1
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Sarvari P, Rubio K, Dobersch S, Ntokou A, Vallejo-Ruiz V. Editorial: Therapeutic targeting of splicing variants in cancer. Front Pharmacol 2023; 14:1206342. [PMID: 37214461 PMCID: PMC10196498 DOI: 10.3389/fphar.2023.1206342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 04/20/2023] [Indexed: 05/24/2023] Open
Affiliation(s)
| | - Karla Rubio
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Mexico
- Laboratoire IMoPA, Université de Lorraine, CNRS, UMR 7365, Nancy, France
| | - Stephanie Dobersch
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Aglaia Ntokou
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, New Haven, CT, United States
- Yale Department of Genetics, New Haven, CT, United States
| | - Verónica Vallejo-Ruiz
- Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social, Puebla, Mexico
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2
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Abedsaeidi M, Hojjati F, Tavassoli A, Sahebkar A. Biology of Tenascin C and its role in physiology and pathology. Curr Med Chem 2023:CMC-EPUB-130686. [PMID: 37021423 DOI: 10.2174/0929867330666230404124229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 01/25/2023] [Accepted: 02/10/2023] [Indexed: 04/07/2023]
Abstract
Tenascin-C (TNC) is a multimodular extracellular matrix (ECM) protein hexameric with several molecular forms (180-250 kDa) produced by alternative splicing at the pre-mRNA level and protein modifications. The molecular phylogeny indicates that the amino acid sequence of TNC is a well-conserved protein among vertebrates. TNC has binding partners, including fibronectin, collagen, fibrillin-2, periostin, proteoglycans, and pathogens. Various transcription factors and intracellular regulators tightly regulate TNC expression. TNC plays an essential role in cell proliferation and migration. Unlike embryonic tissues, TNC protein is distributed over a few tissues in adults. However, higher TNC expression is observed in inflammation, wound healing, cancer, and other pathological conditions. It is widely expressed in a variety of human malignancies and is recognized as a pivotal factor in cancer progression and metastasis. Moreover, TNC increases both pro-and anti-inflammatory signaling pathways. It has been identified as an essential factor in tissue injuries such as damaged skeletal muscle, heart disease, and kidney fibrosis. This multimodular hexameric glycoprotein modulates both innate and adaptive immune responses regulating the expression of numerous cytokines. Moreover, TNC is an important regulatory molecule that affects the onset and progression of neuronal disorders through many signaling pathways. We provide a comprehensive overview of the structural and expression properties of TNC and its potential functions in physiological and pathological conditions.
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Affiliation(s)
- Malihehsadat Abedsaeidi
- Department of Basic Sciences, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Farzaneh Hojjati
- Division of industrial and environmental biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Amin Tavassoli
- Division of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Amirhossein Sahebkar
- Division of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
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3
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Barraza SJ, Bhattacharyya A, Trotta CR, Woll MG. Targeting strategies for modulating pre-mRNA splicing with small molecules: Recent advances. Drug Discov Today 2023; 28:103431. [PMID: 36356786 DOI: 10.1016/j.drudis.2022.103431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/27/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022]
Abstract
The concept of using small molecules to therapeutically modulate pre-mRNA splicing was validated with the US Food and Drug Administration (FDA) approval of Evrysdi® (risdiplam) in 2020. Since then, efforts have continued unabated toward the discovery of new splicing-modulating drugs. However, the drug development world has evolved in the 10 years since risdiplam precursors were first identified in high-throughput screening (HTS). Now, new mechanistic insights into RNA-processing pathways and regulatory networks afford increasingly feasible targeted approaches. In this review, organized into classes of biological target, we compile and summarize small molecules discovered, devised, and developed since 2020 to alter pre-mRNA splicing.
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Affiliation(s)
- Scott J Barraza
- PTC Therapeutics, Inc., 100 Corporate Court, South Plainfield, NJ, USA.
| | | | | | - Matthew G Woll
- PTC Therapeutics, Inc., 100 Corporate Court, South Plainfield, NJ, USA
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4
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Hatch ST, Smargon AA, Yeo GW. Engineered U1 snRNAs to modulate alternatively spliced exons. Methods 2022; 205:140-148. [PMID: 35764245 DOI: 10.1016/j.ymeth.2022.06.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 05/30/2022] [Accepted: 06/23/2022] [Indexed: 10/17/2022] Open
Abstract
Alternative splicing accounts for a considerable portion of transcriptomic diversity, as most protein-coding genes are spliced into multiple mRNA isoforms. However, errors in splicing patterns can give rise to mis-splicing with pathological consequences, such as the congenital diseases familial dysautonomia, Duchenne muscular dystrophy, and spinal muscular atrophy. Small nuclear RNA (snRNA) components of the U snRNP family have been proposed as a therapeutic modality for the treatment of mis-splicing. U1 snRNAs offer great promise, with prior studies demonstrating in vivo efficacy, suggesting additional preclinical development is merited. Improvements in enabling technologies, including screening methodologies, gene delivery vectors, and relevant considerations from gene editing approaches justify further advancement of U1 snRNA as a therapeutic and research tool. With the goal of providing a user-friendly protocol, we compile and demonstrate a methodological toolkit for sequence-specific targeted perturbation of alternatively spliced pre-mRNA with engineered U1 snRNAs. We observe robust modulation of endogenous pre-mRNA transcripts targeted in two contrasting splicing contexts, SMN2 exon 7 and FAS exon 6, exhibiting the utility and applicability of engineered U1 snRNA to both inclusion and exclusion of targeted exons. We anticipate that these demonstrations will contribute to the usability of U1 snRNA in investigating splicing modulation in eukaryotic cells, increasing accessibility to the broader research community.
