1
|
Yustis JC, Devoucoux M, Côté J. The Functional Relationship Between RNA Splicing and the Chromatin Landscape. J Mol Biol 2024; 436:168614. [PMID: 38762032 DOI: 10.1016/j.jmb.2024.168614] [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: 03/04/2024] [Revised: 04/27/2024] [Accepted: 05/13/2024] [Indexed: 05/20/2024]
Abstract
Chromatin is a highly regulated and dynamic structure that has been shown to play an essential role in transcriptional and co-transcriptional regulation. In the context of RNA splicing, early evidence suggested a loose connection between the chromatin landscape and splicing. More recently, it has been shown that splicing occurs in a co-transcriptional manner, meaning that the splicing process occurs in the context of chromatin. Experimental and computational evidence have also shown that chromatin dynamics can influence the splicing process and vice versa. However, much of this evidence provides mainly correlative relationships between chromatin and splicing with just a few concrete examples providing defined molecular mechanisms by which these two processes are functionally related. Nevertheless, it is clear that chromatin and RNA splicing are tightly interconnected to one another. In this review, we highlight the current state of knowledge of the relationship between chromatin and splicing.
Collapse
Affiliation(s)
- Juan-Carlos Yustis
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of the CHU de Québec-Université Laval Research Center, Quebec City, Quebec G1R 3S3, Canada
| | - Maëva Devoucoux
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of the CHU de Québec-Université Laval Research Center, Quebec City, Quebec G1R 3S3, Canada
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of the CHU de Québec-Université Laval Research Center, Quebec City, Quebec G1R 3S3, Canada.
| |
Collapse
|
2
|
Zeng X, Tang J, Zhang Q, Wang C, Qi J, Wei Y, Xu J, Yang K, Zhou Z, Wu H, Luo J, Jiang Y, Song Z, Wu J, Wu J. CircHIPK2 Contributes Cell Growth in Intestinal Epithelial of Colitis and Colorectal Cancer through Promoting TAZ Translation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401588. [PMID: 38981023 DOI: 10.1002/advs.202401588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 06/13/2024] [Indexed: 07/11/2024]
Abstract
Colorectal cancer (CRC) and inflammatory bowel disease (IBD) are escalating global health concerns. Despite their distinct clinical presentations, both disorders share intricate genetic and molecular interactions. The Hippo signaling pathway plays a crucial role in regulating cell processes and is implicated in the pathogenesis of IBD and CRC. Circular RNAs (circRNAs) have gained attention for their roles in various diseases, including IBD and CRC. However, a comprehensive understanding of specific circRNAs involved in both IBD and CRC, and their functional roles is lacking. Here, it is found that circHIPK2 (hsa_circRNA_104507) is a bona fide circRNA consistently upregulated in both IBD and CRC suggesting its potential as a biomarker. Furthermore, silencing of circHIPK2 suppressed the growth of CRC cells in vitro and in vivo. Interestingly, decreased circHipk2 potentiated dextran sulfate sodium (DSS)-induced colitis but alleviated colitis-associated tumorigenesis. Most significantly, mechanistic investigations further unveil that circHIPK2, mediated by FUS, interacting with EIF4A3 to promote the translation of TAZ, ultimately increasing the transcription of downstream target genes CCN1 and CCN2. Taken together, circHIPK2 emerges as a key player in the shared mechanisms of IBD and CRC, modulating the Hippo signaling pathway. CircHIPK2-EIF4A3 axis contributes to cell growth in intestinal epithelial of colitis and CRC by enhancing TAZ translation.
Collapse
Affiliation(s)
- Xixi Zeng
- Key Laboratory of Laboratory Medicine, Ministry of Education, Institute of Genomic Medicine, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Zhejiang, 325035, China
- Zhejiang Key Laboratory of Intelligent Cancer Biomarker Discovery and Translation, First Affiliated Hospital, Wenzhou Medical University, Zhejiang, 325035, China
- The Joint Innovation Center for Health and Medicine, Quzhou People's Hospital, The Quzhou Affiliated Hospital of Wenzhou Medical University, Zhejiang, 324000, China
| | - Jielin Tang
- Chemical Biology Research Center at School of Pharmaceutical Sciences, Wenzhou Medical University, Zhejiang, 325035, China
| | - Qian Zhang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Institute of Genomic Medicine, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Zhejiang, 325035, China
- Zhejiang Key Laboratory of Intelligent Cancer Biomarker Discovery and Translation, First Affiliated Hospital, Wenzhou Medical University, Zhejiang, 325035, China
| | - Chenxing Wang
- Department of Gastroenterology, The Second Affiliated Hospital and Yuying Children of Wenzhou Medical University, Zhejiang, 325003, China
| | - Ji Qi
- Key Laboratory of Laboratory Medicine, Ministry of Education, Institute of Genomic Medicine, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Zhejiang, 325035, China
- Zhejiang Key Laboratory of Intelligent Cancer Biomarker Discovery and Translation, First Affiliated Hospital, Wenzhou Medical University, Zhejiang, 325035, China
| | - Yusi Wei
- Key Laboratory of Laboratory Medicine, Ministry of Education, Institute of Genomic Medicine, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Zhejiang, 325035, China
- Zhejiang Key Laboratory of Intelligent Cancer Biomarker Discovery and Translation, First Affiliated Hospital, Wenzhou Medical University, Zhejiang, 325035, China
| | - Jiali Xu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Institute of Genomic Medicine, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Zhejiang, 325035, China
- Zhejiang Key Laboratory of Intelligent Cancer Biomarker Discovery and Translation, First Affiliated Hospital, Wenzhou Medical University, Zhejiang, 325035, China
| | - Kaiyuan Yang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Institute of Genomic Medicine, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Zhejiang, 325035, China
- Zhejiang Key Laboratory of Intelligent Cancer Biomarker Discovery and Translation, First Affiliated Hospital, Wenzhou Medical University, Zhejiang, 325035, China
| | - Zuolin Zhou
- Key Laboratory of Laboratory Medicine, Ministry of Education, Institute of Genomic Medicine, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Zhejiang, 325035, China
- Zhejiang Key Laboratory of Intelligent Cancer Biomarker Discovery and Translation, First Affiliated Hospital, Wenzhou Medical University, Zhejiang, 325035, China
| | - Hao Wu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Institute of Genomic Medicine, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Zhejiang, 325035, China
- Zhejiang Key Laboratory of Intelligent Cancer Biomarker Discovery and Translation, First Affiliated Hospital, Wenzhou Medical University, Zhejiang, 325035, China
| | - Jiarong Luo
- Key Laboratory of Laboratory Medicine, Ministry of Education, Institute of Genomic Medicine, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Zhejiang, 325035, China
- Zhejiang Key Laboratory of Intelligent Cancer Biomarker Discovery and Translation, First Affiliated Hospital, Wenzhou Medical University, Zhejiang, 325035, China
| | - Yi Jiang
- Department of Gastroenterology, The Second Affiliated Hospital and Yuying Children of Wenzhou Medical University, Zhejiang, 325003, China
| | - Zengqiang Song
- Chemical Biology Research Center at School of Pharmaceutical Sciences, Wenzhou Medical University, Zhejiang, 325035, China
| | - Jinyu Wu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Institute of Genomic Medicine, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Zhejiang, 325035, China
| | - Jianmin Wu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Institute of Genomic Medicine, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Zhejiang, 325035, China
- Zhejiang Key Laboratory of Intelligent Cancer Biomarker Discovery and Translation, First Affiliated Hospital, Wenzhou Medical University, Zhejiang, 325035, China
- Cixi Biomedical Research Institute, Wenzhou Medical University, Zhejiang, 315302, China
| |
Collapse
|
3
|
Bonnet C, Dian AL, Espie-Caullet T, Fabbri L, Lagadec L, Pivron T, Dutertre M, Luco R, Navickas A, Vagner S, Verga D, Uguen P. Post-transcriptional gene regulation: From mechanisms to RNA chemistry and therapeutics. Bull Cancer 2024; 111:782-790. [PMID: 38824069 DOI: 10.1016/j.bulcan.2024.04.005] [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: 02/13/2024] [Revised: 03/22/2024] [Accepted: 04/03/2024] [Indexed: 06/03/2024]
Abstract
A better understanding of the RNA biology and chemistry is necessary to then develop new RNA therapeutic strategies. This review is the synthesis of a series of conferences that took place during the 6th international course on post-transcriptional gene regulation at Institut Curie. This year, the course made a special focus on RNA chemistry.
Collapse
Affiliation(s)
- Clara Bonnet
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Ana Luisa Dian
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Tristan Espie-Caullet
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Lucilla Fabbri
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Lucie Lagadec
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Thibaud Pivron
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Martin Dutertre
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Reini Luco
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Albertas Navickas
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Stephan Vagner
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Daniela Verga
- CNRS UMR9187, Inserm U1196, Chemistry and Modelling for the Biology of Cancer, Institut Curie, université Paris-Saclay, 91405 Orsay, France
| | - Patricia Uguen
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France.
| |
Collapse
|
4
|
Langer LM, Kurscheidt K, Basquin J, Bonneau F, Iermak I, Basquin C, Conti E. UPF1 helicase orchestrates mutually exclusive interactions with the SMG6 endonuclease and UPF2. Nucleic Acids Res 2024; 52:6036-6048. [PMID: 38709891 PMCID: PMC11162806 DOI: 10.1093/nar/gkae323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 04/06/2024] [Accepted: 04/25/2024] [Indexed: 05/08/2024] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a conserved co-translational mRNA surveillance and turnover pathway across eukaryotes. NMD has a central role in degrading defective mRNAs and also regulates the stability of a significant portion of the transcriptome. The pathway is organized around UPF1, an RNA helicase that can interact with several NMD-specific factors. In human cells, degradation of the targeted mRNAs begins with a cleavage event that requires the recruitment of the SMG6 endonuclease to UPF1. Previous studies have identified functional links between SMG6 and UPF1, but the underlying molecular mechanisms have remained elusive. Here, we used mass spectrometry, structural biology and biochemical approaches to identify and characterize a conserved short linear motif in SMG6 that interacts with the cysteine/histidine-rich (CH) domain of UPF1. Unexpectedly, we found that the UPF1-SMG6 interaction is precluded when the UPF1 CH domain is engaged with another NMD factor, UPF2. Based on cryo-EM data, we propose that the formation of distinct SMG6-containing and UPF2-containing NMD complexes may be dictated by different conformational states connected to the RNA-binding status of UPF1. Our findings rationalize a key event in metazoan NMD and advance our understanding of mechanisms regulating activity and guiding substrate recognition by the SMG6 endonuclease.
Collapse
Affiliation(s)
- Lukas M Langer
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried/Munich D-82152, Germany
| | - Katharina Kurscheidt
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried/Munich D-82152, Germany
| | - Jérôme Basquin
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried/Munich D-82152, Germany
| | - Fabien Bonneau
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried/Munich D-82152, Germany
| | - Iuliia Iermak
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried/Munich D-82152, Germany
| | - Claire Basquin
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried/Munich D-82152, Germany
| | - Elena Conti
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried/Munich D-82152, Germany
| |
Collapse
|
5
|
Temaj G, Chichiarelli S, Telkoparan-Akillilar P, Saha S, Nuhii N, Hadziselimovic R, Saso L. Advances in molecular function of UPF1 in Cancer. Arch Biochem Biophys 2024; 756:109989. [PMID: 38621446 DOI: 10.1016/j.abb.2024.109989] [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: 02/06/2024] [Revised: 03/23/2024] [Accepted: 04/10/2024] [Indexed: 04/17/2024]
Abstract
It is known that more than 10 % of genetic diseases are caused by a mutation in protein-coding mRNA (premature termination codon; PTC). mRNAs with an early stop codon are degraded by the cellular surveillance process known as nonsense-mediated mRNA decay (NMD), which prevents the synthesis of C-terminally truncated proteins. Up-frameshift-1 (UPF1) has been reported to be involved in the downregulation of various cancers, and low expression of UPF1 was shown to correlate with poor prognosis. It is known that UPF1 is a master regulator of nonsense-mediated mRNA decay (NMD). UPF1 may also function as an E3 ligase and degrade target proteins without using mRNA decay mechanisms. Increasing evidence indicates that UPF1 could serve as a good biomarker for cancer diagnosis and treatment for future therapeutic applications. Long non-coding RNAs (lncRNAs) have the ability to bind different proteins and regulate gene expression; this role in cancer cells has already been identified by different studies. This article provides an overview of the aberrant expression of UPF1, its functional properties, and molecular processes during cancer for clinical applications in cancer. We also discussed the interactions of lncRNA with UPF1 for cell growth during tumorigenesis.
