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Wang Y, Zhai Y, Zhang M, Song C, Zhang Y, Zhang G. Escaping from CRISPR-Cas-mediated knockout: the facts, mechanisms, and applications. Cell Mol Biol Lett 2024; 29:48. [PMID: 38589794 PMCID: PMC11003099 DOI: 10.1186/s11658-024-00565-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 03/21/2024] [Indexed: 04/10/2024] Open
Abstract
Clustered regularly interspaced short palindromic repeats and associated Cas protein (CRISPR-Cas), a powerful genome editing tool, has revolutionized gene function investigation and exhibits huge potential for clinical applications. CRISPR-Cas-mediated gene knockout has already become a routine method in research laboratories. However, in the last few years, accumulating evidences have demonstrated that genes knocked out by CRISPR-Cas may not be truly silenced. Functional residual proteins could be generated in such knockout organisms to compensate the putative loss of function, termed herein knockout escaping. In line with this, several CRISPR-Cas-mediated knockout screenings have discovered much less abnormal phenotypes than expected. How does knockout escaping happen and how often does it happen have not been systematically reviewed yet. Without knowing this, knockout results could easily be misinterpreted. In this review, we summarize these evidences and propose two main mechanisms allowing knockout escaping. To avoid the confusion caused by knockout escaping, several strategies are discussed as well as their advantages and disadvantages. On the other hand, knockout escaping also provides convenient tools for studying essential genes and treating monogenic disorders such as Duchenne muscular dystrophy, which are discussed in the end.
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Affiliation(s)
- Ying Wang
- The Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
- School of Public Health, Qingdao University, Qingdao, China
| | - Yujing Zhai
- The Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
- School of Public Health, Qingdao University, Qingdao, China
| | - Mingzhe Zhang
- The Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Chunlin Song
- The Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Yuqing Zhang
- The Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Gang Zhang
- The Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.
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2
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Da Cunha D, Miro J, Van Goethem C, Notarnicola C, Hugon G, Carnac G, Cossée M, Koenig M, Tuffery-Giraud S. The exon junction complex is required for DMD gene splicing fidelity and myogenic differentiation. Cell Mol Life Sci 2024; 81:150. [PMID: 38512499 PMCID: PMC10957711 DOI: 10.1007/s00018-024-05188-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 02/14/2024] [Accepted: 02/28/2024] [Indexed: 03/23/2024]
Abstract
Deposition of the exon junction complex (EJC) upstream of exon-exon junctions helps maintain transcriptome integrity by preventing spurious re-splicing events in already spliced mRNAs. Here we investigate the importance of EJC for the correct splicing of the 2.2-megabase-long human DMD pre-mRNA, which encodes dystrophin, an essential protein involved in cytoskeletal organization and cell signaling. Using targeted RNA-seq, we show that knock-down of the eIF4A3 and Y14 core components of EJC in a human muscle cell line causes an accumulation of mis-splicing events clustered towards the 3' end of the DMD transcript (Dp427m). This deregulation is conserved in the short Dp71 isoform expressed ubiquitously except in adult skeletal muscle and is rescued with wild-type eIF4A3 and Y14 proteins but not with an EJC assembly-defective mutant eIF4A3. MLN51 protein and EJC-associated ASAP/PSAP complexes independently modulate the inclusion of the regulated exons 71 and 78. Our data confirm the protective role of EJC in maintaining splicing fidelity, which in the DMD gene is necessary to preserve the function of the critical C-terminal protein-protein interaction domain of dystrophin present in all tissue-specific isoforms. Given the role of the EJC in maintaining the integrity of dystrophin, we asked whether the EJC could also be involved in the regulation of a mechanism as complex as skeletal muscle differentiation. We found that eIF4A3 knockdown impairs myogenic differentiation by blocking myotube formation. Collectively, our data provide new insights into the functional roles of EJC in human skeletal muscle.
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Affiliation(s)
- Dylan Da Cunha
- PhyMedExp, Univ Montpellier, CNRS, INSERM, Montpellier, France
| | - Julie Miro
- PhyMedExp, Univ Montpellier, CNRS, INSERM, Montpellier, France
| | - Charles Van Goethem
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France
- Montpellier BioInformatique Pour Le Diagnostic Clinique (MOBIDIC), Plateau de Médecine Moléculaire Et Génomique (PMMG), CHU Montpellier, 34295, Montpellier, France
| | | | - Gérald Hugon
- PhyMedExp, Univ Montpellier, CNRS, INSERM, Montpellier, France
| | - Gilles Carnac
- PhyMedExp, Univ Montpellier, CNRS, INSERM, Montpellier, France
| | - Mireille Cossée
- PhyMedExp, Univ Montpellier, CNRS, INSERM, Montpellier, France
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France
| | - Michel Koenig
- PhyMedExp, Univ Montpellier, CNRS, INSERM, Montpellier, France
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France
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3
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Ebersberger S, Hipp C, Mulorz MM, Buchbender A, Hubrich D, Kang HS, Martínez-Lumbreras S, Kristofori P, Sutandy FXR, Llacsahuanga Allcca L, Schönfeld J, Bakisoglu C, Busch A, Hänel H, Tretow K, Welzel M, Di Liddo A, Möckel MM, Zarnack K, Ebersberger I, Legewie S, Luck K, Sattler M, König J. FUBP1 is a general splicing factor facilitating 3' splice site recognition and splicing of long introns. Mol Cell 2023:S1097-2765(23)00516-6. [PMID: 37506698 DOI: 10.1016/j.molcel.2023.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 05/19/2023] [Accepted: 07/03/2023] [Indexed: 07/30/2023]
Abstract
Splicing of pre-mRNAs critically contributes to gene regulation and proteome expansion in eukaryotes, but our understanding of the recognition and pairing of splice sites during spliceosome assembly lacks detail. Here, we identify the multidomain RNA-binding protein FUBP1 as a key splicing factor that binds to a hitherto unknown cis-regulatory motif. By collecting NMR, structural, and in vivo interaction data, we demonstrate that FUBP1 stabilizes U2AF2 and SF1, key components at the 3' splice site, through multivalent binding interfaces located within its disordered regions. Transcriptional profiling and kinetic modeling reveal that FUBP1 is required for efficient splicing of long introns, which is impaired in cancer patients harboring FUBP1 mutations. Notably, FUBP1 interacts with numerous U1 snRNP-associated proteins, suggesting a unique role for FUBP1 in splice site bridging for long introns. We propose a compelling model for 3' splice site recognition of long introns, which represent 80% of all human introns.