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Affiliation(s)
- Samuel T Hatch
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA; Stem Cell Program, University of California San Diego, Sanford Consortium for Regenerative Medicine, La Jolla, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA; Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Aaron A Smargon
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA; Stem Cell Program, University of California San Diego, Sanford Consortium for Regenerative Medicine, La Jolla, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA; Stem Cell Program, University of California San Diego, Sanford Consortium for Regenerative Medicine, La Jolla, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA; Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA.
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5
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Pan YJ, Liu BW, Pei DS. The Role of Alternative Splicing in Cancer: Regulatory Mechanism, Therapeutic Strategy, and Bioinformatics Application. DNA Cell Biol 2022; 41:790-809. [PMID: 35947859 DOI: 10.1089/dna.2022.0322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
[Formula: see text] Alternative splicing (AS) can generate distinct transcripts and subsequent isoforms that play differential functions from the same pre-mRNA. Recently, increasing numbers of studies have emerged, unmasking the association between AS and cancer. In this review, we arranged AS events that are closely related to cancer progression and presented promising treatments based on AS for cancer therapy. Obtaining proliferative capacity, acquiring invasive properties, gaining angiogenic features, shifting metabolic ability, and getting immune escape inclination are all splicing events involved in biological processes. Spliceosome-targeted and antisense oligonucleotide technologies are two novel strategies that are hopeful in tumor therapy. In addition, bioinformatics applications based on AS were summarized for better prediction and elucidation of regulatory routines mingled in. Together, we aimed to provide a better understanding of complicated AS events associated with cancer biology and reveal AS a promising target of cancer treatment in the future.
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Affiliation(s)
- Yao-Jie Pan
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, China
| | - Bo-Wen Liu
- Department of General Surgery, Xuzhou Medical University, Xuzhou, China
| | - Dong-Sheng Pei
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, China
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6
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Rosenkranz RRE, Ullrich S, Löchli K, Simm S, Fragkostefanakis S. Relevance and Regulation of Alternative Splicing in Plant Heat Stress Response: Current Understanding and Future Directions. Front Plant Sci 2022; 13:911277. [PMID: 35812973 PMCID: PMC9260394 DOI: 10.3389/fpls.2022.911277] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 05/26/2022] [Indexed: 05/26/2023]
Abstract
Alternative splicing (AS) is a major mechanism for gene expression in eukaryotes, increasing proteome diversity but also regulating transcriptome abundance. High temperatures have a strong impact on the splicing profile of many genes and therefore AS is considered as an integral part of heat stress response. While many studies have established a detailed description of the diversity of the RNAome under heat stress in different plant species and stress regimes, little is known on the underlying mechanisms that control this temperature-sensitive process. AS is mainly regulated by the activity of splicing regulators. Changes in the abundance of these proteins through transcription and AS, post-translational modifications and interactions with exonic and intronic cis-elements and core elements of the spliceosomes modulate the outcome of pre-mRNA splicing. As a major part of pre-mRNAs are spliced co-transcriptionally, the chromatin environment along with the RNA polymerase II elongation play a major role in the regulation of pre-mRNA splicing under heat stress conditions. Despite its importance, our understanding on the regulation of heat stress sensitive AS in plants is scarce. In this review, we summarize the current status of knowledge on the regulation of AS in plants under heat stress conditions. We discuss possible implications of different pathways based on results from non-plant systems to provide a perspective for researchers who aim to elucidate the molecular basis of AS under high temperatures.
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Affiliation(s)
| | - Sarah Ullrich
- Molecular Cell Biology of Plants, Goethe University Frankfurt, Frankfurt, Germany
| | - Karin Löchli
- Molecular Cell Biology of Plants, Goethe University Frankfurt, Frankfurt, Germany
| | - Stefan Simm
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
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7
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Liu Y, Sheng W, Wu J, Zheng J, Zhi X, Zhang S, Gu C, Guo D, Wang W. Case report: Altered pre-mRNA splicing caused by intronic variant c.1499 + 1G > A in the SLC4A4 gene. Front Pediatr 2022; 10:890147. [PMID: 36061388 PMCID: PMC9428394 DOI: 10.3389/fped.2022.890147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 07/25/2022] [Indexed: 11/29/2022] Open
Abstract
Proximal renal tubular acidosis (pRTA) with ocular abnormalities is an autosomal recessive disease caused by variants in the Solute Carrier Family 4 Member 4 (SLC4A4) gene. Patients present with metabolic acidosis and low plasma bicarbonate concentration (3∼17 mmol/L). In addition, they are often accompanied by ocular abnormalities, intellectual disability, and growth retardation. The patient underwent whole exome sequencing (WES) and bioinformatics analysis of variant pathogenicity in this study. Then, a minigene assay was conducted to analyze the splicing site variant further. Compound heterozygous variants in the SLC4A4 gene (NM_003759.3), c.145C > T (p.Arg49*) and c.1499 + 1G > A, were detected by WES. The minigene assay showed an mRNA splicing aberration caused by the c.1499 + 1G > A variant. Compared with the wild type, the mutant type caused 4-base insertion between exons 10 and 11 of SLC4A4 after expression in HEK293 cells. In conclusion, the c.1499 + 1G > A variant in the SLC4A4 gene may be one of the genetic causes in the patient. Moreover, our study provides the foundation for future gene therapy of such pathogenic variants.