Collapse
Affiliation(s)
- Gazmend Temaj
- Faculty of Pharmacy, College UBT, 10000, Prishtina, Republic of Kosovo.
| | - Silvia Chichiarelli
- Department of Biochemical Sciences "A. Rossi-Fanelli", Sapienza University of Rome, 00185, Rome, Italy.
| | | | - Sarmistha Saha
- Department of Biotechnology, Institute of Applied Sciences & Humanities, GLA University, Mathura, Uttar Pradesh, India.
| | - Nexhibe Nuhii
- Department of Pharmacy, Faculty of Medical Sciences, State University of Tetovo, 1200, Tetovo, Macedonia.
| | - Rifat Hadziselimovic
- Faculty of Science, University of Sarajevo, 71000, Sarajevo, Bosnia and Herzegovina.
| | - Luciano Saso
- Department of Physiology and Pharmacology "Vittorio Erspamer", La Sapienza University, 00185, Rome, Italy.
| |
Collapse
|
6
|
Yadav P, Tamilselvan R, Mani H, Singh KK. MicroRNA-mediated regulation of nonsense-mediated mRNA decay factors: Insights into microRNA prediction tools and profiling techniques. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195022. [PMID: 38437914 DOI: 10.1016/j.bbagrm.2024.195022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 03/06/2024]
Abstract
Nonsense-mediated mRNA decay (NMD) stands out as a prominent RNA surveillance mechanism within eukaryotes, meticulously overseeing both RNA abundance and integrity by eliminating aberrant transcripts. These defective transcripts are discerned through the concerted efforts of translating ribosomes, eukaryotic release factors (eRFs), and trans-acting NMD factors, with Up-Frameshift 3 (UPF3) serving as a noteworthy component. Remarkably, in humans, UPF3 exists in two paralogous forms, UPF3A (UPF3) and UPF3B (UPF3X). Beyond its role in quality control, UPF3 wields significant influence over critical cellular processes, including neural development, synaptic plasticity, and axon guidance. However, the precise regulatory mechanisms governing UPF3 remain elusive. MicroRNAs (miRNAs) emerge as pivotal post-transcriptional gene regulators, exerting substantial impact on diverse pathological and physiological pathways. This comprehensive review encapsulates our current understanding of the intricate regulatory nexus between NMD and miRNAs, with particular emphasis on the essential role played by UPF3B in neurodevelopment. Additionally, we bring out the significance of the 3'-untranslated region (3'-UTR) as the molecular bridge connecting NMD and miRNA-mediated gene regulation. Furthermore, we provide an in-depth exploration of diverse computational tools tailored for the prediction of potential miRNA targets. To complement these computational approaches, we delineate experimental techniques designed to validate predicted miRNA-mRNA interactions, empowering readers with the knowledge necessary to select the most appropriate methodology for their specific research objectives.
Collapse
Affiliation(s)
- Priyanka Yadav
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Raja Tamilselvan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Harita Mani
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Kusum Kumari Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
| |
Collapse
|
7
|
Hwang HJ, Kim YK. Molecular mechanisms of circular RNA translation. Exp Mol Med 2024; 56:1272-1280. [PMID: 38871818 PMCID: PMC11263353 DOI: 10.1038/s12276-024-01220-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 06/15/2024] Open
Abstract
Circular RNAs (circRNAs) are covalently closed single-stranded RNAs without a 5' cap structure and a 3' poly(A) tail typically present in linear mRNAs of eukaryotic cells. CircRNAs are predominantly generated through a back-splicing process within the nucleus. CircRNAs have long been considered non-coding RNAs seemingly devoid of protein-coding potential. However, many recent studies have challenged this idea and have provided substantial evidence that a subset of circRNAs can associate with polysomes and indeed be translated. Therefore, in this review, we primarily highlight the 5' cap-independent internal initiation of translation that occurs on circular RNAs. Several molecular features of circRNAs, including the internal ribosome entry site, N6-methyladenosine modification, and the exon junction complex deposited around the back-splicing junction after back-splicing event, play pivotal roles in their efficient internal translation. We also propose a possible relationship between the translatability of circRNAs and their stability, with a focus on nonsense-mediated mRNA decay and nonstop decay, both of which are well-characterized mRNA surveillance mechanisms. An in-depth understanding of circRNA translation will reshape and expand our current knowledge of proteomics.
Collapse
Affiliation(s)
- Hyun Jung Hwang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Yoon Ki Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
| |
Collapse
|
8
|
Chen X, Fansler MM, Janjoš U, Ule J, Mayr C. The FXR1 network acts as signaling scaffold for actomyosin remodeling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.05.565677. [PMID: 37961296 PMCID: PMC10635158 DOI: 10.1101/2023.11.05.565677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
It is currently not known whether mRNAs fulfill structural roles in the cytoplasm. Here, we report the FXR1 network, an mRNA-protein (mRNP) network present throughout the cytoplasm, formed by FXR1-mediated packaging of exceptionally long mRNAs. These mRNAs serve as underlying condensate scaffold and concentrate FXR1 molecules. The FXR1 network contains multiple protein binding sites and functions as a signaling scaffold for interacting proteins. We show that it is necessary for RhoA signaling-induced actomyosin reorganization to provide spatial proximity between kinases and their substrates. Point mutations in FXR1, found in its homolog FMR1, where they cause Fragile X syndrome, disrupt the network. FXR1 network disruption prevents actomyosin remodeling-an essential and ubiquitous process for the regulation of cell shape, migration, and synaptic function. These findings uncover a structural role for cytoplasmic mRNA and show how the FXR1 RNA-binding protein as part of the FXR1 network acts as organizer of signaling reactions.
Collapse
Affiliation(s)
- Xiuzhen Chen
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Mervin M Fansler
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Urška Janjoš
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
- Biosciences PhD Program, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Jernej Ule
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
- UK Dementia Research Institute at King's College London, London, SE5 9NU, UK
| | - Christine Mayr
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
| |
Collapse
|
9
|
Bensaude O, Barbosa I, Morillo L, Dikstein R, Le Hir H. Exon-junction complex association with stalled ribosomes and slow translation-independent disassembly. Nat Commun 2024; 15:4209. [PMID: 38760352 PMCID: PMC11101648 DOI: 10.1038/s41467-024-48371-5] [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: 08/05/2023] [Accepted: 04/29/2024] [Indexed: 05/19/2024] Open
Abstract
Exon junction complexes are deposited at exon-exon junctions during splicing. They are primarily known to activate non-sense mediated degradation of transcripts harbouring premature stop codons before the last intron. According to a popular model, exon-junction complexes accompany mRNAs to the cytoplasm where the first translating ribosome pushes them out. However, they are also removed by uncharacterized, translation-independent mechanisms. Little is known about kinetic and transcript specificity of these processes. Here we tag core subunits of exon-junction complexes with complementary split nanoluciferase fragments to obtain sensitive and quantitative assays for complex formation. Unexpectedly, exon-junction complexes form large stable mRNPs containing stalled ribosomes. Complex assembly and disassembly rates are determined after an arrest in transcription and/or translation. 85% of newly deposited exon-junction complexes are disassembled by a translation-dependent mechanism. However as this process is much faster than the translation-independent one, only 30% of the exon-junction complexes present in cells at steady state require translation for disassembly. Deep RNA sequencing shows a bias of exon-junction complex bound transcripts towards microtubule and centrosome coding ones and demonstrate that the lifetimes of exon-junction complexes are transcript-specific. This study provides a dynamic vision of exon-junction complexes and uncovers their unexpected stable association with ribosomes.
Collapse
Affiliation(s)
- Olivier Bensaude
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France.
| | - Isabelle Barbosa
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Lucia Morillo
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Rivka Dikstein
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Hervé Le Hir
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France.
| |
Collapse
|
10
|
van den Akker GGH, Chabronova A, Housmans BAC, van der Vloet L, Surtel DAM, Cremers A, Marchand V, Motorin Y, Caron MMJ, Peffers MJ, Welting TJM. TGF-β2 Induces Ribosome Activity, Alters Ribosome Composition and Inhibits IRES-Mediated Translation in Chondrocytes. Int J Mol Sci 2024; 25:5031. [PMID: 38732249 PMCID: PMC11084827 DOI: 10.3390/ijms25095031] [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: 03/12/2024] [Revised: 04/29/2024] [Accepted: 05/01/2024] [Indexed: 05/13/2024] Open
Abstract
Alterations in cell fate are often attributed to (epigenetic) regulation of gene expression. An emerging paradigm focuses on specialized ribosomes within a cell. However, little evidence exists for the dynamic regulation of ribosome composition and function. Here, we stimulated a chondrocytic cell line with transforming growth factor beta (TGF-β2) and mapped changes in ribosome function, composition and ribosomal RNA (rRNA) epitranscriptomics. 35S Met/Cys incorporation was used to evaluate ribosome activity. Dual luciferase reporter assays were used to assess ribosomal modus. Ribosomal RNA expression and processing were determined by RT-qPCR, while RiboMethSeq and HydraPsiSeq were used to determine rRNA modification profiles. Label-free protein quantification of total cell lysates, isolated ribosomes and secreted proteins was done by LC-MS/MS. A three-day TGF-β2 stimulation induced total protein synthesis in SW1353 chondrocytic cells and human articular chondrocytes. Specifically, TGF-β2 induced cap-mediated protein synthesis, while IRES-mediated translation was not (P53 IRES) or little affected (CrPv IGR and HCV IRES). Three rRNA post-transcriptional modifications (PTMs) were affected by TGF-β2 stimulation (18S-Gm1447 downregulated, 18S-ψ1177 and 28S-ψ4598 upregulated). Proteomic analysis of isolated ribosomes revealed increased interaction with eIF2 and tRNA ligases and decreased association of eIF4A3 and heterogeneous nuclear ribonucleoprotein (HNRNP)s. In addition, thirteen core ribosomal proteins were more present in ribosomes from TGF-β2 stimulated cells, albeit with a modest fold change. A prolonged stimulation of chondrocytic cells with TGF-β2 induced ribosome activity and changed the mode of translation. These functional changes could be coupled to alterations in accessory proteins in the ribosomal proteome.
Collapse
Affiliation(s)
- Guus G. H. van den Akker
- Laboratory of Experimental Orthopedics, Department of Orthopedic Surgery, Research School CAPHRI, Faculty of Healthy Medicine and Life Sciences, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.C.); (M.M.J.C.); (T.J.M.W.)
| | - Alzbeta Chabronova
- Laboratory of Experimental Orthopedics, Department of Orthopedic Surgery, Research School CAPHRI, Faculty of Healthy Medicine and Life Sciences, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.C.); (M.M.J.C.); (T.J.M.W.)
- Department of Musculoskeletal Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
| | - Bas A. C. Housmans
- Laboratory of Experimental Orthopedics, Department of Orthopedic Surgery, Research School CAPHRI, Faculty of Healthy Medicine and Life Sciences, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.C.); (M.M.J.C.); (T.J.M.W.)
| | - Laura van der Vloet
- Laboratory of Experimental Orthopedics, Department of Orthopedic Surgery, Research School CAPHRI, Faculty of Healthy Medicine and Life Sciences, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.C.); (M.M.J.C.); (T.J.M.W.)
| | - Don A. M. Surtel
- Laboratory of Experimental Orthopedics, Department of Orthopedic Surgery, Research School CAPHRI, Faculty of Healthy Medicine and Life Sciences, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.C.); (M.M.J.C.); (T.J.M.W.)
| | - Andy Cremers
- Laboratory of Experimental Orthopedics, Department of Orthopedic Surgery, Research School CAPHRI, Faculty of Healthy Medicine and Life Sciences, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.C.); (M.M.J.C.); (T.J.M.W.)
| | - Virginie Marchand
- UAR2008 IBSLor CNRS-INSERM, Université de Lorraine, BioPole, F54000 Nancy, France; (V.M.); (Y.M.)
| | - Yuri Motorin
- UAR2008 IBSLor CNRS-INSERM, Université de Lorraine, BioPole, F54000 Nancy, France; (V.M.); (Y.M.)
- UMR7365 IMoPA, CNRS, Université de Lorraine, BioPole, F54000 Nancy, France
| | - Marjolein M. J. Caron
- Laboratory of Experimental Orthopedics, Department of Orthopedic Surgery, Research School CAPHRI, Faculty of Healthy Medicine and Life Sciences, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.C.); (M.M.J.C.); (T.J.M.W.)
| | - Mandy J. Peffers
- Department of Musculoskeletal Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
| | - Tim J. M. Welting
- Laboratory of Experimental Orthopedics, Department of Orthopedic Surgery, Research School CAPHRI, Faculty of Healthy Medicine and Life Sciences, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.C.); (M.M.J.C.); (T.J.M.W.)
- Laboratory of Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University Medical Center +, 6229 HX Maastricht, The Netherlands
| |
Collapse
|
11
|
Singh AK. Rules and impacts of nonsense-mediated mRNA decay in the degradation of long noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1853. [PMID: 38741356 DOI: 10.1002/wrna.1853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024]
Abstract
Nonsense-mediated mRNA decay (NMD) is a quality-control process that selectively degrades mRNAs having premature termination codon, upstream open reading frame, or unusually long 3'UTR. NMD detects such mRNAs and rapidly degrades them during initial rounds of translation in the eukaryotic cells. Since NMD is a translation-dependent cytoplasmic mRNA surveillance process, the noncoding RNAs were initially believed to be NMD-resistant. The sequence feature-based analysis has revealed that many putative long noncoding RNAs (lncRNAs) have short open reading frames, most of which have translation potential. Subsequent transcriptome-based molecular studies showed an association of a large set of such putative lncRNAs with translating ribosomes, and some of them produce stable and functionally active micropeptides. The translationally active lncRNAs typically have relatively longer and unprotected 3'UTR, which can induce their NMD-dependent degradation. This review defines the mechanism and regulation of NMD-dependent degradation of lncRNAs and its impact on biological processes related to the functions of lncRNAs or their encoded micropeptides. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Turnover and Surveillance > Regulation of RNA Stability RNA in Disease and Development > RNA in Disease.
