1
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Duan H, Zhang J, Gui R, Lu Y, Pang A, Chen B, Shen L, Yu H, Li J, Xu T, Wang Y, Yao X, Zhang B, Lin N, Dong X, Zhou Y, Che J. Discovery of a Highly Potent and Selective BRD9 PROTAC Degrader Based on E3 Binder Investigation for the Treatment of Hematological Tumors. J Med Chem 2024; 67:11326-11353. [PMID: 38913763 DOI: 10.1021/acs.jmedchem.4c00883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
BRD9 is a pivotal epigenetic factor involved in cancers and inflammatory diseases. Still, the limited selectivity and poor phenotypic activity of targeted agents make it an atypically undruggable target. PROTAC offers an alternative strategy for overcoming the issue. In this study, we explored diverse E3 ligase ligands for the contribution of BRD9 PROTAC degradation. Through molecular docking, binding affinity analysis, and structure-activity relationship study, we identified a highly potent PROTAC E5, with excellent BRD9 degradation (DC50 = 16 pM) and antiproliferation in MV4-11 cells (IC50 = 0.27 nM) and OCI-LY10 cells (IC50 = 1.04 nM). E5 can selectively degrade BRD9 and induce cell cycle arrest and apoptosis. Moreover, the therapeutic efficacy of E5 was confirmed in xenograft tumor models, accompanied by further RNA-seq analysis. Therefore, these results may pave the way and provide the reference for the discovery and investigation of highly effective PROTAC degraders.
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Affiliation(s)
- Haiting Duan
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Jingyu Zhang
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
- Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Hangzhou First People's Hospital, Cancer Center of Zhejiang University, Hangzhou 310006, P. R. China
- Department of Clinical Pharmacology, Hangzhou Geriatric Hospital, Hangzhou, Zhejiang 310022, P. R. China
| | - Renzhao Gui
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Tsuihang New District, Zhongshan, Guangdong 528400, P. R. China
- School of Pharmacy, Zunyi Medical University, Zunyi 563000, P. R. China
| | - Yang Lu
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Ao Pang
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Beijing Chen
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Tsuihang New District, Zhongshan, Guangdong 528400, P. R. China
| | - Liteng Shen
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Hengyuan Yu
- State Key Laboratory of Advanced Drug Delivery Systems of Zhejiang Province, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Jia Li
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Tsuihang New District, Zhongshan, Guangdong 528400, P. R. China
- School of Pharmacy, Zunyi Medical University, Zunyi 563000, P. R. China
- National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai 264117, P. R. China
| | - Tengfei Xu
- State Key Laboratory of Advanced Drug Delivery Systems of Zhejiang Province, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Yuwei Wang
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang 712000, P. R. China
| | - Xiaojun Yao
- Centre for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao 999078, P. R. China
| | - Bo Zhang
- Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Hangzhou First People's Hospital, Cancer Center of Zhejiang University, Hangzhou 310006, P. R. China
- Department of Clinical Pharmacology, Hangzhou Geriatric Hospital, Hangzhou, Zhejiang 310022, P. R. China
| | - Nengming Lin
- Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Hangzhou First People's Hospital, Cancer Center of Zhejiang University, Hangzhou 310006, P. R. China
- Department of Clinical Pharmacology, Hangzhou Geriatric Hospital, Hangzhou, Zhejiang 310022, P. R. China
| | - Xiaowu Dong
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
- State Key Laboratory of Advanced Drug Delivery Systems of Zhejiang Province, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Yubo Zhou
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Tsuihang New District, Zhongshan, Guangdong 528400, P. R. China
- School of Pharmacy, Zunyi Medical University, Zunyi 563000, P. R. China
- National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
| | - Jinxin Che
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
- State Key Laboratory of Advanced Drug Delivery Systems of Zhejiang Province, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
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Polinski JM, Castellano KR, Buckley KM, Bodnar AG. Genomic signatures of exceptional longevity and negligible aging in the long-lived red sea urchin. Cell Rep 2024; 43:114021. [PMID: 38564335 DOI: 10.1016/j.celrep.2024.114021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 02/12/2024] [Accepted: 03/15/2024] [Indexed: 04/04/2024] Open
Abstract
The red sea urchin (Mesocentrotus franciscanus) is one of the Earth's longest-living animals, reported to live more than 100 years with indeterminate growth, life-long reproduction, and no increase in mortality rate with age. To understand the genetic underpinnings of longevity and negligible aging, we constructed a chromosome-level assembly of the red sea urchin genome and compared it to that of short-lived sea urchin species. Genome-wide syntenic alignments identified chromosome rearrangements that distinguish short- and long-lived species. Expanded gene families in long-lived species play a role in innate immunity, sensory nervous system, and genome stability. An integrated network of genes under positive selection in the red sea urchin was involved in genomic regulation, mRNA fidelity, protein homeostasis, and mitochondrial function. Our results implicated known longevity genes in sea urchin longevity but also revealed distinct molecular signatures that may promote long-term maintenance of tissue homeostasis, disease resistance, and negligible aging.