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Affiliation(s)
- Yan Liu
- Department of Nephrology, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China
| | - Wenchao Sheng
- Graduate College of Tianjin Medical University, Tianjin Medical University, Tianjin, China.,Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China.,Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, China
| | - Jinying Wu
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China.,Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, China
| | - Jie Zheng
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China.,Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, China
| | - Xiufang Zhi
- Graduate College of Tianjin Medical University, Tianjin Medical University, Tianjin, China.,Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China.,Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, China
| | - Shuyue Zhang
- Graduate College of Tianjin Medical University, Tianjin Medical University, Tianjin, China.,Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China.,Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, China
| | - Chunyu Gu
- Graduate College of Tianjin Medical University, Tianjin Medical University, Tianjin, China.,Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China.,Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, China
| | - Detong Guo
- Graduate College of Tianjin Medical University, Tianjin Medical University, Tianjin, China.,Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China.,Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, China
| | - Wenhong Wang
- Department of Nephrology, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China
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8
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Punzo P, Grillo S, Batelli G. Alternative splicing in plant abiotic stress responses. Biochem Soc Trans 2020; 48:2117-26. [PMID: 32869832 DOI: 10.1042/BST20200281] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 08/05/2020] [Accepted: 08/07/2020] [Indexed: 02/06/2023]
Abstract
Modifications of the cellular proteome pool upon stress allow plants to tolerate environmental changes. Alternative splicing is the most significant mechanism responsible for the production of multiple protein isoforms from a single gene. The spliceosome, a large ribonucleoprotein complex, together with several associated proteins, controls this pre-mRNA processing, adding an additional level of regulation to gene expression. Deep sequencing of transcriptomes revealed that this co- or post-transcriptional mechanism is highly induced by abiotic stress, and concerns vast numbers of stress-related genes. Confirming the importance of splicing in plant stress adaptation, key players of stress signaling have been shown to encode alternative transcripts, whereas mutants lacking splicing factors or associated components show a modified sensitivity and defective responses to abiotic stress. Here, we examine recent literature on alternative splicing and splicing alterations in response to environmental stresses, focusing on its role in stress adaptation and analyzing the future perspectives and directions for research.
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9
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Ma J, Du WW, Zeng K, Wu N, Fang L, Lyu J, Yee AJ, Yang BB. An antisense circular RNA circSCRIB enhances cancer progression by suppressing parental gene splicing and translation. Mol Ther 2021; 29:2754-2768. [PMID: 34365033 DOI: 10.1016/j.ymthe.2021.08.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/29/2021] [Accepted: 07/31/2021] [Indexed: 11/25/2022] Open
Abstract
Circular RNAs (circRNAs) represent a large group of non-coding RNAs that are widely detected in mammalian cells. Although most circRNAs are generated in a sense orientation, there is a group of circRNAs that are synthesized in an antisense orientation. High-throughput analysis of breast cancer specimens revealed a significant enrichment of 209 antisense circRNAs. The tumor suppressor SCRIB was shown to potentially produce thirteen circRNAs, three of which are in an antisense orientation. Among these three circRNAs, circSCRIB (hsa_circ_0001831) was the most enriched in the breast cancer panel. This antisense SCRIB circRNA was shown to span one intron and two exons. We hypothesized that this circRNA could decrease pre-mRNA splicing and mRNA translation. To test this, we generated a hsa_circ_0001831 expression construct. We found that there was decreased SCRIB mRNA production but increased cancer cell proliferation, migration, and invasion. In comparison, an exonic sequence construct did not affect mRNA splicing but decreased protein translation, leading to increased E-cadherin expression and decreased expression of N-cadherin and vimentin. Thus, there was increased cell migration, invasion, proliferation, colony formation, and tumorigenesis. Our study suggests a novel modulatory role of antisense circRNAs on their parental transcripts. This may represent a promising approach for developing circRNA-directed therapy.
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Affiliation(s)
- Jian Ma
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, ON, Canada
| | - William W Du
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, ON, Canada
| | - Kaixuan Zeng
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, ON, Canada
| | - Nan Wu
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, ON, Canada
| | - Ling Fang
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, ON, Canada; China-Japan Union Hospital of Jilin University, Jilin, China
| | - Juanjuan Lyu
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, ON, Canada
| | - Albert J Yee
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, ON, Canada
| | - Burton B Yang
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
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10
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Skalska L, Begley V, Beltran M, Lukauskas S, Khandelwal G, Faull P, Bhamra A, Tavares M, Wellman R, Tvardovskiy A, Foster BM, Ruiz de Los Mozos I, Herrero J, Surinova S, Snijders AP, Bartke T, Jenner RG. Nascent RNA antagonizes the interaction of a set of regulatory proteins with chromatin. Mol Cell 2021; 81:2944-2959.e10. [PMID: 34166609 DOI: 10.1016/j.molcel.2021.05.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 05/19/2021] [Accepted: 05/23/2021] [Indexed: 12/30/2022]
Abstract
A number of regulatory factors are recruited to chromatin by specialized RNAs. Whether RNA has a more general role in regulating the interaction of proteins with chromatin has not been determined. We used proteomics methods to measure the global impact of nascent RNA on chromatin in embryonic stem cells. Surprisingly, we found that nascent RNA primarily antagonized the interaction of chromatin modifiers and transcriptional regulators with chromatin. Transcriptional inhibition and RNA degradation induced recruitment of a set of transcriptional regulators, chromatin modifiers, nucleosome remodelers, and regulators of higher-order structure. RNA directly bound to factors, including BAF, NuRD, EHMT1, and INO80 and inhibited their interaction with nucleosomes. The transcriptional elongation factor P-TEFb directly bound pre-mRNA, and its recruitment to chromatin upon Pol II inhibition was regulated by the 7SK ribonucleoprotein complex. We postulate that by antagonizing the interaction of regulatory proteins with chromatin, nascent RNA links transcriptional output with chromatin composition.