Collapse
Affiliation(s)
- Anand Kumar Singh
- Department of Biology, Indian Institute of Science Education and Research Tirupati, Tirupati, Andhra Pradesh, India
| |
Collapse
|
12
|
Fanara S, Schloesser M, Joris M, De Franco S, Vandevenne M, Kerff F, Hanikenne M, Motte P. The Arabidopsis SR45 splicing factor bridges the splicing machinery and the exon-exon junction complex. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2280-2298. [PMID: 38180875 DOI: 10.1093/jxb/erae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 01/04/2024] [Indexed: 01/07/2024]
Abstract
The Arabidopsis splicing factor serine/arginine-rich 45 (SR45) contributes to several biological processes. The sr45-1 loss-of-function mutant exhibits delayed root development, late flowering, unusual numbers of floral organs, shorter siliques with decreased seed sets, narrower leaves and petals, and altered metal distribution. SR45 bears a unique RNA recognition motif (RRM) flanked by one serine/arginine-rich (RS) domain on both sides. Here, we studied the function of each SR45 domains by examining their involvement in: (i) the spatial distribution of SR45; (ii) the establishment of a protein-protein interaction network including spliceosomal and exon-exon junction complex (EJC) components; and (iii) the RNA binding specificity. We report that the endogenous SR45 promoter is active during vegetative and reproductive growth, and that the SR45 protein localizes in the nucleus. We demonstrate that the C-terminal arginine/serine-rich domain is a determinant of nuclear localization. We show that the SR45 RRM domain specifically binds purine-rich RNA motifs via three residues (H101, H141, and Y143), and is also involved in protein-protein interactions. We further show that SR45 bridges both mRNA splicing and surveillance machineries as a partner of EJC core components and peripheral factors, which requires phosphoresidues probably phosphorylated by kinases from both the CLK and SRPK families. Our findings provide insights into the contribution of each SR45 domain to both spliceosome and EJC assemblies.
Collapse
Affiliation(s)
- Steven Fanara
- InBioS-PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000, Liège, Belgium
| | - Marie Schloesser
- InBioS-PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000, Liège, Belgium
| | - Marine Joris
- InBioS-PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000, Liège, Belgium
| | - Simona De Franco
- InBioS-Center for Protein Engineering, Laboratory of Biological Macromolecules, University of Liège, 4000, Liège, Belgium
| | - Marylène Vandevenne
- InBioS-Center for Protein Engineering, Laboratory of Biological Macromolecules, University of Liège, 4000, Liège, Belgium
| | - Frédéric Kerff
- InBioS-Center for Protein Engineering, Laboratory of Crystallography, University of Liège, 4000, Liège, Belgium
| | - Marc Hanikenne
- InBioS-PhytoSystems, Translational Plant Biology, University of Liège, 4000, Liège, Belgium
| | - Patrick Motte
- InBioS-PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000, Liège, Belgium
| |
Collapse
|
13
|
Verma SK, Kuyumcu-Martinez MN. RNA binding proteins in cardiovascular development and disease. Curr Top Dev Biol 2024; 156:51-119. [PMID: 38556427 DOI: 10.1016/bs.ctdb.2024.01.007] [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] [Indexed: 04/02/2024]
Abstract
Congenital heart disease (CHD) is the most common birth defect affecting>1.35 million newborn babies worldwide. CHD can lead to prenatal, neonatal, postnatal lethality or life-long cardiac complications. RNA binding protein (RBP) mutations or variants are emerging as contributors to CHDs. RBPs are wizards of gene regulation and are major contributors to mRNA and protein landscape. However, not much is known about RBPs in the developing heart and their contributions to CHD. In this chapter, we will discuss our current knowledge about specific RBPs implicated in CHDs. We are in an exciting era to study RBPs using the currently available and highly successful RNA-based therapies and methodologies. Understanding how RBPs shape the developing heart will unveil their contributions to CHD. Identifying their target RNAs in the embryonic heart will ultimately lead to RNA-based treatments for congenital heart disease.
Collapse
Affiliation(s)
- Sunil K Verma
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine Charlottesville, VA, United States.
| | - Muge N Kuyumcu-Martinez
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine Charlottesville, VA, United States; Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, United States; University of Virginia Cancer Center, Charlottesville, VA, United States.
| |
Collapse
|
14
|
He PC, He C. mRNA accessibility within mRNPs as a determinant of gene expression. Trends Biochem Sci 2024; 49:199-207. [PMID: 38071089 PMCID: PMC10939938 DOI: 10.1016/j.tibs.2023.11.003] [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: 07/31/2023] [Revised: 11/05/2023] [Accepted: 11/10/2023] [Indexed: 01/31/2024]
Abstract
Gene expression is a complex process requiring many control mechanisms to achieve a desired phenotype. DNA accessibility within chromatin is well established as an important determinant of gene expression. By contrast, while mRNA also associates with a complement of proteins, the exact nature of messenger ribonucleoprotein (mRNP) packaging and its functional relevance is not as clear. Recent reports indicate that exon junction complex (EJC)-mediated mRNP packaging renders exon junction-proximal regions inaccessible for m6A methylation, and that EJCs reside within the inaccessible interior of globular transcription and export (TREX) complex-associated nuclear mRNPs. We propose that 'mRNA accessibility' within mRNPs is an important determinant of gene expression that may modulate the specificity of a broad array of regulatory processes including but not limited to m6A methylation.
Collapse
Affiliation(s)
- P Cody He
- Pritzker School of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Committee on Immunology, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA.
| |
Collapse
|
15
|
Miliara S, Cozzi E, Zhong X, Chan I, Ekwall K, Lehmann S, Lennartsson A, Bartek J, Kanellis DC. The exon-junction complex helicase eIF4A3 holds therapeutic potential in acute myeloid leukemia. Leukemia 2024; 38:663-666. [PMID: 38036629 PMCID: PMC10912025 DOI: 10.1038/s41375-023-02098-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 11/08/2023] [Accepted: 11/21/2023] [Indexed: 12/02/2023]
Affiliation(s)
- Sophia Miliara
- Department of Biosciences and Nutrition, Neo, Karolinska Institute, Huddinge, Sweden
| | - Elisabetta Cozzi
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Xiangfu Zhong
- Department of Biosciences and Nutrition, Neo, Karolinska Institute, Huddinge, Sweden
| | - Isaac Chan
- Department of Biosciences and Nutrition, Neo, Karolinska Institute, Huddinge, Sweden
| | - Karl Ekwall
- Department of Biosciences and Nutrition, Neo, Karolinska Institute, Huddinge, Sweden
| | - Sören Lehmann
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Medical Sciences, Hematology Unit, Uppsala University, Uppsala, Sweden
- Hematology Centre, Karolinska University Hospital, Stockholm, Sweden
| | - Andreas Lennartsson
- Department of Biosciences and Nutrition, Neo, Karolinska Institute, Huddinge, Sweden
| | - Jiri Bartek
- Danish Cancer Institute, Danish Cancer Society, DK-2100, Copenhagen, Denmark.
- Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Division of Genome Biology, Karolinska Institutet, S-171 21, Stockholm, Sweden.
| | - Dimitris C Kanellis
- Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Division of Genome Biology, Karolinska Institutet, S-171 21, Stockholm, Sweden.
| |
Collapse
|
16
|
Cui H, Shi Q, Macarios CM, Schimmel P. Metabolic regulation of mRNA splicing. Trends Cell Biol 2024:S0962-8924(24)00025-4. [PMID: 38431493 DOI: 10.1016/j.tcb.2024.02.002] [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: 11/07/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 03/05/2024]
Abstract
Alternative mRNA splicing enables the diversification of the proteome from a static genome and confers plasticity and adaptiveness on cells. Although this is often explored in development, where hard-wired programs drive the differentiation and specialization, alternative mRNA splicing also offers a way for cells to react to sudden changes in outside stimuli such as small-molecule metabolites. Fluctuations in metabolite levels and availability in particular convey crucial information to which cells react and adapt. We summarize and highlight findings surrounding the metabolic regulation of mRNA splicing. We discuss the principles underlying the biochemistry and biophysical properties of mRNA splicing, and propose how these could intersect with metabolite levels. Further, we present examples in which metabolites directly influence RNA-binding proteins and splicing factors. We also discuss the interplay between alternative mRNA splicing and metabolite-responsive signaling pathways. We hope to inspire future research to obtain a holistic picture of alternative mRNA splicing in response to metabolic cues.
Collapse
Affiliation(s)
- Haissi Cui
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.
| | - Qingyu Shi
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | | | - Paul Schimmel
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA.
| |
Collapse
|
17
|
Das R, Panigrahi GK. Messenger RNA Surveillance: Current Understanding, Regulatory Mechanisms, and Future Implications. Mol Biotechnol 2024:10.1007/s12033-024-01062-4. [PMID: 38411790 DOI: 10.1007/s12033-024-01062-4] [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: 10/10/2023] [Accepted: 01/02/2024] [Indexed: 02/28/2024]
Abstract
Nonsense-mediated mRNA decay (NMD) is an evolutionarily conserved surveillance mechanism in eukaryotes primarily deployed to ensure RNA quality control by eliminating aberrant transcripts and also involved in modulating the expression of several physiological transcripts. NMD, the mRNA surveillance pathway, is a major form of gene regulation in eukaryotes. NMD serves as one of the most significant quality control mechanisms as it primarily scans the newly synthesized transcripts and differentiates the aberrant and non-aberrant transcripts. The synthesis of truncated proteins is restricted, which would otherwise lead to cellular dysfunctions. The up-frameshift factors (UPFs) play a central role in executing the NMD event, largely by recognizing and recruiting multiple protein factors that result in the decay of non-physiological mRNAs. NMD exhibits astounding variability in its ability across eukaryotes in an array of pathological and physiological contexts. The detailed understanding of NMD and the underlying molecular mechanisms remains blurred. This review outlines our current understanding of NMD, in regulating multifaceted cellular events during development and disease. It also attempts to identify unanswered questions that deserve further investigation.
Collapse
Affiliation(s)
- Rutupurna Das
- Department of Zoology, School of Applied Sciences, Centurion University of Technology and Management, Jatni, Khordha, Odisha, India
| | - Gagan Kumar Panigrahi
- Department of Zoology, School of Applied Sciences, Centurion University of Technology and Management, Jatni, Khordha, Odisha, India.
| |
Collapse
|
18
|
Uctepe E, Vona B, Esen FN, Sonmez FM, Smol T, Tümer S, Mancılar H, Geylan Durgun DE, Boute O, Moghbeli M, Ghayoor Karimiani E, Hashemi N, Bakhshoodeh B, Kim HG, Maroofian R, Yesilyurt A. Bi-allelic truncating variants in CASP2 underlie a neurodevelopmental disorder with lissencephaly. Eur J Hum Genet 2024; 32:52-60. [PMID: 37880421 PMCID: PMC10772072 DOI: 10.1038/s41431-023-01461-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/24/2023] [Accepted: 09/11/2023] [Indexed: 10/27/2023] Open
Abstract
Lissencephaly (LIS) is a malformation of cortical development due to deficient neuronal migration and abnormal formation of cerebral convolutions or gyri. Thirty-one LIS-associated genes have been previously described. Recently, biallelic pathogenic variants in CRADD and PIDD1, have associated with LIS impacting the previously established role of the PIDDosome in activating caspase-2. In this report, we describe biallelic truncating variants in CASP2, another subunit of PIDDosome complex. Seven patients from five independent families presenting with a neurodevelopmental phenotype were identified through GeneMatcher-facilitated international collaborations. Exome sequencing analysis was carried out and revealed two distinct novel homozygous (NM_032982.4:c.1156delT (p.Tyr386ThrfsTer25), and c.1174 C > T (p.Gln392Ter)) and compound heterozygous variants (c.[130 C > T];[876 + 1 G > T] p.[Arg44Ter];[?]) in CASP2 segregating within the families in a manner compatible with an autosomal recessive pattern. RNA studies of the c.876 + 1 G > T variant indicated usage of two cryptic splice donor sites, each introducing a premature stop codon. All patients from whom brain MRIs were available had a typical fronto-temporal LIS and pachygyria, remarkably resembling the CRADD and PIDD1-related neuroimaging findings. Other findings included developmental delay, attention deficit hyperactivity disorder, hypotonia, seizure, poor social skills, and autistic traits. In summary, we present patients with CASP2-related ID, anterior-predominant LIS, and pachygyria similar to previously reported patients with CRADD and PIDD1-related disorders, expanding the genetic spectrum of LIS and lending support that each component of the PIDDosome complex is critical for normal development of the human cerebral cortex and brain function.