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Affiliation(s)
| | | | | | - Andrea G Bodnar
- Gloucester Marine Genomics Institute, Gloucester, MA 01930, USA.
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3
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Huseby CJ, Delvaux E, Brokaw DL, Coleman PD. Blood RNA transcripts reveal similar and differential alterations in fundamental cellular processes in Alzheimer's disease and other neurodegenerative diseases. Alzheimers Dement 2022. [DOI: 10.1002/alz.12880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 09/30/2022] [Accepted: 10/21/2022] [Indexed: 12/24/2022]
Affiliation(s)
- Carol J. Huseby
- ASU‐Banner Neurodegenerative Disease Research Center Arizona State University Tempe Arizona USA
| | - Elaine Delvaux
- ASU‐Banner Neurodegenerative Disease Research Center Arizona State University Tempe Arizona USA
| | - Danielle L. Brokaw
- University of Pennsylvania Perelman School of Medicine Philadelphia Pennsylvania USA
| | - Paul D. Coleman
- ASU‐Banner Neurodegenerative Disease Research Center Arizona State University Tempe Arizona USA
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4
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Gañez-Zapater A, Mackowiak SD, Guo Y, Tarbier M, Jordán-Pla A, Friedländer MR, Visa N, Östlund Farrants AK. The SWI/SNF subunit BRG1 affects alternative splicing by changing RNA binding factor interactions with nascent RNA. Mol Genet Genomics 2022; 297:463-484. [PMID: 35187582 PMCID: PMC8960663 DOI: 10.1007/s00438-022-01863-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 01/23/2022] [Indexed: 11/29/2022]
Abstract
BRG1 and BRM are ATPase core subunits of the human SWI/SNF chromatin remodelling complexes mainly associated with transcriptional initiation. They also have a role in alternative splicing, which has been shown for BRM-containing SWI/SNF complexes at a few genes. Here, we have identified a subset of genes which harbour alternative exons that are affected by SWI/SNF ATPases by expressing the ATPases BRG1 and BRM in C33A cells, a BRG1- and BRM-deficient cell line, and analysed the effect on splicing by RNA sequencing. BRG1- and BRM-affected sub-sets of genes favouring both exon inclusion and exon skipping, with only a minor overlap between the ATPase. Some of the changes in alternative splicing induced by BRG1 and BRM expression did not require the ATPase activity. The BRG1-ATPase independent included exons displayed an exon signature of a high GC content. By investigating three genes with exons affected by the BRG-ATPase-deficient variant, we show that these exons accumulated phosphorylated RNA pol II CTD, both serine 2 and serine 5 phosphorylation, without an enrichment of the RNA polymerase II. The ATPases were recruited to the alternative exons, together with both core and signature subunits of SWI/SNF complexes, and promoted the binding of RNA binding factors to chromatin and RNA at the alternative exons. The interaction with the nascent RNP, however, did not reflect the association to chromatin. The hnRNPL, hnRNPU and SAM68 proteins associated with chromatin in cells expressing BRG1 and BRM wild type, but the binding of hnRNPU to the nascent RNP was excluded. This suggests that SWI/SNF can regulate alternative splicing by interacting with splicing-RNA binding factor and influence their binding to the nascent pre-mRNA particle.
