and PINK1 are differentially misregulated in TDP-43 proteinopathy at RNA and protein levels. Using knock-in flies, mouse primary neurons, and TDP-43Q331K transgenic mice, we further unveil that TDP-43 downregulates Parkin mRNA, which involves an unidentified, intron-independent mechanism and requires the RNA-binding and the protein–protein interaction functions of TDP-43. Unlike Parkin, TDP-43 does not regulate PINK1 at an RNA level. Instead, excess of TDP-43 causes cytosolic accumulation of cleaved PINK1 due to impaired proteasomal activity, leading to compromised mitochondrial functions. Consistent with the alterations at the molecular and cellular levels, we show that transgenic upregulation of Parkin but downregulation of PINK1 suppresses TDP-43-induced degenerative phenotypes in a Drosophila model of ALS. Together, these findings highlight the challenge associated with the heterogeneity and complexity of ALS pathogenesis, while pointing to Parkin–PINK1 as a common pathway that may be differentially misregulated in TDP-43 proteinopathy.
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63
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Hannigan MM, Zagore LL, Licatalosi DD. Mapping transcriptome-wide protein-RNA interactions to elucidate RNA regulatory programs. QUANTITATIVE BIOLOGY 2018; 6:228-238. [PMID: 31098334 PMCID: PMC6516777 DOI: 10.1007/s40484-018-0145-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 03/27/2018] [Accepted: 04/03/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Our understanding of post-transcriptional gene regulation has increased exponentially with the development of robust methods to define protein-RNA interactions across the transcriptome. In this review, we highlight the evolution and successful applications of crosslinking and immunoprecipitation (CLIP) methods to interrogate protein-RNA interactions in a transcriptome-wide manner. RESULTS Here, we survey the vast array of in vitro and in vivo approaches used to identify protein-RNA interactions, including but not limited to electrophoretic mobility shift assays, systematic evolution of ligands by exponential enrichment (SELEX), and RIP-seq. We particularly emphasize the advancement of CLIP technologies, and detail protocol improvements and computational tools used to analyze the output data. Importantly, we discuss how profiling protein-RNA interactions can delineate biological functions including splicing regulation, alternative polyadenylation, cytoplasmic decay substrates, and miRNA targets. CONCLUSIONS In summary, this review summarizes the benefits of characterizing RNA-protein networks to further understand the regulation of gene expression and disease pathogenesis. Our review comments on how future CLIP technologies can be adapted to address outstanding questions related to many aspects of RNA metabolism and further advance our understanding of RNA biology.
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Affiliation(s)
- Molly M Hannigan
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Leah L Zagore
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Donny D Licatalosi
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH 44106, USA
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64
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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: 86] [Impact Index Per Article: 14.3] [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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Ule J, Hwang HW, Darnell RB. The Future of Cross-Linking and Immunoprecipitation (CLIP). Cold Spring Harb Perspect Biol 2018; 10:a032243. [PMID: 30068528 PMCID: PMC6071486 DOI: 10.1101/cshperspect.a032243] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
To understand the assembly and functional outcomes of protein-RNA regulation, it is crucial to precisely identify the positions of such interactions. Cross-linking and immunoprecipitation (CLIP) serves this purpose by exploiting covalent protein-RNA cross-linking and RNA fragmentation, along with a series of stringent purification and quality control steps to prepare complementary DNA (cDNA) libraries for sequencing. Here we describe the core steps of CLIP, its primary variations, and the approaches to data analysis. We present the application of CLIP to studies of specific cell types in genetically engineered mice and discuss the mechanistic and physiologic insights that have already been gained from studies using CLIP. We conclude by discussing the future opportunities for CLIP, including studies of human postmortem tissues from disease patients and controls, RNA epigenetic modifications, and RNA structure. These and other applications of CLIP will continue to unravel fundamental gene regulatory mechanisms while providing important biologic and clinically relevant insights.