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Affiliation(s)
- Lenka Skalska
- UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London WC1E 6BT, UK
| | - Victoria Begley
- UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London WC1E 6BT, UK
| | - Manuel Beltran
- UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London WC1E 6BT, UK
| | - Saulius Lukauskas
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Garima Khandelwal
- UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London WC1E 6BT, UK
| | - Peter Faull
- The Francis Crick Institute, London NW1 1AT, UK
| | - Amandeep Bhamra
- Proteomics Research Translational Technology Platform, UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London WC1E 6BT, UK
| | - Manuel Tavares
- UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London WC1E 6BT, UK
| | - Rachel Wellman
- UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London WC1E 6BT, UK
| | - Andrey Tvardovskiy
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Benjamin M Foster
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Igor Ruiz de Los Mozos
- The Francis Crick Institute, London NW1 1AT, UK; Institute of Neurology, UCL, London WC1N 3BG, UK
| | - Javier Herrero
- UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London WC1E 6BT, UK
| | - Silvia Surinova
- Proteomics Research Translational Technology Platform, UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London WC1E 6BT, UK
| | | | - Till Bartke
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Richard G Jenner
- UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London WC1E 6BT, UK.
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11
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Tomski A, Zakarczemny M. Stochastic Gene Expression Revisited. Genes (Basel) 2021; 12:648. [PMID: 33926131 PMCID: PMC8145461 DOI: 10.3390/genes12050648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/20/2021] [Accepted: 04/22/2021] [Indexed: 11/17/2022] Open
Abstract
We investigate the model of gene expression in the form of Iterated Function System (IFS), where the probability of choice of any iterated map depends on the state of the phase space. Random jump times of the process mark activation periods of the gene when pre-mRNA molecules are produced before mRNA and protein processing phases occur. The main idea is inspired by the continuous-time piecewise deterministic Markov process describing stochastic gene expression. We show that for our system there exists a unique invariant limit measure. We provide full probabilistic description of the process with a comparison of our results to those obtained for the model with continuous time.
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Affiliation(s)
- Andrzej Tomski
- Institute of Mathematics, University of Silesia in Katowice, 40-007 Katowice, Poland;
| | - Maciej Zakarczemny
- Department of Applied Mathematics, Faculty of Computer Science and Telecommunications, Cracow University of Technology, 31-155 Cracow, Poland
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12
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Fang N, Ding GW, Ding H, Li J, Liu C, Lv L, Shi YJ. Research Progress of Circular RNA in Gastrointestinal Tumors. Front Oncol 2021; 11:665246. [PMID: 33937077 PMCID: PMC8082141 DOI: 10.3389/fonc.2021.665246] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 03/15/2021] [Indexed: 01/17/2023] Open
Abstract
circular RNA (circRNA) is a closed ring structure formed by cyclic covalent bonds connecting the 5’-end and 3’-end of pre-mRNA. circRNA is widely distributed in eukaryotic cells. Recent studies have shown that circRNA is involved in the pathogenesis and development of multiple types of diseases, including tumors. circRNA is specifically expressed in tissues. And the stability of circRNA is higher than that of linear RNA, which can play biological roles through sponge adsorption of miRNA, interaction with RNA binding protein, regulation of gene transcription, the mRNA and protein translation brake, and translation of protein and peptides. These characteristics render circRNAs as biomarkers and therapeutic targets of tumors. Gastrointestinal tumors are common malignancies worldwide, which seriously threaten human health. In this review, we summarize the generation and biological characteristics of circRNA, molecular regulation mechanism and related effects of circRNA in gastrointestinal tumors.
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Affiliation(s)
- Na Fang
- Department of Oncology, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China
| | - Guo-Wen Ding
- Department of Thoracic and Cardiovascular Surgery, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China
| | - Hao Ding
- Department of Respiratory, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China
| | - Juan Li
- Department of Oncology, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China
| | - Chao Liu
- Department of Thoracic and Cardiovascular Surgery, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China
| | - Lu Lv
- Department of Thoracic and Cardiovascular Surgery, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China
| | - Yi-Jun Shi
- Department of Thoracic and Cardiovascular Surgery, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China
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13
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Rosenkranz RRE, Bachiri S, Vraggalas S, Keller M, Simm S, Schleiff E, Fragkostefanakis S. Identification and Regulation of Tomato Serine/Arginine-Rich Proteins Under High Temperatures. Front Plant Sci 2021; 12:645689. [PMID: 33854522 PMCID: PMC8039515 DOI: 10.3389/fpls.2021.645689] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/03/2021] [Indexed: 05/15/2023]
Abstract
Alternative splicing is an important mechanism for the regulation of gene expression in eukaryotes during development, cell differentiation or stress response. Alterations in the splicing profiles of genes under high temperatures that cause heat stress (HS) can impact the maintenance of cellular homeostasis and thermotolerance. Consequently, information on factors involved in HS-sensitive alternative splicing is required to formulate the principles of HS response. Serine/arginine-rich (SR) proteins have a central role in alternative splicing. We aimed for the identification and characterization of SR-coding genes in tomato (Solanum lycopersicum), a plant extensively used in HS studies. We identified 17 canonical SR and two SR-like genes. Several SR-coding genes show differential expression and altered splicing profiles in different organs as well as in response to HS. The transcriptional induction of five SR and one SR-like genes is partially dependent on the master regulator of HS response, HS transcription factor HsfA1a. Cis-elements in the promoters of these SR genes were predicted, which can be putatively recognized by HS-induced transcription factors. Further, transiently expressed SRs show reduced or steady-state protein levels in response to HS. Thus, the levels of SRs under HS are regulated by changes in transcription, alternative splicing and protein stability. We propose that the accumulation or reduction of SRs under HS can impact temperature-sensitive alternative splicing.