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Affiliation(s)
| | - Clara Hipp
- Institute of Structural Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany; Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, 85747 Garching, Germany
| | - Miriam M Mulorz
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | | | - Dalmira Hubrich
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Hyun-Seo Kang
- Institute of Structural Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany; Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, 85747 Garching, Germany
| | - Santiago Martínez-Lumbreras
- Institute of Structural Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany; Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, 85747 Garching, Germany
| | - Panajot Kristofori
- Department of Systems Biology, Institute for Biomedical Genetics (IBMG), University of Stuttgart, 70569 Stuttgart, Germany
| | | | | | - Jonas Schönfeld
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Cem Bakisoglu
- Buchmann Institute for Molecular Life Sciences & Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Anke Busch
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Heike Hänel
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Kerstin Tretow
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Mareen Welzel
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | | | - Martin M Möckel
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences & Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany; CardioPulmonary Institute (CPI), 35392 Gießen, Germany
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany; Senckenberg Biodiversity and Climate Research Center (S-BIK-F), 60325 Frankfurt am Main, Germany; LOEWE Center for Translational Biodiversity Genomics (TBG), 60325 Frankfurt am Main, Germany
| | - Stefan Legewie
- Department of Systems Biology, Institute for Biomedical Genetics (IBMG), University of Stuttgart, 70569 Stuttgart, Germany; Stuttgart Research Center for Systems Biology (SRCSB), University of Stuttgart, 70569 Stuttgart, Germany
| | - Katja Luck
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany.
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany; Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, 85747 Garching, Germany.
| | - Julian König
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany.
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4
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Ruan X, Hu K, Zhang X. PIE-seq: identifying RNA-binding protein targets by dual RNA-deaminase editing and sequencing. Nat Commun 2023; 14:3275. [PMID: 37280234 DOI: 10.1038/s41467-023-39054-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 05/26/2023] [Indexed: 06/08/2023] Open
Abstract
RNA-binding proteins (RBPs) are essential for gene regulation, but it remains a challenge to identify their RNA targets across cell types. Here we present PIE-Seq to investigate Protein-RNA Interaction with dual-deaminase Editing and Sequencing by conjugating C-to-U and A-to-I base editors to RBPs. We benchmark PIE-Seq and demonstrate its sensitivity in single cells, its application in the developing brain, and its scalability with 25 human RBPs. Bulk PIE-Seq identifies canonical binding features for RBPs such as PUM2 and NOVA1, and nominates additional target genes for most tested RBPs such as SRSF1 and TDP-43/TARDBP. Homologous RBPs frequently edit similar sequences and gene sets in PIE-Seq while different RBP families show distinct targets. Single-cell PIE-PUM2 uncovers comparable targets to bulk samples and applying PIE-PUM2 to the developing mouse neocortex identifies neural-progenitor- and neuron-specific target genes such as App. In summary, PIE-Seq provides an orthogonal approach and resource to uncover RBP targets in mice and human cells.
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Affiliation(s)
- Xiangbin Ruan
- Department of Human Genetics and The Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - Kaining Hu
- Department of Human Genetics and The Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - Xiaochang Zhang
- Department of Human Genetics and The Neuroscience Institute, University of Chicago, Chicago, IL, USA.
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5
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Zaytseva O, Mitchell NC, Muckle D, Delandre C, Nie Z, Werner JK, Lis JT, Eyras E, Hannan RD, Levens DL, Marshall OJ, Quinn LM. Psi promotes Drosophila wing growth via direct transcriptional activation of cell cycle targets and repression of growth inhibitors. Development 2023; 150:286725. [PMID: 36692218 PMCID: PMC10110491 DOI: 10.1242/dev.201563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 01/03/2023] [Indexed: 01/25/2023]
Abstract
The first characterised FUSE Binding Protein family member, FUBP1, binds single-stranded DNA to activate MYC transcription. Psi, the sole FUBP protein in Drosophila, binds RNA to regulate P-element and mRNA splicing. Our previous work revealed pro-growth functions for Psi, which depend, in part, on transcriptional activation of Myc. Genome-wide functions for FUBP family proteins in transcriptional control remain obscure. Here, through the first genome-wide binding and expression profiles obtained for a FUBP family protein, we demonstrate that, in addition to being required to activate Myc to promote cell growth, Psi also directly binds and activates stg to couple growth and cell division. Thus, Psi knockdown results in reduced cell division in the wing imaginal disc. In addition to activating these pro-proliferative targets, Psi directly represses transcription of the growth inhibitor tolkin (tok, a metallopeptidase implicated in TGFβ signalling). We further demonstrate tok overexpression inhibits proliferation, while tok loss of function increases mitosis alone and suppresses impaired cell division caused by Psi knockdown. Thus, Psi orchestrates growth through concurrent transcriptional activation of the pro-proliferative genes Myc and stg, in combination with repression of the growth inhibitor tok.
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Affiliation(s)
- Olga Zaytseva
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia
| | - Naomi C Mitchell
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia
| | - Damien Muckle
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia
| | - Caroline Delandre
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania 7000, Australia
| | - Zuqin Nie
- National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | | | - John T Lis
- Cornell University, Ithaca, NY 14850, USA
| | - Eduardo Eyras
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia
| | - Ross D Hannan
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia
| | | | - Owen J Marshall
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania 7000, Australia
| | - Leonie M Quinn
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia
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6
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RNA-Targeting Splicing Modifiers: Drug Development and Screening Assays. Molecules 2021; 26:molecules26082263. [PMID: 33919699 PMCID: PMC8070285 DOI: 10.3390/molecules26082263] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/05/2021] [Accepted: 04/09/2021] [Indexed: 02/06/2023] Open
Abstract
RNA splicing is an essential step in producing mature messenger RNA (mRNA) and other RNA species. Harnessing RNA splicing modifiers as a new pharmacological modality is promising for the treatment of diseases caused by aberrant splicing. This drug modality can be used for infectious diseases by disrupting the splicing of essential pathogenic genes. Several antisense oligonucleotide splicing modifiers were approved by the U.S. Food and Drug Administration (FDA) for the treatment of spinal muscular atrophy (SMA) and Duchenne muscular dystrophy (DMD). Recently, a small-molecule splicing modifier, risdiplam, was also approved for the treatment of SMA, highlighting small molecules as important warheads in the arsenal for regulating RNA splicing. The cellular targets of these approved drugs are all mRNA precursors (pre-mRNAs) in human cells. The development of novel RNA-targeting splicing modifiers can not only expand the scope of drug targets to include many previously considered “undruggable” genes but also enrich the chemical-genetic toolbox for basic biomedical research. In this review, we summarized known splicing modifiers, screening methods for novel splicing modifiers, and the chemical space occupied by the small-molecule splicing modifiers.