Collapse
Affiliation(s)
- Eyyup Uctepe
- Acibadem Ankara Tissue Typing Laboratory, Ankara, Türkiye
| | - Barbara Vona
- Institute of Human Genetics, University Medical Center Göttingen, Heinrich-Düker-Weg 12, 37073, Göttingen, Germany
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | | | - F Mujgan Sonmez
- Department of Child Neurology, Faculty of Medicine, Retired lecturer, Karadeniz Technical University, Trabzon, Türkiye
- Private Office, Ankara, Türkiye
| | - Thomas Smol
- Institut de Génétique Médicale, Université de Lille, ULR7364 RADEME, CHU Lille, F-59000, Lille, France
| | - Sait Tümer
- Acibadem Labgen Genetic Diagnosis Center, Istanbul, Türkiye
| | | | | | - Odile Boute
- Clinique de Génétique, Université de Lille, ULR7364 RADEME, CHU Lille, F-59000, Lille, France
| | - Meysam Moghbeli
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ehsan Ghayoor Karimiani
- Molecular and Clinical Sciences Institute, St. George's, University of London, Cranmer Terrace, London, SW17 0RE, UK
- Department of Medical Genetics, Next Generation Genetic Polyclinic, Mashhad, Iran
| | - Narges Hashemi
- Department of Pediatrics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Hyung Goo Kim
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Ahmet Yesilyurt
- Acibadem Labgen Genetic Diagnosis Center, Istanbul, Türkiye.
- Acibadem Maslak Hospital, Istanbul, Türkiye.
| |
Collapse
|
19
|
Corre M, Boehm V, Besic V, Kurowska A, Viry A, Mohammad A, Sénamaud-Beaufort C, Thomas-Chollier M, Lebreton A. Alternative splicing induced by bacterial pore-forming toxins sharpens CIRBP-mediated cell response to Listeria infection. Nucleic Acids Res 2023; 51:12459-12475. [PMID: 37941135 PMCID: PMC10711537 DOI: 10.1093/nar/gkad1033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 10/09/2023] [Accepted: 10/20/2023] [Indexed: 11/10/2023] Open
Abstract
Cell autonomous responses to intracellular bacteria largely depend on reorganization of gene expression. To gain isoform-level resolution of these modes of regulation, we combined long- and short-read transcriptomic analyses of the response of intestinal epithelial cells to infection by the foodborne pathogen Listeria monocytogenes. Among the most striking isoform-based types of regulation, expression of the cellular stress response regulator CIRBP (cold-inducible RNA-binding protein) and of several SRSFs (serine/arginine-rich splicing factors) switched from canonical transcripts to nonsense-mediated decay-sensitive isoforms by inclusion of 'poison exons'. We showed that damage to host cell membranes caused by bacterial pore-forming toxins (listeriolysin O, perfringolysin, streptolysin or aerolysin) led to the dephosphorylation of SRSFs via the inhibition of the kinase activity of CLK1, thereby driving CIRBP alternative splicing. CIRBP isoform usage was found to have consequences on infection, since selective repression of canonical CIRBP reduced intracellular bacterial load while that of the poison exon-containing isoform exacerbated it. Consistently, CIRBP-bound mRNAs were shifted towards stress-relevant transcripts in infected cells, with increased mRNA levels or reduced translation efficiency for some targets. Our results thus generalize the alternative splicing of CIRBP and SRSFs as a common response to biotic or abiotic stresses by extending its relevance to the context of bacterial infection.
Collapse
Affiliation(s)
- Morgane Corre
- Group Bacterial infection, response & dynamics, Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Volker Boehm
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Vinko Besic
- Group Bacterial infection, response & dynamics, Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Anna Kurowska
- Group Bacterial infection, response & dynamics, Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Anouk Viry
- Group Bacterial infection, response & dynamics, Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Ammara Mohammad
- GenomiqueENS, Institut de Biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Catherine Sénamaud-Beaufort
- GenomiqueENS, Institut de Biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Morgane Thomas-Chollier
- Group Bacterial infection, response & dynamics, Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
- GenomiqueENS, Institut de Biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Alice Lebreton
- Group Bacterial infection, response & dynamics, Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
- INRAE, Micalis Institute, 78350 Jouy-en-Josas, France
| |
Collapse
|
20
|
Roth JF, Braunschweig U, Wu M, Li JD, Lin ZY, Larsen B, Weatheritt RJ, Gingras AC, Blencowe BJ. Systematic analysis of alternative exon-dependent interactome remodeling reveals multitasking functions of gene regulatory factors. Mol Cell 2023; 83:4222-4238.e10. [PMID: 38065061 DOI: 10.1016/j.molcel.2023.10.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 08/09/2023] [Accepted: 10/24/2023] [Indexed: 12/18/2023]
Abstract
Alternative splicing significantly expands biological complexity, particularly in the vertebrate nervous system. Increasing evidence indicates that developmental and tissue-dependent alternative exons often control protein-protein interactions; yet, only a minor fraction of these events have been characterized. Using affinity purification-mass spectrometry (AP-MS), we show that approximately 60% of analyzed neural-differential exons in proteins previously implicated in transcriptional regulation result in the gain or loss of interaction partners, which in some cases form unexpected links with coupled processes. Notably, a neural exon in Chtop regulates its interaction with the Prmt1 methyltransferase and DExD-Box helicases Ddx39b/a, affecting its methylation and activity in promoting RNA export. Additionally, a neural exon in Sap30bp affects interactions with RNA processing factors, modulating a critical function of Sap30bp in promoting the splicing of <100 nt "mini-introns" that control nuclear RNA levels. AP-MS is thus a powerful approach for elucidating the multifaceted functions of proteins imparted by context-dependent alternative exons.
Collapse
Affiliation(s)
- Jonathan F Roth
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | | | - Mingkun Wu
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Jack Daiyang Li
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Zhen-Yuan Lin
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada
| | - Brett Larsen
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada
| | - Robert J Weatheritt
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; EMBL Australia, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
| |
Collapse
|
21
|
Carrard J, Lejeune F. Nonsense-mediated mRNA decay, a simplified view of a complex mechanism. BMB Rep 2023; 56:625-632. [PMID: 38052423 PMCID: PMC10761751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/31/2023] [Accepted: 11/17/2023] [Indexed: 12/07/2023] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is both a quality control mechanism and a gene regulation pathway. It has been studied for more than 30 years, with an accumulation of many mechanistic details that have often led to debate and hence to different models of NMD activation, particularly in higher eukaryotes. Two models seem to be opposed, since the first requires intervention of the exon junction complex (EJC) to recruit NMD factors downstream of the premature termination codon (PTC), whereas the second involves an EJC-independent mechanism in which NMD factors concentrate in the 3'UTR to initiate NMD in the presence of a PTC. In this review we describe both models, giving recent molecular details and providing experimental arguments supporting one or the other model. In the end it is certainly possible to imagine that these two mechanisms co-exist, rather than viewing them as mutually exclusive. [BMB Reports 2023; 56(12): 625-632].
Collapse
Affiliation(s)
- Julie Carrard
- Univ. Lille, CNRS, Inserm, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, Lille F-59000, France
| | - Fabrice Lejeune
- Univ. Lille, CNRS, Inserm, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, Lille F-59000, France
| |
Collapse
|
22
|
Chen Z, Wang R, Zhu Y, Huang Z, Yang X, Li Q, Zhong M, Zhang W, Chen L, Wu W, Feng L, An N, Yan Y. A novel circular RNA, circSQSTM1, protects the endothelial function in atherosclerosis. Free Radic Biol Med 2023; 209:301-319. [PMID: 37865306 DOI: 10.1016/j.freeradbiomed.2023.10.398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/11/2023] [Accepted: 10/18/2023] [Indexed: 10/23/2023]
Abstract
A novel circRNA named circSQSTM1 (hsa_circRNA_075320) was screened out in atorvastatin (ATV) stimulated endothelial cells (ECs) by our group. Considering the anti-atherosclerotic function of ATV, we hypothesized the circSQSTM1 could protect ECs functions in AS progression. The effects of circSQSTM1 on ECs inflammation, oxidative stress and autophagy were measured by qRT-PCR, Western blotting, monocyte-endothelial adhesion assay, dichloro-dihydro-fluorescein diacetate and mCherry-GFP-LC3 labeling. A luciferase reporter assay, RNA immunoprecipitation, MS2-tagging system and fluorescence in situ hybridization were performed to identify the biological functions of circSQSTM1. The partial left carotid artery ligation model and atherosclerosis model were established to analyze the effects of circSQSTM1 on atherosclerosis progression in vivo. Our results revealed that ATV induced the accumulation of circSQSTM1 in ECs via suppressing m6A modified degradation. In the cytoplasm, circSQSTM1 could relieve Sirt1 by competitively sponging miR-23b-3p. In the nucleus, circSQSTM1 directly interacts with eIF4A3 and promoting the efficient nuclear export of FOXO1 mRNA, which encodes FOXO1 transcription factor to directly activate Sirt1 promoter activity. Hence, circSQSTM1 reduced inflammation, inhibited oxidative stress and promoted autophagy by upregulating Sirt1 in ECs. Moreover, circSQSTM1 overexpression in ECs attenuated the progression of atherosclerosis in ApoE-/- mice. Taken together, the unique noncoding RNA known as circSQSTM1 took a protective role to the ECs in atherosclerosis.
Collapse
Affiliation(s)
- Ziqi Chen
- Department of Cardiology, Translational Research Center for Regenerative Medicine and 3D Printing Technologies, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Ruoyu Wang
- Department of Cardiology, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518033, China
| | - Yinghong Zhu
- Department of Cardiology, Translational Research Center for Regenerative Medicine and 3D Printing Technologies, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Ziyao Huang
- Department of Cardiology, Translational Research Center for Regenerative Medicine and 3D Printing Technologies, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Xuewen Yang
- Department of Cardiology, Translational Research Center for Regenerative Medicine and 3D Printing Technologies, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Qiushi Li
- Department of Cardiology, Translational Research Center for Regenerative Medicine and 3D Printing Technologies, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Meijun Zhong
- Department of Cardiology, Translational Research Center for Regenerative Medicine and 3D Printing Technologies, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Wei Zhang
- Department of Cardiology, Translational Research Center for Regenerative Medicine and 3D Printing Technologies, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Lin Chen
- Department of Cardiology, Translational Research Center for Regenerative Medicine and 3D Printing Technologies, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Wei Wu
- Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Li Feng
- Department of Cardiology, Zhongshan Hospital of Sun Yat-sen University, Zhongshan, 528400, China.
| | - Ningbo An
- Dermatology Hospital of Southern Medical University, Southern Medical University, Guangzhou, 510515, China.
| | - Yi Yan
- Department of Cardiology, Translational Research Center for Regenerative Medicine and 3D Printing Technologies, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
| |
Collapse
|
23
|
Chang J, Shin MK, Park J, Hwang HJ, Locker N, Ahn J, Kim D, Baek D, Park Y, Lee Y, Boo SH, Kim HI, Kim YK. An interaction between eIF4A3 and eIF3g drives the internal initiation of translation. Nucleic Acids Res 2023; 51:10950-10969. [PMID: 37811880 PMCID: PMC10639049 DOI: 10.1093/nar/gkad763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 08/30/2023] [Accepted: 09/08/2023] [Indexed: 10/10/2023] Open
Abstract
An RNA structure or modified RNA sequences can provide a platform for ribosome loading and internal translation initiation. The functional significance of internal translation has recently been highlighted by the discovery that a subset of circular RNAs (circRNAs) is internally translated. However, the molecular mechanisms underlying the internal initiation of translation in circRNAs remain unclear. Here, we identify eIF3g (a subunit of eIF3 complex) as a binding partner of eIF4A3, a core component of the exon-junction complex (EJC) that is deposited onto spliced mRNAs and plays multiple roles in the regulation of gene expression. The direct interaction between eIF4A3-eIF3g serves as a molecular linker between the eIF4A3 and eIF3 complex, thereby facilitating internal ribosomal entry. Protein synthesis from in vitro-synthesized circRNA demonstrates eIF4A3-driven internal translation, which relies on the eIF4A3-eIF3g interaction. Furthermore, our transcriptome-wide analysis shows that efficient polysomal association of endogenous circRNAs requires eIF4A3. Notably, a subset of endogenous circRNAs can express a full-length intact protein, such as β-catenin, in an eIF4A3-dependent manner. Collectively, our results expand the understanding of the protein-coding potential of the human transcriptome, including circRNAs.