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Affiliation(s)
- Remus R. E. Rosenkranz
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt am Main, Germany
| | - Samia Bachiri
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt am Main, Germany
| | - Stavros Vraggalas
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt am Main, Germany
| | - Mario Keller
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt am Main, Germany
| | - Stefan Simm
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Enrico Schleiff
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt am Main, Germany
- Frankfurt Institute of Advanced Studies, Frankfurt am Main, Germany
- *Correspondence: Enrico Schleiff
| | - Sotirios Fragkostefanakis
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt am Main, Germany
- Sotirios Fragkostefanakis
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14
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Yoshida T, Naito Y, Yasuhara H, Sasaki K, Kawaji H, Kawai J, Naito M, Okuda H, Obika S, Inoue T. Evaluation of off-target effects of gapmer antisense oligonucleotides using human cells. Genes Cells 2019; 24:827-835. [PMID: 31637814 PMCID: PMC6915909 DOI: 10.1111/gtc.12730] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 09/30/2019] [Accepted: 10/18/2019] [Indexed: 12/21/2022]
Abstract
Antisense oligonucleotide (ASO) has the potential to induce off‐target effects due to complementary binding between the ASO and unintended RNA with a sequence similar to the target RNA. Conventional animal studies cannot be used to assess toxicity induced by off‐target effects because of differences in the genome sequence between humans and other animals. Consequently, the assessment of off‐target effects with in silico analysis using a human RNA database and/or in vitro expression analysis using human cells has been proposed. Our previous study showed that the number of complementary regions of ASOs with mismatches in the human RNA sequences increases dramatically as the number of tolerated mismatches increases. However, to what extent the expression of genes with mismatches is affected by off‐target effects at the cellular level is not clear. In this study, we evaluated off‐target effects of gapmer ASOs, which cleave the target RNA in an RNase H‐dependent manner, by introducing the ASO into human cells and performing microarray analysis. Our data indicate that gapmer ASOs induce off‐target effects depending on the degree of complementarity between the ASO and off‐target candidate genes. Based on our results, we also propose a scheme for the assessment of off‐target effects of gapmer ASOs.
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Affiliation(s)
- Tokuyuki Yoshida
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Yuki Naito
- Database Center for Life Science (DBCLS), Mishima, Shizuoka, Japan.,National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Hidenori Yasuhara
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Kiyomi Sasaki
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Hideya Kawaji
- Tokyo Metropolitan Institute of Medical Science, Tokyo, Setagaya-ku, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Yokohama, Kanagawa, Japan.,Preventive Medicine and Applied Genomics Unit, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Jun Kawai
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Yokohama, Kanagawa, Japan
| | - Mikihiko Naito
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Haruhiro Okuda
- National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Takao Inoue
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
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15
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Hill CH, Boreikaitė V, Kumar A, Casañal A, Kubík P, Degliesposti G, Maslen S, Mariani A, von Loeffelholz O, Girbig M, Skehel M, Passmore LA. Activation of the Endonuclease that Defines mRNA 3' Ends Requires Incorporation into an 8-Subunit Core Cleavage and Polyadenylation Factor Complex. Mol Cell 2019; 73:1217-1231.e11. [PMID: 30737185 PMCID: PMC6436931 DOI: 10.1016/j.molcel.2018.12.023] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/02/2018] [Accepted: 12/21/2018] [Indexed: 01/19/2023]
Abstract
Cleavage and polyadenylation factor (CPF/CPSF) is a multi-protein complex essential for formation of eukaryotic mRNA 3' ends. CPF cleaves pre-mRNAs at a specific site and adds a poly(A) tail. The cleavage reaction defines the 3' end of the mature mRNA, and thus the activity of the endonuclease is highly regulated. Here, we show that reconstitution of specific pre-mRNA cleavage with recombinant yeast proteins requires incorporation of the Ysh1 endonuclease into an eight-subunit "CPFcore" complex. Cleavage also requires the accessory cleavage factors IA and IB, which bind substrate pre-mRNAs and CPF, likely facilitating assembly of an active complex. Using X-ray crystallography, electron microscopy, and mass spectrometry, we determine the structure of Ysh1 bound to Mpe1 and the arrangement of subunits within CPFcore. Together, our data suggest that the active mRNA 3' end processing machinery is a dynamic assembly that is licensed to cleave only when all protein factors come together at the polyadenylation site.
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Affiliation(s)
- Chris H Hill
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | | | - Ana Casañal
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Peter Kubík
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | - Sarah Maslen
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | - Ottilie von Loeffelholz
- Centre for Integrative Biology, Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology, Illkirch, Université de Strasbourg, Strasbourg, France; Centre National de la Recherche Scientifique UMR 7104, Illkirch, Université de Strasbourg, Strasbourg, France; INSERM U964, Illkirch, Université de Strasbourg, Strasbourg, France
| | - Mathias Girbig
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Mark Skehel
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
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16
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Hansen SR, Nikolai BJ, Spreacker PJ, Carrocci TJ, Hoskins AA. Chemical Inhibition of Pre-mRNA Splicing in Living Saccharomyces cerevisiae. Cell Chem Biol 2019; 26:443-448.e3. [PMID: 30639260 DOI: 10.1016/j.chembiol.2018.11.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 10/30/2018] [Accepted: 11/15/2018] [Indexed: 12/22/2022]
Abstract
The spliceosome mediates precursor mRNA splicing in eukaryotes, including the model organism Saccharomyces cerevisiae (yeast). Despite decades of study, no chemical inhibitors of yeast splicing in vivo are available. We have developed a system to efficiently inhibit splicing and block proliferation in living yeast cells using compounds that target the human spliceosome protein SF3B1. Potent inhibition is observed in yeast expressing a chimeric protein containing portions of human SF3B1. However, only a single point mutation in the yeast homolog of SF3B1 is needed for selective inhibition of splicing by pladienolide B, herboxidiene, or meayamycin in liquid culture. Mutations that enable inhibition also improve splicing of branch sites containing mismatches between the intron and small nuclear RNA-suggesting a link between inhibitor sensitivity and usage of weak branch sites in humans. This approach provides powerful new tools for manipulating splicing in live yeast and studies of spliceosome inhibitors.