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Affiliation(s)
- Antoni Gañez-Zapater
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, The Arrhenius Laboratories F4, 106 91, Stockholm, Sweden
- Center for Genomic Regulation, 08003, Barcelona, Spain
| | - Sebastian D Mackowiak
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91, Stockholm, Sweden
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195, Berlin, Germany
| | - Yuan Guo
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, The Arrhenius Laboratories F4, 106 91, Stockholm, Sweden
| | - Marcel Tarbier
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91, Stockholm, Sweden
| | - Antonio Jordán-Pla
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, The Arrhenius Laboratories F4, 106 91, Stockholm, Sweden
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencies Biológicas, Valencia University, C/Dr. Moliner, 50, 46100, Burjassot, Spain
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91, Stockholm, Sweden
| | - Neus Visa
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, The Arrhenius Laboratories F4, 106 91, Stockholm, Sweden
| | - Ann-Kristin Östlund Farrants
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, The Arrhenius Laboratories F4, 106 91, Stockholm, Sweden.
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5
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Biology of the mRNA Splicing Machinery and Its Dysregulation in Cancer Providing Therapeutic Opportunities. Int J Mol Sci 2021; 22:ijms22105110. [PMID: 34065983 PMCID: PMC8150589 DOI: 10.3390/ijms22105110] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/07/2021] [Accepted: 05/07/2021] [Indexed: 12/13/2022] Open
Abstract
Dysregulation of messenger RNA (mRNA) processing—in particular mRNA splicing—is a hallmark of cancer. Compared to normal cells, cancer cells frequently present aberrant mRNA splicing, which promotes cancer progression and treatment resistance. This hallmark provides opportunities for developing new targeted cancer treatments. Splicing of precursor mRNA into mature mRNA is executed by a dynamic complex of proteins and small RNAs called the spliceosome. Spliceosomes are part of the supraspliceosome, a macromolecular structure where all co-transcriptional mRNA processing activities in the cell nucleus are coordinated. Here we review the biology of the mRNA splicing machinery in the context of other mRNA processing activities in the supraspliceosome and present current knowledge of its dysregulation in lung cancer. In addition, we review investigations to discover therapeutic targets in the spliceosome and give an overview of inhibitors and modulators of the mRNA splicing process identified so far. Together, this provides insight into the value of targeting the spliceosome as a possible new treatment for lung cancer.
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6
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Ayestaran I, Galhoz A, Spiegel E, Sidders B, Dry JR, Dondelinger F, Bender A, McDermott U, Iorio F, Menden MP. Identification of Intrinsic Drug Resistance and Its Biomarkers in High-Throughput Pharmacogenomic and CRISPR Screens. PATTERNS (NEW YORK, N.Y.) 2020; 1:100065. [PMID: 33205120 PMCID: PMC7660407 DOI: 10.1016/j.patter.2020.100065] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/14/2020] [Accepted: 06/08/2020] [Indexed: 12/15/2022]
Abstract
High-throughput drug screens in cancer cell lines test compounds at low concentrations, thereby enabling the identification of drug-sensitivity biomarkers, while resistance biomarkers remain underexplored. Dissecting meaningful drug responses at high concentrations is challenging due to cytotoxicity, i.e., off-target effects, thus limiting resistance biomarker discovery to frequently mutated cancer genes. To address this, we interrogate subpopulations carrying sensitivity biomarkers and consecutively investigate unexpectedly resistant (UNRES) cell lines for unique genetic alterations that may drive resistance. By analyzing the GDSC and CTRP datasets, we find 53 and 35 UNRES cases, respectively. For 24 and 28 of them, we highlight putative resistance biomarkers. We find clinically relevant cases such as EGFRT790M mutation in NCI-H1975 or PTEN loss in NCI-H1650 cells, in lung adenocarcinoma treated with EGFR inhibitors. Interrogating the underpinnings of drug resistance with publicly available CRISPR phenotypic assays assists in prioritizing resistance drivers, offering hypotheses for drug combinations.