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7
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Dai W, Qu H, Zhang J, Thongkum A, Dinh TN, Kappeler KV, Chen QM. Far Upstream Binding Protein 1 (FUBP1) participates in translational regulation of Nrf2 protein under oxidative stress. Redox Biol 2021; 41:101906. [PMID: 33676361 PMCID: PMC7937566 DOI: 10.1016/j.redox.2021.101906] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/10/2021] [Accepted: 02/16/2021] [Indexed: 01/04/2023] Open
Abstract
Oxidative stress is ubiquitously involved in disease etiology or progression. While the damaging effects have been well characterized, how cells deal with oxidative stress for prevention or removal of damage remains to be fully elucidated. Works from our laboratory have revealed de novo Nrf2 protein translation when cells are encountering low to mild levels of oxidative stress. Nrf2 encodes a transcription factor controlling a myriad of genes important for antioxidation, detoxification, wound repair and tissue remodeling. Here we report a role of FUBP1 in regulating de novo Nrf2 protein translation. An increase of FUBP1 binding to Nrf2 5′UTR due to H2O2 treatment has been found by LC-MS/MS, Far Western blot and ribonucleoprotein immunoprecipitation assays. Blocking FUBP1 expression using siRNA abolished H2O2 from inducing Nrf2 protein elevation or Nrf2 5′UTR activity. While no nuclear to cytoplasmic translocation was detected, cytosolic redistribution to the ribosomal fractions was observed due to oxidant treatment. The presence of FUBP1 in 40/43S ribosomal fractions confirm its involvement in translation initiation of Nrf2 protein. When tested by co-immunoprecipitation with eIF4E, eIF2a, eIF3η and eIF1, only eIF3η was found to gain physical interaction with FUBP1 due to H2O2 treatment. Our data support a role of FUBP1 for promoting the attachment of 40S ribosomal subunit to Nrf2 mRNA and formation of 43S pre-initiation complex for translation initiation of Nrf2 protein under oxidative stress.
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Affiliation(s)
- Wujing Dai
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, 85724, USA; Department of Pharmacy Practice and Science, College of Pharmacy, University of Arizona, Tucson, AZ, 85721, USA
| | - Han Qu
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, 85724, USA; Department of Pharmacy Practice and Science, College of Pharmacy, University of Arizona, Tucson, AZ, 85721, USA
| | - Jack Zhang
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, 85724, USA
| | - Angkana Thongkum
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, 85724, USA
| | - Thai Nho Dinh
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, 85724, USA
| | - Kyle V Kappeler
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, 85724, USA
| | - Qin M Chen
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, 85724, USA; Department of Pharmacy Practice and Science, College of Pharmacy, University of Arizona, Tucson, AZ, 85721, USA.
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8
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First Identification of RNA-Binding Proteins That Regulate Alternative Exons in the Dystrophin Gene. Int J Mol Sci 2020; 21:ijms21207803. [PMID: 33096920 PMCID: PMC7589424 DOI: 10.3390/ijms21207803] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/16/2020] [Accepted: 10/19/2020] [Indexed: 12/29/2022] Open
Abstract
The Duchenne muscular dystrophy (DMD) gene has a complex expression pattern regulated by multiple tissue-specific promoters and by alternative splicing (AS) of the resulting transcripts. Here, we used an RNAi-based approach coupled with DMD-targeted RNA-seq to identify RNA-binding proteins (RBPs) that regulate splicing of its skeletal muscle isoform (Dp427m) in a human muscular cell line. A total of 16 RBPs comprising the major regulators of muscle-specific splicing events were tested. We show that distinct combinations of RBPs maintain the correct inclusion in the Dp427m of exons that undergo spatio-temporal AS in other dystrophin isoforms. In particular, our findings revealed the complex networks of RBPs contributing to the splicing of the two short DMD exons 71 and 78, the inclusion of exon 78 in the adult Dp427m isoform being crucial for muscle function. Among the RBPs tested, QKI and DDX5/DDX17 proteins are important determinants of DMD exon inclusion. This is the first large-scale study to determine which RBP proteins act on the physiological splicing of the DMD gene. Our data shed light on molecular mechanisms contributing to the expression of the different dystrophin isoforms, which could be influenced by a change in the function or expression level of the identified RBPs.
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9
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RNA Binding Motif Protein RBM45 Regulates Expression of the 11-Kilodalton Protein of Parvovirus B19 through Binding to Novel Intron Splicing Enhancers. mBio 2020; 11:mBio.00192-20. [PMID: 32156816 PMCID: PMC7064759 DOI: 10.1128/mbio.00192-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Human parvovirus B19 (B19V) is a human pathogen that causes severe hematological disorders in immunocompromised individuals. B19V infection has a remarkable tropism with respect to human erythroid progenitor cells (EPCs) in human bone marrow and fetal liver. During B19V infection, only one viral precursor mRNA (pre-mRNA) is transcribed by a single promoter of the viral genome and is alternatively spliced and alternatively polyadenylated, a process which plays a key role in expression of viral proteins. Our studies revealed that a cellular RNA binding protein, RBM45, binds to two intron splicing enhancers and is essential for the maturation of the small nonstructural protein 11-kDa-encoding mRNA. The 11-kDa protein plays an important role not only in B19V infection-induced apoptosis but also in viral DNA replication. Thus, the identification of the RBM45 protein and its cognate binding site in B19V pre-mRNA provides a novel target for antiviral development to combat B19V infection-caused severe hematological disorders. During infection of human parvovirus B19 (B19V), one viral precursor mRNA (pre-mRNA) is transcribed by a single promoter and is alternatively spliced and alternatively polyadenylated. Here, we identified a novel cis-acting sequence (5′-GUA AAG CUA CGG GAC GGU-3′), intronic splicing enhancer 3 (ISE3), which lies 72 nucleotides upstream of the second splice acceptor (A2-2) site of the second intron that defines the exon of the mRNA encoding the 11-kDa viral nonstructural protein. RNA binding motif protein 45 (RBM45) specifically binds to ISE3 with high affinity (equilibrium dissociation constant [KD] = 33 nM) mediated by its RNA recognition domain and 2-homo-oligomer assembly domain (RRM2-HOA). Knockdown of RBM45 expression or ectopic overexpression of RRM2-HOA in human erythroid progenitor cells (EPCs) expanded ex vivo significantly decreased the level of viral mRNA spliced at the A2-2 acceptor but not that of the mRNA spliced at A2-1 that encodes VP2. Moreover, silent mutations of ISE3 in an infectious DNA of B19V significantly reduced 11-kDa expression. Notably, RBM45 also specifically interacts in vitro with ISE2, which shares the octanucleotide (GGGACGGU) with ISE3. Taken together, our results suggest that RBM45, through binding to both ISE2 and ISE3, is an essential host factor for maturation of 11-kDa-encoding mRNA.