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Affiliation(s)
- Sarah R Hansen
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Integrated Program in Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Brandon J Nikolai
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Peyton J Spreacker
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Integrated Program in Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Tucker J Carrocci
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Integrated Program in Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Integrated Program in Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
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17
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Delorme JE, Kodoth V, Aton SJ. Sleep loss disrupts Arc expression in dentate gyrus neurons. Neurobiol Learn Mem 2018; 160:73-82. [PMID: 29635031 DOI: 10.1016/j.nlm.2018.04.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 04/05/2018] [Accepted: 04/06/2018] [Indexed: 01/24/2023]
Abstract
Sleep loss affects many aspects of cognition, and memory consolidation processes occurring in the hippocampus seem particularly vulnerable to sleep loss. The immediate-early gene Arc plays an essential role in both synaptic plasticity and memory formation, and its expression is altered by sleep. Here, using a variety of techniques, we have characterized the effects of brief (3-h) periods of sleep vs. sleep deprivation (SD) on the expression of Arc mRNA and Arc protein in the mouse hippocampus and cortex. By comparing the relative abundance of mature Arc mRNA with unspliced pre-mRNA, we see evidence that during SD, increases in Arc across the cortex, but not hippocampus, reflect de novo transcription. Arc increases in the hippocampus during SD are not accompanied by changes in pre-mRNA levels, suggesting that increases in mRNA stability, not transcription, drives this change. Using in situ hybridization (together with behavioral observation to quantify sleep amounts), we find that in the dorsal hippocampus, SD minimally affects Arc mRNA expression, and decreases the number of dentate gyrus (DG) granule cells expressing Arc. This is in contrast to neighboring cortical areas, which show large increases in neuronal Arc expression after SD. Using immunohistochemistry, we find that Arc protein expression is also differentially affected in the cortex and DG with SD - while larger numbers of cortical neurons are Arc+, fewer DG granule cells are Arc+, relative to the same regions in sleeping mice. These data suggest that with regard to expression of plasticity-regulating genes, sleep (and SD) can have differential effects in hippocampal and cortical areas. This may provide a clue regarding the susceptibility of performance on hippocampus-dependent tasks to deficits following even brief periods of sleep loss.
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Affiliation(s)
- James E Delorme
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109, United States
| | - Varna Kodoth
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, United States
| | - Sara J Aton
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, United States.
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18
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Abstract
This Outlook discusses the study published in this issue by Ke et al., which clarifies the role of N6-methyladenosine (m6A) in mRNA biogenesis and function and shows that m6A methylation levels negatively correlate with transcript half-life but are not required for most pre-mRNA splicing events. Post-transcriptional modification of RNA nucleosides has been implicated as a pivotal regulator of mRNA biology. In this issue of Genes & Development, Ke and colleagues (pp. 990–1006) provide insights into the temporal and spatial distribution of N6-methyladenosine (m6A) in RNA transcripts by analyzing different subcellular fractions. Using a recently developed biochemical approach for detecting m6A, the researchers show that m6A methylations are enriched in exons and are added to transcripts prior to splicing. Although m6A addition is widely thought to be readily reversible, they demonstrate in HeLa cells that once RNA is released from chromatin, the modifications are surprisingly static. This study integrates data from previous publications to clarify conflicting conclusions regarding the role of m6A in mRNA biogenesis and function. Ke and colleagues found that m6A methylation levels negatively correlate with transcript half-life but are not required for most pre-mRNA splicing events.
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Affiliation(s)
- Nicolle A Rosa-Mercado
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA
| | - Johanna B Withers
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA.,Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA
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19
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Ke S, Pandya-Jones A, Saito Y, Fak JJ, Vågbø CB, Geula S, Hanna JH, Black DL, Darnell JE, Darnell RB. m 6A mRNA modifications are deposited in nascent pre-mRNA and are not required for splicing but do specify cytoplasmic turnover. Genes Dev 2017. [PMID: 28637692 PMCID: PMC5495127 DOI: 10.1101/gad.301036.117] [Citation(s) in RCA: 372] [Impact Index Per Article: 53.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Understanding the biologic role of N6-methyladenosine (m6A) RNA modifications in mRNA requires an understanding of when and where in the life of a pre-mRNA transcript the modifications are made. We found that HeLa cell chromatin-associated nascent pre-mRNA (CA-RNA) contains many unspliced introns and m6A in exons but very rarely in introns. The m6A methylation is essentially completed upon the release of mRNA into the nucleoplasm. Furthermore, the content and location of each m6A modification in steady-state cytoplasmic mRNA are largely indistinguishable from those in the newly synthesized CA-RNA or nucleoplasmic mRNA. This result suggests that quantitatively little methylation or demethylation occurs in cytoplasmic mRNA. In addition, only ∼10% of m6As in CA-RNA are within 50 nucleotides of 5' or 3' splice sites, and the vast majority of exons harboring m6A in wild-type mouse stem cells is spliced the same in cells lacking the major m6A methyltransferase Mettl3. Both HeLa and mouse embryonic stem cell mRNAs harboring m6As have shorter half-lives, and thousands of these mRNAs have increased half-lives (twofold or more) in Mettl3 knockout cells compared with wild type. In summary, m6A is added to exons before or soon after exon definition in nascent pre-mRNA, and while m6A is not required for most splicing, its addition in the nascent transcript is a determinant of cytoplasmic mRNA stability.