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Affiliation(s)
- Iñigo Ayestaran
- Institute of Computational Biology, Helmholtz Zentrum München GmbH—German Research Center for Environmental Health, Neuherberg 85764, Germany
- CRUK Cambridge Centre Early Detection Programme, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Ana Galhoz
- Institute of Computational Biology, Helmholtz Zentrum München GmbH—German Research Center for Environmental Health, Neuherberg 85764, Germany
- Department of Biology, Ludwig-Maximilians University Munich, Martinsried 82152, Germany
| | - Elmar Spiegel
- Institute of Computational Biology, Helmholtz Zentrum München GmbH—German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Ben Sidders
- Research and Early Development, Oncology, AstraZeneca, Cambridge CB4 0WG, UK
| | - Jonathan R. Dry
- Research and Early Development, Oncology, AstraZeneca, Boston, MA 02451, USA
- Tempus Labs, Boston, MA, USA
| | - Frank Dondelinger
- Centre for Health Informatics, Computation and Statistics, Lancaster Medical School, Lancaster University, Lancaster LA1 4YW, UK
| | - Andreas Bender
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Ultan McDermott
- Research and Early Development, Oncology, AstraZeneca, Cambridge CB4 0WG, UK
| | - Francesco Iorio
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1RQ, UK
- Human Technopole, Palazzo Italia Via Cristina Belgioioso 171, Milano 20157, Italy
| | - Michael P. Menden
- Institute of Computational Biology, Helmholtz Zentrum München GmbH—German Research Center for Environmental Health, Neuherberg 85764, Germany
- Department of Biology, Ludwig-Maximilians University Munich, Martinsried 82152, Germany
- German Centre for Diabetes Research (DZD e.V.), Neuherberg 85764, Germany
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7
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Crisci A, Raleff F, Bagdiul I, Raabe M, Urlaub H, Rain JC, Krämer A. Mammalian splicing factor SF1 interacts with SURP domains of U2 snRNP-associated proteins. Nucleic Acids Res 2015; 43:10456-73. [PMID: 26420826 PMCID: PMC4666396 DOI: 10.1093/nar/gkv952] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 09/10/2015] [Indexed: 02/03/2023] Open
Abstract
Splicing factor 1 (SF1) recognizes the branch point sequence (BPS) at the 3′ splice site during the formation of early complex E, thereby pre-bulging the BPS adenosine, thought to facilitate subsequent base-pairing of the U2 snRNA with the BPS. The 65-kDa subunit of U2 snRNP auxiliary factor (U2AF65) interacts with SF1 and was shown to recruit the U2 snRNP to the spliceosome. Co-immunoprecipitation experiments of SF1-interacting proteins from HeLa cell extracts shown here are consistent with the presence of SF1 in early splicing complexes. Surprisingly almost all U2 snRNP proteins were found associated with SF1. Yeast two-hybrid screens identified two SURP domain-containing U2 snRNP proteins as partners of SF1. A short, evolutionarily conserved region of SF1 interacts with the SURP domains, stressing their role in protein–protein interactions. A reduction of A complex formation in SF1-depleted extracts could be rescued with recombinant SF1 containing the SURP-interaction domain, but only partial rescue was observed with SF1 lacking this sequence. Thus, SF1 can initially recruit the U2 snRNP to the spliceosome during E complex formation, whereas U2AF65 may stabilize the association of the U2 snRNP with the spliceosome at later times. In addition, these findings may have implications for alternative splicing decisions.