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10
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Elman JS, Ni TK, Mengwasser KE, Jin D, Wronski A, Elledge SJ, Kuperwasser C. Identification of FUBP1 as a Long Tail Cancer Driver and Widespread Regulator of Tumor Suppressor and Oncogene Alternative Splicing. Cell Rep 2019; 28:3435-3449.e5. [PMID: 31553912 PMCID: PMC7297508 DOI: 10.1016/j.celrep.2019.08.060] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 06/10/2019] [Accepted: 08/20/2019] [Indexed: 12/13/2022] Open
Abstract
Comprehensive sequencing approaches have allowed for the identification of the most frequent contributors to cancer, known as drivers. They have also revealed a class of mutations in understudied, infrequently altered genes, referred to as "long tail" (LT) drivers. A key challenge has been to find clinically relevant LT drivers and to understand how they cooperate to drive disease. Here, we identified far upstream binding protein 1 (FUBP1) as an LT driver using an in vivo CRISPR screen. FUBP1 cooperates with other tumor suppressor genes to transform mammary epithelial cells by disrupting cellular differentiation and tissue architecture. Mechanistically, FUBP1 participates in regulating N6-methyladenosine (m6A) RNA methylation, and its loss leads to global changes in RNA splicing and widespread expression of aberrant driver isoforms. These findings suggest that somatic alteration of a single gene involved in RNA splicing and m6A methylation can produce the necessary panoply of contributors for neoplastic transformation.
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Affiliation(s)
- Jessica S Elman
- Department of Developmental, Chemical and Molecular Biology, Tufts University School of Medicine, 136 Harrison Ave, Boston, MA 02111, USA; Raymond & Beverly Sackler Convergence Laboratory, Tufts University School of Medicine, 136 Harrison Ave, Boston, MA 02111, USA
| | - Thomas K Ni
- Department of Developmental, Chemical and Molecular Biology, Tufts University School of Medicine, 136 Harrison Ave, Boston, MA 02111, USA; Raymond & Beverly Sackler Convergence Laboratory, Tufts University School of Medicine, 136 Harrison Ave, Boston, MA 02111, USA
| | - Kristen E Mengwasser
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Dexter Jin
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ania Wronski
- Department of Developmental, Chemical and Molecular Biology, Tufts University School of Medicine, 136 Harrison Ave, Boston, MA 02111, USA; Raymond & Beverly Sackler Convergence Laboratory, Tufts University School of Medicine, 136 Harrison Ave, Boston, MA 02111, USA
| | - Stephen J Elledge
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Ludwig Center at Harvard, Boston, MA, USA; Department of Genetics, Program in Virology, Harvard Medical School, Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Charlotte Kuperwasser
- Department of Developmental, Chemical and Molecular Biology, Tufts University School of Medicine, 136 Harrison Ave, Boston, MA 02111, USA; Raymond & Beverly Sackler Convergence Laboratory, Tufts University School of Medicine, 136 Harrison Ave, Boston, MA 02111, USA.
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11
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Zhu Y, Deng H, Chen X, Li H, Yang C, Li S, Pan X, Tian S, Feng S, Tan X, Matsuo M, Zhang Z. Skipping of an exon with a nonsense mutation in the DMD gene is induced by the conversion of a splicing enhancer to a splicing silencer. Hum Genet 2019; 138:771-785. [DOI: 10.1007/s00439-019-02036-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 05/29/2019] [Indexed: 01/23/2023]
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12
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Kang M, Lee SM, Kim W, Lee KH, Kim DY. Fubp1 supports the lactate-Akt-mTOR axis through the upregulation of Hk1 and Hk2. Biochem Biophys Res Commun 2019; 512:93-99. [PMID: 30871777 DOI: 10.1016/j.bbrc.2019.03.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 12/21/2022]
Abstract
Cells require energy for homeostatic activities, growth and division. By utilizing glucose as the main energy source, cells generate ATP and metabolic precursors through glycolysis and citric acid cycle. Although the oxidative phosphorylation can produce more ATP molecules from one molecule of glucose than glycolysis, rapidly growing cells primarily metabolize glucose via aerobic glycolysis. This aerobic glycolysis makes cells to uptake glucose at a higher rate and to efficiently convert glucose into the macromolecules required for new daughter cells. Recent evidence suggests that Fubp1 promotes cell proliferation and survival, and it is overexpressed in a variety of cancers. However, the role of Fubp1 in cellular metabolism remains unclear. In the present study, we demonstrated that Fubp1 upregulates the mRNA levels of two hexokinase genes, Hk1 and Hk2. We also found the positive correlation in mRNA expression between Fubp1 and both of hexokinase genes in several types of cancers. We suggest that Fubp1 contributes to cell survival through supporting lactate-Akt-mTOR axis.
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Affiliation(s)
- Mingyu Kang
- Department of Pharmacology, School of Dentistry, Kyungpook National University, Daegu, 41940, Republic of Korea
| | - Sang Min Lee
- Department of Pharmacology, School of Dentistry, Kyungpook National University, Daegu, 41940, Republic of Korea
| | - Wanil Kim
- Department of Cosmetic Science and Technology, College of Bio-industry, Daegu Haany University, Gyeongsan, 38610, Republic of Korea
| | - Kyung-Ha Lee
- Department of Cosmetic Science and Technology, College of Bio-industry, Daegu Haany University, Gyeongsan, 38610, Republic of Korea
| | - Do-Yeon Kim
- Department of Pharmacology, School of Dentistry, Kyungpook National University, Daegu, 41940, Republic of Korea; Brain Science and Engineering Institute, Kyungpook National University, Daegu, 41940, Republic of Korea.
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13
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Debaize L, Troadec MB. The master regulator FUBP1: its emerging role in normal cell function and malignant development. Cell Mol Life Sci 2019; 76:259-281. [PMID: 30343319 PMCID: PMC11105487 DOI: 10.1007/s00018-018-2933-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 09/06/2018] [Accepted: 10/01/2018] [Indexed: 12/20/2022]
Abstract
The human Far Upstream Element (FUSE) Binding Protein 1 (FUBP1) is a multifunctional DNA- and RNA-binding protein involved in diverse cellular processes. FUBP1 is a master regulator of transcription, translation, and RNA splicing. FUBP1 has been identified as a potent pro-proliferative and anti-apoptotic factor by modulation of complex networks. FUBP1 is also described either as an oncoprotein or a tumor suppressor. Especially, FUBP1 overexpression is observed in a growing number of cancer and leads to a deregulation of targets that includes the fine-tuned MYC oncogene. Moreover, recent loss-of-function analyses of FUBP1 establish its essential functions in hematopoietic stem cell maintenance and survival. Therefore, FUBP1 appears as an emerging suspect in hematologic disorders in addition to solid tumors. The scope of the present review is to describe the advances in our understanding of the molecular basis of FUBP1 functions in normal cells and carcinogenesis. We also delineate the recent progresses in the understanding of the master role of FUBP1 in normal and pathological hematopoiesis. We conclude that FUBP1 is not only worth studying biologically but is also of clinical relevance through its pivotal role in regulating multiple cellular processes and its involvement in oncogenesis.