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Affiliation(s)
- Jernej Ule
- The Francis Crick Institute, London NW1 1AT, United Kingdom
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London WC1N 3BG, United Kingdom
| | - Hun-Way Hwang
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15261
| | - Robert B Darnell
- Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, New York 10065
- Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065
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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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Synaptic Paths to Neurodegeneration: The Emerging Role of TDP-43 and FUS in Synaptic Functions. Neural Plast 2018; 2018:8413496. [PMID: 29755516 PMCID: PMC5925147 DOI: 10.1155/2018/8413496] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 02/08/2018] [Accepted: 02/27/2018] [Indexed: 12/13/2022] Open
Abstract
TAR DNA-binding protein-43 KDa (TDP-43) and fused in sarcoma (FUS) as the defining pathological hallmarks for amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), coupled with ALS-FTD-causing mutations in both genes, indicate that their dysfunctions damage the motor system and cognition. On the molecular level, TDP-43 and FUS participate in the biogenesis and metabolism of coding and noncoding RNAs as well as in the transport and translation of mRNAs as part of cytoplasmic mRNA-ribonucleoprotein (mRNP) granules. Intriguingly, many of the RNA targets of TDP-43 and FUS are involved in synaptic transmission and plasticity, indicating that synaptic dysfunction could be an early event contributing to motor and cognitive deficits in ALS and FTD. Furthermore, the ability of the low-complexity prion-like domains of TDP-43 and FUS to form liquid droplets suggests a potential mechanism for mRNP assembly and conversion. This review will discuss the role of TDP-43 and FUS in RNA metabolism, with an emphasis on the involvement of this process in synaptic function and neuroprotection. This will be followed by a discussion of the potential phase separation mechanism for forming RNP granules and pathological inclusions.
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Discovery of physiological and cancer-related regulators of 3' UTR processing with KAPAC. Genome Biol 2018; 19:44. [PMID: 29592812 PMCID: PMC5875010 DOI: 10.1186/s13059-018-1415-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 02/28/2018] [Indexed: 11/10/2022] Open
Abstract
3' Untranslated regions (3' UTRs) length is regulated in relation to cellular state. To uncover key regulators of poly(A) site use in specific conditions, we have developed PAQR, a method for quantifying poly(A) site use from RNA sequencing data and KAPAC, an approach that infers activities of oligomeric sequence motifs on poly(A) site choice. Application of PAQR and KAPAC to RNA sequencing data from normal and tumor tissue samples uncovers motifs that can explain changes in cleavage and polyadenylation in specific cancers. In particular, our analysis points to polypyrimidine tract binding protein 1 as a regulator of poly(A) site choice in glioblastoma.
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Szkop KJ, Nobeli I. Untranslated Parts of Genes Interpreted: Making Heads or Tails of High-Throughput Transcriptomic Data via Computational Methods: Computational methods to discover and quantify isoforms with alternative untranslated regions. Bioessays 2017; 39. [PMID: 29052251 DOI: 10.1002/bies.201700090] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 09/12/2017] [Indexed: 01/07/2023]
Abstract
In this review we highlight the importance of defining the untranslated parts of transcripts, and present a number of computational approaches for the discovery and quantification of alternative transcription start and poly-adenylation events in high-throughput transcriptomic data. The fate of eukaryotic transcripts is closely linked to their untranslated regions, which are determined by the position at which transcription starts and ends at a genomic locus. Although the extent of alternative transcription starts and alternative poly-adenylation sites has been revealed by sequencing methods focused on the ends of transcripts, the application of these methods is not yet widely adopted by the community. We suggest that computational methods applied to standard high-throughput technologies are a useful, albeit less accurate, alternative to the expertise-demanding 5' and 3' sequencing and they are the only option for analysing legacy transcriptomic data. We review these methods here, focusing on technical challenges and arguing for the need to include better normalization of the data and more appropriate statistical models of the expected variation in the signal.
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Affiliation(s)
- Krzysztof J Szkop
- Institute of Structural and Molecular Biology, Department of Biological Sciences Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Irene Nobeli
- Institute of Structural and Molecular Biology, Department of Biological Sciences Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
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