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Affiliation(s)
- Angela Crisci
- Department of Cell Biology, Faculty of Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Flore Raleff
- Department of Cell Biology, Faculty of Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Ivona Bagdiul
- Department of Cell Biology, Faculty of Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Monika Raabe
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, D-37075 Göttingen, Germany
| | | | - Angela Krämer
- Department of Cell Biology, Faculty of Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland
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hPso4/hPrp19: a critical component of DNA repair and DNA damage checkpoint complexes. Oncogene 2015; 35:2279-86. [PMID: 26364595 DOI: 10.1038/onc.2015.321] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 07/16/2015] [Accepted: 07/19/2015] [Indexed: 12/15/2022]
Abstract
Genome integrity is vital to cellular homeostasis and its forfeiture is linked to deleterious consequences-cancer, immunodeficiency, genetic disorders and premature aging. The human ubiquitin ligase Pso4/Prp19 has emerged as a critical component of multiple DNA damage response (DDR) signaling networks. It not only senses DNA damage, binds double-stranded DNA in a sequence-independent manner, facilitates processing of damaged DNA, promotes DNA end joining, regulates replication protein A (RPA2) phosphorylation and ubiquitination at damaged DNA, but also regulates RNA splicing and mitotic spindle formation in its integral capacity as a scaffold for a multimeric core complex. Accordingly, by virtue of its regulatory and structural interactions with key proteins critical for genome integrity-DNA double-strand break (DSB) repair, DNA interstrand crosslink repair, repair of stalled replication forks and DNA end joining-it fills a unique niche in restoring genomic integrity after multiple types of DNA damage and thus has a vital role in maintaining chromatin integrity and cellular functions. These properties may underlie its ability to thwart replicative senescence and, not surprisingly, have been linked to the self-renewal and colony-forming ability of murine hematopoietic stem cells. This review highlights recent advances in hPso4 research that provides a fascinating glimpse into the pleiotropic activities of a ubiquitously expressed multifunctional E3 ubiquitin ligase.
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Chen PH, Lee CI, Weng YT, Tarn WY, Tsao YP, Kuo PC, Hsu PH, Huang CW, Huang CS, Lee HH, Wu JT, Chen SL. BCAS2 is essential for Drosophila viability and functions in pre-mRNA splicing. RNA (NEW YORK, N.Y.) 2013; 19:208-218. [PMID: 23249746 PMCID: PMC3543084 DOI: 10.1261/rna.034835.112] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2012] [Accepted: 11/14/2012] [Indexed: 06/01/2023]
Abstract
Here, we show that dBCAS2 (CG4980, human Breast Carcinoma Amplified Sequence 2 ortholog) is essential for the viability of Drosophila melanogaster. We find that ubiquitous or tissue-specific depletion of dBCAS2 leads to larval lethality, wing deformities, impaired splicing, and apoptosis. More importantly, overexpression of hBCAS2 rescues these defects. Furthermore, the C-terminal coiled-coil domain of hBCAS2 binds directly to CDC5L and recruits hPrp19/PLRG1 to form a core complex for splicing in mammalian cells and can partially restore wing damage induced by knocking down dBCAS2 in flies. In summary, Drosophila and human BCAS2 share a similar function in RNA splicing, which affects cell viability.