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Affiliation(s)
- Lydie Debaize
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)-UMR 6290, F-35000, Rennes, France
| | - Marie-Bérengère Troadec
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)-UMR 6290, F-35000, Rennes, France.
- Univ Brest, INSERM, EFS, UMR 1078, GGB, F-29200, Brest, France.
- CHRU de Brest, laboratoire de cytogénétique, F-29200, Brest, France.
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14
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Debaize L, Jakobczyk H, Avner S, Gaudichon J, Rio AG, Sérandour AA, Dorsheimer L, Chalmel F, Carroll JS, Zörnig M, Rieger MA, Delalande O, Salbert G, Galibert MD, Gandemer V, Troadec MB. Interplay between transcription regulators RUNX1 and FUBP1 activates an enhancer of the oncogene c-KIT and amplifies cell proliferation. Nucleic Acids Res 2018; 46:11214-11228. [PMID: 30500954 PMCID: PMC6265458 DOI: 10.1093/nar/gky756] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 08/07/2018] [Accepted: 08/10/2018] [Indexed: 12/31/2022] Open
Abstract
Runt-related transcription factor 1 (RUNX1) is a well-known master regulator of hematopoietic lineages but its mechanisms of action are still not fully understood. Here, we found that RUNX1 localizes on active chromatin together with Far Upstream Binding Protein 1 (FUBP1) in human B-cell precursor lymphoblasts, and that both factors interact in the same transcriptional regulatory complex. RUNX1 and FUBP1 chromatin localization identified c-KIT as a common target gene. We characterized two regulatory regions, at +700 bp and +30 kb within the first intron of c-KIT, bound by both RUNX1 and FUBP1, and that present active histone marks. Based on these regions, we proposed a novel FUBP1 FUSE-like DNA-binding sequence on the +30 kb enhancer. We demonstrated that FUBP1 and RUNX1 cooperate for the regulation of the expression of the oncogene c-KIT. Notably, upregulation of c-KIT expression by FUBP1 and RUNX1 promotes cell proliferation and renders cells more resistant to the c-KIT inhibitor imatinib mesylate, a common therapeutic drug. These results reveal a new mechanism of action of RUNX1 that implicates FUBP1, as a facilitator, to trigger transcriptional regulation of c-KIT and to regulate cell proliferation. Deregulation of this regulatory mechanism may explain some oncogenic function of RUNX1 and FUBP1.
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Affiliation(s)
- Lydie Debaize
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) – UMR 6290, F-35000 Rennes, France
| | - Hélène Jakobczyk
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) – UMR 6290, F-35000 Rennes, France
| | - Stéphane Avner
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) – UMR 6290, F-35000 Rennes, France
| | - Jérémie Gaudichon
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) – UMR 6290, F-35000 Rennes, France
| | - Anne-Gaëlle Rio
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) – UMR 6290, F-35000 Rennes, France
| | - Aurélien A Sérandour
- CRCINA, INSERM, CNRS, Université d’Angers, Université de Nantes, 44035 Nantes, France
- Ecole Centrale de Nantes, Nantes, France
| | - Lena Dorsheimer
- Department of Medicine, Hematology/Oncology, Goethe University Frankfurt, Frankfurt, Germany
| | - Frédéric Chalmel
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) – UMR_S 1085, F-35000 Rennes, France
| | - Jason S Carroll
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Martin Zörnig
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, D-60528 Frankfurt, Germany
| | - Michael A Rieger
- Department of Medicine, Hematology/Oncology, Goethe University Frankfurt, Frankfurt, Germany
| | - Olivier Delalande
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) – UMR 6290, F-35000 Rennes, France
| | - Gilles Salbert
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) – UMR 6290, F-35000 Rennes, France
| | - Marie-Dominique Galibert
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) – UMR 6290, F-35000 Rennes, France
- Génétique Somatique des Cancers, Centre Hospitalier Universitaire, 35033 Rennes, France
| | - Virginie Gandemer
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) – UMR 6290, F-35000 Rennes, France
- Department of pediatric oncohematology, Centre Hospitalier Universitaire, 35203 Rennes, France
| | - Marie-Bérengère Troadec
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) – UMR 6290, F-35000 Rennes, France
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15
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The Isoquinoline Alkaloid Dauricine Targets Multiple Molecular Pathways to Ameliorate Alzheimer-Like Pathological Changes In Vitro. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:2025914. [PMID: 30057671 PMCID: PMC6051032 DOI: 10.1155/2018/2025914] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 03/02/2018] [Accepted: 04/22/2018] [Indexed: 12/22/2022]
Abstract
Alzheimer's disease (AD), the most common neurodegenerative disease, has no effective treatment. Dauricine (DAU), a benzyl tetrahydroisoquinoline alkaloid isolated from the root of Menispermum dauricum DC, reportedly has neuroprotective effects in cerebral ischemia. Here, we investigated the effects of DAU on N2a cells stably transfected with Swedish mutant amyloid precursor protein (N2a/APP), an AD-like cell model. ELISA and Western blot analysis revealed that DAU inhibited APP processing and reduced Aβ accumulation. In addition, DAU ameliorated tau hyperphosphorylation via PP2A, p35/25, and CDK5 pathways in N2a/APP cells. The amelioration of tau hyperphosphorylation by DAU was also validated in HEK293/Tau cells, another cell line with tau hyperphosphorylation. Proteomic analysis revealed 85 differentially expressed proteins in the lysates between the wild-type N2a cells (N2a/WT) and the N2a/APP cells in the presence or absence of DAU; these were classified into 6 main categories according to their functions: endoplasmic reticulum (ER) stress-associated proteins, oxidative stress-associated proteins, cytoskeleton proteins, molecular chaperones, mitochondrial respiration and metabolism-related proteins, and signaling proteins. Taken together, we demonstrated that DAU treatment reduces AD-like pathology, thereby suggesting that DAU has potential therapeutic utility in AD.
