1
|
Zhang Y, Huang Z, Lu W, Liu Z. Alternative polyadenylation in cancer: Molecular mechanisms and clinical application. Crit Rev Oncol Hematol 2024; 206:104599. [PMID: 39701503 DOI: 10.1016/j.critrevonc.2024.104599] [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: 11/05/2024] [Accepted: 12/13/2024] [Indexed: 12/21/2024] Open
Abstract
Alternative polyadenylation (APA) serves as a crucial mechanism for the posttranscriptional regulation of gene expression and influences gene expression by generating diverse mRNA isoforms. This process is regulated by a diverse array of RNA-binding proteins (RBPs), which selectively bind to specific sequences or structures within the pre-mRNA molecule. Dysregulation of APA and its associated RBPs has been implicated in numerous diseases, including cardiovascular diseases, nervous system disease, and cancer. For instance, aberrant APA events have been observed in several types of tumors, contributing to tumor heterogeneity and affecting key cellular pathways involved in cell proliferation, invasion, metastasis, and response to therapy. This review critically evaluates the current understanding of APA mechanisms and the multifaceted roles of RBPs in orchestrating this intricate process. We highlight recent advancements in high-throughput sequencing and bioinformatics tools that have enhanced our ability to study APA on a genome-wide scale. Moreover, we explored the pathological consequences of APA dysregulation, emphasizing its role in oncogenesis. By elucidating the intricate relationships between APA and RBPs, this review aims to underscore the potential of targeting the APA machinery and RBPs for therapeutic intervention. Understanding these molecular processes holds promise for developing novel diagnostic markers and treatment strategies for a range of human cancers.
Collapse
Affiliation(s)
- Ying Zhang
- Department of Radiotherapy, Cancer Hospital of Shantou University Medical College, No.7 Raoping Road, Shantou, Guangdong 515041, China; Clinical Research Center, Cancer Hospital of Shantou University Medical College, No.7 Raoping Road, Shantou, Guangdong 515041, China.
| | - Zikun Huang
- Department of Orthopedics, First Affiliated Hospital of Shantou University Medical College, No.57 Changping Road, Shantou, Guangdong 515041, China
| | - Weiqing Lu
- Department of Radiotherapy, Cancer Hospital of Shantou University Medical College, No.7 Raoping Road, Shantou, Guangdong 515041, China
| | - Zhaoyong Liu
- Department of Orthopedics, First Affiliated Hospital of Shantou University Medical College, No.57 Changping Road, Shantou, Guangdong 515041, China.
| |
Collapse
|
2
|
Taniue K, Sugawara A, Zeng C, Han H, Gao X, Shimoura Y, Ozeki AN, Onoguchi-Mizutani R, Seki M, Suzuki Y, Hamada M, Akimitsu N. The MTR4/hnRNPK complex surveils aberrant polyadenylated RNAs with multiple exons. Nat Commun 2024; 15:8684. [PMID: 39419981 PMCID: PMC11487169 DOI: 10.1038/s41467-024-51981-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 08/21/2024] [Indexed: 10/19/2024] Open
Abstract
RNA surveillance systems degrade aberrant RNAs that result from defective transcriptional termination, splicing, and polyadenylation. Defective RNAs in the nucleus are recognized by RNA-binding proteins and MTR4, and are degraded by the RNA exosome complex. Here, we detect aberrant RNAs in MTR4-depleted cells using long-read direct RNA sequencing and 3' sequencing. MTR4 destabilizes intronic polyadenylated transcripts generated by transcriptional read-through over one or more exons, termed 3' eXtended Transcripts (3XTs). MTR4 also associates with hnRNPK, which recognizes 3XTs with multiple exons. Moreover, the aberrant protein translated from KCTD13 3XT is a target of the hnRNPK-MTR4-RNA exosome pathway and forms aberrant condensates, which we name KCTD13 3eXtended Transcript-derived protein (KeXT) bodies. Our results suggest that RNA surveillance in human cells inhibits the formation of condensates of a defective polyadenylated transcript-derived protein.
Collapse
Affiliation(s)
- Kenzui Taniue
- Isotope Science Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.
- Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa, Hokkaido, 078-8510, Japan.
| | - Anzu Sugawara
- Isotope Science Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Chao Zeng
- Faculty of Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Han Han
- Isotope Science Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Xinyue Gao
- Isotope Science Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Yuki Shimoura
- Isotope Science Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Atsuko Nakanishi Ozeki
- Isotope Science Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Rena Onoguchi-Mizutani
- Isotope Science Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Masahide Seki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Michiaki Hamada
- Faculty of Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
- AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Nobuyoshi Akimitsu
- Isotope Science Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.
| |
Collapse
|
3
|
Rambout X, Maquat LE. Nuclear mRNA decay: regulatory networks that control gene expression. Nat Rev Genet 2024; 25:679-697. [PMID: 38637632 PMCID: PMC11408106 DOI: 10.1038/s41576-024-00712-2] [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] [Accepted: 02/19/2024] [Indexed: 04/20/2024]
Abstract
Proper regulation of mRNA production in the nucleus is critical for the maintenance of cellular homoeostasis during adaptation to internal and environmental cues. Over the past 25 years, it has become clear that the nuclear machineries governing gene transcription, pre-mRNA processing, pre-mRNA and mRNA decay, and mRNA export to the cytoplasm are inextricably linked to control the quality and quantity of mRNAs available for translation. More recently, an ever-expanding diversity of new mechanisms by which nuclear RNA decay factors finely tune the expression of protein-encoding genes have been uncovered. Here, we review the current understanding of how mammalian cells shape their protein-encoding potential by regulating the decay of pre-mRNAs and mRNAs in the nucleus.
Collapse
Affiliation(s)
- Xavier Rambout
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA.
- Center for RNA Biology, University of Rochester, Rochester, NY, USA.
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA.
- Center for RNA Biology, University of Rochester, Rochester, NY, USA.
| |
Collapse
|
4
|
Gordon J, Phizicky D, Schärfen L, Brown C, Arias Escayola D, Kanyo J, Lam T, Simon M, Neugebauer K. Phosphorylation of the nuclear poly(A) binding protein (PABPN1) during mitosis protects mRNA from hyperadenylation and maintains transcriptome dynamics. Nucleic Acids Res 2024; 52:9886-9903. [PMID: 38943343 PMCID: PMC11381358 DOI: 10.1093/nar/gkae562] [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: 01/08/2024] [Revised: 05/23/2024] [Accepted: 06/28/2024] [Indexed: 07/01/2024] Open
Abstract
Polyadenylation controls mRNA biogenesis, nucleo-cytoplasmic export, translation and decay. These processes are interdependent and coordinately regulated by poly(A)-binding proteins (PABPs), yet how PABPs are themselves regulated is not fully understood. Here, we report the discovery that human nuclear PABPN1 is phosphorylated by mitotic kinases at four specific sites during mitosis, a time when nucleoplasm and cytoplasm mix. To understand the functional consequences of phosphorylation, we generated a panel of stable cell lines inducibly over-expressing PABPN1 with point mutations at these sites. Phospho-inhibitory mutations decreased cell proliferation, highlighting the importance of PABPN1 phosphorylation in cycling cells. Dynamic regulation of poly(A) tail length and RNA stability have emerged as important modes of gene regulation. We therefore employed long-read sequencing to determine how PABPN1 phospho-site mutants affected poly(A) tails lengths and TimeLapse-seq to monitor mRNA synthesis and decay. Widespread poly(A) tail lengthening was observed for phospho-inhibitory PABPN1 mutants. In contrast, expression of phospho-mimetic PABPN1 resulted in shorter poly(A) tails with increased non-A nucleotides, in addition to increased transcription and reduced stability of a distinct cohort of mRNAs. Taken together, PABPN1 phosphorylation remodels poly(A) tails and increases mRNA turnover, supporting the model that enhanced transcriptome dynamics reset gene expression programs across the cell cycle.