Collapse
Affiliation(s)
- Jeeyoon Chang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Min-Kyung Shin
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Joori Park
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hyun Jung Hwang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Nicolas Locker
- Department of Microbial and Cellular Sciences, University of Surrey, Guildford GU2 7HX, UK
| | - Junhak Ahn
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Doyeon Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Daehyun Baek
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Yeonkyoung Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yujin Lee
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Sung Ho Boo
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hyeong-In Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yoon Ki Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| |
Collapse
|
24
|
Morillo L, Paternina T, Alasseur Q, Genovesio A, Schwartz S, Le Hir H. Comprehensive mapping of exon junction complex binding sites reveals universal EJC deposition in Drosophila. BMC Biol 2023; 21:246. [PMID: 37936138 PMCID: PMC10630996 DOI: 10.1186/s12915-023-01749-1] [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: 08/04/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUND The exon junction complex (EJC) is involved in most steps of the mRNA life cycle, ranging from splicing to nonsense-mediated mRNA decay (NMD). It is assembled by the splicing machinery onto mRNA in a sequence-independent manner. A fundamental open question is whether the EJC is deposited onto all exon‒exon junctions or only on a subset of them. Several previous studies have made observations supportive of the latter, yet these have been limited by methodological constraints. RESULTS In this study, we sought to overcome these limitations via the integration of two different approaches for transcriptome-wide mapping of EJCs. Our results revealed that nearly all, if not all, internal exons consistently harbor an EJC in Drosophila, demonstrating that EJC presence is an inherent consequence of the splicing reaction. Furthermore, our study underscores the limitations of eCLIP methods in fully elucidating the landscape of RBP binding sites. Our findings highlight how highly specific (low false positive) methodologies can lead to erroneous interpretations due to partial sensitivity (high false negatives). CONCLUSIONS This study contributes to our understanding of EJC deposition and its association with pre-mRNA splicing. The universal presence of EJC on internal exons underscores its significance in ensuring proper mRNA processing. Additionally, our observations highlight the need to consider both specificity and sensitivity in RBP mapping methodologies.
Collapse
Affiliation(s)
- Lucía Morillo
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Toni Paternina
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Quentin Alasseur
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Auguste Genovesio
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7630031, Israel
| | - Hervé Le Hir
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France.
| |
Collapse
|
25
|
Jung I, Kim YK. Exon Junction Complex Is a Molecular Compass of N 6-Methyladenosine Modification. Mol Cells 2023; 46:589-591. [PMID: 37853685 PMCID: PMC10590705 DOI: 10.14348/molcells.2023.0101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/09/2023] [Accepted: 07/09/2023] [Indexed: 10/20/2023] Open
Affiliation(s)
- Inhong Jung
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Yoon Ki Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| |
Collapse
|
26
|
Bohnsack KE, Yi S, Venus S, Jankowsky E, Bohnsack MT. Cellular functions of eukaryotic RNA helicases and their links to human diseases. Nat Rev Mol Cell Biol 2023; 24:749-769. [PMID: 37474727 DOI: 10.1038/s41580-023-00628-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2023] [Indexed: 07/22/2023]
Abstract
RNA helicases are highly conserved proteins that use nucleoside triphosphates to bind or remodel RNA, RNA-protein complexes or both. RNA helicases are classified into the DEAD-box, DEAH/RHA, Ski2-like, Upf1-like and RIG-I families, and are the largest class of enzymes active in eukaryotic RNA metabolism - virtually all aspects of gene expression and its regulation involve RNA helicases. Mutation and dysregulation of these enzymes have been linked to a multitude of diseases, including cancer and neurological disorders. In this Review, we discuss the regulation and functional mechanisms of RNA helicases and their roles in eukaryotic RNA metabolism, including in transcription regulation, pre-mRNA splicing, ribosome assembly, translation and RNA decay. We highlight intriguing models that link helicase structure, mechanisms of function (such as local strand unwinding, translocation, winching, RNA clamping and displacing RNA-binding proteins) and biological roles, including emerging connections between RNA helicases and cellular condensates formed through liquid-liquid phase separation. We also discuss associations of RNA helicases with human diseases and recent efforts towards the design of small-molecule inhibitors of these pivotal regulators of eukaryotic gene expression.
Collapse
Affiliation(s)
- Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany.
| | - Soon Yi
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Sarah Venus
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Eckhard Jankowsky
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Moderna, Cambridge, MA, USA.
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany.
- Göttingen Centre for Molecular Biosciences, University of Göttingen, Göttingen, Germany.
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
| |
Collapse
|
27
|
Schertzer MD, Stirn A, Isaev K, Pereira L, Das A, Harbison C, Park SH, Wessels HH, Sanjana NE, Knowles DA. Cas13d-mediated isoform-specific RNA knockdown with a unified computational and experimental toolbox. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.557474. [PMID: 37745416 PMCID: PMC10515814 DOI: 10.1101/2023.09.12.557474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Alternative splicing is an essential mechanism for diversifying proteins, in which mature RNA isoforms produce proteins with potentially distinct functions. Two major challenges in characterizing the cellular function of isoforms are the lack of experimental methods to specifically and efficiently modulate isoform expression and computational tools for complex experimental design. To address these gaps, we developed and methodically tested a strategy which pairs the RNA-targeting CRISPR/Cas13d system with guide RNAs that span exon-exon junctions in the mature RNA. We performed a high-throughput essentiality screen, quantitative RT-PCR assays, and PacBio long read sequencing to affirm our ability to specifically target and robustly knockdown individual RNA isoforms. In parallel, we provide computational tools for experimental design and screen analysis. Considering all possible splice junctions annotated in GENCODE for multi-isoform genes and our gRNA efficacy predictions, we estimate that our junction-centric strategy can uniquely target up to 89% of human RNA isoforms, including 50,066 protein-coding and 11,415 lncRNA isoforms. Importantly, this specificity spans all splicing and transcriptional events, including exon skipping and inclusion, alternative 5' and 3' splice sites, and alternative starts and ends.
Collapse
Affiliation(s)
- Megan D Schertzer
- New York Genome Center, New York, NY
- Department of Computer Science, Columbia University, New York, NY
| | - Andrew Stirn
- New York Genome Center, New York, NY
- Department of Computer Science, Columbia University, New York, NY
| | - Keren Isaev
- New York Genome Center, New York, NY
- Department of Systems Biology, Columbia University, New York, NY
| | | | - Anjali Das
- New York Genome Center, New York, NY
- Department of Computer Science, Columbia University, New York, NY
| | | | - Stella H Park
- New York Genome Center, New York, NY
- Department of Biomedical Engineering, Columbia University, New York, NY
| | - Hans-Hermann Wessels
- New York Genome Center, New York, NY
- Department of Biology, New York University, New York, NY
| | - Neville E Sanjana
- New York Genome Center, New York, NY
- Department of Biology, New York University, New York, NY
| | - David A Knowles
- New York Genome Center, New York, NY
- Department of Computer Science, Columbia University, New York, NY
- Department of Systems Biology, Columbia University, New York, NY
- Data Science Institute, Columbia University, New York, NY
| |
Collapse
|
28
|
Halbout M, Bury M, Hanet A, Gerin I, Graff J, Killian T, Gatto L, Vertommen D, Bommer GT. SUZ domain-containing proteins have multiple effects on nonsense-mediated decay target transcripts. J Biol Chem 2023; 299:105095. [PMID: 37507022 PMCID: PMC10470013 DOI: 10.1016/j.jbc.2023.105095] [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: 01/31/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Many transcripts are targeted by nonsense-mediated decay (NMD), leading to their degradation and the inhibition of their translation. We found that the protein SUZ domain-containing protein 1 (SZRD1) interacts with the key NMD factor up-frameshift 1. When recruited to NMD-sensitive reporter gene transcripts, SZRD1 increased protein production, at least in part, by relieving translational inhibition. The conserved SUZ domain in SZRD1 was required for this effect. The SUZ domain is present in only three other human proteins besides SZRD1: R3H domain-containing protein 1 and 2 (R3HDM1, R3HDM2) and cAMP-regulated phosphoprotein 21 (ARPP21). We found that ARPP21, similarly to SZRD1, can increase protein production from NMD-sensitive reporter transcripts in an SUZ domain-dependent manner. This indicated that the SUZ domain-containing proteins could prevent translational inhibition of transcripts targeted by NMD. Consistent with the idea that SZRD1 mainly prevents translational inhibition, we did not observe a systematic decrease in the abundance of NMD targets when we knocked down SZRD1. Surprisingly, knockdown of SZRD1 in two different cell lines led to reduced levels of the NMD component UPF3B, which was accompanied by increased levels in a subset of NMD targets. This suggests that SZRD1 is required to maintain normal UPF3B levels and indicates that the effect of SZRD1 on NMD targets is not limited to a relief from translational inhibition. Overall, our study reveals that human SUZ domain-containing proteins play a complex role in regulating protein output from transcripts targeted by NMD.
Collapse
Affiliation(s)
- Mathias Halbout
- Department of Physiological Chemistry, de Duve Institute, UCLouvain, Brussels, Belgium; WELBIO, Brussels, Belgium
| | - Marina Bury
- Department of Physiological Chemistry, de Duve Institute, UCLouvain, Brussels, Belgium; WELBIO, Brussels, Belgium
| | - Aoife Hanet
- Department of Physiological Chemistry, de Duve Institute, UCLouvain, Brussels, Belgium
| | - Isabelle Gerin
- Department of Physiological Chemistry, de Duve Institute, UCLouvain, Brussels, Belgium; WELBIO, Brussels, Belgium
| | - Julie Graff
- Department of Physiological Chemistry, de Duve Institute, UCLouvain, Brussels, Belgium; WELBIO, Brussels, Belgium
| | - Theodore Killian
- Computational Biology Laboratory, de Duve Institute, UCLouvain, Bruxelles, Belgium
| | - Laurent Gatto
- Computational Biology Laboratory, de Duve Institute, UCLouvain, Bruxelles, Belgium
| | - Didier Vertommen
- Protein Phosphorylation Unit, de Duve Institute, UCLouvain, Brussels, Belgium
| | - Guido T Bommer
- Department of Physiological Chemistry, de Duve Institute, UCLouvain, Brussels, Belgium; WELBIO, Brussels, Belgium.
| |
Collapse
|
29
|
Beusch I, Rao B, Studer MK, Luhovska T, Šukytė V, Lei S, Oses-Prieto J, SeGraves E, Burlingame A, Jonas S, Madhani HD. Targeted high-throughput mutagenesis of the human spliceosome reveals its in vivo operating principles. Mol Cell 2023; 83:2578-2594.e9. [PMID: 37402368 PMCID: PMC10484158 DOI: 10.1016/j.molcel.2023.06.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 03/15/2023] [Accepted: 06/02/2023] [Indexed: 07/06/2023]
Abstract
The spliceosome is a staggeringly complex machine, comprising, in humans, 5 snRNAs and >150 proteins. We scaled haploid CRISPR-Cas9 base editing to target the entire human spliceosome and investigated the mutants using the U2 snRNP/SF3b inhibitor, pladienolide B. Hypersensitive substitutions define functional sites in the U1/U2-containing A complex but also in components that act as late as the second chemical step after SF3b is dissociated. Viable resistance substitutions map not only to the pladienolide B-binding site but also to the G-patch domain of SUGP1, which lacks orthologs in yeast. We used these mutants and biochemical approaches to identify the spliceosomal disassemblase DHX15/hPrp43 as the ATPase ligand for SUGP1. These and other data support a model in which SUGP1 promotes splicing fidelity by triggering early spliceosome disassembly in response to kinetic blocks. Our approach provides a template for the analysis of essential cellular machines in humans.
Collapse
Affiliation(s)
- Irene Beusch
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, USA
| | - Beiduo Rao
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, USA
| | - Michael K Studer
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Tetiana Luhovska
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Viktorija Šukytė
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Susan Lei
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, USA
| | - Juan Oses-Prieto
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, USA
| | - Em SeGraves
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, USA
| | - Alma Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, USA
| | - Stefanie Jonas
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, USA.
| |
Collapse
|
30
|
Busselez J, Uzbekov RE, Franco B, Pancione M. New insights into the centrosome-associated spliceosome components as regulators of ciliogenesis and tissue identity. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1776. [PMID: 36717357 DOI: 10.1002/wrna.1776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 12/20/2022] [Accepted: 12/27/2022] [Indexed: 02/01/2023]
Abstract
Biomolecular condensates are membrane-less assemblies of proteins and nucleic acids. Centrosomes are biomolecular condensates that play a crucial role in nuclear division, cytoskeletal remodeling, and cilia formation in animal cells. Spatial omics technology is providing new insights into the dynamic exchange of spliceosome components between the nucleus and the centrosome/cilium. Intriguingly, centrosomes are emerging as cytoplasmic sites for information storage, enriched with RNA molecules and RNA-processing proteins. Furthermore, growing evidence supports the view that nuclear spliceosome components assembled at the centrosome function as potential coordinators of splicing subprograms, pluripotency, and cell differentiation. In this article, we first discuss the current understanding of the centrosome/cilium complex, which controls both stem cell differentiation and pluripotency. We next explore the molecular mechanisms that govern splicing factor assembly and disassembly around the centrosome and examine how RNA processing pathways contribute to ciliogenesis. Finally, we discuss numerous unresolved compelling questions regarding the centrosome-associated spliceosome components and transcript variants within the cytoplasm as sources of RNA-based secondary messages in the regulation of cell identity and cell fate determination. This article is categorized under: RNA-Based Catalysis > RNA Catalysis in Splicing and Translation RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Processing > Splicing Regulation/Alternative Splicing RNA Processing > RNA Processing.