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16
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Miro J, Bourgeois CF, Claustres M, Koenig M, Tuffery-Giraud S. Identification of Splicing Factors Involved in DMD Exon Skipping Events Using an In Vitro RNA Binding Assay. Methods Mol Biol 2018; 1687:157-169. [PMID: 29067662 DOI: 10.1007/978-1-4939-7374-3_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Mutation-induced exon skipping in the DMD gene can modulate the severity of the phenotype in patients with Duchenne or Becker Muscular Dystrophy. These alternative splicing events are most likely the result of changes in recruitment of splicing factors at cis-acting elements in the mutated DMD pre-mRNA. The identification of proteins involved can be achieved by an affinity purification procedure. Here, we provide a detailed protocol for the in vitro RNA binding assay that we routinely apply to explore molecular mechanisms underlying splicing defects in the DMD gene. In vitro transcribed RNA probes containing either the wild type or mutated sequence are oxidized and bound to adipic acid dihydrazide-agarose beads. Incubation with a nuclear extract allows the binding of nuclear proteins to the RNA probes. The unbound proteins are washed off and then the specifically RNA-bound proteins are released from the beads by an RNase treatment. After separation by SDS-PAGE, proteins that display differential binding affinities for the wild type and mutant RNA probes are identified by mass spectrometry.
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Affiliation(s)
- Julie Miro
- Laboratoire de Génétique de Maladies Rares (LGMR), EA7402, Université de Montpellier, Montpellier, 34000, France
| | - Cyril F Bourgeois
- INSERM U1210, CNRS UMR 5239, Laboratory of Biology and Modelling of the Cell, Ecole Normale Supérieure de Lyon, Université de Lyon, 69007, Lyon, France
| | - Mireille Claustres
- Laboratoire de Génétique de Maladies Rares (LGMR), EA7402, Université de Montpellier, Montpellier, 34000, France.,Laboratoire de Génétique Moléculaire, CHU Montpellier, Hôpital Arnaud de Villeneuve, Montpellier, 34000, France
| | - Michel Koenig
- Laboratoire de Génétique de Maladies Rares (LGMR), EA7402, Université de Montpellier, Montpellier, 34000, France.,Laboratoire de Génétique Moléculaire, CHU Montpellier, Hôpital Arnaud de Villeneuve, Montpellier, 34000, France
| | - Sylvie Tuffery-Giraud
- Laboratoire de Génétique de Maladies Rares (LGMR), EA7402, Université de Montpellier, Montpellier, 34000, France.
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17
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Wang J, Schultz PG, Johnson KA. Mechanistic studies of a small-molecule modulator of SMN2 splicing. Proc Natl Acad Sci U S A 2018; 115:E4604-E4612. [PMID: 29712837 PMCID: PMC5960314 DOI: 10.1073/pnas.1800260115] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
RG-7916 is a first-in-class drug candidate for the treatment of spinal muscular atrophy (SMA) that functions by modulating pre-mRNA splicing of the SMN2 gene, resulting in a 2.5-fold increase in survival of motor neuron (SMN) protein level, a key protein lacking in SMA patients. RG-7916 is currently in three interventional phase 2 clinical trials for various types of SMA. In this report, we show that SMN-C2 and -C3, close analogs of RG-7916, act as selective RNA-binding ligands that modulate pre-mRNA splicing. Chemical proteomic and genomic techniques reveal that SMN-C2 directly binds to the AGGAAG motif on exon 7 of the SMN2 pre-mRNA, and promotes a conformational change in two to three unpaired nucleotides at the junction of intron 6 and exon 7 in both in vitro and in-cell models. This change creates a new functional binding surface that increases binding of the splicing modulators, far upstream element binding protein 1 (FUBP1) and its homolog, KH-type splicing regulatory protein (KHSRP), to the SMN-C2/C3-SMN2 pre-mRNA complex and enhances SMN2 splicing. These findings underscore the potential of small-molecule drugs to selectively bind RNA and modulate pre-mRNA splicing as an approach to the treatment of human disease.
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Affiliation(s)
- Jingxin Wang
- California Institute for Biomedical Research, La Jolla, CA 92037
| | - Peter G Schultz
- California Institute for Biomedical Research, La Jolla, CA 92037;
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037
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18
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Sutandy FXR, Ebersberger S, Huang L, Busch A, Bach M, Kang HS, Fallmann J, Maticzka D, Backofen R, Stadler PF, Zarnack K, Sattler M, Legewie S, König J. In vitro iCLIP-based modeling uncovers how the splicing factor U2AF2 relies on regulation by cofactors. Genome Res 2018; 28:699-713. [PMID: 29643205 PMCID: PMC5932610 DOI: 10.1101/gr.229757.117] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 02/09/2018] [Indexed: 01/26/2023]
Abstract
Alternative splicing generates distinct mRNA isoforms and is crucial for proteome diversity in eukaryotes. The RNA-binding protein (RBP) U2AF2 is central to splicing decisions, as it recognizes 3′ splice sites and recruits the spliceosome. We establish “in vitro iCLIP” experiments, in which recombinant RBPs are incubated with long transcripts, to study how U2AF2 recognizes RNA sequences and how this is modulated by trans-acting RBPs. We measure U2AF2 affinities at hundreds of binding sites and compare in vitro and in vivo binding landscapes by mathematical modeling. We find that trans-acting RBPs extensively regulate U2AF2 binding in vivo, including enhanced recruitment to 3′ splice sites and clearance of introns. Using machine learning, we identify and experimentally validate novel trans-acting RBPs (including FUBP1, CELF6, and PCBP1) that modulate U2AF2 binding and affect splicing outcomes. Our study offers a blueprint for the high-throughput characterization of in vitro mRNP assembly and in vivo splicing regulation.