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Affiliation(s)
- Shengdong Ke
- Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, New York 10065, USA.,Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA
| | - Amy Pandya-Jones
- Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Yuhki Saito
- Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, New York 10065, USA.,Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA
| | - John J Fak
- Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, New York 10065, USA.,Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA
| | - Cathrine Broberg Vågbø
- Proteomics and Metabolomics Core Facility, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, 7489 Trondheim, Norway
| | - Shay Geula
- The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Jacob H Hanna
- The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Douglas L Black
- Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - James E Darnell
- Laboratory of Molecular Cell Biology, The Rockefeller University, New York, New York 10065, USA
| | - Robert B Darnell
- Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, New York 10065, USA.,Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA
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20
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Abstract
Deregulation of precursor mRNA splicing is associated with many illnesses and has been linked to age-related chronic diseases. Here we review recent progress documenting how defects in the machinery that performs intron removal and controls splice site selection contribute to cellular senescence and organismal aging. We discuss the functional association linking p53, IGF-1, SIRT1, and ING-1 splice variants with senescence and aging, and review a selection of splicing defects occurring in accelerated aging (progeria), vascular aging, and Alzheimer's disease. Overall, it is becoming increasingly clear that changes in the activity of splicing factors and in the production of key splice variants can impact cellular senescence and the aging phenotype.
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Affiliation(s)
- Mathieu Deschênes
- Department of Microbiology and Infectious DiseasesFaculty of Medicine and Health SciencesUniversité de SherbrookeSherbrookeQuebecJ1E 4K8Canada
| | - Benoit Chabot
- Department of Microbiology and Infectious DiseasesFaculty of Medicine and Health SciencesUniversité de SherbrookeSherbrookeQuebecJ1E 4K8Canada
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21
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Lee B, Sahoo A, Marchica J, Holzhauser E, Chen X, Li JL, Seki T, Govindarajan SS, Markey FB, Batish M, Lokhande SJ, Zhang S, Ray A, Perera RJ. The long noncoding RNA SPRIGHTLY acts as an intranuclear organizing hub for pre-mRNA molecules. Sci Adv 2017; 3:e1602505. [PMID: 28508063 PMCID: PMC5415337 DOI: 10.1126/sciadv.1602505] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 03/03/2017] [Indexed: 05/13/2023]
Abstract
Molecular mechanisms by which long noncoding RNA (lncRNA) molecules may influence cancerous condition are poorly understood. The aberrant expression of SPRIGHTLY lncRNA, encoded within the drosophila gene homolog Sprouty-4 intron, is correlated with a variety of cancers, including human melanomas. We demonstrate by SHAPE-seq and dChIRP that SPRIGHTLY RNA secondary structure has a core pseudoknotted domain. This lncRNA interacts with the intronic regions of six pre-mRNAs: SOX5, SMYD3, SND1, MEOX2, DCTN6, and RASAL2, all of which have cancer-related functions. Hemizygous knockout of SPRIGHTLY by CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 in melanoma cells significantly decreases SPRIGHTLY lncRNA levels, simultaneously decreases the levels of its interacting pre-mRNA molecules, and decreases anchorage-independent growth rate of cells and the rate of in vivo tumor growth in mouse xenografts. These results provide the first demonstration of an lncRNA's three-dimensional coordinating role in facilitating cancer-related gene expression in human melanomas.
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Affiliation(s)
- Bongyong Lee
- Sanford Burnham Prebys Medical Discovery Institute, 6400 Sanger Road, Orlando, FL 32827, USA
| | - Anupama Sahoo
- Sanford Burnham Prebys Medical Discovery Institute, 6400 Sanger Road, Orlando, FL 32827, USA
| | - John Marchica
- Sanford Burnham Prebys Medical Discovery Institute, 6400 Sanger Road, Orlando, FL 32827, USA
| | - Erwin Holzhauser
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Xiaoli Chen
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Jian-Liang Li
- Sanford Burnham Prebys Medical Discovery Institute, 6400 Sanger Road, Orlando, FL 32827, USA
| | - Tatsuya Seki
- Sanford Burnham Prebys Medical Discovery Institute, 6400 Sanger Road, Orlando, FL 32827, USA
- Medical and Biological Laboratories, Nagoya 460-0008, Japan
| | | | - Fatu Badiane Markey
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers Biomedical and Health Sciences, Rutgers University, Newark, NJ 07103, USA
| | - Mona Batish
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers Biomedical and Health Sciences, Rutgers University, Newark, NJ 07103, USA
| | | | - Shaojie Zhang
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Animesh Ray
- Keck Graduate Institute, 535 Watson Drive, Claremont, CA 91711, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ranjan J. Perera
- Sanford Burnham Prebys Medical Discovery Institute, 6400 Sanger Road, Orlando, FL 32827, USA
- Corresponding author.