Collapse
Affiliation(s)
- Johan Busselez
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch-Graffenstaden, France
| | - Rustem E Uzbekov
- Faculté de Médecine, Université de Tours, Tours, France
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia
| | - Brunella Franco
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Department of Translational Medicine, Medical Genetics, University of Naples "Federico II", Naples, Italy
- Scuola Superiore Meridionale (SSM, School of Advanced Studies), Genomics and Experimental Medicine program, University of Naples Federico II, Naples, Italy
| | - Massimo Pancione
- Department of Sciences and Technologies, University of Sannio, Benevento, Italy
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Complutense University Madrid, Madrid, Spain
| |
Collapse
|
31
|
Song J, Ge Y, Dong M, Guan Q, Ju M, Song X, Han J, Zhao L. Molecular interplay between EIF4 family and circular RNAs in cancer: Mechanisms and therapeutics. Eur J Pharmacol 2023:175867. [PMID: 37369297 DOI: 10.1016/j.ejphar.2023.175867] [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: 04/05/2023] [Revised: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023]
Abstract
The eukaryotic translation initiation factor 4 (EIF4) family is a major contributor to the recruitment of mRNAs to ribosomes during the initial translation stage in eukaryotes, whose dysregulation either allows for cancer transformation or prevents disordered cancerous cell growth. Circular RNAs (circRNAs), which exhibit distinctive structures and are widely expressed in eukaryotes, are anticipated to be a clinical diagnostic biomarker for cancer therapy. There is considerable evidence that EIF4s can influence the biogenesis, transport, and function of circRNAs and, in turn, circRNAs can control the expressions of EIF4s through certain molecular pathways. Herein, we primarily review the emerging studies of the EIF4 family and pinpoint the roles of dysregulated EIF4s in cancer. We also evaluate the patterns of intricate interactions between circRNAs and EIF4s and discuss the potential utility of circRNA-based therapeutics targeting EIF4s in clinical cancer research.
Collapse
Affiliation(s)
- Jia Song
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, PR China; Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, China Medical University, Shenyang, 110122, PR China.
| | - Yuexin Ge
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, PR China; Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, China Medical University, Shenyang, 110122, PR China.
| | - Mingyan Dong
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, PR China; Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, China Medical University, Shenyang, 110122, PR China.
| | - Qiutong Guan
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, PR China; Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, China Medical University, Shenyang, 110122, PR China.
| | - Mingyi Ju
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, PR China; Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, China Medical University, Shenyang, 110122, PR China.
| | - Xueyi Song
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, PR China; Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, China Medical University, Shenyang, 110122, PR China.
| | - Jiali Han
- Department of Otolaryngology, The First Hospital of China Medical University, Shenyang, Liaoning, 110001, PR China.
| | - Lin Zhao
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, PR China; Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, China Medical University, Shenyang, 110122, PR China.
| |
Collapse
|
32
|
Nagarajan VK, Stuart CJ, DiBattista AT, Accerbi M, Caplan JL, Green PJ. RNA degradome analysis reveals DNE1 endoribonuclease is required for the turnover of diverse mRNA substrates in Arabidopsis. THE PLANT CELL 2023; 35:1936-1955. [PMID: 37070465 PMCID: PMC10226599 DOI: 10.1093/plcell/koad085] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 03/01/2023] [Accepted: 03/04/2023] [Indexed: 05/30/2023]
Abstract
In plants, cytoplasmic mRNA decay is critical for posttranscriptionally controlling gene expression and for maintaining cellular RNA homeostasis. Arabidopsis DCP1-ASSOCIATED NYN ENDORIBONUCLEASE 1 (DNE1) is a cytoplasmic mRNA decay factor that interacts with proteins involved in mRNA decapping and nonsense-mediated mRNA decay (NMD). There is limited information on the functional role of DNE1 in RNA turnover, and the identities of its endogenous targets are unknown. In this study, we utilized RNA degradome approaches to globally investigate DNE1 substrates. Monophosphorylated 5' ends, produced by DNE1, should accumulate in mutants lacking the cytoplasmic exoribonuclease XRN4, but be absent from DNE1 and XRN4 double mutants. In seedlings, we identified over 200 such transcripts, most of which reflect cleavage within coding regions. While most DNE1 targets were NMD-insensitive, some were upstream ORF (uORF)-containing and NMD-sensitive transcripts, indicating that this endoribonuclease is required for turnover of a diverse set of mRNAs. Transgenic plants expressing DNE1 cDNA with an active-site mutation in the endoribonuclease domain abolished the in planta cleavage of transcripts, demonstrating that DNE1 endoribonuclease activity is required for cleavage. Our work provides key insights into the identity of DNE1 substrates and enhances our understanding of DNE1-mediated mRNA decay.
Collapse
Affiliation(s)
- Vinay K Nagarajan
- Delaware Biotechnology Institute, University of Delaware,
Newark, DE 19713-1316, USA
| | - Catherine J Stuart
- Delaware Biotechnology Institute, University of Delaware,
Newark, DE 19713-1316, USA
| | - Anna T DiBattista
- Delaware Biotechnology Institute, University of Delaware,
Newark, DE 19713-1316, USA
| | - Monica Accerbi
- Delaware Biotechnology Institute, University of Delaware,
Newark, DE 19713-1316, USA
| | - Jeffrey L Caplan
- Bio-Imaging Center, Delaware Biotechnology Institute, University of
Delaware, Newark, DE 19713-1316, USA
| | - Pamela J Green
- Delaware Biotechnology Institute, University of Delaware,
Newark, DE 19713-1316, USA
| |
Collapse
|
33
|
Lupan BM, Solecki RA, Musso CM, Alsina FC, Silver DL. The exon junction complex component EIF4A3 is essential for mouse and human cortical progenitor mitosis and neurogenesis. Development 2023; 150:dev201619. [PMID: 37139782 PMCID: PMC10233715 DOI: 10.1242/dev.201619] [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: 01/13/2023] [Accepted: 04/24/2023] [Indexed: 05/05/2023]
Abstract
Mutations in components of the exon junction complex (EJC) are associated with neurodevelopment and disease. In particular, reduced levels of the RNA helicase EIF4A3 cause Richieri-Costa-Pereira syndrome (RCPS) and copy number variations are linked to intellectual disability. Consistent with this, Eif4a3 haploinsufficient mice are microcephalic. Altogether, this implicates EIF4A3 in cortical development; however, the underlying mechanisms are poorly understood. Here, we use mouse and human models to demonstrate that EIF4A3 promotes cortical development by controlling progenitor mitosis, cell fate and survival. Eif4a3 haploinsufficiency in mice causes extensive cell death and impairs neurogenesis. Using Eif4a3;p53 compound mice, we show that apoptosis has the most impact on early neurogenesis, while additional p53-independent mechanisms contribute to later stages. Live imaging of mouse and human neural progenitors reveals that Eif4a3 controls mitosis length, which influences progeny fate and viability. These phenotypes are conserved, as cortical organoids derived from RCPS iPSCs exhibit aberrant neurogenesis. Finally, using rescue experiments we show that EIF4A3 controls neuron generation via the EJC. Altogether, our study demonstrates that EIF4A3 mediates neurogenesis by controlling mitosis duration and cell survival, implicating new mechanisms that underlie EJC-mediated disorders.
Collapse
Affiliation(s)
- Bianca M. Lupan
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Rachel A. Solecki
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Camila M. Musso
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Fernando C. Alsina
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Debra L. Silver
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
- Departments of Cell Biology and Neurobiology, Duke University Medical Center, Durham, NC 27710, USA
- Duke Institute for Brain Sciences and Duke Regeneration Center, Duke University Medical Center, Durham, NC 27710, USA
| |
Collapse
|
34
|
Atmakuru PS, Dhawan J. The cilium-centrosome axis in coupling cell cycle exit and cell fate. J Cell Sci 2023; 136:308872. [PMID: 37144419 DOI: 10.1242/jcs.260454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023] Open
Abstract
The centrosome is an evolutionarily conserved, ancient organelle whose role in cell division was first described over a century ago. The structure and function of the centrosome as a microtubule-organizing center, and of its extracellular extension - the primary cilium - as a sensory antenna, have since been extensively studied, but the role of the cilium-centrosome axis in cell fate is still emerging. In this Opinion piece, we view cellular quiescence and tissue homeostasis from the vantage point of the cilium-centrosome axis. We focus on a less explored role in the choice between distinct forms of mitotic arrest - reversible quiescence and terminal differentiation, which play distinct roles in tissue homeostasis. We outline evidence implicating the centrosome-basal body switch in stem cell function, including how the cilium-centrosome complex regulates reversible versus irreversible arrest in adult skeletal muscle progenitors. We then highlight exciting new findings in other quiescent cell types that suggest signal-dependent coupling of nuclear and cytoplasmic events to the centrosome-basal body switch. Finally, we propose a framework for involvement of this axis in mitotically inactive cells and identify future avenues for understanding how the cilium-centrosome axis impacts central decisions in tissue homeostasis.
Collapse
Affiliation(s)
- Priti S Atmakuru
- CSIR Centre for Cellular and Molecular Biology, Hyderabad 500 007, India
| | - Jyotsna Dhawan
- CSIR Centre for Cellular and Molecular Biology, Hyderabad 500 007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| |
Collapse
|
35
|
McSweeney C, Chen M, Dong F, Sebastian A, Reynolds DJ, Mott J, Pei Z, Zou J, Shi Y, Mao Y. Transcriptomic Analyses of Brains of RBM8A Conditional Knockout Mice at Different Developmental Stages Reveal Conserved Signaling Pathways Contributing to Neurodevelopmental Diseases. Int J Mol Sci 2023; 24:4600. [PMID: 36902031 PMCID: PMC10003467 DOI: 10.3390/ijms24054600] [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: 12/31/2022] [Revised: 02/20/2023] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Abstract
RNA-binding motif 8A (RBM8A) is a core component of the exon junction complex (EJC) that binds pre-mRNAs and regulates their splicing, transport, translation, and nonsense-mediated decay (NMD). Dysfunction in the core proteins has been linked to several detriments in brain development and neuropsychiatric diseases. To understand the functional role of Rbm8a in brain development, we have generated brain-specific Rbm8a knockout mice and used next-generation RNA-sequencing to identify differentially expressed genes (DEGs) in mice with heterozygous, conditional knockout (cKO) of Rbm8a in the brain at postnatal day 17 (P17) and at embryonic day 12. Additionally, we analyzed enriched gene clusters and signaling pathways within the DEGs. At the P17 time point, between the control and cKO mice, about 251 significant DEGs were identified. At E12, only 25 DEGs were identified in the hindbrain samples. Bioinformatics analyses have revealed many signaling pathways related to the central nervous system (CNS). When E12 and P17 results were compared, three DEGs, Spp1, Gpnmb, and Top2a, appeared to peak at different developmental time points in the Rbm8a cKO mice. Enrichment analyses suggested altered activity in pathways affecting cellular proliferation, differentiation, and survival. The results support the hypothesis that loss of Rbm8a causes decreased cellular proliferation, increased apoptosis, and early differentiation of neuronal subtypes, which may lead ultimately to an altered neuronal subtype composition in the brain.
Collapse
Affiliation(s)
- Colleen McSweeney
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Miranda Chen
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Fengping Dong
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Aswathy Sebastian
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Derrick James Reynolds
- Department of Microbiology & Molecular Genetics, School of Medicine, University of California, Irvine, CA 92697, USA
| | - Jennifer Mott
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Zifei Pei
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Jizhong Zou
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, Rockville, MD 20892, USA
| | - Yongsheng Shi
- Department of Microbiology & Molecular Genetics, School of Medicine, University of California, Irvine, CA 92697, USA
| | - Yingwei Mao
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| |
Collapse
|
36
|
He PC, Wei J, Dou X, Harada BT, Zhang Z, Ge R, Liu C, Zhang LS, Yu X, Wang S, Lyu R, Zou Z, Chen M, He C. Exon architecture controls mRNA m 6A suppression and gene expression. Science 2023; 379:677-682. [PMID: 36705538 PMCID: PMC9990141 DOI: 10.1126/science.abj9090] [Citation(s) in RCA: 73] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 01/16/2023] [Indexed: 01/28/2023]
Abstract
N6-methyladenosine (m6A) is the most abundant messenger RNA (mRNA) modification and plays crucial roles in diverse physiological processes. Using a massively parallel assay for m6A (MPm6A), we discover that m6A specificity is globally regulated by suppressors that prevent m6A deposition in unmethylated transcriptome regions. We identify exon junction complexes (EJCs) as m6A suppressors that protect exon junction-proximal RNA within coding sequences from methylation and regulate mRNA stability through m6A suppression. EJC suppression of m6A underlies multiple global characteristics of mRNA m6A specificity, with the local range of EJC protection sufficient to suppress m6A deposition in average-length internal exons but not in long internal and terminal exons. EJC-suppressed methylation sites colocalize with EJC-suppressed splice sites, which suggests that exon architecture broadly determines local mRNA accessibility to regulatory complexes.