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Affiliation(s)
| | | | - Lu Huang
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Anke Busch
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Maximilian Bach
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Hyun-Seo Kang
- Institute of Structural Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany.,Biomolecular NMR and Center for Integrated Protein Science Munich at Department of Chemistry, Technical University of Munich, 85747 Garching, Germany
| | - Jörg Fallmann
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107 Leipzig, Germany
| | - Daniel Maticzka
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany.,Centre for Biological Signalling Studies (BIOSS), University of Freiburg, 79104 Freiburg, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107 Leipzig, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, 60438 Frankfurt a.M., Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany.,Biomolecular NMR and Center for Integrated Protein Science Munich at Department of Chemistry, Technical University of Munich, 85747 Garching, Germany
| | - Stefan Legewie
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Julian König
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
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19
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Hwang I, Cao D, Na Y, Kim DY, Zhang T, Yao J, Oh H, Hu J, Zheng H, Yao Y, Paik J. Far Upstream Element-Binding Protein 1 Regulates LSD1 Alternative Splicing to Promote Terminal Differentiation of Neural Progenitors. Stem Cell Reports 2018; 10:1208-1221. [PMID: 29606613 PMCID: PMC5998560 DOI: 10.1016/j.stemcr.2018.02.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 02/26/2018] [Accepted: 02/28/2018] [Indexed: 01/08/2023] Open
Abstract
Loss of a cell's ability to terminally differentiate because of mutations is a selected genetic event in tumorigenesis. Genomic analyses of low-grade glioma have reported recurrent mutations of far upstream element-binding protein 1 (FUBP1). Here, we show that FUBP1 expression is dynamically regulated during neurogenesis and that its downregulation in neural progenitors impairs terminal differentiation and promotes tumorigenesis collaboratively with expression of IDH1R132H. Mechanistically, collaborative action between SRRM4 and FUBP1 is necessary for mini-exon splicing of the neurospecific LSD1+8a isoform. LSD1+8a was downregulated upon loss of FUBP1 in neural progenitors, thereby impairing terminal neuronal differentiation and maturation. Reinforcing LSD1+8a expression in FUBP1-downregulated neural progenitors restored terminal differentiation and suppressed tumorigenesis; hence, LSD1+8a is an obligatory effector of FUBP1-dependent neuronal differentiation. These findings establish a direct role for FUBP1 in neuronal differentiation and also explain its tumor-suppressor function in the nervous system. FUBP1 is the tumor suppressor necessary for terminal differentiation of neurons FUBP1 promotes inclusion of neuron-specific LSD1 exon 8a FUBP1 and IDH1 mutations converge on impaired differentiation of neural progenitors
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Affiliation(s)
- Inah Hwang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Dongqing Cao
- Neurosurgical Immunology Laboratory, Neurosurgical Institute of Fudan University, Shanghai, China
| | - Yoonmi Na
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Do-Yeon Kim
- Department of Pharmacology, School of Dentistry, Kyungpook National University, Daegu, Korea
| | - Tuo Zhang
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY 10065, USA
| | - Jun Yao
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Hwanhee Oh
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Jian Hu
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Hongwu Zheng
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Yu Yao
- Neurosurgical Immunology Laboratory, Neurosurgical Institute of Fudan University, Shanghai, China; Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China.
| | - Jihye Paik
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA.
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20
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Zaytseva O, Quinn LM. DNA Conformation Regulates Gene Expression: The MYC Promoter and Beyond. Bioessays 2018; 40:e1700235. [PMID: 29504137 DOI: 10.1002/bies.201700235] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 01/29/2018] [Indexed: 01/07/2023]
Abstract
Emerging evidence suggests that DNA topology plays an instructive role in cell fate control through regulation of gene expression. Transcription produces torsional stress, and the resultant supercoiling of the DNA molecule generates an array of secondary structures. In turn, local DNA architecture is harnessed by the cell, acting within sensory feedback mechanisms to mediate transcriptional output. MYC is a potent oncogene, which is upregulated in the majority of cancers; thus numerous studies have focused on detailed understanding of its regulation. Dissection of regulatory regions within the MYC promoter provided the first hint that intimate feedback between DNA topology and associated DNA remodeling proteins is critical for moderating transcription. As evidence of such regulation is also found in the context of many other genes, here we expand on the prototypical example of the MYC promoter, and also explore DNA architecture in a genome-wide context as a global mechanism of transcriptional control.
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Affiliation(s)
- Olga Zaytseva
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, ACT 2600, Canberra City, Australia.,School of Biomedical Sciences, University of Melbourne, 3010, Parkville, Australia
| | - Leonie M Quinn
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, ACT 2600, Canberra City, Australia.,School of Biomedical Sciences, University of Melbourne, 3010, Parkville, Australia
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21
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Normal and altered pre-mRNA processing in the DMD gene. Hum Genet 2017; 136:1155-1172. [DOI: 10.1007/s00439-017-1820-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 06/02/2017] [Indexed: 12/11/2022]
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22
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Targeted RNA-Seq profiling of splicing pattern in the DMD gene: exons are mostly constitutively spliced in human skeletal muscle. Sci Rep 2017; 7:39094. [PMID: 28045018 PMCID: PMC5206723 DOI: 10.1038/srep39094] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 11/17/2016] [Indexed: 02/08/2023] Open
Abstract
We have analysed the splicing pattern of the human Duchenne Muscular Dystrophy (DMD) NB transcript in normal skeletal muscle. To achieve depth of coverage required for the analysis of this lowly expressed gene in muscle, we designed a targeted RNA-Seq procedure that combines amplification of the full-length 11.3 kb DMD cDNA sequence and 454 sequencing technology. A high and uniform coverage of the cDNA sequence was obtained that allowed to draw up a reliable inventory of the physiological alternative splicing events in the muscular DMD transcript. In contrast to previous assumptions, we evidenced that most of the 79 DMD exons are constitutively spliced in skeletal muscle. Only a limited number of 12 alternative splicing events were identified, all present at a very low level. These include previously known exon skipping events but also newly described pseudoexon inclusions and alternative 3′ splice sites, of which one is the first functional NAGNAG splice site reported in the DMD gene. This study provides the first RNA-Seq-based reference of DMD splicing pattern in skeletal muscle and reports on an experimental procedure well suited to detect condition-specific differences in this low abundance transcript that may prove useful for diagnostic, research or RNA-based therapeutic applications.
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23
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Kralovicova J, Vorechovsky I. Alternative splicing of U2AF1 reveals a shared repression mechanism for duplicated exons. Nucleic Acids Res 2016; 45:417-434. [PMID: 27566151 PMCID: PMC5224494 DOI: 10.1093/nar/gkw733] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 08/10/2016] [Accepted: 08/11/2016] [Indexed: 12/30/2022] Open
Abstract
The auxiliary factor of U2 small nuclear ribonucleoprotein (U2AF) facilitates branch point (BP) recognition and formation of lariat introns. The gene for the 35-kD subunit of U2AF gives rise to two protein isoforms (termed U2AF35a and U2AF35b) that are encoded by alternatively spliced exons 3 and Ab, respectively. The splicing recognition sequences of exon 3 are less favorable than exon Ab, yet U2AF35a expression is higher than U2AF35b across tissues. We show that U2AF35b repression is facilitated by weak, closely spaced BPs next to a long polypyrimidine tract of exon Ab. Each BP lacked canonical uridines at position -2 relative to the BP adenines, with efficient U2 base-pairing interactions predicted only for shifted registers reminiscent of programmed ribosomal frameshifting. The BP cluster was compensated by interactions involving unpaired cytosines in an upstream, EvoFold-predicted stem loop (termed ESL) that binds FUBP1/2. Exon Ab inclusion correlated with predicted free energies of mutant ESLs, suggesting that the ESL operates as a conserved rheostat between long inverted repeats upstream of each exon. The isoform-specific U2AF35 expression was U2AF65-dependent, required interactions between the U2AF-homology motif (UHM) and the α6 helix of U2AF35, and was fine-tuned by exon Ab/3 variants. Finally, we identify tandem homologous exons regulated by U2AF and show that their preferential responses to U2AF65-related proteins and SRSF3 are associated with unpaired pre-mRNA segments upstream of U2AF-repressed 3′ss. These results provide new insights into tissue-specific subfunctionalization of duplicated exons in vertebrate evolution and expand the repertoire of exon repression mechanisms that control alternative splicing.