Collapse
Affiliation(s)
- Jackson M Gordon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - David V Phizicky
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Leonard Schärfen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Courtney L Brown
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Dahyana Arias Escayola
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Jean Kanyo
- Keck MS & Proteomics Resource, Yale School of Medicine, New Haven, CT 06520, USA
| | - TuKiet T Lam
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Keck MS & Proteomics Resource, Yale School of Medicine, New Haven, CT 06520, USA
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| |
Collapse
|
5
|
González-Iglesias A, Arcas A, Domingo-Muelas A, Mancini E, Galcerán J, Valcárcel J, Fariñas I, Nieto MA. Intron detention tightly regulates the stemness/differentiation switch in the adult neurogenic niche. Nat Commun 2024; 15:2837. [PMID: 38565566 PMCID: PMC10987655 DOI: 10.1038/s41467-024-47092-z] [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: 12/06/2021] [Accepted: 03/13/2024] [Indexed: 04/04/2024] Open
Abstract
The adult mammalian brain retains some capacity to replenish neurons and glia, holding promise for brain regeneration. Thus, understanding the mechanisms controlling adult neural stem cell (NSC) differentiation is crucial. Paradoxically, adult NSCs in the subependymal zone transcribe genes associated with both multipotency maintenance and neural differentiation, but the mechanism that prevents conflicts in fate decisions due to these opposing transcriptional programmes is unknown. Here we describe intron detention as such control mechanism. In NSCs, while multiple mRNAs from stemness genes are spliced and exported to the cytoplasm, transcripts from differentiation genes remain unspliced and detained in the nucleus, and the opposite is true under neural differentiation conditions. We also show that m6A methylation is the mechanism that releases intron detention and triggers nuclear export, enabling rapid and synchronized responses. m6A RNA methylation operates as an on/off switch for transcripts with antagonistic functions, tightly controlling the timing of NSCs commitment to differentiation.
Collapse
Affiliation(s)
| | - Aida Arcas
- Instituto de Neurociencias (CSIC-UMH), Sant Joan d'Alacant, 03550, Spain
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, 31008, Spain
| | - Ana Domingo-Muelas
- Departamento de Biología Celular, Biología Funcional y Antropología Física and Instituto de Biotecnología y Biomedicina, Universidad de Valencia, Burjassot, 46100, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28029, Madrid, Spain
- Carlos Simon Foundation, 46980, Paterna, Valencia, Spain
- Department of Cell and Developmental Biology, Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Igenomix Foundation, 46980, Paterna, Valencia, Spain
| | - Estefania Mancini
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, 08003, Spain
| | - Joan Galcerán
- Instituto de Neurociencias (CSIC-UMH), Sant Joan d'Alacant, 03550, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Raras (CIBERER), 28029, Madrid, Spain
| | - Juan Valcárcel
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, 08003, Spain
- Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Spain
| | - Isabel Fariñas
- Departamento de Biología Celular, Biología Funcional y Antropología Física and Instituto de Biotecnología y Biomedicina, Universidad de Valencia, Burjassot, 46100, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28029, Madrid, Spain
| | - M Angela Nieto
- Instituto de Neurociencias (CSIC-UMH), Sant Joan d'Alacant, 03550, Spain.
- Centro de Investigación Biomédica en Red sobre Enfermedades Raras (CIBERER), 28029, Madrid, Spain.
| |
Collapse
|
6
|
Ntasis VF, Guigó R. Studying relative RNA localization From nucleus to the cytosol. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.06.583744. [PMID: 38559161 PMCID: PMC10979850 DOI: 10.1101/2024.03.06.583744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The precise coordination of important biological processes, such as differentiation and development, is highly dependent on the regulation of expression of the genetic information. The flow of the genetic information is tightly regulated on multiple levels. Among them, RNA export to cytosol is an essential step for the production of proteins in eukaryotic cells. Hence, estimating the relative concentration of RNA molecules of a given transcript species in the nucleus and in the cytosol is of major significance as it contributes to the understanding of the dynamics of RNA trafficking between the nucleus and the cytosol. The most efficient way to estimate the levels of RNA species genome-wide is through RNA sequencing (RNAseq). While RNAseq can be performed separately in the nucleus and in the cytosol, because measured transcript levels are relative to the total volume of RNA in these compartments, and because this volume is usually unknown, the transcript levels in the nucleus and in the cytosol cannot be directly compared. Here we show theoretically that if, in addition to nuclear and cytosolic RNA-seq, whole cell RNA-seq is also performed, then accurate estimations of the localization of transcripts can be obtained. Based on this, we designed a method that estimates, first the fraction of the total RNA volume in the cytosol (nucleus), and then, this fraction for every transcript. We evaluate our methodology on simulated data and nuclear and cytosolic single cell data available. Finally, we use our method to investigate the cellular localization of transcripts using bulk RNAseq data from the ENCODE project.