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Affiliation(s)
- Po-Han Chen
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Chia-I Lee
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Yu-Tzu Weng
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Woan-Yuh Tarn
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Yeou-Ping Tsao
- Department of Ophthalmology, Mackay Memorial Hospital, Taipei 104, Taiwan
| | - Ping-Chang Kuo
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Pang-Hung Hsu
- Department of Life Science, College of Life Sciences, National Taiwan Ocean University, Keelung 202, Taiwan
- Institute of Bioscience and Biotechnology, College of Life Sciences, National Taiwan Ocean University, Keelung 202, Taiwan
| | - Chu-Wei Huang
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Chiun-Sheng Huang
- Department of Surgery, College of Medicine, National Taiwan University and Hospital, Taipei 100, Taiwan
| | - Hsiu-Hsiang Lee
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - June-Tai Wu
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
- Department of Medical Research, National Taiwan University Hospital, Taipei 100, Taiwan
| | - Show-Li Chen
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
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10
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Löscher M, Schosserer M, Dausse E, Lee K, Ajuh P, Grillari-Voglauer R, Lamond AI, Toulmé JJ, Grillari J. Inhibition of pre-mRNA splicing by a synthetic Blom7α-interacting small RNA. PLoS One 2012; 7:e47497. [PMID: 23144703 PMCID: PMC3483155 DOI: 10.1371/journal.pone.0047497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 09/17/2012] [Indexed: 12/02/2022] Open
Abstract
Originally the novel protein Blom7α was identified as novel pre-mRNA splicing factor that interacts with SNEVPrp19/Pso4, an essential protein involved in extension of human endothelial cell life span, DNA damage repair, the ubiquitin-proteasome system, and pre-mRNA splicing. Blom7α belongs to the heteronuclear ribonucleoprotein K homology (KH) protein family, displaying 2 KH domains, a well conserved and widespread RNA-binding motif. In order to identify specific sequence binding motifs, we here used Systematic Evolution of Ligands by Exponential Enrichment (SELEX) with a synthetic RNA library. Besides sequence motifs like (U/A)1–4 C2–6 (U/A)1–5, we identified an AC-rich RNA-aptamer that we termed AK48 (Aptamer KH-binding 48), binding to Blom7α with high affinity. Addition of AK48 to pre-mRNA splicing reactions in vitro inhibited the formation of mature spliced mRNA and led to a slight accumulation of the H complex of the spliceosome. These results suggest that the RNA binding activity of Blom7α might be required for pre-mRNA splicing catalysis. The inhibition of in-vitro splicing by the small RNA AK48 indicates the potential use of small RNA molecules in targeting the spliceosome complex as a novel target for drug development.
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Affiliation(s)
- Marlies Löscher
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Markus Schosserer
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Eric Dausse
- INSERM U869, European Institute of Chemistry and Biology, Pessac, France
- University of Bordeaux, Bordeaux, France
| | - Kiseok Lee
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Paul Ajuh
- School of Life Sciences, Welcome Trust Biocentre, University of Dundee, Dundee, United Kingdom
| | - Regina Grillari-Voglauer
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
- ACIB, Vienna, Austria
- Evercyte GmbH, Vienna, Austria
| | - Angus I. Lamond
- School of Life Sciences, Welcome Trust Biocentre, University of Dundee, Dundee, United Kingdom
| | - Jean-Jacques Toulmé
- INSERM U869, European Institute of Chemistry and Biology, Pessac, France
- University of Bordeaux, Bordeaux, France
| | - Johannes Grillari
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
- Evercyte GmbH, Vienna, Austria
- * E-mail:
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11
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Yin J, Zhu JM, Shen XZ. New insights into pre-mRNA processing factor 19: A multi-faceted protein in humans. Biol Cell 2012; 104:695-705. [DOI: 10.1111/boc.201200011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2011] [Accepted: 09/06/2012] [Indexed: 11/27/2022]
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12
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Koncz C, deJong F, Villacorta N, Szakonyi D, Koncz Z. The spliceosome-activating complex: molecular mechanisms underlying the function of a pleiotropic regulator. FRONTIERS IN PLANT SCIENCE 2012; 3:9. [PMID: 22639636 PMCID: PMC3355604 DOI: 10.3389/fpls.2012.00009] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 01/09/2012] [Indexed: 05/18/2023]
Abstract
Correct interpretation of the coding capacity of RNA polymerase II transcribed eukaryotic genes is determined by the recognition and removal of intronic sequences of pre-mRNAs by the spliceosome. Our current knowledge on dynamic assembly and subunit interactions of the spliceosome mostly derived from the characterization of yeast, Drosophila, and human spliceosomal complexes formed on model pre-mRNA templates in cell extracts. In addition to sequential structural rearrangements catalyzed by ATP-dependent DExH/D-box RNA helicases, catalytic activation of the spliceosome is critically dependent on its association with the NineTeen Complex (NTC) named after its core E3 ubiquitin ligase subunit PRP19. NTC, isolated recently from Arabidopsis, occurs in a complex with the essential RNA helicase and GTPase subunits of the U5 small nuclear RNA particle that are required for both transesterification reactions of splicing. A compilation of mass spectrometry data available on the composition of NTC and spliceosome complexes purified from different organisms indicates that about half of their conserved homologs are encoded by duplicated genes in Arabidopsis. Thus, while mutations of single genes encoding essential spliceosome and NTC components lead to cell death in other organisms, differential regulation of some of their functionally redundant Arabidopsis homologs permits the isolation of partial loss of function mutations. Non-lethal pleiotropic defects of these mutations provide a unique means for studying the roles of NTC in co-transcriptional assembly of the spliceosome and its crosstalk with DNA repair and cell death signaling pathways.