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Affiliation(s)
- Jana Kralovicova
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Igor Vorechovsky
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
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Wang J, Li X, Wang L, Li J, Zhao Y, Bou G, Li Y, Jiao G, Shen X, Wei R, Liu S, Xie B, Lei L, Li W, Zhou Q, Liu Z. A novel long intergenic noncoding RNA indispensable for the cleavage of mouse two-cell embryos. EMBO Rep 2016; 17:1452-1470. [PMID: 27496889 DOI: 10.15252/embr.201642051] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 07/07/2016] [Indexed: 01/30/2023] Open
Abstract
Endogenous retroviruses (ERVs) are transcriptionally active in cleavage stage embryos, yet their functions are unknown. ERV sequences are present in the majority of long intergenic noncoding RNAs (lincRNAs) in mouse and humans, playing key roles in many cellular processes and diseases. Here, we identify LincGET as a nuclear lincRNA that is GLN-, MERVL-, and ERVK-associated and essential for mouse embryonic development beyond the two-cell stage. LincGET is expressed in late two- to four-cell mouse embryos. Its depletion leads to developmental arrest at the late G2 phase of the two-cell stage and to MAPK signaling pathway inhibition. LincGET forms an RNA-protein complex with hnRNP U, FUBP1, and ILF2, promoting the cis-regulatory activity of long terminal repeats (LTRs) in GLN, MERVL, and ERVK (GLKLTRs), and inhibiting RNA alternative splicing, partially by downregulating hnRNP U, FUBP1, and ILF2 protein levels. Hnrnpu or Ilf2 mRNA injection at the pronuclear stage also decreases the preimplantation developmental rate, and Fubp1 mRNA injection at the pronuclear stage causes a block at the two-cell stage. Thus, as the first functional ERV-associated lincRNA, LincGET provides clues for ERV functions in cleavage stage embryonic development.
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Affiliation(s)
- Jiaqiang Wang
- College of Life Science, Northeast Agricultural University, Harbin, China State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xin Li
- College of Life Science, Northeast Agricultural University, Harbin, China State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Leyun Wang
- College of Life Science, Northeast Agricultural University, Harbin, China State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jingyu Li
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Yanhua Zhao
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Gerelchimeg Bou
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Yufei Li
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Guanyi Jiao
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xinghui Shen
- Department of Histology and Embryology, Harbin Medical University, Harbin, China
| | - Renyue Wei
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Shichao Liu
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Bingteng Xie
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Lei Lei
- Department of Histology and Embryology, Harbin Medical University, Harbin, China
| | - Wei Li
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qi Zhou
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zhonghua Liu
- College of Life Science, Northeast Agricultural University, Harbin, China
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Abstract
Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) are caused by mutations in the DMD gene that encodes the cytoskeletal protein, dystrophin. Dystrophinopathies are inherited in an X-linked recessive manner. Due to the tremendous size of the gene (2.2 megabases), the DMD locus has a high spontaneous mutation rate, and one third of sporadic cases of DMD are due to a de novo mutation. There are seven tissue-specific promoters in the gene. The skeletal muscular transcript contains 79 exons and encode the full-length protein (427-kDa) located at the inner face of the sarcolemma of muscle fibers. DMD gene mutations are highly heterogeneous. Large rearrangements (deletions or duplications of one or more exons) are most frequently involved while point mutations account for 20 %-30 % of cases. A survey of current strategies of molecular diagnosis is presented here. In particular, the role of muscle biopsy (for dystrophin and RNA analyses) in the diagnosis of dystrophinopathies is discussed. In more than 90 % of cases, the clinical severity is correlated with the impact of the mutations on the reading frame and the expression of the dystrophin (absence or residual amount of mutated protein). Various mechanisms contribute to the exceptions. Besides the clinical interest for the patient, the identification of the mutation allows accurate genetic counseling in the familles, and is a necessary prerequisite for the inclusion of the patient in the genotype-based clinical trials.
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Affiliation(s)
- F Leturcq
- Laboratoire de biochimie et génétique, moléculaire, Hôpital Cochin et Institut de Myologie, Groupe hospitalier La Pitié Salpétrière, APHP, France
| | - S Tuffery-Giraud
- Laboratoire de Génétique de Maladies Rares, Université de Montpellier, IURC, 641 av du Doyen G. Giraud, 34093 Montpellier cedex 5, France.
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Functional Analysis of Mutations in Exon 9 of NF1 Reveals the Presence of Several Elements Regulating Splicing. PLoS One 2015; 10:e0141735. [PMID: 26509978 PMCID: PMC4624989 DOI: 10.1371/journal.pone.0141735] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 10/11/2015] [Indexed: 11/19/2022] Open
Abstract
Neurofibromatosis type 1 (NF1) is one of the most common human hereditary disorders, predisposing individuals to the development of benign and malignant tumors in the nervous system, as well as other clinical manifestations. NF1 is caused by heterozygous mutations in the NF1 gene and around 25% of the pathogenic changes affect pre-mRNA splicing. Since the molecular mechanisms affected by these mutations are poorly understood, we have analyzed the splicing mutations identified in exon 9 of NF1, which is particularly prone to such changes, to better define the possible splicing regulatory elements. Using a minigene approach, we studied the effect of five splicing mutations in this exon described in patients. These highlighted three regulatory motifs within the exon. An in vivo splicing analysis of an extensive collection of changes generated in the minigene demonstrated that the CG motif at c.910-911 is critical for the recognition of exon 9. We also found that the GC motif at c.945-946 is involved in exon recognition through SRSF2 and that this motif is part of a Composite Exon Splicing Regulatory Element made up of physically overlapping enhancer and silencer elements. Finally, through an in vivo splicing analysis and in vitro binding assays, we demonstrated that the c.1007G>A mutation creates an Exonic Splicing Silencer element that binds the hnRNPA1 protein. The complexity of the splicing regulatory elements present in exon 9 is most likely responsible for the fact that mutations in this region represent 25% of all exonic changes that affect splicing in the NF1 gene.
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