Collapse
Affiliation(s)
- P. Cody He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Committee on Immunology, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Jiangbo Wei
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Xiaoyang Dou
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Bryan T. Harada
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Zijie Zhang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
- State Key Laboratory for Conservation and Utilization of Bio-Resources, School of Life Sciences, Yunnan University, Kunming, Yunnan 650091, China
| | - Ruiqi Ge
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Chang Liu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Li-Sheng Zhang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Xianbin Yu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Shuai Wang
- Department of Neurobiology, The University of Chicago, Chicago, IL 60637, USA
| | - Ruitu Lyu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Zhongyu Zou
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Mengjie Chen
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Committee on Immunology, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| |
Collapse
|
37
|
Uzonyi A, Dierks D, Nir R, Kwon OS, Toth U, Barbosa I, Burel C, Brandis A, Rossmanith W, Le Hir H, Slobodin B, Schwartz S. Exclusion of m6A from splice-site proximal regions by the exon junction complex dictates m6A topologies and mRNA stability. Mol Cell 2023; 83:237-251.e7. [PMID: 36599352 DOI: 10.1016/j.molcel.2022.12.026] [Citation(s) in RCA: 66] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 11/04/2022] [Accepted: 12/21/2022] [Indexed: 01/05/2023]
Abstract
N6-methyladenosine (m6A), a widespread destabilizing mark on mRNA, is non-uniformly distributed across the transcriptome, yet the basis for its selective deposition is unknown. Here, we propose that m6A deposition is not selective. Instead, it is exclusion based: m6A consensus motifs are methylated by default, unless they are within a window of ∼100 nt from a splice junction. A simple model which we extensively validate, relying exclusively on presence of m6A motifs and exon-intron architecture, allows in silico recapitulation of experimentally measured m6A profiles. We provide evidence that exclusion from splice junctions is mediated by the exon junction complex (EJC), potentially via physical occlusion, and that previously observed associations between exon-intron architecture and mRNA decay are mechanistically mediated via m6A. Our findings establish a mechanism coupling nuclear mRNA splicing and packaging with the covalent installation of m6A, in turn controlling cytoplasmic decay.
Collapse
Affiliation(s)
- Anna Uzonyi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7630031, Israel
| | - David Dierks
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7630031, Israel
| | - Ronit Nir
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7630031, Israel
| | - Oh Sung Kwon
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Ursula Toth
- Center for Anatomy & Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Isabelle Barbosa
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Cindy Burel
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Alexander Brandis
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7630031, Israel
| | - Walter Rossmanith
- Center for Anatomy & Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Hervé Le Hir
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Boris Slobodin
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7630031, Israel; Department of Biochemistry, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa 31096, Israel.
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7630031, Israel.
| |
Collapse
|
38
|
Lupan BM, Solecki RA, Musso CM, Alsina FC, Silver DL. The exon junction complex component EIF4A3 is essential for mouse and human cortical progenitor mitosis and neurogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.13.524010. [PMID: 36711736 PMCID: PMC9882224 DOI: 10.1101/2023.01.13.524010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Mutations in components of the exon junction complex (EJC) are associated with neurodevelopment and disease. In particular, reduced levels of the RNA helicase EIF4A3 cause Richieri-Costa-Pereira Syndrome (RCPS) and CNVs are linked to intellectual disability. Consistent with this, Eif4a3 haploinsufficient mice are microcephalic. Altogether, this implicates EIF4A3 in cortical development; however, the underlying mechanisms are poorly understood. Here, we use mouse and human models to demonstrate that EIF4A3 promotes cortical development by controlling progenitor mitosis, cell fate, and survival. Eif4a3 haploinsufficiency in mice causes extensive cell death and impairs neurogenesis. Using Eif4a3 ; p53 compound mice, we show that apoptosis is most impactful for early neurogenesis, while additional p53-independent mechanisms contribute to later stages. Live imaging of mouse and human neural progenitors reveals Eif4a3 controls mitosis length, which influences progeny fate and viability. These phenotypes are conserved as cortical organoids derived from RCPS iPSCs exhibit aberrant neurogenesis. Finally, using rescue experiments we show that EIF4A3 controls neuron generation via the EJC. Altogether, our study demonstrates that EIF4A3 mediates neurogenesis by controlling mitosis duration and cell survival, implicating new mechanisms underlying EJC-mediated disorders. Summary statement This study shows that EIF4A3 mediates neurogenesis by controlling mitosis duration in both mouse and human neural progenitors, implicating new mechanisms underlying neurodevelopmental disorders.
Collapse
|
39
|
V M DD, Sivaramakrishnan V, Arvind Kumar K. Structural systems biology approach delineate the functional implications of SNPs in exon junction complex interaction network. J Biomol Struct Dyn 2023; 41:11969-11986. [PMID: 36617892 DOI: 10.1080/07391102.2022.2164355] [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: 02/03/2022] [Accepted: 12/26/2022] [Indexed: 01/10/2023]
Abstract
In eukaryotes, transcripts that carry premature termination codons (PTC) leading to truncated proteins are degraded by the Nonsense Mediated Decay (NMD) machinery. Missense and nonsense Single Nucleotide Polymorphisms (SNPs) in proteins belonging to Exon junction complex (EJC) and up-frameshift protein (UPF) will compromise NMD leading to the accumulation of truncated proteins in various diseases. The EJC and UPF which are involved in NMD is a good model system to study the effect of SNPs at a system level. Despite the availability of crystal structures, computational tools, and data on mutational and deletion studies, with functional implications, an integrated effort to understand the impact of SNPs at the systems level is lacking. To study the functional consequences of missense SNPs, sequence-based techniques like SIFT and PolyPhen which classify SNPs as deleterious or non-deleterious and structure-based methods like FoldX which calculate the Delta Delta G, (ddGs, ∆∆G) are used. Using FoldX, the ddG for mutations with experimentally validated functional effects is calculated and compared with those calculated for SNPs in the same protein-protein interaction interface. Further, a model is conceived to explain the functional implications of SNPs based on the effects observed for known mutants. The results are visualized in a network format. The effects of nonsense mutations are discerned by comparing with deletion mutation studies and loss of interaction in the crystal structure. The present work not only integrates genomics, proteomics, and classical genetics with 'Structural Biology' but also helps to integrate it into a 'systems-level functional network'.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Datta Darshan V M
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
| | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
| | - K Arvind Kumar
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| |
Collapse
|
40
|
Yang X, Triboulet R, Liu Q, Sendinc E, Gregory RI. Exon junction complex shapes the m 6A epitranscriptome. Nat Commun 2022; 13:7904. [PMID: 36550132 PMCID: PMC9780246 DOI: 10.1038/s41467-022-35643-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
N6-methyladenosine (m6A), the most abundant modification of mRNA, is essential for normal development and dysregulation promotes cancer. m6A is highly enriched in the 3' untranslated region (UTR) of a large subset of mRNAs to influence mRNA stability and/or translation. However, the mechanism responsible for the observed m6A distribution remains enigmatic. Here we find the exon junction complex shapes the m6A landscape by blocking METTL3-mediated m6A modification close to exon junctions within coding sequence (CDS). Depletion of EIF4A3, a core component of the EJC, causes increased METTL3 binding and m6A modification of short internal exons, and sites close to exon-exon junctions within mRNA. Reporter gene experiments further support the role of splicing and EIF4A3 deposition in controlling m6A modification via the local steric blockade of METTL3. Our results explain how characteristic patterns of m6A mRNA modification are established and uncover a role of the EJC in shaping the m6A epitranscriptome.
Collapse
Affiliation(s)
- Xin Yang
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Robinson Triboulet
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Twentyeight-Seven Therapeutics, Watertown, MA, 02472, USA
| | - Qi Liu
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
| | - Erdem Sendinc
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Richard I Gregory
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, 02115, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
- Harvard Initiative for RNA Medicine, Boston, MA, 02115, USA.
| |
Collapse
|
41
|
Li D, Yang J, Malik V, Huang Y, Huang X, Zhou H, Wang J. An RNAi screen of RNA helicases identifies eIF4A3 as a regulator of embryonic stem cell identity. Nucleic Acids Res 2022; 50:12462-12479. [PMID: 36416264 PMCID: PMC9757061 DOI: 10.1093/nar/gkac1084] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 10/21/2022] [Accepted: 10/26/2022] [Indexed: 11/24/2022] Open
Abstract
RNA helicases are involved in multiple steps of RNA metabolism to direct their roles in gene expression, yet their functions in pluripotency control remain largely unexplored. Starting from an RNA interference (RNAi) screen of RNA helicases, we identified that eIF4A3, a DEAD-box (Ddx) helicase component of the exon junction complex (EJC), is essential for the maintenance of embryonic stem cells (ESCs). Mechanistically, we show that eIF4A3 post-transcriptionally controls the pluripotency-related cell cycle regulators and that its depletion causes the loss of pluripotency via cell cycle dysregulation. Specifically, eIF4A3 is required for the efficient nuclear export of Ccnb1 mRNA, which encodes Cyclin B1, a key component of the pluripotency-promoting pathway during the cell cycle progression of ESCs. Our results reveal a previously unappreciated role for eIF4A3 and its associated EJC in maintaining stem cell pluripotency through post-transcriptional control of the cell cycle.
Collapse
Affiliation(s)
- Dan Li
- Department of Medicine, Columbia Center for Human Development and Stem Cell Therapies, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Cell, Developmental and Regenerative Biology; The Black Family Stem Cell Institute; Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jihong Yang
- Department of Medicine, Columbia Center for Human Development and Stem Cell Therapies, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Vikas Malik
- Department of Medicine, Columbia Center for Human Development and Stem Cell Therapies, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Yuting Huang
- Department of Medicine, Columbia Center for Human Development and Stem Cell Therapies, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Xin Huang
- Department of Medicine, Columbia Center for Human Development and Stem Cell Therapies, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Hongwei Zhou
- Department of Medicine, Columbia Center for Human Development and Stem Cell Therapies, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jianlong Wang
- Department of Medicine, Columbia Center for Human Development and Stem Cell Therapies, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| |
Collapse
|
42
|
Jakt LM, Dubin A, Johansen SD. Intron size minimisation in teleosts. BMC Genomics 2022; 23:628. [PMID: 36050638 PMCID: PMC9438311 DOI: 10.1186/s12864-022-08760-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 07/13/2022] [Indexed: 11/17/2022] Open
Abstract
Background Spliceosomal introns are parts of primary transcripts that are removed by RNA splicing. Although introns apparently do not contribute to the function of the mature transcript, in vertebrates they comprise the majority of the transcribed region increasing the metabolic cost of transcription. The persistence of long introns across evolutionary time suggests functional roles that can offset this metabolic cost. The teleosts comprise one of the largest vertebrate clades. They have unusually compact and variable genome sizes and provide a suitable system for analysing intron evolution. Results We have analysed intron lengths in 172 vertebrate genomes and show that teleost intron lengths are relatively short, highly variable and bimodally distributed. Introns that were long in teleosts were also found to be long in mammals and were more likely to be found in regulatory genes and to contain conserved sequences. Our results argue that intron length has decreased in parallel in a non-random manner throughout teleost evolution and represent a deviation from the ancestral state. Conclusion Our observations indicate an accelerated rate of intron size evolution in the teleosts and that teleost introns can be divided into two classes by their length. Teleost intron sizes have evolved primarily as a side-effect of genome size evolution and small genomes are dominated by short introns (<256 base pairs). However, a non-random subset of introns has resisted this process across the teleosts and these are more likely have functional roles in all vertebrate clades. Supplementary Information The online version contains supplementary material available at (10.1186/s12864-022-08760-w).
Collapse
Affiliation(s)
- Lars Martin Jakt
- Faculty for bioscience and aquaculture, Nord University, Universitetsalléen 11, Bodoe, 8026, Norway.
| | - Arseny Dubin
- Faculty for bioscience and aquaculture, Nord University, Universitetsalléen 11, Bodoe, 8026, Norway.,Currently at: Parental Investment and Immune Dynamics, GEOMAR Helmholtz Centre for Ocean Research, Düsternbrookerweg 20, Kiel, D-24105, Germany
| | - Steinar Daae Johansen
- Faculty for bioscience and aquaculture, Nord University, Universitetsalléen 11, Bodoe, 8026, Norway
| |
Collapse
|
43
|
Karousis ED, Mühlemann O. The broader sense of nonsense. Trends Biochem Sci 2022; 47:921-935. [PMID: 35780009 DOI: 10.1016/j.tibs.2022.06.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/30/2022] [Accepted: 06/08/2022] [Indexed: 12/21/2022]
Abstract
The term 'nonsense-mediated mRNA decay' (NMD) was initially coined to describe the translation-dependent degradation of mRNAs harboring premature termination codons (PTCs), but it is meanwhile known that NMD also targets many canonical mRNAs with numerous biological implications. The molecular mechanisms determining on which RNAs NMD ensues are only partially understood. Considering the broad range of NMD-sensitive RNAs and the variable degrees of their degradation, we highlight here the hallmarks of mammalian NMD and point out open questions. We review the links between NMD and disease by summarizing the role of NMD in cancer, neurodegeneration, and viral infections. Finally, we describe strategies to modulate NMD activity and specificity as potential therapeutic approaches for various diseases.