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Affiliation(s)
- Csaba Koncz
- Department of Plant Developmental Biology, Max-Planck Institute for Plant Breeding ResearchCologne, Germany
- Institute of Plant Biology, Biological Research Center of Hungarian Academy of SciencesSzeged, Hungary
- *Correspondence: Csaba Koncz, Department of Plant Developmental Biology, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, D-59829 Cologne, Germany. e-mail:
| | - Femke deJong
- Department of Plant Developmental Biology, Max-Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Nicolas Villacorta
- Department of Plant Developmental Biology, Max-Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Dóra Szakonyi
- Department of Plant Developmental Biology, Max-Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Zsuzsa Koncz
- Department of Plant Developmental Biology, Max-Planck Institute for Plant Breeding ResearchCologne, Germany
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Dellago H, Löscher M, Ajuh P, Ryder U, Kaisermayer C, Grillari-Voglauer R, Fortschegger K, Gross S, Gstraunthaler A, Borth N, Eisenhaber F, Lamond AI, Grillari J. Exo70, a subunit of the exocyst complex, interacts with SNEV(hPrp19/hPso4) and is involved in pre-mRNA splicing. Biochem J 2011; 438:81-91. [PMID: 21639856 PMCID: PMC3708444 DOI: 10.1042/bj20110183] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The Cdc5L (cell division cycle 5-like) complex is a spliceosomal subcomplex that also plays a role in DNA repair. The complex contains the splicing factor hPrp19, also known as SNEV or hPso4, which is involved in cellular life-span regulation and proteasomal breakdown. In a recent large-scale proteomics analysis for proteins associated with this complex, proteins involved in transcription, cell-cycle regulation, DNA repair, the ubiquitin-proteasome system, chromatin remodelling, cellular aging, the cytoskeleton and trafficking, including four members of the exocyst complex, were identified. In the present paper we report that Exo70 interacts directly with SNEV(hPrp19/hPso4) and shuttles to the nucleus, where it associates with the spliceosome. We mapped the interaction site to the N-terminal 100 amino acids of Exo70, which interfere with pre-mRNA splicing in vitro. Furthermore, Exo70 influences the splicing of a model substrate as well as of its own pre-mRNA in vivo. In addition, we found that Exo70 is alternatively spliced in a cell-type- and cell-age- dependent way. These results suggest a novel and unexpected role of Exo70 in nuclear mRNA splicing, where it might signal membrane events to the splicing apparatus.
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Affiliation(s)
- Hanna Dellago
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Marlies Löscher
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Paul Ajuh
- Department of Gene Expression and Regulation, University of Dundee, Dundee, Scotland, U.K
| | - Ursula Ryder
- Department of Gene Expression and Regulation, University of Dundee, Dundee, Scotland, U.K
| | - Christian Kaisermayer
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | | | - Klaus Fortschegger
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Stefan Gross
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Anna Gstraunthaler
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Nicole Borth
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Singapore 138671
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, Singapore 117597
- School of Computater Engineering (SCE), Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore 637553
| | - Angus I. Lamond
- Department of Gene Expression and Regulation, University of Dundee, Dundee, Scotland, U.K
| | - Johannes Grillari
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
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