Collapse
Affiliation(s)
- Vasilis F. Ntasis
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Catalonia, Spain
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Catalonia, Spain
- Department of Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
| |
Collapse
|
7
|
Sáez-Martínez P, Porcel-Pastrana F, Montero-Hidalgo AJ, Lozano de la Haba S, Sanchez-Sanchez R, González-Serrano T, Gómez-Gómez E, Martínez-Fuentes AJ, Jiménez-Vacas JM, Gahete MD, Luque RM. Dysregulation of RNA-Exosome machinery is directly linked to major cancer hallmarks in prostate cancer: Oncogenic role of PABPN1. Cancer Lett 2024; 584:216604. [PMID: 38244911 DOI: 10.1016/j.canlet.2023.216604] [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: 10/05/2023] [Revised: 12/01/2023] [Accepted: 12/15/2023] [Indexed: 01/22/2024]
Abstract
Novel biomarkers and therapeutic strategies for prostate-cancer (PCa) are required to overcome its lethal progression. The dysregulation/implication of the RNA-Exosome-complex (REC; cellular machinery controlling the 3'-5'processing/degradation of most RNAs) in different cancer-types, including PCa, is poorly known. Herein, different cellular/molecular/preclinical approaches with human PCa-samples (tissues and/or plasma of 7 independent cohorts), and in-vitro/in-vivo PCa-models were used to comprehensively characterize the REC-profile and explore its role in PCa. Moreover, isoginkgetin (REC-inhibitor) effects were evaluated on PCa-cells. We demonstrated a specific dysregulation of the REC-components in PCa-tissues, identifying the Poly(A)-Binding-Protein-Nuclear 1 (PABPN1) factor as a critical regulator of major cancer hallmarks. PABPN1 is consistently overexpressed in different human PCa-cohorts and associated with poor-progression, invasion and metastasis. PABPN1 silencing decreased relevant cancer hallmarks in multiple PCa-models (proliferation/migration/tumourspheres/colonies, etc.) through the modulation of key cancer-related lncRNAs (PCA3/FALEC/DLEU2) and mRNAs (CDK2/CDK6/CDKN1A). Plasma PABPN1 levels were altered in patients with metastatic and tumour-relapse. Finally, pharmacological inhibition of REC-activity drastically inhibited PCa-cell aggressiveness. Altogether, the REC is drastically dysregulated in PCa, wherein this novel molecular event/mechanism, especially PABPN1 alteration, may be potentially exploited as a novel prognostic and therapeutic tool for PCa.
Collapse
Affiliation(s)
- Prudencio Sáez-Martínez
- Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain; Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain; Hospital Universitario Reina Sofía (HURS), Cordoba, Spain; Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), Cordoba, Spain
| | - Francisco Porcel-Pastrana
- Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain; Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain; Hospital Universitario Reina Sofía (HURS), Cordoba, Spain; Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), Cordoba, Spain
| | - Antonio J Montero-Hidalgo
- Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain; Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain; Hospital Universitario Reina Sofía (HURS), Cordoba, Spain; Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), Cordoba, Spain
| | - Samanta Lozano de la Haba
- Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain; Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain; Hospital Universitario Reina Sofía (HURS), Cordoba, Spain; Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), Cordoba, Spain
| | - Rafael Sanchez-Sanchez
- Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain; Hospital Universitario Reina Sofía (HURS), Cordoba, Spain; Anatomical Pathology Service, HURS, Cordoba, Spain
| | - Teresa González-Serrano
- Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain; Hospital Universitario Reina Sofía (HURS), Cordoba, Spain; Anatomical Pathology Service, HURS, Cordoba, Spain
| | - Enrique Gómez-Gómez
- Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain; Hospital Universitario Reina Sofía (HURS), Cordoba, Spain; Urology Service, HURS/IMIBIC, Cordoba, Spain
| | - Antonio J Martínez-Fuentes
- Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain; Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain; Hospital Universitario Reina Sofía (HURS), Cordoba, Spain; Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), Cordoba, Spain
| | | | - Manuel D Gahete
- Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain; Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain; Hospital Universitario Reina Sofía (HURS), Cordoba, Spain; Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), Cordoba, Spain
| | - Raúl M Luque
- Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain; Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain; Hospital Universitario Reina Sofía (HURS), Cordoba, Spain; Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), Cordoba, Spain.