Collapse
Affiliation(s)
- Evangelos D Karousis
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.
| | - Oliver Mühlemann
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.
| |
Collapse
|
44
|
Luo D, Singh NN, Singh RN. Internal Introns Promote Backsplicing to Generate Circular RNAs from Spinal Muscular Atrophy Gene. Genes (Basel) 2022; 13:1145. [PMID: 35885927 PMCID: PMC9323214 DOI: 10.3390/genes13071145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 06/23/2022] [Accepted: 06/23/2022] [Indexed: 01/27/2023] Open
Abstract
Human survival motor neuron 1 (SMN1) codes for SMN, an essential housekeeping protein involved in most aspects of RNA metabolism. Deletions or mutations of SMN1 lead to spinal muscular atrophy (SMA), a devastating neurodegenerative disease linked to a high rate of infant mortality. SMN2, a near identical copy of SMN1 present in humans, cannot compensate for the loss of SMN1 due to predominant skipping of SMN2 exon 7. Restoration of SMN by splicing modulation of SMN2 exon 7 or gene replacement are currently approved therapies of SMA. Human SMN genes produce a vast repertoire of circular RNAs (circRNAs). However, the mechanism of SMN circRNA generation has not yet been examined in detail. For example, it remains unknown if forward splicing impacts backsplicing that generates circRNAs containing multiple exons. Here, we employed SMN as a model system to examine the impact of intronic sequences on the generation of circRNAs. We performed our experiments in HeLa cells transiently transfected with minigenes expressing three abundantly represented circRNAs containing two or more SMN exons. We observed an enhanced rate of circRNA generation when introns joining exons to be incorporated into circRNAs were present as compared to the intronless context. These results underscore the stimulatory effect of forward splicing in the generation of circRNAs containing multiple exons. These findings are consistent with the reported low abundance of SMN circRNAs comprised of single exons. We confirmed our findings using inducible HEK 293 cells stably expressing the SMN circRNAs. Our results support the role of the exon junction complex in the generation of the exon-only-containing circRNAs. We showed that SMN circRNAs were preferentially localized in the cytoplasm. These findings provide new insights regarding our understanding of circRNA generation and open avenues to uncover novel functions of the SMN genes.
Collapse
Affiliation(s)
| | | | - Ravindra Narayan Singh
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (D.L.); (N.N.S.)
| |
Collapse
|
45
|
Qu Z, Yang KD, Luo BH, Zhang F. CAFs-secreted exosomal cricN4BP2L2 promoted colorectal cancer stemness and chemoresistance by interacting with EIF4A3. Exp Cell Res 2022; 418:113266. [PMID: 35752345 DOI: 10.1016/j.yexcr.2022.113266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 06/13/2022] [Accepted: 06/19/2022] [Indexed: 02/07/2023]
Abstract
Cancer-associated fibroblasts secreted exosomes (CAFs-exo) are important for tumor carcinogenesis and chemoresistance, but its underlying mechanism in colorectal cancer (CRC) has not yet been clarified. In this study, we investigated the regulatory mechanism of CAFs-exo cricN4BP2L2 on the proliferation, apoptosis, stemness and chemoresistance of LoVo cells. We found that CAFs-exo promoted the oxaliplatin resistance and stemness of LoVo cells, while inhibited the LoVo cell apoptosis. Moreover, knockdown of cricN4BP2L2 in CAFs-exo inhibited the oxaliplatin resistance and stemness characteristics of LoVo cells. Mechanistically, cricN4BP2L2 regulated PI3K/AKT/mTOR axis by binding to EIF4A3. Rescue experiments proved that CAFs-derived exosomal cricN4BP2L2 promoted CRC cells stemness and oxaliplatin resistance by upregulating EIF4A3. Moreover, in vivo experiments showed that depletion of cricN4BP2L2 suppressed CRC tumorigenesis growth. In conclusion, CAFs-exo cricN4BP2L2 promoted the CRC cells stemness and oxaliplatin resistance through EIF4A3/PI3K/AKT/mTOR pathway.
Collapse
Affiliation(s)
- Zhan Qu
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, PR China
| | - Ke-Da Yang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, PR China
| | - Bai-Hua Luo
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, PR China
| | - Fan Zhang
- Department of Gynecology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, PR China.
| |
Collapse
|
46
|
Kim YJ, Nomakuchi T, Papaleonidopoulou F, Yang L, Zhang Q, Krainer AR. Gene-specific nonsense-mediated mRNA decay targeting for cystic fibrosis therapy. Nat Commun 2022; 13:2978. [PMID: 35624092 PMCID: PMC9142507 DOI: 10.1038/s41467-022-30668-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 05/06/2022] [Indexed: 12/20/2022] Open
Abstract
Low CFTR mRNA expression due to nonsense-mediated mRNA decay (NMD) is a major hurdle in developing a therapy for cystic fibrosis (CF) caused by the W1282X mutation in the CFTR gene. CFTR-W1282X truncated protein retains partial function, so increasing its levels by inhibiting NMD of its mRNA will likely be beneficial. Because NMD regulates the normal expression of many genes, gene-specific stabilization of CFTR-W1282X mRNA expression is more desirable than general NMD inhibition. Synthetic antisense oligonucleotides (ASOs) designed to prevent binding of exon junction complexes (EJC) downstream of premature termination codons (PTCs) attenuate NMD in a gene-specific manner. We describe cocktails of three ASOs that specifically increase the expression of CFTR-W1282X mRNA and CFTR protein upon delivery into human bronchial epithelial cells. This treatment increases the CFTR-mediated chloride current. These results set the stage for clinical development of an allele-specific therapy for CF caused by the W1282X mutation. The W1282X nonsense mutation in the CFTR gene causes cystic fibrosis by reducing its mRNA and functional protein levels. Here the authors developed antisense-oligonucleotide cocktails that restore CFTR protein function by gene-specific stabilization of CFTR mRNA.
Collapse
Affiliation(s)
- Young Jin Kim
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.,Graduate Program in Genetics, Stony Brook University, Stony Brook, NY, 11794, USA.,Medical Scientist Training Program, Stony Brook University School of Medicine, Stony Brook, NY, 11794, USA
| | - Tomoki Nomakuchi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.,Medical Scientist Training Program, Stony Brook University School of Medicine, Stony Brook, NY, 11794, USA.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Foteini Papaleonidopoulou
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.,Francis Crick Institute, London, 1140062, UK
| | - Lucia Yang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.,Graduate Program in Genetics, Stony Brook University, Stony Brook, NY, 11794, USA.,Medical Scientist Training Program, Stony Brook University School of Medicine, Stony Brook, NY, 11794, USA
| | - Qian Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.,Graduate Program in Molecular and Cell Biology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.
| |
Collapse
|
47
|
Biswas B, Chaaban R, Chakraborty S, Devaux A, Dian AL, Minello A, Singh JK, Vagner S, Uguen P, Lambert S, Dutertre M, Carreira A. At the crossroads of RNA biology, genome integrity and cancer. Bull Cancer 2022; 109:728-735. [PMID: 35597618 DOI: 10.1016/j.bulcan.2022.02.014] [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: 12/20/2021] [Revised: 02/16/2022] [Accepted: 02/21/2022] [Indexed: 10/18/2022]
Abstract
This article is the synthesis of the scientific presentations that took place during two international courses at Institute Curie, one on post-transcriptional gene regulation and the other on genome instability and human disease, that were joined together in their 2021 edition. This joined course brought together the knowledge on RNA metabolism and the maintenance of genome stability.
Collapse
Affiliation(s)
- Biswendu Biswas
- CNRS UMR 3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Rady Chaaban
- CNRS UMR 3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Shrena Chakraborty
- CNRS UMR 3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Alexandre Devaux
- CNRS UMR 3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Ana Luisa Dian
- CNRS UMR 3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Anna Minello
- CNRS UMR 3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Jenny Kaur Singh
- CNRS UMR 3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Stephan Vagner
- CNRS UMR 3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Patricia Uguen
- CNRS UMR 3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France.
| | - Sarah Lambert
- CNRS UMR 3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Martin Dutertre
- CNRS UMR 3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Aura Carreira
- CNRS UMR 3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| |
Collapse
|
48
|
No-nonsense: insights into the functional interplay of nonsense-mediated mRNA decay factors. Biochem J 2022; 479:973-993. [PMID: 35551602 PMCID: PMC9162471 DOI: 10.1042/bcj20210556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 04/10/2022] [Accepted: 04/12/2022] [Indexed: 11/22/2022]
Abstract
Nonsense-mediated messenger RNA decay (NMD) represents one of the main surveillance pathways used by eukaryotic cells to control the quality and abundance of mRNAs and to degrade viral RNA. NMD recognises mRNAs with a premature termination codon (PTC) and targets them to decay. Markers for a mRNA with a PTC, and thus NMD, are a long a 3′-untranslated region and the presence of an exon-junction complex (EJC) downstream of the stop codon. Here, we review our structural understanding of mammalian NMD factors and their functional interplay leading to a branched network of different interconnected but specialised mRNA decay pathways. We discuss recent insights into the potential impact of EJC composition on NMD pathway choice. We highlight the coexistence and function of different isoforms of up-frameshift protein 1 (UPF1) with an emphasis of their role at the endoplasmic reticulum and during stress, and the role of the paralogs UPF3B and UPF3A, underscoring that gene regulation by mammalian NMD is tightly controlled and context-dependent being conditional on developmental stage, tissue and cell types.
Collapse
|
49
|
Yi Z, Arvola RM, Myers S, Dilsavor CN, Abu Alhasan R, Carter BN, Patton RD, Bundschuh R, Singh G. Mammalian UPF3A and UPF3B can activate nonsense-mediated mRNA decay independently of their exon junction complex binding. EMBO J 2022; 41:e109202. [PMID: 35451102 PMCID: PMC9108626 DOI: 10.15252/embj.2021109202] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 03/21/2022] [Accepted: 03/31/2022] [Indexed: 12/30/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is governed by the three conserved factors-UPF1, UPF2, and UPF3. While all three are required for NMD in yeast, UPF3B is dispensable for NMD in mammals, and its paralog UPF3A is suggested to only weakly activate or even repress NMD due to its weaker binding to the exon junction complex (EJC). Here, we characterize the UPF3A/B-dependence of NMD in human cell lines deleted of one or both UPF3 paralogs. We show that in human colorectal cancer HCT116 cells, NMD can operate in a UPF3B-dependent and -independent manner. While UPF3A is almost dispensable for NMD in wild-type cells, it strongly activates NMD in cells lacking UPF3B. Notably, NMD remains partially active in cells lacking both UPF3 paralogs. Complementation studies in these cells show that EJC-binding domain of UPF3 paralogs is dispensable for NMD. Instead, the conserved "mid" domain of UPF3 paralogs is consequential for their NMD activity. Altogether, our results demonstrate that the mammalian UPF3 proteins play a more active role in NMD than simply bridging the EJC and the UPF complex.
Collapse
Affiliation(s)
- Zhongxia Yi
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA.,Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - René M Arvola
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA.,Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - Sean Myers
- Department of Physics, The Ohio State University, Columbus, OH, USA
| | - Corinne N Dilsavor
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - Rabab Abu Alhasan
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA.,Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - Bayley N Carter
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - Robert D Patton
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA.,Department of Physics, The Ohio State University, Columbus, OH, USA
| | - Ralf Bundschuh
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA.,Department of Physics, The Ohio State University, Columbus, OH, USA.,Department of Chemistry and Biochemistry, The Ohio State University , Columbus, OH, USA.,Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Guramrit Singh
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA.,Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| |
Collapse
|
50
|
Oshizuki S, Matsumoto E, Tanaka S, Kataoka N. Mutations equivalent to Drosophila
mago nashi
mutants imply reduction of Magoh protein incorporation into exon junction complex. Genes Cells 2022; 27:505-511. [DOI: 10.1111/gtc.12941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/07/2022] [Accepted: 04/12/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Saya Oshizuki
- Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences Graduate School of Agriculture and Life Sciences, The University of Tokyo Japan
| | - Eri Matsumoto
- Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences Graduate School of Agriculture and Life Sciences, The University of Tokyo Japan
| | - Satoshi Tanaka
- Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences Graduate School of Agriculture and Life Sciences, The University of Tokyo Japan
| | - Naoyuki Kataoka
- Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences Graduate School of Agriculture and Life Sciences, The University of Tokyo Japan
- Laboratory for Malignancy Control Research, Medical Innovation Center Kyoto University Graduate School of Medicine Kyoto Japan
- Institute for Virus Research Kyoto University Kyoto Japan
| |
Collapse
|