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22
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Bain J, Cho M, Telegrafi A, Wilson A, Brooks S, Botti C, Gowans G, Autullo L, Krishnamurthy V, Willing M, Toler T, Ben-Zev B, Elpeleg O, Shen Y, Retterer K, Monaghan K, Chung W. Variants in HNRNPH2 on the X Chromosome Are Associated with a Neurodevelopmental Disorder in Females. Am J Hum Genet 2016; 99:728-734. [PMID: 27545675 DOI: 10.1016/j.ajhg.2016.06.028] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 06/27/2016] [Indexed: 01/07/2023] Open
Abstract
Via whole-exome sequencing, we identified six females from independent families with a common neurodevelopmental phenotype including developmental delay, intellectual disability, autism, hypotonia, and seizures, all with de novo predicted deleterious variants in the nuclear localization signal of Heterogeneous Nuclear Ribonucleoprotein H2, encoded by HNRNPH2, a gene located on the X chromosome. Many of the females also have seizures, psychiatric co-morbidities, and orthopedic, gastrointestinal, and growth problems as well as common dysmorphic facial features. HNRNPs are a large group of ubiquitous proteins that associate with pre-mRNAs in eukaryotic cells to produce a multitude of alternatively spliced mRNA products during development and play an important role in controlling gene expression. The failure to identify affected males, the severity of the neurodevelopmental phenotype in females, and the essential role of this gene suggests that male conceptuses with these variants may not be viable.
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23
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Abstract
The number of factors known to participate in the DNA damage response (DDR) has expanded considerably in recent years to include splicing and alternative splicing factors. While the binding of splicing proteins and ribonucleoprotein complexes to nascent transcripts prevents genomic instability by deterring the formation of RNA/DNA duplexes, splicing factors are also recruited to, or removed from, sites of DNA damage. The first steps of the DDR promote the post-translational modification of splicing factors to affect their localization and activity, while more downstream DDR events alter their expression. Although descriptions of molecular mechanisms remain limited, an emerging trend is that DNA damage disrupts the coupling of constitutive and alternative splicing with the transcription of genes involved in DNA repair, cell-cycle control and apoptosis. A better understanding of how changes in splice site selection are integrated into the DDR may provide new avenues to combat cancer and delay aging.
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Affiliation(s)
- Lulzim Shkreta
- Microbiologie et d'Infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada.
| | - Benoit Chabot
- Microbiologie et d'Infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada.
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24
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Abstract
The 3' ends of most eukaryotic messenger RNAs must undergo a maturation step that includes an endonuc-leolytic cleavage followed by addition of a polyadenylate tail. While this reaction is catalyzed by the action of only two enzymes it is supported by an unexpectedly large number of proteins. This complexity reflects the necessity of coordinating this process with other nuclear events, and growing evidence indicates that even more factors than previously thought are necessary to connect 3' processing to additional cellular pathways. In this review we summarize the current understanding of the molecular machinery involved in this step of mRNA maturation, focusing on new core and auxiliary proteins that connect polyadenylation to splicing, DNA damage, transcription and cancer.
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Affiliation(s)
| | - James L Manley
- Columbia University, Department of Biological Sciences, New York NY, 10027, USA
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25
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Ma WK, Cloutier SC, Tran EJ. The DEAD-box protein Dbp2 functions with the RNA-binding protein Yra1 to promote mRNP assembly. J Mol Biol 2013; 425:3824-38. [PMID: 23721653 DOI: 10.1016/j.jmb.2013.05.016] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 05/01/2013] [Accepted: 05/18/2013] [Indexed: 11/25/2022]
Abstract
Eukaryotic gene expression involves numerous biochemical steps that are dependent on RNA structure and ribonucleoprotein (RNP) complex formation. The DEAD-box class of RNA helicases plays fundamental roles in formation of RNA and RNP structure in every aspect of RNA metabolism. In an effort to explore the diversity of biological roles for DEAD-box proteins, our laboratory recently demonstrated that the DEAD-box protein Dbp2 associates with actively transcribing genes and is required for normal gene expression in Saccharomyces cerevisiae. We now provide evidence that Dbp2 interacts genetically and physically with the mRNA export factor Yra1. In addition, we find that Dbp2 is required for in vivo assembly of mRNA-binding proteins Yra1, Nab2, and Mex67 onto poly(A)+ RNA. Strikingly, we also show that Dbp2 is an efficient RNA helicase in vitro and that Yra1 decreases the efficiency of ATP-dependent duplex unwinding. We provide a model whereby messenger ribonucleoprotein (mRNP) assembly requires Dbp2 unwinding activity and once the mRNP is properly assembled, inhibition by Yra1 prevents further rearrangements. Both Yra1 and Dbp2 are conserved in multicellular eukaryotes, suggesting that this constitutes a broadly conserved mechanism for stepwise assembly of mature mRNPs in the nucleus.
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Affiliation(s)
- Wai Kit Ma
- Department of Biochemistry, Purdue University, BCHM 305, 175 South University Street, West Lafayette, IN 47907-2063, USA; Purdue University Center for Cancer Research, Purdue University, Hansen Life Sciences Research Building, Room 141, 201 South University Street, West Lafayette, IN 47907-2064, USA
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26
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Abstract
Eukaryotic cells transcribe a vast number of noncoding RNA species. Among them, long noncoding RNAs (lncRNAs) have been widely implicated in the regulation of gene transcription. However, examples of posttranscriptional gene regulation by lncRNAs are emerging. Through extended base-pairing, lncRNAs can stabilize or promote the translation of target mRNAs, while partial base-pairing facilitates mRNA decay or inhibits target mRNA translation. In the absence of complementarity, lncRNAs can suppress precursor mRNA splicing and translation by acting as decoys of RNA-binding proteins or microRNAs and can compete for microRNA-mediated inhibition leading to increased expression of the mRNA. Through these regulatory mechanisms, lncRNAs can elicit differentiation, proliferation, and cytoprotective programs, underscoring the rising recognition of lncRNA roles in human disease. In this review, we summarize the mechanisms of posttranscriptional gene regulation by lncRNAs identified until now.
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Affiliation(s)
- Je-Hyun Yoon
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
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