| |
Collapse
|
8
|
Jönsson J, Wang L, Kajitani N, Schwartz S. A novel HPV16 splicing enhancer critical for viral oncogene expression and cell immortalization. Nucleic Acids Res 2024; 52:316-336. [PMID: 37994701 PMCID: PMC10783526 DOI: 10.1093/nar/gkad1099] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 10/18/2023] [Accepted: 11/03/2023] [Indexed: 11/24/2023] Open
Abstract
High-risk carcinogenic human papillomaviruses (HPVs), e.g. HPV16, express the E6 and E7 oncogenes from two mRNAs that are generated in a mutually exclusive manner by splicing. The HPV16 E7 mRNA, also known as the E6*I/E7 mRNA, is produced by splicing between splice sites SD226 and SA409, while E6 mRNAs retain the intron between these splice sites. We show that splicing between HPV16 splice sites SD226 and SA409 is controlled by a splicing enhancer consisting of a perfect repeat of an adenosine-rich, 11 nucleotide sequence: AAAAGCAAAGA. Two nucleotide substitutions in both 11 nucleotide sequences specifically inhibited production of the spliced E6*I/E7 mRNA. As a result, production of E7 protein was reduced and the ability of HPV16 to immortalize human primary keratinocytes was abolished. The splicing-enhancing effect was mediated by the cellular TRAP150/THRAP3 protein that also enhanced splicing of other high-risk HPV E6*I/E7 mRNAs, but had no effect on low-risk HPV mRNAs. In summary, we have identified a novel splicing enhancer in the E6 coding region that is specific for high-risk HPVs and that is critically linked to HPV16 carcinogenic properties.
Collapse
Affiliation(s)
- Johanna Jönsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC-B9, 751 23 Uppsala, Sweden
| | - Lianqing Wang
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC-B9, 751 23 Uppsala, Sweden
- Center of Translational Medicine, Zibo Central Hospital, 255036 Zibo, China
| | - Naoko Kajitani
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC-B9, 751 23 Uppsala, Sweden
| | - Stefan Schwartz
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC-B9, 751 23 Uppsala, Sweden
| |
Collapse
|
9
|
Kases K, Schubert E, Hajikhezri Z, Larsson M, Devi P, Darweesh M, Andersson L, Akusjärvi G, Punga T, Younis S. The RNA-binding protein ZC3H11A interacts with the nuclear poly(A)-binding protein PABPN1 and alters polyadenylation of viral transcripts. J Biol Chem 2023; 299:104959. [PMID: 37356722 PMCID: PMC10371797 DOI: 10.1016/j.jbc.2023.104959] [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: 03/09/2023] [Revised: 06/09/2023] [Accepted: 06/14/2023] [Indexed: 06/27/2023] Open
Abstract
Nuclear mRNA metabolism is regulated by multiple proteins, which either directly bind to RNA or form multiprotein complexes. The RNA-binding protein ZC3H11A is involved in nuclear mRNA export, NF-κB signaling, and is essential during mouse embryo development. Furthermore, previous studies have shown that ZC3H11A is important for nuclear-replicating viruses. However, detailed biochemical characterization of the ZC3H11A protein has been lacking. In this study, we established the ZC3H11A protein interactome in human and mouse cells. We demonstrate that the nuclear poly(A)-binding protein PABPN1 interacts specifically with the ZC3H11A protein and controls ZC3H11A localization into nuclear speckles. We report that ZC3H11A specifically interacts with the human adenovirus type 5 (HAdV-5) capsid mRNA in a PABPN1-dependent manner. Notably, ZC3H11A uses the same zinc finger motifs to interact with PABPN1 and viral mRNA. Further, we demonstrate that the lack of ZC3H11A alters the polyadenylation of HAdV-5 capsid mRNA. Taken together, our results suggest that the ZC3H11A protein may act as a novel regulator of polyadenylation of nuclear mRNA.
Collapse
Affiliation(s)
- Katharina Kases
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Erik Schubert
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Zamaneh Hajikhezri
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Mårten Larsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Priya Devi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Mahmoud Darweesh
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden; Department of Microbiology and Immunology, Al-Azhr University, Assiut, Egypt
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Göran Akusjärvi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Tanel Punga
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
| | - Shady Younis
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden; Division of Immunology and Rheumatology, Stanford University, Stanford, California, USA.
| |
Collapse
|